https://www.na-mic.org/w/api.php?action=feedcontributions&user=JChris.FillionR&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-28T15:17:28ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=Wiki_page_for_2013_Progress_Report_Assignments&diff=98931Wiki page for 2013 Progress Report Assignments2023-04-11T21:13:38Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]<br />
<br />
<br />
=Assignments=<br />
Reporting Interval: 7/1/2012- 6/30/2013<br />
{| class="wikitable sortable labelpage labelpagetable" border="1" width="100%" cellpadding="5"<br />
|- style="background:#c2c2c2; color:black" align="left" <br />
| style="width:20%" | Task<br />
| style="width:20%" | Owner<br />
| style="width:60%" | Title, comments <br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|1. INTRODUCTION<br />
| style="background:#c4f4af; color:black"|Ann<br />
| style="background:#fff6a6; color:black"|Update Figure 1-1. Geo-anatomical Map of NA-MIC Collaborations, Recent changes and Center (administrative) highlights<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|2. [[2012_Progress_Report_HIGHLIGHTS | HIGHLIGHTS]]<br />
| style="background:#c4f4af; color:black"|Will Schroeder, Kitware<br />
| style="background:#b4e4d4; color:black"|2.1 Algorithms, 2.2 Engineering, 2.3 NA-MIC Kit.<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/23/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|3. [[2012_Progress_Report_IMPACT | IMPACT AND VALUE TO BIOCOMPUTING]]<br />
| style="background:#c4f4af; color:black"|Jim Miller, GE<br />
| style="background:#b4e4d4; color:black"|3.1 Impact within the Center, 3.2 Impact within NIH-Funded Research, 3.3 National and International Impact<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4. RESEARCH PROGRESS SUMMARIES<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#fff6a6; color:black"| <br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1 DRIVING BIOLOGICAL PROJECTS<br />
| style="background:#c4f4af; color:black"|DBP PIs<br />
| style="background:#fff6a6; color:black"| <br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1.1 [[2012_Progress_Report_DBP Atrial_Fibrillation | Atrial Fibrillation]]<br />
| style="background:#c4f4af; color:black"|Rob MacLeod, Utah<br />
| style="background:#b4ebd4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1.2 [[2012_Progress_Report_DBP Huntington's Disease | Huntington's Disease]]<br />
| style="background:#c4f4af; color:black"|Hans Johnson, Iowa<br />
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/18/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1.3 [[2012_Progress_Report_DBP Adaptive Radiotherapy | Adaptive Radiotherapy for Head and Neck Cancer]]<br />
| style="background:#c4f4af; color:black"|Gregory C. Sharp, MGH<br />
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/17/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1.4 [[2012_Progress_Report_DBP_TBI | Traumatic Brain Injury]]<br />
| style="background:#c4f4af; color:black"|Jack Van Horn, UCLA<br />
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|5. COMPUTER SCIENCE CORE<br />
| style="background:#c4f4af; color:black"|Ross Whitaker<br />
| style="background:#fff6a6; color:black"|Brief Introduction: Algorithms, Engineering, NA-MIC Kit<br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|5.1 Algorithms<br />
| style="background:#c4f4af; color:black"|Polina Golland, Guido Gerig, Allen Tannenbaum, Martin Styner<br />
| style="background:#b4e4d4; color:black"|5.1.1 Statistical Models of Anatomy and Pathology, Polina Golland<br>A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black"|5.1.2. Geometric Correspondence, Guido Gerig<br>A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br><br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black"|5.1.3. User Interactive Segmentation, Allen Tannenbaum<br>A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br><br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black"|5.1.4. Longitudinal and Time Series Analysis, Martin Styner<br>A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|5.2 <br />
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller<br />
| style="background:#b4e4d4; color:black"|5.2.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | End-user Platform, Steve Pieper]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black" align="center"|5.2.2. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Computational Platform, Jim Miller]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black" align="center"|5.2.3. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Data Management Platform, Dan Marcus]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black" align="center"|5.2.4.[[2012_Progress_Report_Science_Wiki_Version_Engineering | Software Process, Stephen R. Aylward ]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|5.3 [[2012_Progress_Report_Science_Wiki_Version_Engineering | NA-MIC Kit]]<br />
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller<br />
| style="background:#b4e4d4; color:black"|5.3.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Expansion<br>5.3.2. Release<br>]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/21/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|6. [[2012_Progress_Report_ARRA_Supplement| ARRA SUPPLEMENT]]<br />
| style="background:#c4f4af; color:black"|Steve Aylward<br />
| style="background:#b4e4d4; color:black"|6.1 Summary of Funded Activity<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|7. [[2012_Progress_Report_Outreach| OUTREACH]]<br />
| style="background:#c4f4af; color:black"|Sonia Pujol<br />
| style="background:#b4e4d4; color:black"|7.1 Summary of Outreach Activities<br><br />
| style="background:#b4e4d4; color:black"|Submitted on 4/13/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|8. NA-MIC PUBLICATIONS <br />
| style="background:#c4f4af; color:black"|Marianna <br />
| style="background:#fff6a6; color:black"|8.1 Papers that Acknowledge NA-MIC, 8.2. Conference Reports [[2012_Progress_Report#Dissemination|Go to All Papers List]]<br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|9. External Advisory Board (EAB) Report<br />
| style="background:#c4f4af; color:black"|Bill Lorensen<br />
| style="background:#fff6a6; color:black"|<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Wiki_page_for_2013_Preliminary_Draft&diff=98930Wiki page for 2013 Preliminary Draft2023-04-11T21:10:41Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div> Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]<br />
<br />
Required elements of the New Research Progress Template<br />
<br />
1. RESEARCH AND RESOURCE METRICS<br />
<br />
1A. Summary of Center Progress<br />
<br />
* Brief description of overall objectives of NA-MIC<br />
<br />
The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary community of computer scientists, software engineers, and medical investigators who share the common goal of improving healthcare through the development of computational tools for the analysis and visualization of medical image data. The Center maintains a robust and flexible infrastructure for developing and applying advanced imaging technologies across a range of important biomedical research disciplines. Our research and development effort is organized around the Computer Science Core, which includes independent teams for Algorithms and Engineering. The Algorithm effort responds to the challenges of the DBPs to expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly experimental, creating new approaches that are rapidly prototyped, tested, and improved. The Engineering effort supports the needs of the Algorithms effort by creating integrated software platforms that support research and eventual deployment of advanced technology. The Engineering team also develops and maintains processes used to build and sustain a large research community. A separate Core oversees operations and maintenance of The NA-MIC Kit, an integrated set of interoperable free open source software (FOSS) packages; developed, supported and deployed using a collaborative, agile, high quality software process. NA-MIC's current DBPs are investigating solutions to problems in patient-specific data analysis in four clinical areas: Atrial Fibrillation, Huntingdon's Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury. NA-MIC further provides enabling technology and resources to XX collaborative research projects.<br />
<br />
* Brief outline indicating strengths of NA-MIC as a national resource<br />
[take from NA-MIC impact statement, August 2012]<br />
<br />
NA-MIC takes seriously the responsibility of representing US medical imaging software development activities in the national and international community. Through our collaborations and outreach programs, we have mobilized like-minded scientists to contribute to open source software development for biomedical image analysis. Attracted to the concept of sharing software development resources, leading international groups have adopted NA-MIC’s engineering framework in lieu of undertaking the costly and redundant option of developing their own. These collaborative efforts have greatly raised awareness of the benefits of open science, and as a result, government-funded efforts that complement NA-MIC are now in place in Canada, Germany, Spain, France, and Italy.<br />
<br />
* Summarize progress made in each Research and Core Project.<br />
<br />
Algorithms. The NA-MIC Computer Science Algorithm effort responds to the challenges of the DBPs to expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly experimental, creating new approaches that are rapidly prototyped, tested, and improved.<br />
<br />
Engineering. The NA-MIC Computer Science Engineering effort supports the needs of the Algorithms effort by creating integrated software platforms that support research and eventual deployment of advanced technology. The Engineering team also develops and maintains processes used to build and sustain a large research community.<br />
<br />
NA-MIC Kit. The NA-MIC Kit consists of an integrated set of interoperable free open source software (FOSS) packages; developed, supported and deployed using a collaborative, agile, high quality software process. The NA-MIC Kit has been constructed as a layered architecture to provide a spectrum of capabilities, ranging from compute-intensive algorithms to easy-to-use applications. Hence users and developers can choose to engage the NA-MIC Kit at a variety of levels, including developing extensions which can be readily deployed to the broader biomedical imaging community.<br />
<br />
In the following subsections we highlight the accomplishments from this reporting period for algorithms, engineering, and NA-MIC Kit.<br />
<br />
2.1. Algorithms<br />
The Algorithms team develops computational methods that support patient-specific analysis of medical<br />
images. This effort requires analysis of images that vary significantly from one patient to another, or from one<br />
time point to another, presenting distinct challenges to existing state-of-art medical image analysis algorithms.<br />
These technical challenges are addressed using four computational approaches: (1) Statistical models of<br />
anatomy and pathology; (2) Geometric correspondence; (3) User interactive tools for segmentation; and (4)<br />
Longitudinal and time-series analysis. Highlights of these efforts are described in the following sections.<br />
<br />
'''Statistical models of anatomy and pathology.''' ''Polina Golland--Please update this section with current progress.''<br />
<br />
'''Geometric correspondence'''<br />
<br />
'''User interactive tools for segmentation<br />
<br />
'''Longitudinal and time series analysis.<br />
<br />
<br />
2.2 Engineering<br />
The Engineering Team builds bridges between the various NA-MIC cores and ultimately to the wider<br />
biomedical computing community. Working with the Algorithms Team, it deploys leading edge biomedical<br />
computing tools back to the DBPs, which are then used to perform impactful health research. In addition, the<br />
tools developed by the Engineering Team are used to train and disseminate technologies across the research<br />
community. The Team places particular focus on developing sustainable communities through the creation of<br />
open platforms, quality-inducing software processes, and integration to a broad variety of computational tools<br />
and databases. The following describes some of the highlights of the past year's work.<br />
<br />
3D Slicer, version 4<br />
<br />
Downloads<br />
<br />
Atlases<br />
<br />
Downloads<br />
<br />
<br />
Community support for NA-MIC and the various NA-MIC Kit tools continues. The goals of this effort are to<br />
transition new technologies to the wider community, to enable community members to contribute back to Slicer<br />
and the NA-MIC Kit, and to ensure high-quality systems. Beyond some of the support activities mentioned<br />
previously, the following are other accomplishments.<br />
<br />
* We have begun integrating the SimpleITK module of ITKv4 into Slicer to ensure simple integration capabilities with emerging algorithms.<br />
<br />
* Additional open data support has been added to Slicer such as ultrasound (e.g., video) and 4D (e.g., gated CT) data.<br />
<br />
* We have integrated the extension writing and the documentation generation processes. The documentation created when an extension is written is now automatically ported to a web host for easier access from within and outside of Slicer, ensuring that documentation resources keep up with the rapid pace of development.<br />
<br />
2.3 NA-MIC Kit<br />
<br />
The NA-MIC Kit is designed to accelerate the pace of research and facilitate clinical evaluation. Along these lines, the past year realized significant milestones toward the creation of a stable research platform, supporting the ability to easily extend and disseminate novel additions, all in the context of a world-wide, broad research community. Beyond the major highlights related to the Slicer4 application platform described in the previous section, the following are a few of the highlights of the past year.<br />
<br />
* CMake and its associated software process tools (CTest, CDash, and CPack) are used to build, test and deploy software in a cross-platform manner. CMake continues one of the most well-known pieces of the NA-MIC Kit, with more than 2,000 known downloads per day (as well as being included by various Linux distributions). CMake 2.8.7 was released with NA-MIC support.<br />
<br />
* CDash Package Manager (CDash 2.0.2) was released with support from NA-MIC. One of the most significant contributions to CDash from NA-MIC was the package upload process. This process enables the many Slicer testing machines to upload the executables and packages created during testing to the main CDash server. This, in turn, allows users to download those testing packages and run additional tests or use them in their research. This complete automation of the test-release cycle is a massive time-saver for the Service core and has greatly reduced the time to discover and resolve bugs and to improve the stability of Slicer.<br />
<br />
* Significant data integration efforts were completed over the past year. XNAT was greatly improved in its usability and interfaces. DICOM support was greatly enhanced, including the ability to embed Slicer MRML scene files as DICOM lollipops, meaning that Slicer data exchange across the DICOM standard is now possible. In addition, DCMTK was integrated into the NA-MIC Kit, meaning that DICOM support and functionality was greatly increased.<br />
<br />
* NA-MIC supports and nurtures an extensive biomedical research community. Along these lines it develops integration tools and interfaces with other communities. CTK, supported by NA-MIC funding,<br />
is one such community and interfaces with other open-source toolkits (e.g., MITK from the German Cancer Research Center in Heidelberg, XIP from Siemens, GIMIAS from UPF in Spain, and OpenMAF<br />
from U of Bologna). CTK now provides several innovative GUI and DICOM elements that specifically save GUI space, user-time, and developer effort when building custom medical applications. The NAMIC Kit also integrated the BRAINSFit system, a collection of programs for registering images with mutual information based metric. BRAINSFit uses the Slicer execution model framework to define the command line arguments and is fully integrated with Slicer using the module discovery capabilities.<br />
<br />
* Recent developments are in the process of being integrated into the NA-MIC Kit and the Slicer application platform.<br />
<br />
* The Slicer Catalog allows users to install, uninstall, search, browse, and rank Slicer extensions. This user experience is available from within Slicer and over the web, much like the Android and Apple App Stores. Developers can contribute, update, document, and post screenshots on their modules and receive community feedback.<br />
<br />
* The analysis infrastructure for Diffusion Weighted MRI (DWI) IO and visualization has been generalized to be used for other time varying acquisitions like multivolume analysis, dynamic contrast enhanced MRI (DCE), and gated cardiac CT.<br />
<br />
* To cover the use of Qt and newer versions of VTK (both part of the NA-MIC Kit), advanced charting and analytics options have been demonstrated in Slicer4, and will be fleshed out in the coming year.<br />
<br />
* Driving Biological Projects:<br />
<br />
The Center worked synergistically with the Driving Biological Projects (DBPs) to achieve fundamental advances in shape representation, shape analysis, groupwise registration, diffusion estimation, segmentation and quantification, functional estimation, distortion correction, and clustering.<br />
<br />
Atrial Fibrillation (Rob MacLeod, progress report)<br />
Huntingdon's Disease (Hans Johnson, progress report)<br />
Adaptive Radiotherapy for Head and Neck Cancer (Greg Sharp, progress report)<br />
Traumatic Brain Injury (Jack Van Horn, progress report0<br />
<br />
<br />
NA-MIC further provides enabling technology and resources to XX collaborative research projects.<br />
<br />
<br />
* Discuss at least 3 Collaborative Research Projects (these may include collaborating R01/R21s or other projects not directly funded by the Center's NCBC grant, but using Center tools or algorithms in a substantial and enabling manner.<br />
<br />
Collaboration 1: TBA<br />
Collaboration 2: TBA<br />
Collaboration 3: TBA<br />
<br />
* Brief description of new training and outreach activities conducted during reporting interval (7/1/2012 - 6/30/2013). Provide web-links if available.<br />
<br />
Sonia Pujol: Please update and revised. This year NA-MIC hosted XX workshops and courses at national universities and international venues, providing training and<br />
exposure to medical researchers in 3D Slicer and other NA-MIC technologies. NA-MIC also xxxx launched the first<br />
DTI Tractography Challenge for Neurosurgical Planning at the XXth International Conference on Medical Image<br />
Computing and Computer Assisted Intervention (MICCAI 2011) conference in Toronto, Canada, demonstrating<br />
its continued commitment to validation. The purpose of the validation effort is to assess the performance of<br />
NA-MIC algorithms in a variety of settings.<br />
<br />
<br />
* Impact of Center (i) on biomedical research and research training and outreach at our institution (BWH) and (i) broader scientific community. Institutional benefits might include, organization of special courses and meetings, attraction of students, and faculty participation. Scientific community benefits may include software released, workshops organized, collaborations established, service performed, technology developed, and technology disseminated through patents, publications, peer-reviewed citations of center collaborations by non-center investigators, and personnel trained.<br />
<br />
Provide a Center Summary Table<br />
<br />
Progress made by innovation and image analysis , and scientific CoresResearch Cores<br />
<br />
The scientific development is driven by 4 DBPs. In addition to activities that sustain the NA-MIC Kit and integrity of the Center’s software infrastructure, NA-MIC has an impressive outreach program that delivers software, data, and innovative science to the broader biomedical community through its publications and training venues. NA-MIC also has instituted a unique validation effort where software developers and end-users participate in hands-on workshops to measure and improve medical image algorithms.<br />
<br />
Required elements: <br />
<br />
Finally, this year saw the release of Slicer version 4.0 and 4.1 (Slicer4) which represents a significant advance in capabilities and underlying technologies. The software was released at RSNA 2011 in<br />
November. As in past years, a detailed presentation of current work was made at the All Hands Meeting in Salt Lake City, Utah, January 9-13, 2012, and can be viewed in detail on the NA-MIC Wiki [http://wiki.namic.org/Wiki/index.php/ 2012_Winter_Project_Week]. This represents the 8th Annual Progress Report and second year of the second cycle of funding. The report includes Highlights and Impact statements, individual progress reports from the four DBPs (Atrial Fibrillation, Huntington’s Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury), a science and technology summary from the Computer Science Core (Algorithms, Engineering, and NA-MIC Kit), and a review of Training activities, including the validation effort. The report concludes with a bibliography of 33 peer-reviewed journal articles and 21 peer-reviewed conference reports and the annual recommendations of the External Advisory Board, which met on January 12, 2012 in Salt Lake City, coincident with Winter Project Week.</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Technical_Information&diff=98929Technical Information2023-04-11T20:59:05Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>=Technical information of 4D Ultrasound=<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]<br />
<br />
<br />
You have to understand the following steps to use 4DUltrasound<br />
<br />
# Fullfill the requirements<br />
# Check out code and build<br />
# Prepare for use<br />
# Understand how to use 4DUltrasound Tutorial<br />
<br />
===Requirement===<br />
In this section you will find requirements to run the software<br />
<br />
==== Software ====<br />
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [https://www.slicer.org/wiki/Slicer3:Build_Instructions here] )''<br />
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''<br />
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''<br />
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''<br />
<br />
===== Modifications =====<br />
* OpenIGTLink Slicer Module:<br />
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module<br />
# Search for "crc" in this file -> You hit find the following lines <br> <br> <code> // If you want to skip CRC check, call Unpack() without argument. </code> <br> <code> int c = imgMsg->Unpack(1); </code> <br> <br><br />
# Change the last line to: <code> int c = imgMsg->Unpack(); </code><br />
# Recompile the OpenIGTLink Module<br />
## Change to the <code> Slicer-build </code> directory and type <code> $make </code><br />
<br />
* OpenIGTLink:<br />
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink<br />
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code><br />
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code><br />
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code><br />
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code><br />
# Recompile OpenIGTLink<br />
## Change to the OpenIGTLink-build directory and type <code> $make </code><br />
<br />
==== Hardware ====<br />
<br />
[[Image:Drawing-System_Design_Hardware.png |600px]]<br />
<br />
''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''<br />
<br />
* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]<br />
** 2 * 6 DOF Sensors<br />
*** 1 Sensor attached to the ultrasound probe<br />
*** 1 Sensor can be used to simulate a tracked surgical instrument<br />
<br />
* Ultrasound machine with Analog video output<br />
<br />
* Frame Grabber Card<br />
The System has successfully been test with the following 2 frame grabber cards:<br />
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]<br />
** Kuroutoshikou KRDM-CX23883<br />
<br />
* Optional: nVidia Cuda compatible graphics card<br />
<br />
===== Hardware Setup =====<br />
<br />
Tracker attached to ultrasound transducer<br />
<br />
[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]<br />
<br />
===Build Instructions===<br />
<br />
<br />
<br />
<br />
<br />
It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.<br />
<br />
A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] <br> <br><br />
<br />
# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound <br> <br><br />
# '''Configure''' via ccmake (version > 2.6) in your build directory <br> <br> ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' <br> <br> If you know how to do this, skip the next steps and procede with ''Compile'' <br> <br> <br />
## Make a new directory in with the name "Build" in the 4DUltrasound dir: <br> <br> <em> .../4DUltrasound$ mkdir Build </em> <br> <br><br />
## Change into the Build directory <br> <br> <em> .../4DUltrasound$ cd Build </em> <br> <br><br />
## Execute ccmake in this directory with the parent directory as parameter <br> <br> <em> .../4DUltrasound/Build$ ccmake ../ </em> <br> <br> If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: <em> .../Slicer3-lib/CMAKE-build/bin/ccmake </em> <br> <br><br />
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message <br> <br><br />
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER <br> <br><br />
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: <em> .../Slicer3-lib/VTK-build </em>) <br> <br> ''(In Ubuntu you must provide the absolute path no relative path will work)'' <br> <br><br />
## Hit "c" to start the configuration <br> <br> -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again <br> <br><br />
## Hit "c" <br> <br><br />
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable <br> <br><br />
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable <br> <br><br />
## Hit "c" <br> <br><br />
## Set "BUILD_SHARED_LIBS" to OFF <br> <br><br />
## Hit "g" to generate the Make files <br> <br><br />
# '''Compile''' 4D Ultrasound: Type <em>$ make </em> in your build directory<br> <br> <em> .../4DUltrasound/Build$ make </em><br />
<br />
=== Preparation to use 4D Ultrasound===<br />
<br />
Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]<br />
<br />
===Running 4D Ultrasound===<br />
<br />
Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]<br />
<br />
You need a working version of Slicer with OpenIGTLink and you must<br />
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code><br />
# Run Slicer<br />
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944<br />
# Run 4DUltrasound on the same machine you run Slicer<br />
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu<br />
<br />
====Commandline Options====<br />
{|border="0" cellpadding="4"<br />
|- bgcolor="silver"<br />
! Command !! Alternative !! Description<br />
|-<br />
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)<br />
|-<br />
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board<br />
|-<br />
| --track-ultrasound || -tu || Enable ultrasound tracking<br />
|-<br />
| --track-instrument || -ti || Enable instrument tracking<br />
|-<br />
| --simulate-instrument || -si || Simulate instrument<br />
|-<br />
| --get-calibration-data || -gcd || Get calibration data<br />
|-<br />
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file<br />
|-<br />
| --verbose || -v || Print more information<br />
|-<br />
|}<br />
<br />
==== TO DO ====<br />
{|border="0" cellpadding="5"<br />
|- bgcolor="silver"<br />
! Priority !! MUST<br />
|-<br />
| align="center" | || <br />
|-<br />
| align="center" | || <br />
|- bgcolor="silver"<br />
! Priority !! SHOULD<br />
|-<br />
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)<br />
|-<br />
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory<br />
|-<br />
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake<br />
|-<br />
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2<br />
|-<br />
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library<br />
|-<br />
|- bgcolor="silver"<br />
! Priority !! COULD<br />
|-<br />
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code<br />
|-<br />
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature<br />
|-<br />
| align="center", width="70px" | || width="600px"| Tracker test feature<br />
|-<br />
| align="center", width="70px" | || width="600px"| Ultrasound test feature<br />
|-<br />
|}<br />
<br />
=== Ultrasound device ===<br />
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.<br />
<br />
==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====<br />
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]<br />
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling<br />
===== Linux (Ubuntu 8.10 , Fedora 5)=====<br />
* The card is automatically correct detected. No further configuration needed.<br />
* Linux Driver: Video4Linux2 bt878<br />
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant<br />
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).<br />
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]<br />
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]<br />
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html<br />
** The Impact VCB has # 10<br />
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"<br />
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"<br />
* The card uses NTSC video interlacing per default<br />
===== Hardware Information =====<br />
* Channel 3 delivers the s-video signal<br />
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):<br />
<code> <br />
int channel = 3;<br />
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))<br />
errno_exit ("VIDIOC_S_INPUT"); <br />
</code><br />
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!<br />
<br />
==== Video4Linux2 ====<br />
Video4Linux is part of the Linux kernel since version 2.6.xx<br />
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]<br />
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]<br />
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver<br />
===== Old links may soon be dead =====<br />
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]<br />
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]<br />
* Link collection for V4L: [http://www.exploits.org/v4l]<br />
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore<br />
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore<br />
<br />
==== Contacts ====<br />
* Christoph Ruetz<br />
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]<br />
<br />
=== Tracking device ===<br />
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.<br />
<br />
=====Contacts=====<br />
* Haiying Liu<br />
<br />
=== Calibration ===<br />
Description: To get the correct information from the ultrasound device it has to be calibrated<br><br />
===== Contacts =====<br />
* Raul San Jose<br />
Information:<br />
* I have serval links and information from Raul on which I have to go through<br />
<br />
== Slicer ==<br />
I am using the Slicer development version, i.e. Slicer trunk. <br />
<br />
=== Python Synchrograb Module ===<br />
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.<br />
<br />
=== Volume Rendering ===<br />
Module '''VolumeRenderingCuda''' was used in Slicer for volume rendering. This module has been moved out of Slicer3 trunk and saved in NAMICSandBox/CUDAForVolumeRendering, and is not actively being developed. Now, we should use '''VolumeRendering''' module. Updated by Haiying Liu on Oct 30, 2009.<br />
<!-- === 3D CUDA ===<br />
I might not use Cuda acceleration since there is no real performance advantage at this point<br />
<br />
==== TO DO ====<br />
* Nothing<br />
<br />
==== Contacts ====<br />
* Ben Grauer: [https://www.slicer.org/wiki/Slicer3:Volume_Rendering_With_Cuda Volume Rendering with CUDA]<br />
* Nicholas Harlambang: CUDA Guru<br />
<br />
==== Documentation: VolumeRenderingCuda Module ====<br />
<br />
* Adjust the '''threshold''' (scroll bar below 'Component Weights Scrollbars') to correct values. Especially the lower value. Normally > 0<br />
* '''Scalar Opacity Mapping''': Shows a histogram of the used values an their transparence. Low transparent, high solid<br />
* '''Scalar Color Mapping''': You can click into and than in the color circle above and select certain colors for a specific value<br />
* '''Composite''': Here you can select different rendering modes<br />
* '''Volume''': You can also select just to display a slice instead of the whole volume. You can transform the slice in the ''Transforms Module'' and than select the ~ transformation matrix in '''Slice Matrix'''<br />
* '''Plus/Minus''': Select if you want to see everything or just the volume on one side of the slice and on the other<br />
--><br />
<br />
=== Links ===<br />
<br />
* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]<br />
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]<br />
<br />
* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]<br />
<br />
* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]<br />
<br />
<br />
<br />
=== Infos on loadable Modules ===<br />
<br />
<br />
<br />
[https://www.slicer.org/wiki/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] <br><br />
<br />
[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI]<br><br />
<br />
[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] <br><br />
<br />
<br />
<br />
=== Subscribe to different meetings ===<br />
<br />
* Journal Club<br />
<br />
* 1st Monday Seminar<br />
<br />
* Office OPRC<br />
<br />
* Radiology Grand Rounds<br />
<br />
* Cimit Forum<br />
<br />
<!--<br />
=== How to "Enable CUDA 2.0 in Fedora 8 for use with Slicer 3.3 Alpha" ===<br />
Date: Sept. 26th 2008<br />
<br />
Fedora 8 is the newest Fedora version for which CUDA is available. The available CUDA Version is 2.0. <br><br />
To enable CUDA 2.0 in Fedora 8 for Slicer 3.3 Alpha follow the steps below:<br />
<br />
==== Installation of Drivers ====<br />
<br />
* Download the CUDA installation files (Driver, Toolkit, SDK) here [http://www.nvidia.com/object/cuda_get.html] and remember the directory in which you downloaded them. I used<br />
for the driver installation binary<br />
~/Download/CUDA/Driver/ <br />
for the tool kit installation binary<br />
~/Download/CUDA/Toolkit/<br />
and for the SDK installation binary<br />
~/Download/CUDA/SDK/<br />
* For the installation there must not run a X-Server. Therefore we have to restart the computer. When you see the GRUB Bootscreen after the reboot press any key to enter the GRUB menu. Highlight the Fedora Version you want to boot and press <br />
a<br />
Then type <br />
Type 3<br />
and hit the 'Enter' key. Fedora will boot up without X Server and drop you at Command Line Login prompt.<br />
* Login and change into root mode via:<br />
su<br />
* Then switch to the directory where you downloaded the driver. For me this means: <br />
cd ~/Download/CUDA/Driver/<br />
* Now we have to change the permissions for the driver-binary and make it executable. This works with <br />
chmod +x BINARY-NAME<br />
(Replace 'BINARY-NAME' with the name of the driver binary)<br />
* Now start the installation with:<br />
./BINARY-NAME<br />
I changed none of the default values during the installation<br />
<br />
* For the sdk compilation follow this reference guide: [http://developer.download.nvidia.com/compute/cuda/2.0-Beta2/docs/SDK_Rel_Notes_Linux_2.0beta2.txt]<br> If you get the error message: "ld: cannot find -lglut", like I did, have a look at the reference under 'IV. Known Issues'<br />
<br />
* In the next step we do the same for the toolkit and for the sdk, e.g chance to the according directory, change the permissions and run the installation with the default values<br />
<br />
<br />
==== Enable CUDA in Slicer 3.3 Alpha ====<br />
<br />
* Start with the installation manual of Ben Grauer. You find it here [http://www.slicer.org/slicerWiki/images/a/ae/Cuda2slicer3.pdf]<br> Below you find corrections to certains points that did not work for me the way it was explained in the manual<br />
<br />
* In 1.1.2 Check out the following slicer branch instead and build it:<br />
<br />
svn co http://svn.slicer.org/Slicer3/trunk Slicer3<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
* Before you can go on with step 1.2.2 you have to Uncomment: <br />
**''CudaSupport'' in Slicer3/Libs/CMakeLists.txt<br />
**''VolumeRenderingCuda'' in Slicer3/Modules/CMakeLists.txt<br />
<br />
* In step 1.2.2 <br />
**you have to use your build directory (Slicer-build) as parameter for ccmake<br />
**for CUDA_INSTALL_PREFIX use /usr/local/cuda<br />
**for FOUND_CUT use $HOME/NVIDIA_CUDA_SDK/common/lib/linux/libcudpp.a<br />
**for FOUND_CUT_INCLUDE use $HOME/NVIDIA_CUDA_SDK/common/inc<br />
<br />
* Step 1.2.3 was not necessary for me<br />
<br />
* Just do a rebuild (run Slicer3/Scripts/getbuildtest.tcl) and the VolumeRenderingCUDA module is available<br />
<br />
This installation worked for me on a DELL machine with XEON Dual Core and a Nvidia G8800. For fast rendering make sure not enable compiz(Desktop Effects).<br />
--></div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Slicer_Team_Color_Map&diff=98928Slicer Team Color Map2023-04-11T20:51:50Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>==Lookup table 2011==<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
! integer_label<br />
! text_label<br />
! color<br />
! notes<br />
|-<br />
|1<br />
|team 1<br />
|style="background:rgb(157,0,0)"|rgb(157,0,0)<br />
|<br />
|-<br />
|2<br />
|team 2<br />
|style="background:rgb(230,169,29)"|rgb(230,169,29)<br />
|<br />
|-<br />
|3<br />
|team 3<br />
|style="background:rgb(255,255,0)"|rgb(255,255,0)<br />
|<br />
|-<br />
|4<br />
|team 4<br />
|style="background:rgb(185,232,61)"|rgb(185,232,61)<br />
|<br />
|-<br />
|5<br />
|team 5<br />
|style="background:rgb(0,226,255)"|rgb(0,226,255)<br />
|<br />
|-<br />
|6<br />
|team 6<br />
|style="background:rgb(0,0,255)"|rgb(0,0,255)<br />
|<br />
|-<br />
|7<br />
|team 7<br />
|style="background:rgb(251,159,255)"|rgb(251,159,255)<br />
|<br />
|-<br />
|8<br />
|team 8<br />
|style="background: rgb(138, 43, 226)"|rgb(138, 43, 226)<br />
|<br />
|}<br />
<br />
==Lookup table 2012==<br />
[[Slicer_Team_Color_2012 | Slicer Team Color 2012]]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=RSNA_2020&diff=98927RSNA 20202023-04-11T20:49:47Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
{| class="wikitable" style="background: white;"<br />
|colspan="3" |[[image:RSNA2020.png|center]]<br />
|-style="text-align: center;"<br />
|style="width:33%" |[[Image:NAMIC.jpg|50px]]<br />
|style="width:33%" |[[Image:NCIGTlogo.gif|120px]]<br />
|style="width:33%" |[[Image:Logo_nac.gif|50px]]<br />
|}<br />
<br />
The [https://rsna2020.rsna.org/ 106th Annual Meeting of the Radiological Society of North America (RSNA 2020)] was held virtually on Nov.19 – Dec.5, 2020.<br />
<br />
==Educational Exhibits==<br />
<br />
*The 3D Slicer open-source platform for medical image analysis and 3D visualization of DICOM data, Sonia Pujol, PhD, Andras Lasso, PhD, Steve Pieper, PhD, Andriy Fedorov, PhD, Ron Kikinis, MD. <br />
*National Cancer Institute Imaging Data Commons. Fedorov A, Longabaugh W, Pot D, Pieper P, Ziegler E, Herrmann M, Clifford W, Aerts H, Homeyer A, Clunie D, Farahani K, Pihl T, Kikinis R. <br />
<br />
==Digital Posters==<br />
<br />
*Representing and Communicating AI Model Results in Standard DICOM Format Using the Python Programming Language. Bridge C, Doyle S, Fedorov A, Pieper S, Ziegler Z, Petts J, Clunie A, Harris G, Andriole K, Lennerz J, Herrmann M. <br />
*Using the Open Health Imaging Foundation (OHIF) Framework to Build Web-based Imaging Applications. Ziegler E, Brown D, Urban T, Petts J, Rukas D, Lewis R, Pieper S, Hafey C, Harris GJ.</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=QIICR_2013&diff=98926QIICR 20132023-04-11T20:48:20Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div> [[Events#2013|Back to events page]]<br />
<br />
{| align="right"<br />
| __TOC__<br />
|}<br />
<br />
{|<br />
|[[Image:QIICR_horizontal.png|450px]]<br />
<br />
'''October 22-23, 2013'''<br />
<br />
'''Brigham and Women's Hospital, Boston, MA'''<br />
<br />
http://qiicr.org<br />
|}<br />
<br />
=Introduction=<br />
<br />
Imaging has enormous untapped potential to improve cancer research through software to extract and process morphometric and functional biomarkers. In the era of non-cytotoxic treatment agents, multi-modality image-guided ablative therapies and rapidly evolving computational resources, quantitative imaging software can be transformative in enabling minimally invasive, objective and reproducible evaluation of cancer treatment response. Post-processing algorithms are integral to high-throughput analysis and fine- grained differentiation of multiple molecular targets. Software tools used for such analyses must be robust and validated across a range of datasets collected for multiple subjects, timepoints and institutions. Ensuring the validity of this software requires unambiguous specification of analysis protocols, documentation of the analysis results, and clear guidelines for their interpretation. <br />
<br />
Yet cancer research data does not exist in formats that facilitate advancement of quantitative analysis and there is lack of an infrastructure to support common data exchange and method sharing. We therefore propose to develop and disseminate interoperable image informatics platform for development of software tools for quantitative imaging biomarker discovery. This platform will enable archival, organization, retrieval, dissemination of the data produced by the novel analysis tools and performance evaluation of quantitative analysis methods. Its functionality will be defined by the needs of the active research projects within the NCI Quantitative Imaging Network (QIN) in quantitative imaging biomarker development for prostate adenocarcinoma, head and neck cancer and glioblastoma multiforme. The infrastructure will be based on 3D Slicer, an NIH funded open source platform for image analysis and visualization, and will be accompanied by sample data and step-by-step documentation. <br />
<br />
In the Quantitative Image Informatics for Cancer Research (QIICR) project we will (1) develop software tools encapsulating analysis and data organization workflows for the specific cancer imaging research applications; (2) implement support for interoperable open formats accepted in the community to enable dissemination and sharing of the analysis results; (3) develop interfaces to community cancer imaging repositories to enable archival and dissemination of the analysis results.<br />
<br />
==Objective==<br />
During the QIICR 2013 meeting in Boston we will: <br />
*review the project as funded, <br />
*hear updates on the current status of the DICOM standard and its support in major open source toolkits and platforms such as ITK and Slicer <br />
*plan the project activities among the participants <br />
*discuss how to communicate and coordinate among the participants<br />
<br />
=Program=<br />
==Day 1 (Oct 22): Public Workshop on DICOM Support for Quantitative Imaging Trials ==<br />
<br />
This meeting is co-organized with [http://nac.spl.harvard.edu/ NAC], [http://ncigt.org/ NCIGT], [http://na-mic.org/ NA-MIC].<br />
<br />
Times in Eastern Daylight Time (EDT). 13:30 EDT = 19:30 Central European Summer Time (CEST)<br />
<br />
* noon: networking and brown bag working lunch (i.e. bring your own lunch - there are many nearby places to buy food) - coffee will be served<br />
* 1:30pm-2:00pm QIICR introduction (Andrey Fedorov) [[Media:2013-QIICR-Boston-Fedorov.pdf|Slides]]<br />
* 2:00pm-2:30pm Existing support of DICOM in 3D Slicer and CTK (Steve Pieper) [[media:Qiicr-kickoff-pieper-slicerdicom.pdf| Slides]]<br />
* 2:30pm-2:55pm DICOM aspects of SlicerRT project (Andras Lasso) [[Media:QIICR2013-SlicerRtDicom.pdf|Slides]]<br />
* 2:55pm-3:05pm break<br />
* 3:05pm-3:30pm Overview of the relevant capabilities of DCMTK (Michael Onken) [[media:DCMTK-in-qiicr final.pdf|Slides]]<br />
* 3:30pm-4:25pm Overview of the relevant parts of DICOM (David Clunie) [[Media:20131022_QIICR_DICOM.pptx| Slides]]<br />
* 4:25pm-4:35pm break<br />
* 4:35pm-5:30pm Structured Report templates for Cancer Clinical Trials DICOM (David Clunie) [[Media:20131022_QIICR_StructuredReportTemplates.pptx| Slides]]<br />
* 5:30pm-6:30pm Open discussion<br />
** [[Projects:ARRA:SlicerWF|Workflow engine]]<br />
* 7:30pm Group dinner (everyone pays for their own, location TBD. Please notify Katie if you will join kmast@bwh.harvard.edu) (Elephant Walk, 900 Beacon St, http://elephantwalk.com/)<br />
<br />
==Day 2 (Oct 23): QIICR Participants Only==<br />
<br><br />
<gallery widths="800px" heights="300px" perrow="3" mode="packed-hover"><br />
image:QIICR-2013-10-23.png|The internal meeting in full swing (photo by Ron)<br />
</gallery><br />
<br />
(this day will be devoted to administrative, logistic, and other details. QIICR funded investigators are required to attend, if you are not a QIICR funded investigator and would like to attend, contact the program committee)<br />
* Closed program<br />
* 8am Working breakfast (bring your own) - coffee will be served<br />
* 8:45am-9:00am Review the agenda for the day (Andrey Fedorov)<br />
* 9am-noon: Presentations from DBPs and brain-storming<br />
** 9:00am-10:00 am [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin/bwhospital Quantitative MRI of prostate cancer as a biomarker and guide for treatment] (Fiona Fennessy, BWH QIN site PI, QIICR investigator) + questions<br />
** 10:00am-10:10am break<br />
** 10:10am-11:00am [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin/mgh Quantitative MRI of Glioblastoma Response] (Jayashree Kalpathy-Cramer, MGH QIN site investigator, QIICR MGH site PI) + questions<br />
** 11:00am-12:00am [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin/iowa Quantitative Imaging to Assess Response in Cancer Therapy Trials] (Reinhard Beichel, Iowa QIN site investigator, QIICR Iowa site PI) + questions<br />
* noon-1pm brown-bag lunch<br />
* 1:00pm-1:20pm Discussion of the DBP and related issues<br />
** Site-specific and common informatics and data organization needs<br />
** Organization of image-related vs clinical data - interaction between DICOM-based storage and databases<br />
** Data sharing<br />
** Integration of structured terminology<br />
** Near term and end of year deliverables<br />
* 1:20pm-3pm Discussions of day-to-day logistics issues<br />
** communication means and frequency<br />
*** every other week - Google hangout ? YES - Except during RSNA week<br />
*** perhaps meet at RSNA - with other folks, perhaps Monday 2.00pm-3.00pm (CST) ?? what room<br />
*** perhaps meet at NA-MIC project week Salt Lake City Jan 6-10<br />
*** wiki for status updates, documentation and record-keeping: NA-MIC wiki (http://wiki.na-mic.org/Wiki/index.php/QIICR_2013), github project wiki (https://github.com/QIICR/qiicr.github.io/wiki/QIICR-Wiki-Home) (AF to demo)<br />
*** github issues for project milestones (AF to demo)<br />
**** large binary files on MIDAS http://www.kitware.com/source/home/post/8<br />
*** web-site for publicity: http://qiicr.org (AF to demo)<br />
**** git crash course and links (Slicer-specific, but many useful links) https://www.slicer.org/wiki/Slicer:git-svn<br />
*** face-to-face meetings: NA-MIC project weeks twice a year, do we need more?<br />
** Development-related activities<br />
*** prioritization of development tasks, SR templates, XML<br />
*** repository of sample DICOM objects (public?)<br />
*** cross-linking of DICOM standard ?<br />
**** related effort: DICOM in XML (~2005) [http://medical.nema.org/Dicom/minutes/Committee/2005/2005-09-29/DICOM%20in%20XML.ppt PPT slides]. March 2013 update: ''The Secretary reported that plans are formulated for a 2013 conversion. More discussion will be needed when a more detailed proposal is available. It was noted however that Pts 3 and 16 are available in XML form, now.'' [[http://medical.nema.org/Dicom/minutes/Committee/2013/DICOM-2013-03-19-Min.docx DSC meeting minutes]<br />
*** means of data sharing (XNAT Central? MIDAS?)<br />
<br />
=Logistics=<br />
==Registration==<br />
This event is intended for the participants in the grant, but open to others as long as they are willing to participate in the DICOM-related discussions. You must have expertise on one or several of the following topics: quantitative image analysis, open source software development, imaging informatics or related topics.<br />
<br />
Unless you received an invitation to attend this event, please [http://goo.gl/48iA94 fill this form] if you are interested to join. Organizing committee (Ron Kikinis, Steve Pieper and Andrey Fedorov) will confirm your registration and you will be added to the registered attendee list. <br />
<br />
Registration is open until October 1 so that we can finalize the logistics.<br />
<br />
Due to space limitations, the number of attendees is limited. After accommodating the participants in the grant, we have a "first come" policy. Please register early if you are interested in attending!<br />
<br />
==Where==<br />
2nd floor Demo Room, 1249 Boylston street, Boston MA ([http://goo.gl/maps/jWd32 Google map link]) <br />
<br />
Room will be finalized subject to the number of attendees registered.<br />
<br />
==When==<br />
October 22 and 23, 2013<br />
==Who==<br />
==What==<br />
<br />
== Lodging and other considerations ==<br />
<br />
There are [https://www.google.com/maps/preview#!q=hotels+near+1249+Boylston+St%2C+Boston%2C+MA+02215&data=!1m4!1m3!1d8747!2d-71.09578!3d42.345416!4m11!1m10!4m8!1m3!1d1517205!2d-71.6835014!3d42.0369215!3m2!1i1024!2i768!4f13.1!17b1 many hotel options near 1249 Boylston]. [http://mbta.com Public transportation in Boston] is pretty good, and you should not have issues commuting from the neighborhoods like Cambridge and Brookline. [http://thehubway.com Hubway] is a popular bike share system that you can use to get around, 24-hour access pass is $6.<br />
<br />
Among the nearby choices:<br />
* The Howard Johnson's next door is convenient, but run down.<br />
* [http://www.residenceinnbackbay.com/ Residence Inn] is new and looks nice.<br />
* People have said good things about [http://www.hotelcommonwealth.com/ the Hotel Commonwealth]<br />
* The [http://www.bostonhotelbuckminster.com/ Hotel Buckminster] has also worked well for visitor.<br />
<br />
'''Please Note: the Red Sox WILL BE in the [http://en.wikipedia.org/wiki/2013_World_Series World Series], which starts at 8:07pm on the second day of our meeting Wednesday, October 23. Because of this exciting event, the neighborhood will be very busy and parking will be impossible. Definitely make your reservations in advance, because rooms will be hard to come by.'''<br />
<br />
The meeting location is easily reachable by cab or bus if the nearby hotels don't work out.<br />
<br />
==Contact==<br />
Andrey Fedorov, Brigham and Women's Hospital<br />
<br />
fedorov AT bwh.harvard.edu<br />
<br />
=Attendees=<br />
==Day 1==<br />
# Ron Kikinis, Brigham and Women's Hospital<br />
# Andrey Fedorov, Brigham and Women's Hospital<br />
# Steve Pieper, Isomics Inc.<br />
# Jayashree Kalpathy-Cramer, Mass General Hospital<br />
# Reinhard Beichel, U. of Iowa<br />
# David Clunie, Pixelmed Publishing<br />
# Michael Onken, Open Connections GmbH and OFFIS<br />
# Andras Lasso, Queens U. and OCAIRO<br />
# Csaba Pinter, Queens U. and OCAIRO<br />
# Gordon Harris, BWH/MGH Tumor Imaging Metrics Core<br />
# Greg Sharp, MGH Radiation Oncology<br />
# Oleg Pianykh, Harvard<br />
# Leonid Syrkin, DFCI<br />
# John Evans, MGH<br />
# Alireza Mehrtash, BWH<br />
# Tobias Penzkofer, BWH<br />
# Nathaniel Reynolds, MGH<br />
# Marco Nolden, DKFZ (by Google hangout)<br />
# Jean-Christophe Fillion-Robin, Kitware Inc. (by Google hangout)<br />
# Jörg Riesmeier, Freelancer and DCMTK (by Google hangout)<br />
# Kevin Wang, Toronto (by Google hangout)<br />
<br />
==Day 2==<br />
# Ron Kikinis, Brigham and Women's Hospital<br />
# Andrey Fedorov, Brigham and Women's Hospital<br />
# Steve Pieper, Isomics Inc.<br />
# Jayashree Kalpathy-Cramer, Mass General Hospital<br />
# Reinhard Beichel, U. of Iowa<br />
# Fiona Fennessy, Brigham and Women's Hospital<br />
# David Clunie, Pixelmed Publishing<br />
# Michael Onken, Open Connections GmbH and OFFIS<br />
# John Evans, MGH<br />
# Alireza Mehrtash, BWH<br />
# Yantian Zhang, NCI (by phone)<br />
<br />
=References=<br />
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin NCI Quantitative Imaging Network]<br />
* [http://projectreporter.nih.gov/project_info_description.cfm?aid=8606944&icde=17789200&ddparam=&ddvalue=&ddsub=&cr=2&csb=default&cs=ASC NIH Reporter info on QIICR]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Projects:Utah2ShapeRegression&diff=98925Projects:Utah2ShapeRegression2023-04-11T20:44:44Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>Back to [[Algorithm:Utah2|Utah 2 Algorithms]]<br />
__NOTOC__<br />
<br />
= Ongoing Work (Updated 8/16/12) =<br />
<br />
== Smooth Growth Trajectories from Time Series Shape Data ==<br />
<br />
Segmentation of multi-time point image data of individual subjects results in serial shape data of structures of interest. Clinical research is interested in the spatiotemporal analysis of shape changes, which potentially leads to improved understanding of the rate of change, locality and growth trajectory of structures of interest.<br />
<br />
== Description ==<br />
<br />
Longitudinal shape analysis often relies on the estimation of a realistic continuous growth scenario from data sparsely distributed in time. In this project, we develop a new type of growth model parameterized by acceleration, whereas standard methods usually control the velocity [1,2]. From this parameterization, we gain one order of differentiability and guarantee that shape evolution is smooth in both space and time. This mimics the behavior of biological tissue as a mechanical system driven by external forces. The growth trajectories are estimated as continuous flows of deformations, which are twice differentiable. The shape regression is based on a correspondence-free technique using ''currents'' [2,3], which calculates diffeomorphic flows between set of shapes represented as surface data.<br />
<br />
[[File:Shape_regression_illustration.png|700px|center|thumb|Shape regression involves estimating a continuous evolution from a set of discrete shapes.]]<br />
<br />
== Results == <br />
<br />
To evaluate our method, we use longitudinal image data from a child that has been scanned 16 times between four and eight years of age. The MRI data is first rigidly aligned to establish a common reference frame. The intracranial volume and lateral ventricles are segmented from each image using an EM based tissue classification algorithm and a level-set based active contour segmentation tool.<br />
<br />
We estimate the evolution of the intracranial surface using a regression model based on the piecewise geodesic flow of diffeomorphisms as in [3]. The standard deviation of the Gaussian kernel controlling deformation is set to 50mm, roughly 30% of the diameter of the baseline intracranial surface. For the scale of currents we use 20mm, with a regularity weight of 0.1. Finally, time is discretized in increments of$0.0425 years. We also produce a growth trajectory using our proposed method with the same parameter settings as above except we weight regularity by 0.01 (the two weighted terms cannot be compared since they have different `physical' dimension). The parameters were tuned empirically to produce regressions of comparable quality with both methods.<br />
<br />
Shape evolution is considerably smoother using our proposed regression model as compared to the piecewise geodesic model. This is particularly evident in the trajectories of the shape points across time, a subset of which are shown below. It is an important distinction that the trajectories estimated by our method are ''not'' a smoothing of the piecewise geodesic method. Rather, the trajectories are the result of fundamentally different assumptions on the underlying model which results in a more realistic estimation of growth.<br />
<br />
[[File:Long_pg_vs_accel.png|600px|center|thumb|Shape evolution from baseline (solid) to final configuration (transparent) <br />
using a model based on piecewise geodesics (top left) and our method (bottom left) with point trajectories for selected particles displayed as black lines.<br />
On the right, the path of a point on the forebrain is decomposed into coordinates. Growth is estimated using 15 target shapes, highlighting the speed discontinuities present in the piecewise<br />
geodesic evolution.]]<br />
<br />
Next, we investigate the application of our model to the study of measurements derived from shape. Here we obtain a continuous non-linear model of volume, shown in the figure below. The results are consistent with a 1D regression model, such as kernel regression, applied to the sparse volume measurements. However, we have focused our modeling efforts on capturing the evolution of shape, with continuous volume measurements resulting naturally from the estimated growth. In addition, the piecewise geodesic method appears to be overfitting, producing unrealistic volume measurements, further suggesting that our method is more robust in the presence of noisy data.<br />
<br />
[[File:Long_accel_volume_w_kernel_reg.png|600px|center|thumb|Volume measurements derived from our growth model are consistent with a kernel regression performed on the sparse volume measurements. Our model describes the continuous evolution of ''shape'' and volume is measured after regression.]]<br />
<br />
We also consider the evolution of the lateral ventricles, which exhibit considerably more complexity than the intracranial surface. The horns of the segmented lateral ventricles are as thin as a few millimeters, making regression particularly challenging. As with the intracranial volume, ventricle growth is estimated using a piecewise geodesic model and our acceleration based model. The scale of deformation is set at 6mm, the scale of currents to 2mm, and regularity is weighted by 0.1 and 0.01, respectively.<br />
<br />
The impact of missing data is examined by performing leave-several-out experiments, the results of which are summarized in the figure below. In all experiments, selected target shapes were chosen as uniformly across time as possible. Our method demonstrates robustness with respect to the number of target shapes, with only minimal increase in the coefficient of determination R^2 when using more than 3 targets. This suggests that our method captures the underlying growth with limited data, as additional target data does not greatly alter the estimation. In contrast, piecewise geodesic regression is more influenced by additional target data and is therefore likely to overfit. <br />
<br />
[[File:Leave_several_out_summary.png|600px|center|thumb|'''Left:''' Snapshots from a continuous shape evolution of lateral ventricles estimated by our regression model. Acceleration vectors are displayed on the surface, with color denoting magnitude. '''Right:''' The impact of the number of target shapes on R^2.]]<br />
<br />
== Application to Autism Research (former DBP partner UNC Psychiatry) == <br />
<br />
Preliminary results seem to indicate a different pattern of growth between the HR+ group (high risk diagnosed with Autism or ASD) and the HR- (high risk not diagnosed with Autism) and LR- (controls not diagnosed with Autism) groups. We observe rapid outward growth of the forebrain in HR+, as compared to more isotropic growth in HR- and LR-. Currently we are working on developing a complete statistical framework for the analysis of shape trajectories as well as the evolution of scalar measurements derived from shape (such as volume or circumference).<br />
<br />
[[File:Hrp_hrm_lrm_mean_scenario_small_first_frame.png|800px|center|thumb|Mean growth scenarios for HR+ (high risk diagnosed with Autism or ASD), HR- (high risk not diagnosed with Autism), and LR- (controls not diagnosed with Autism). [[Media:Hrp_hrm_lrm_mean_scenario_small.gif|Click here for an animation.]] ]]<br />
<br />
[[File:Mean_scenarios_volume_and_circumference.png|800px|center|thumb|Volume and circumference measured from mean growth scenarios.]]<br />
<br />
== Application to Huntington's Disease (DBP partner Iowa) == <br />
<br />
We are investigating the application of our shape regression framework to the study of Huntington's disease. Here we estimate the evolution of a shape complex consisting of 6 sets of sub-cortical structures (12 total shapes). We observe a volume loss over time in all the structures except the ventricles, which are expected to grow if the other structures shrink (they are fluid). These preliminary results on a single subject are promising, and we are beginning to experiment on many additional subjects.<br />
<br />
[[Image:Sub_cort_evo_snapshot.png|thumb|800px|center| Snapshots of the evolution of several sub-cortical structures. Color denotes magnitude of velocity. [[Media:Sub_cort_evolution_sigmaV_10_sigmaW_10_gammaR_0p1.gif|Click here for an animation.]] ]]<br />
<br />
[[Image:Volume_sigmaV_10_sigmaW_10_gammaR_0p1.png|thumb|500px|center| Volume measured after shape regression. Plus signs denote target volume.]]<br />
<br />
= Software Tools = <br />
<br />
At the NAMIC summer project week 2012, we mt with current and prospective users to get their input on what they expect from the software.<br />
<br />
We considered the input format, which presents a trade off between ease of use and robustness. The easiest input format from a user's point of view would be segmentation label images. However, this choice leads to issues with mesh extraction, simplification, smoothing, etc. We have concluded that the most realistic input to the system should be aligned, simplified meshes. It is up to the user to provide aligned meshes of adequate quality and reasonable complexity. However, the users have requested documentation for the preprocessing steps, with specific tools provided for each step.<br />
<br />
We considered the output format as well. We have decided on outputting shapes and corresponding vector fields in ascii VTK format.<br />
<br />
A page for downloading the software and documentation for building/using it can be found http://www.cs.utah.edu/~jfishbau/shapereg.html.<br />
<br />
The software was used successfully by Beatriz Paniagua at UNC to estimate a healthy atlas from over 400 shapes. The results can be seen below. <br />
<br />
{| class="wikitable" style="margin: 1em auto 1em auto;"<br />
|-<br />
| [[Image:cranio_all_exp_small.gif|thumb|500px|center|Atlas of healthy evolution from birth to ~2 years, estimated from over 400 surfaces. Velocity is displayed on the surface. ]] || [[Image:volume.png|thumb|500px|center|Volume measured continuously after regression.]] <br />
|-<br />
|}<br />
<br />
= Former Work =<br />
<br />
In pilot tests on an infant growth study, we demonstrate that volume measurements taken out of our 3D shape regression are compatible with a 1D regression of these measurements. This implies that also other morphometric measurements of interest for clinicians might be smooth and thus model biological change in a realistic way. Leave-several-out experiments demonstrate that the new method better interpolates between data and is therefore more robust to missing observations. This suggests a greater ability to capture the underlying growth of the anatomical structures.<br />
<br />
We plan to apply this method to anatomical shapes of image data on Huntington diseases (HD) provided the IOWA DBP partner. Preliminary studies showed an inflection of change rapid decrease of striatal volume trajectory, and application of this methodology to three time point data might reveal morphological characteristics of such volume loss.<br />
<br />
== Results ==<br />
<br />
Tests of the prototype shape regression software on synthetic and real image data shows smooth shape evolution based on only few discrete time points. This property will be important when comparing shape change trajectories between different subjects, in particular if images/shapes are not taken at the same time. The regression is based on a correspondence-free method that uses the "currents" method for estimation of diffeomorphic registration. This property might be important when shapes with slightly different topology due to segmentation noise and biological change (see e.g. ventricles) are compared.<br />
<br />
The following images show the example of brain ventricles and intracranial volumes (ICV) measured at 6 month, 1 year and 2 years of age and the resulting smooth shape evolution. <br />
<br />
{| border="0" style="background:transparent;"<br />
|[[File:VentShape-Regression.PNG|320px|center|thumb|Brain ventricle change 6mo/1yr/2yrs.]]<br />
|[[File:Vent-volume.png|300px|center|thumb|Ventricle volumes and surface area at discrete time points]]<br />
|[[File:Vent-volume-regression.png|250px|center|thumb|Ventricle and ICV volumes calculated from shape regression]]<br />
|-<br />
|}<br />
<br />
{| border="0" style="background:transparent;"<br />
| [[File:VentShape-Regression-Movie.gif|700px|thumb|left| Shape regression for individual subject from 6 months to 2 years. [[Media:VentShape-Regression-Movie.gif|Click here for full size.]] ]]<br />
|-<br />
|}<br />
<br />
= Literature =<br />
<br />
[1] Miller, M, I., Trouve, A., Younes, L.: On the metrics and Euler-Lagrange equations of Computational Anatomy. Annual Review of Biomedical Engineering 4 (2002), 375–405<br />
<br />
[2] Vaillant, M., Glaunes, J.: Surface matching via currents. In: Proceedings of IPMI.<br />
(2005) 381–392<br />
<br />
[3] Durrleman, S., Pennec, X., Trouve, A., Gerig, G., Ayache, N.: Spatiotemporal atlas estimation for developmental delay detection in longitudinal datasets. In: Proc. of MICCAI’09, Part I. (2009) 297–304<br />
<br />
<br />
<br />
<br />
==Key Investigators==<br />
* Utah: James Fishbaugh, Stanley Durrleman, Guido Gerig<br />
* IOWA: Hans Johnson<br />
<br />
<br />
[http://www.na-mic.org/Wiki/index.php/Algorithm:Utah2 Back to Utah 2 Algorithm Core]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures/ROI_Definitions&diff=98924Projects/Diffusion/2007 Project Week Contrasting Tractography Measures/ROI Definitions2023-04-11T20:40:02Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>{|<br />
|<br />
|-<br />
|<br />
<br />
<br />
'''NOTE: FORNIX LABELS UPDATED ON AUGUST 3rd.'''<br />
This page describes the definition of the regions of interest for five fiber bundles: the Internal Capsule, the Uncinate Fasciculus, the Fornix, the Arcuate Fasciculus and the Cingulum Bundle.[[Image:ColorPalette.png|thumb|right|300px|Color Palette]] <br />
Seed points were defined using a two ROIs approach. Each ROI was drawn on FA and color by orientation maps according to the criteria defined below:<br />
<br />
== Internal Capsule (IC) ==<br />
'''Connects thalamus with frontal lobe. Involved in executive functions and working memory, both of these cognitive skills are abnormal in schizophrenia.'''<br />
<br />
Anterior limb of internal capsule, specifically interested in thalamocortical connections to frontal cortex.<br />
<br />
'''ROI1''' <br />
<br />
The inferior boundary of ROI1 was defined by an axial slice containing the anterior commisure (Fig.1). <br />
<br />
The left and right ROI1s were drawn on a coronal slice containing the anterior commisure, on each side of the midsagittal line (Fig.2). The superior boundary of each ROI1 was defined by the caudate/putamen line <br />
<br />
[[Image:InternalCapsule.jpg|thumb|right|300px|Internal Capsule]] <br />
[[Image:IC_axial.png|thumb|left|300px|Figure1. Axial View of the Anterior Commisure, which serves as the bottom boundary of ROI 1]] <br />
[[Image:IC_ROI1.png|thumb|left|300px|Figure 2. Coronal View of ROI 1 (left and right), showing the inferior boundary (in purple)]] <br />
<br />
|-<br />
|<br />
<br />
'''ROI2'''<br />
<br />
The most anterior coronal slice of the corpus collosum was selected using a sagittal view (Fig 3), and the ROI2s were defined by the whole sections of the left and right hemispheres of the brain (Fig 4).<br />
<br />
[[Image:InternalCapsuleROIs.png|thumb|left|300px|Figure 3.Internal Capsule ROI's 1 and 2 (left)]] [[Image:IC_ROI2.png|thumb|left|300px|Figure 4.Coronal View of ROI 2 (left and right)]]<br />
<br />
|-<br />
|<br />
<br />
The color coding of the resulting ROIs is as follows:<br />
::ROI 1: Left(7) - Right(8)<br />
::ROI 2: Left(11) - Right(12)<br />
<br />
==Uncinate Fasciculus (UNC)==<br />
'''Connects temporal pole and orbito-frontal gyrus. Involved in episodic memory, verbal learning, and emotion. Related to affective flattening and episodic memory dysfunctions in schizophrenia.''' <br><br />
[[Image:Uncinate.jpg|thumb|right|300px|Uncinate Fasciculus]]<br />
The most prominant (central) slice of the fornix was identified using a sagittal view (Fig. 5), and the ROI1s and ROI2s were drawn on the coronal slice adjacent to the most anterior point of the fornix (Fig. 6).<br />
<br />
<p> [[Image:unc_fornROI.png|thumb|left|300px|Figure 5. Sagittal view of the fornix, located centrally in the brain]] [[Image:unc_ROIs.png|thumb|left|300px|Figure 6. Coronal View of ROI 1 and ROI 2, (left and right)]]</p><br />
<br />
|-<br />
|<br />
<br />
<p> [[Image:UncinateROIs.png|thumb|left|300px|Figure 7.Uncinate Fasciculus ROI's 1 and 2 (left)]] </p><br />
<br />
|-<br />
|<br />
<br />
The color coding of the resulting ROIs is as follows:<br />
::ROI 1: Left(7) - Right(8)<br />
::ROI 2: Left(11) - Right(12)<br />
<br />
==Fornix==<br />
'''Connects hippocampus with other brain regions (thalamus, prefrontal cortex). Involved in spatial learning and memory. Related to memory deficits in schizophrenia.''' <br />
[[Image:Fornix.jpg|thumb|right|300px|Fornix]]<br />
<br />
ROI 1 was drawn on the sagittal slice, 5 slices superior to the anterior commisure (Fig. 8 & 10). <br />
ROI 2 was drawn on a coronal slice where the crux of the fornix was present. It was not always the same slice for both sides (Fig. 9 & 11).<br />
<br />
<br />
[[Image:ROI1_ax.png|left|thumb|300px|Figure 8. Axial View of ROI 1]][[Image:ROI2_cor.png|left|thumb|300px|Figure 9. Coronal View of ROI 2 (left=11, right=13)]]<br />
<br />
|-<br />
|<br />
<br />
[[Image:ROI1_sag.png|left|thumb|300px|Figure 10. Sagittal View of Fornix, ROI 1 (both left and right)]] [[Image:ROI2_sag.png|left|thumb|300px|Figure 11. Sagittal View of Fornix, ROI 2 (right)]]<br />
<br />
|-<br />
|<br />
<br />
The color coding of the resulting ROIs is as follows:<br />
::ROI 1: Left & Right (7)<br />
::ROI 2: Left(8) - Right(6)<br />
<br />
==Arcuate Fasciculus==<br />
'''Connects Broca’s and Wernicke’s areas. Involved in language processing. Abnormalities here could be related to thought disorder and semantic processing disruptions that are hallmarks of schizophrenia.'''<br />
[[Image:Arcuate.jpg|thumb|right|300px|Arcuate Fasciculus]] <br />
These labelmaps ('caseD00XXX-FS-arcuate-final.nhdr') were created using automatic gray matter parcellation in Freesurfer and coregistered in Slicer to corresponding DTI dataset. The labelmaps were dilated in Slicer to increase coverage of gray matter.<br />
<br />
<br />
[[Image:Arcuate.png|thumb|left|300px|Figure 12. Gray matter ROI's for Arcuate Fasciculus tractography]] [[Image:Arcuate3d.png|thumb|left|300px|Figure 13. Gray matter ROIs (right side) in 3D]] <br />
<br />
|-<br />
|<br />
<br />
The color coding of the resulting ROIs is as follows:<br />
::ROI 1: Superior Temporal Gyrus - Left(5) - Right(6)<br />
::ROI 2:Inferior Frontal Gyrus- Left(13) - Right (14)<br />
<br />
'''Second generation ROI'''<br />
<br />
The ROIs were generated based on the FreeSurfer cortical parcellation, dilated to include the underlying white matter and mapped back into the DWI-Ed-EPI space:<br />
:: left side: source: Inferior Frontal Gyrus and Sulcus (label #2) ; sink: Superior Temporal Gyrus and Sulcus(label #7)<br />
:: right side: source: Inferior Frontal Gyrus and Sulcus (label #8); sink: Superior Temporal Gyrus and Sulcus (label #9 ).<br />
<br />
==Cingulum Bundle==<br />
'''Interconnects limbic structures (DLPFC, cingulate gyrus, parahippocampal gyrus). Involved in attention, emotions, spatial orientation, memory. Abnormalities here could be related to negative symptoms, hallucinations, memory and executive attentional deficits in schizophrenia.''' <br />
<br />
Tractography - 4 ROIs define<br />
Connectivity - Orbital frontal cortex to amygdala<br />
<br />
[[Image:Cingulum1.jpg|thumb|right|300px|Cingulum]] <br />
<br />
'''ROI 1)''' A coronal plane in the most anterior point of the corpus callosum was selected using the mid-saggital plane (Fig.18), and the left and right ROI1s were drawn on the superior side of the corpus callosum (Fig.15)<br />
<br />
'''ROI 2) & ROI 3)''' The first coronal slice where the left and right corpus connect was selected: the left and right ROI2s were drawn on the superior side of the corpus and the left and right ROI3s were drawn on the inferior side of the corpus (Fig. 16 & 18) <br />
<br />
'''ROI 4)''' The first coronal slice showing where the middle cerebellar peduncle was slected, and the left and right ROI4s were drawn(Fig. 17 & 19) <br />
<br />
<br />
[[Image:cing_roi1.png|left|thumb|300px|Figure 15. Coronal View of Cingulum Bundle ROI 1, Left and Right]] [[Image:cing_roi23.png|left|thumb|300px|Figure 16. Coronal View of Cingulum Bundle ROI's 2 & 3, left and right]][[Image:cing_roi4.png|left|thumb|300px|Figure 17. Coronal View of Cingulum Bundle ROI 4, left and right]]<br />
<br />
|-<br />
|<br />
<br />
[[Image:Cing1ROIs.png|left|thumb|300px|Figure 18. Cingulum Bundle ROI's 1, 2, and 3]] [[Image:Cing2ROIs.png|left|thumb|300px|Figure 19. Cingulum Bundle ROI 4]]<br />
<br />
|-<br />
|<br />
The color coding of the resulting ROIs is as follows:<br />
::ROI 1: Left(7) - Right(8)<br />
::ROI 2: Left(9) - Right(16)<br />
::ROI 3: Left(11) - Right(12)<br />
::ROI 4: Left(13) - Right(14)<br />
<br />
<br />
|}<br />
<br />
<br />
Return to [[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures | Contrasting Tractography Project page]]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Project_Week_25/Steerable_Catheters_Path_Planner_Extension_for_Brain_Surgery_Applications&diff=98923Project Week 25/Steerable Catheters Path Planner Extension for Brain Surgery Applications2023-04-11T20:37:09Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
<br />
Back to [[Project_Week_25#Projects|Projects List]]<br />
<br />
==Key Investigators==<br />
<!-- Key Investigator bullet points --><br />
*[http://nearlab.polimi.it/medical/albertof/ Alberto Favaro] (Polytechnic University of Milan, Italy)<br />
*[http://www.imperial.ac.uk/mechatronics-in-medicine/people/ Marlene Pinzi] (Imperial College, UK)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<!-- Objective bullet points --><br />
The project consists in a reliable and time-efficient pre-operative path planner for steerable catheters, intended to be used in neurosurgical applications. The algorithm estimates a pathway from an entry to a target point within the 3D space defined by the brain volume in accordance to specific optimality parameters and constraints, as the geometric and kynodynamic characteristics of the catheter, the distance from inner brain structures (e.g. the main blood vessels) and the total path length.<br />
<br />
|<!-- Approach and Plan bullet points --><br />
The workflow consists in the following steps:<br />
* Definition of a risk-based distance map based on a multimodal brain imaging<br />
* Piecewise-linear path estimation, exploiting the 3D implementation of [1]<br />
* Path interpolation via NURBS curves (a 2D application of the method can be found in [2]) accounting for catheter cinematic and safety constraints<br />
* Uncertainties map computation, to account for path tracking error during the catheter insertion<br />
|<!-- Progress and Next steps (fill out at the end of project week), bullet points --><br />
Goals achieved:<br />
* Deformable image registration via Plastimatch<br />
* Blood vessel segmentation through VMTK<br />
* 3D BIT* path planner implementation<br />
* Path interpolation<br />
* Surgeon eye view<br />
Future steps:<br />
# DTI data integration<br />
# Robust path interpolation considering catheter cinematic constraints<br />
# Uncertainties map<br />
[[File:FavaroPinzi_interface.png|320px]]<br />
[[File:FavaroPinzi_path.mov]]<br />
<br />
<br />
|}<br />
<br />
==Illustrations==<br />
<!--http://i0.wp.com/www.eden2020.eu/wp-content/uploads/2016/06/2.5mm-catheter-blue-long-2.png?fit=1200%2C456--><br />
<br />
{|<br />
| Eden2020 steerable catheter:<br />
|[[image:2.5mm-catheter-blue-long-2.png|left|600px|thumb|2.5mm Blue Catheter]]<br />
|}<br />
<br />
==Video==<br />
Surgeon eye view:<br />
[[File:FavaroPinzi_view.gif]]<br />
<br />
==Background and References==<br />
The proposed path planning solution finds a possible direct implementation in the [http://www.eden2020.eu EDEN2020 project], a recently founded EU project (GA No. 688279), which aims to develop an innovative system from treating glioblastoma – a highly malignant tumor involving the central nervous system – through a pioneering steerable catheter (see figure above).<br />
<br />
#Gammell, Jonathan D., Siddhartha S. Srinivasa, and Timothy D. Barfoot. "Batch informed trees (BIT*): Sampling-based optimal planning via the heuristically guided search of implicit random geometric graphs." Robotics and Automation (ICRA), 2015 IEEE International Conference on. IEEE, 2015<br />
#Jalel, Sawssen, Philippe Marthon, and Atef Hamouda. "A new path generation algorithm based on accurate NURBS curves." International Journal of Advanced Robotic Systems 13.2 (2016): 75.</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=October_08_2009_Meeting:_VT-NAMIC_Revised_atlas_construction_workflow&diff=98922October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflow2023-04-11T20:26:04Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>== TODOs ==<br />
<br />
== Software ==<br />
<br />
== Workflow ==<br />
<br />
=== Template Tommy (deprecated) ===<br />
<br />
'''Step 1''': Prepare the data using the instructions -- LINK<br />
<br />
'''Step 2''': Gradient anisotropic diffusion. Tools: Slicer GAD module. Parameters: time step: 0.0625, iterations: 5, conductance: 1. ''Note: Should try with and without GAD. Sandy suggested GAD can cause troubles for EM.''<br />
<br />
'''Step 3''': Initial registration 6+9+12 DOF registration. Tools: BRAINSFit svn r301. Parameters: default except CenterOfHead initializer with ROIAUTO sampling region. Comments: failure to recover the pose for Hugo and Valentino (both have severe head tilt in all three planes). Execution time: ~2 min per subject.<br />
<br />
'''Step 4''': Manual pose alignment for Hugo and Valentino. Transforms "hardened" in Slicer MRML, volumes saved and re-registered same way as described in Step 3. Registration issue resolved. Tools: Slicer Transforms module, BRAINSFit.<br />
<br />
'''Step 5 -- Ginger''': Manual ICC for Tommy. Tools: itkSNAP, manual editing by Ginger. Tried Xiaodong's SkullStrippingModule, no luck.<br />
<br />
'''Step 6''': Editing of ICC label map. Tools: Slicer smoothing label map module. Parameters: 10 iterations.<br />
<br />
'''Step 7''': Manual mask dilation, so that each brain of each subject following registration in Step is contained. Tools: Slicer Editor module. Parameters: 8-neighbor, repeated 3 times.<br />
<br />
'''Step 8''': Resampling of the ICC to each subject. Tools: Slicer ResampleVolume2 command line module. Parameters: NN interpolation.<br />
<br />
'''Step 9''': Bias field correction with ICC. Tools: Slicer N3MRILightCLI extension. Parameters: default values except number of iterations increased from 50 to 100, convergence threshold decreased from 0.001 to 0.0001, ICC label from Step 8. Execution time: < 2 min per subject. Comments: There are some parameters in N3 which we understand and can play with. Subjective (?) trying to evaluate if the result is better. ''Note: should also try not correcting for bias field outside EM.''<br />
<br />
'''Step 10 -- we are here right now''': Pipelined registration (6+9+12+BSpline). Tried: (1) ICC ROI from step for moving floating, BSpline step segfaults; (2) ROIAUTO (same as in Step 3), BSpline completes, but resampled volume does not make any sense. AF: I suspect BSpline registration may not be able to handle non-axis-aligned volumes. Comments: When resampling, do not forget to use higher order interpolator. Debugging data: [[File:Tommy-Calvin-bspline_registration.tgz]]<br />
<br />
'''Step 11''': Average all subjects to get average template.<br />
<br />
'''Step 12''': Manually edit ICC labels for each subject, skull strip here or after Step 9, edit and repeat all steps to improve registration.<br />
<br />
'''Remaining steps''': <br />
<br />
* Segment GM/WM/CSF+Putamen/Caudate/Hippocampus in the averaged template. <br />
* Invert the deformation field from Step 10 (Step 12?), and map the segmentations to the individual subjects. <br />
* Manually edit each subject labels. Map back to the average template and calculate the probabilities atlas. <br />
* Run EM Segmenter to get the bias field. Repeat again?<br />
<br />
=== Template Gucci ===<br />
<br />
Following the discussion during Oct'09 meeting, the agreement is that Gucci is the best subject to be used as a template for atlas building (see meeting notes). The current progress in atlas construction will be reported here.<br />
<br />
Transforms, scripts and other relevant material (except data) will be maintained on the NAMIC Sandbox here: [http://viewvc.slicer.org/viewcvs.cgi/trunk/VervetAtlas/?root=NAMICSandBox http://viewvc.slicer.org/viewcvs.cgi/trunk/VervetAtlas/?root=NAMICSandBox]<br />
<br />
'''Step 1''' Prepare the data using [[October_07_2009_Meeting:_VT-NAMIC_Data_load_protocol_and_comments|instructions]]. Result: ''<Subject>-raw.nrrd''<br />
<br />
'''Step 2''' Discard the directions matrix from the input data using [http://viewvc.slicer.org/viewcvs.cgi/trunk/VervetAtlas/Tools/DiscardDirectionCosines DiscardDirectionCosines Slicer extension]. Images with non-orthogonal orientation result in poor performance of B-spline registration at a later step. Result: ''<Subject>-axial.nrrd''<br />
<br />
'''Step 2''' Segment Gucci (template) ICC manually using [http://www.itksnap.org ITK-SNAP] (spline editing capabilities, not available in Slicer). Result: ''Gucci-ICC.nrrd''<br />
<br />
'''Step 3''' Register subjects to template with BRAINSFit. (Important modifications to the default parameters: ''--transformType Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine,BSpline --initializeTransformMode CenterOfHead''). Save the resulting affine and affine+bspline bulk transforms as .tfm (problems reading .mat transforms have been observed with different tools).<br />
<br />
'''Step 4''' Invert the transform using [http://viewvc.slicer.org/viewcvs.cgi/trunk/VervetAtlas/Tools/AtlasTools/InvertBSpline.cxx InvertBSpline tool], recover ICC for each subject by applying the inverse transform to the ICC of Gucci. Resampling should be performed with ApplyWarp tool from [http://www.nitrc.org/projects/brainsdemonwarp/ BRAINSDemonWarp package]. ResampleVolume2 from Slicer does not give consistent results and has not been tested with bulk Affine+BSpline transform ([http://na-mic.org/Mantis/view.php?id=709 bug report #709 submitted])<br />
<br />
'''Step 5''' Perform bias correction for each subject with [http://www.insight-journal.org/browse/publication/640 N4] using the recovered ICC as the mask. <br />
<br />
'''Step 6''' Apply histogram matching of each ICC-masked subject to the template (Gucci) with [http://viewvc.slicer.org/viewcvs.cgi/trunk/VervetAtlas/Tools/AtlasTools/HistogramMatchICC.cxx HistogramMatchICC tool]. The resulting images are skull-stripped, bias-corrected, post histogram matching.<br />
<br />
'''Step 7''' Manually segment RIGHT SIDE subcortical structures using Gucci and the average template as the guide. This was done by Andrey under guidance of Ron. The following numbering conventions have been adopted:<br />
<br />
<pre><br />
Assumption: The enhancing area on the image outside monkey head marks the RIGHT side of the subject.<br />
<br />
Label conventions:<br />
<br />
1: CSF<br />
2: GM<br />
3: WM<br />
<br />
11 and 12: Right and Left Thalamus<br />
13 and 14: Right and Left Caudate<br />
15 and 16: Right and Left Putamen<br />
17 and 18: Right and Left Globus Pallidus<br />
19 and 20: Right and Left Hippocampus<br />
<br />
</pre><br />
<br />
'''Step 8''' Use [http://viewvc.slicer.org/viewcvs.cgi/trunk/VervetAtlas/Tools/ThreePointMirror ThreePointMirror extension] to reflect the RIGHT SIDE labels for subcortical structures to the left side. This was done by manually placing three fiducials at the average template midline, and running the tool. The reflected LEFT SIDE labels were not in perfect alignment, and were manually edited by Andrey. ''Note: at this stage, these segmentations are in the original space of Gucci after discarding direction cosines from the orientation matrix.''<br />
<br />
'''Step 7''' Align AC-PC line of the average template manually.<br />
<br />
'''Step 8''' Register (up to B-spline) masked, bias-corrected input subjects to the AC-PC aligned average template from the previous step. This is done with BRAINSFit tool, same parameters as in Step 3.<br />
<br />
'''Step 9''' Resample the axial subject images (1) with the Affine+BSpline transform and (2) with Affine transform component only, which were obtained in the previous step. Note: at this step, BSpline interpolator was used for greyscale images. Also, ICC for each subject was resampled, as well as the segmentations of subcortical structures in Gucci space. ''At this step, we have subcorticals in the space of the second iteration average image.''<br />
<br />
'''Step 10''' Perform histogram matching of bias-corrected, resampled to average template space, subjects to the average template, use resampled ICC mask. The output is 10 skull-stripped subjects in the space of average template. Recompute the average templates using ''affinely registered'' and ''bspline registered'' masked scans. ''The result of the averaging affinely aligned subjects is the final average template, and the bspline average is the image used to segment CSF/WM/GM, and back-propagate all structures to the subjct images.''<br />
<br />
'''Step 11''' Segment CSF,GM,WM in the bspline average using Slicer Editor module with thresholding. Approximate threshold values -- CSF: [100,7000], GM:[7000,14000], WM[1400,inf]. Use ImageLabelCombine Slicer module to merge CSF/GM/WM labels with the projected segmentations of subcortical structures. ''Note: subcortical segmentations overwrite 3class segmentations!'' UPDATE: Threshold based segmentation was substituted for semi-manual 3-class segmentation prepared by Ginger in this step of the workflow!<br />
<br />
'''Step 12''' Given the segmentation of subcorticals in the space of ''bspline registered average'', use InvertBSpline tool to map subcorticals from bspline average to the space of affine average. ''At this step we have 3class + subcortical segmentations for all subjects affinely aligned to the initial averaged template''<br />
<br />
'''Step 13''' Evaluate probability for each label as follows: smooth the label with ~0.5 variance Gaussian kernel, add labels from 10 subjects, divide by the number of subjects. This results in the image with intensities [0,1] for each structure.<br />
<br />
{|<br />
|[[Image:atlas_axial.jpg|thumb|200px|Affine atlas slice]]<br />
|[[Image:atlas_csf_axial.jpg|thumb|200px|Affine atlas CSF]]<br />
|[[Image:atlas_gm_axial.jpg|thumb|200px|Affine atlas GM]]<br />
|[[Image:atlas_wm_axial.jpg|thumb|200px|Affine atlas WM]]<br />
|[[Image:atlas_subcortical models.jpg|thumb|200px|Models of subcortical structures overlap over all subjects for the atlas image]]<br />
|}<br />
<br />
== Progress ==<br />
<br />
''Most recent first''<br />
<br />
* Rhesus atlas registration improved with 2-level bspline<br />
<br />
{|<br />
| Rhesus atlas registered to Calvin<br />
|-<br />
|[[Image:rhesus2calvin-ax.jpg|thumb|200px|]]<br />
|[[Image:rhesus2calvin-sag.jpg|thumb|200px|]]<br />
|[[Image:rhesus2calvin-cor.jpg|thumb|200px|]]<br />
|-<br />
|Rhesus atlas seems to have a deeper sulcus, which is not recovered by registration (can it be recovered?)<br />
|-<br />
|[[Image:calvin-sulcus.jpg|thumb|200px|]]<br />
|[[Image:template2calvin-sulcus.jpg|thumb|200px|]]<br />
|}<br />
<br />
<br />
<br />
* Current effort: register rhesus atlas to vervet subjects. Preliminary results: overlay of the Gucci ''manual'' 3-class segmentation with the rhesus atlas post-affine before bspline registration (first row) and multilevel registration including bspline using BRAINSFit (second row), and another slice from the same volume, not so successful (third row).<br />
<br />
Rhesus has the frontal part bent down, and registration does not seem to capture this sufficiently. More experimentation is needed.<br />
<br />
Also note the differences in the gyration patterns post-registration.<br />
<br />
{|<br />
| '''(1) Overlay of vervet manual segmentation with rhesus atlas after registration up to 12 DOF (affine)'''<br />
|-<br />
|[[Image:vervet-rhesus-axial1.jpg|thumb|200px|]]<br />
|[[Image:vervet-rhesus-saggital1.jpg|thumb|200px|]]<br />
|[[Image:vervet-rhesus-coronal1.jpg|thumb|200px|]]<br />
|-<br />
|'''(2) Same, but after registration up to bspline transform'''<br />
|-<br />
|[[Image:vervet-rhesus-axial2.jpg|thumb|200px|]]<br />
|[[Image:vervet-rhesus-saggital2.jpg|thumb|200px|]]<br />
|[[Image:vervet-rhesus-coronal2.jpg|thumb|200px|]]<br />
|-<br />
|'''(3) Same registration volume as (2), but different slice'''<br />
|-<br />
|[[Image:vervet-rhesus-axial3.jpg|thumb|200px|]]<br />
|[[Image:vervet-rhesus-saggital3.jpg|thumb|200px|]]<br />
|[[Image:vervet-rhesus-coronal3.jpg|thumb|200px|]]<br />
|}<br />
<br />
<br />
* Dec 7, 2009: Initial version of the atlas ready and submitted for review to VT. v0.1: 3class segmentations were produced in the average affine template by thresholding. v0.2: 3class segmentations are resampled from semi-manual labels created by Ginger (cerebellum marked as WM). Both atlases contain: probabilistic segmentations of GM/WM/CSF + subcortical structures and average atlas image. Next steps:<br />
** Ginger will experiment with segmentation using the new atlas, consider itkEMS ([http://wiki.na-mic.org/Wiki/index.php/DBP2:UNC:Tissue_Segmentation_Evaluation relevant study])<br />
** Andrey will work on trying to register the [http://www.na-mic.org/publications/item/view/1555 UNC rhesus atlas] to vervet subjects<br />
<br />
* Nov 30, 2009:<br />
** subcorticals now with hippocampus for one hemisphere)<br />
** label image mirror tool in Sandbox (to simplify second hemisphere segmentation)<br />
* Nov 23, 2009: <br />
** [[Vervet Atlas Construction:Debugging bspline registration]]<br />
** bspline deformation inversion tool in Sandbox (Ginger)<br />
* Nov 19, 2009: <br />
** ApplyWarp tool from [http://www.nitrc.org/projects/brainsdemonwarp/ BRAINSDemonWarp] produces resampled image consistent with the output of BRAINSFit for affine+bspline bundled transform. <br />
** N4 bias correction tested. <br />
** ICC segmentations for subjects are ready for the subjects registered to template, bspline deformation inversion tool is in progress (Ginger)<br />
** initial subcortical segmentations are ready (one hemisphere)<br />
<br />
* Nov 16, 2009: Average template ready, started working on subcortical structures segmentation (AF under Ron's guidance)<br />
<br />
{|<br />
|[[Image:gucci_slice.jpg|thumb|200px|Gucci axial slice (#94) showing contrast for thalamus, globus pallidus, putamen]]<br />
|[[Image:average_registered.jpg|thumb|200px|Same slice, template averaged from registered images]]<br />
|[[Image:average_resampled.jpg|thumb|200px|Same slice, template averaged from resampled images]]<br />
|[[Image:average_subtract.jpg|thumb|200px|Same slice, difference between 2 and 3]]<br />
|}<br />
<br />
* Nov 13, 2009: A significant non-rigid discrepancy between the registered image produced by BRAINSFit and the image resampled with the ResampleVolume2 and the transform produced by BRAINSFit.<br />
<br />
{|<br />
|<gallery perrow="4" heights="200px" widths="300px"><br />
Image:calvin-brainsfit.jpg|'''Calvin registered to Gucci, image produced by BRAINSFit'''<br />
Image:calvin-resampled.jpg|'''Calvin registered to Gucci, image produced by ResampleVolume2 using the transform saved by BRAINSFit'''<br />
Image:calvin-difference.jpg|'''Difference image'''<br />
</gallery><br />
|}<br />
<br />
* Oct 29, 2009: experiments with the input data resampled to be axis-aligned showed significant improvement of the performanc in BSplpine registration. Added a module to discard direction cosines from the input images ([http://svn.na-mic.org/NAMICSandBox/trunk/VervetAtlas/Tools/DiscardDirectionCosines/ http://svn.na-mic.org/NAMICSandBox/trunk/VervetAtlas/Tools/DiscardDirectionCosines/]). Need to re-think the workflow in light of this. Likely, we will not be able to impose AC-PC alignment on the template subject.<br />
<br />
* Oct 27, 2009: discussed the possibility of applying groupwise registration to the vervet data with Lilla Zollei. Lilla has the data, <br />
<br />
* Oct, 2009: <br />
** AF: Progress with workflow stalled, since BSpline registration does not perform well with the current data<br />
** GL: ICC prepared for Gucci, initial attempts to manually segment GM/WM. Difficulties identifying basal ganglia.<br />
** GL: Watershed segmentation considered as a tool to help with manual segmentation. CLI module in preparation.<br />
** AF: Experiments with EM Segmenter to segment GM/WM, ECC+CSF masked out. Not successful.<br />
** AF: ITK 3.16 is required to handle image orientation. Slicer updated accordingly, initial problems with BRAINSFit resolved, but the results are not satisfying (TODO: put images)</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=MegasonLab&diff=98921MegasonLab2023-04-11T20:19:28Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
<br />
{|<br />
| style="width:10%" | [[Image:GoFigure-Zebrafish-Ear-Image.jpg|thumb|left|200px|confocal microscopy image of a Zebrafish embryo .]]<br />
| style="width:90%" |<br />
<br />
== The Megason Lab ==<br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<h1>Intro</h1><br />
. [http://gofigure.caltech.edu]<br />
</div> <br />
<br />
<div style="width: 49%; float: left; padding-right: 3%;"><br />
<h1>Key Investigators</h1><br />
* Sean Megason (Caltech - Harvard Medical School)<br />
* Alex. Gouaillard (Caltech - Harvard Medical School)<br />
* Titus Brown (Caltech - U of Mich.)<br />
* Kishore Mosanliganti (Harvard Medical School)<br />
* Arnaud Gelas (Harvard Medical School)<br />
</div><br />
<br />
|- <br />
|| ... <br />
||<br />
<br />
<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "Level Set Segmentation: Active Contours without edge", [[http://hdl.handle.net/1926/1532 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Meshes Smoothing", [[http://hdl.handle.net/1926/1518 Insight Journal]]<br />
*Mosaliganti, Gelas, Gouaillard, Megason, "Microscopy Image Analysis: Blob Segmentation using Geodesic Active Contours", [[http://hdl.handle.net/1926/1531 Insight Journal]]<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes", [[http://hdl.handle.net/10380/3055 Insight Journal]]<br />
*Mosaliganti, Smith, Gelas, Gouaillard, Megason, "level set segmentation using coupled active surfaces", [[http://hdl.handle.net/1926/1533 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Mesh Discrete Curvature Estimators", [[http://hdl.handle.net/1926/1494 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Mesh Normals Filter", [[http://hdl.handle.net/1926/1495 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Surface Meshes Incremental Decimation Framework", [[http://hdl.handle.net/1926/1488 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Triangular Meshes Delaunay Conforming Filter", [[http://hdl.handle.net/1926/1489 Insight Journal]]<br />
*Gelas, Gouaillard, Megason, "Mutable Priority Queue Container", [[http://hdl.handle.net/1926/1395 Insight Journal]]<br />
*Gelas, Gouaillard, "Parameterization of discrete surfaces", [[http://hdl.handle.net/1926/1315 Insight Journal]]<br />
*Gouaillard , Brown, Bronner-Fraser, Fraser, Megason, "GoFigure and The Digital Fish Project: Open tools and open data for an imaging based approach to system biology", [[http://hdl.handle.net/1926/565 Insight Journal]]<br />
*Gouaillard, Florez, Boix, “A rigorous orientable 2-Manifold Data Structure for optimal Volume and discrete surface interaction”, [[http://hdl.handle.net/1926/306 Insight Journal ]]<br />
|-<br />
<br />
|| [[Image:NAMIC-SLC.jpg|thumb|left|200px|]]<br />
||<br />
<br />
== [[2009_Winter_Project_Week|2009 January: Project Event 8]] ==<br />
This event is scheduled for January 5-11, 2009 in Salt Lake City, Utah. [[2009_Winter_Project_Week|More...]]<br />
<br />
----<br />
[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti) <br><br />
[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard) <br><br />
[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas) <br><br />
<br />
<br />
----<br />
[[AHM2009:Cell Segmentation|Cell Segmentation breakout session]] (Alex G, arnaud G, Kishore M)<br />
<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Summer_Project_Week|2008 June: Project Event 7]] ==<br />
This event is scheduled for <br />
<br />
----<br />
<br />
<br />
----<br />
<br />
|-<br />
<br />
|| [[Image:ProjectWeek-2008.png|thumb|left|200px|]]<br />
||<br />
<br />
== [[2008_Winter_Project_Week|2008 January: Project Event 6]] ==<br />
This event is scheduled for January 7-11, 2008 in Salt Lake City, Utah. [[2008_Winter_Project_Week|More...]]<br />
<br />
----<br />
<br />
The GoFigure project will be present and will focus on finishing a cross-plateform / 64 bits version of the Code. The GUI need to be ported to KWwidget, and the core code to be freed of MFC. [[2008_Winter_Project_Week:GoFigure | The corresponding GoFigure project page]]<br />
<br />
----<br />
<br />
We will also lead a "Geometry and Topology processing of meshes" breakout session in collaboration with Prof. GU from SUNY STonny Brook, and Luca Antiga, from Italia. [[2008_Winter_Project_Week_Geometry_and_Topology_processing_of_Meshes | the breakout session page]].<br />
<br />
|-<br />
| |[[Image:ProjectWeek-2007.png|thumb|200px|left|<small>Picture of the event taken by Jeffrey Hawley</small>]]<br />
| |<br />
<br />
== [[2007_Programming/Project_Week_MIT|2007 June: Project Event 5]] ==<br />
<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.[[2007_Programming/Project_Week_MIT|More...]]<br />
<br />
----<br />
<br />
The Megason Lab was represented by Alex. Gouaillard and sean Megason. It was the first official appearance of GoFigure as an external project and the beginning of a collaboration with NA-MIC.[[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | The corresponding GoFigure project page]]<br />
<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Lung_Segments_Color_Map&diff=98920Lung Segments Color Map2023-04-11T20:07:39Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
! integer_label<br />
! text_label<br />
! color<br />
! notes<br />
|-<br />
|1<br />
|R_UpperLobe_Apical<br />
|style="background:rgb(255,0,0)"|rgb(255,0,0)<br />
|<br />
|-<br />
|2<br />
|R_UpperLobe_Anterior<br />
|style="background:rgb(0,255,0)"|rgb(0,255,0)<br />
|<br />
|-<br />
|3<br />
|R_UpperLobe_Posterior<br />
|style="background:rgb(255,200,0)"|rgb(255,200,0)<br />
|<br />
|-<br />
|4<br />
|R_MiddleLobe_Medial<br />
|style="background:rgb(50,100,255)"|rgb(50,100,255)<br />
|<br />
|-<br />
|5<br />
|R_MiddleLobe_Lateral<br />
|style="background:rgb(255,0,255)"|rgb(255,0,255)<br />
|<br />
|-<br />
|6<br />
|R_LowerLobe_Superior<br />
|style="background:rgb(0,128,0)"|rgb(0,128,0)<br />
|<br />
|-<br />
|7<br />
|R_LowerLobe_AnteriorBasal<br />
|style="background:rgb(255,255,0)"|rgb(255,255,0)<br />
|<br />
|-<br />
|8<br />
|R_LowerLobe_LateralBasal<br />
|style="background:rgb(0,255,255)"|rgb(0,255,255)<br />
|<br />
|-<br />
|9<br />
|R_LowerLobe_PosteriorBasal<br />
|style="background:rgb(255,100,0)"|rgb(255,100,0)<br />
|<br />
|-<br />
|10<br />
|R_LowerLobe_MedialBasal<br />
|style="background:rgb(255,180,180)"|rgb(255,180,180)<br />
|<br />
|-<br />
|11<br />
|L_UpperLobe_Apical<br />
|style="background:rgb(255,0,0)"|rgb(255,0,0)<br />
|<br />
|-<br />
|12<br />
|L_UpperLobe_Anterior<br />
|style="background:rgb(0,255,0)"|rgb(0,255,0)<br />
|<br />
|-<br />
|13<br />
|L_UpperLobe_Posterior<br />
|style="background:rgb(255,200,0)"|rgb(255,200,0)<br />
|<br />
|-<br />
|14<br />
|L_MiddleLobe_Medial<br />
|style="background:rgb(50,100,255)"|rgb(50,100,255)<br />
|<br />
|-<br />
|15<br />
|L_MiddleLobe_Lateral<br />
|style="background:rgb(255,0,255)"|rgb(255,0,255)<br />
|<br />
|-<br />
|16<br />
|L_LowerLobe_Superior<br />
|style="background:rgb(0,128,0)"|rgb(0,128,0)<br />
|<br />
|-<br />
|17<br />
|L_LowerLobe_AnteriorBasal<br />
|style="background:rgb(255,255,0)"|rgb(255,255,0)<br />
|<br />
|-<br />
|18<br />
|L_LowerLobe_LateralBasal<br />
|style="background:rgb(0,255,255)"|rgb(0,255,255)<br />
|<br />
|-<br />
|19<br />
|L_LowerLobe_PosteriorBasal<br />
|style="background:rgb(255,100,0)"|rgb(255,100,0)<br />
|<br />
|-<br />
|20<br />
|L_LowerLobe_MedialBasal<br />
|style="background:rgb(255,180,180)"|rgb(255,180,180)<br />
|<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=KarinW%C3%A5rdell_Visit_2018&diff=98919KarinWårdell Visit 20182023-04-11T20:05:47Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>{| class="wikitable" style="background: white;"<br />
|-style="text-align: center;"<br />
|style="width:50%" |[[Image:Logo_nac.gif|80px]]<br />
|style="width:50%" |[[Image:logosvg.png|80px]]<br />
|}<br />
==Linköping University Guest==<br />
* Professor Karin Wärdell, Ph.D., Professor of Biomedical Engineering, Linköping University, Sweden<br />
<br />
==Brigham and Women's Hospital Hosts ==<br />
*Sonia Pujol, Ph.D., Brigham and Women's Hospital, Harvard Medical School<br />
*Carl-Fredrik Westin, Ph.D.,Brigham and Women's Hospital, Harvard Medical School</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Technical_Information&diff=98918Technical Information2023-04-11T20:01:29Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>=Technical information of 4D Ultrasound=<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]<br />
<br />
<br />
You have to understand the following steps to use 4DUltrasound<br />
<br />
# Fullfill the requirements<br />
# Check out code and build<br />
# Prepare for use<br />
# Understand how to use 4DUltrasound Tutorial<br />
<br />
===Requirement===<br />
In this section you will find requirements to run the software<br />
<br />
==== Software ====<br />
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [https://www.slicer.org/wiki/Slicer3:Build_Instructions here] )''<br />
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''<br />
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''<br />
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''<br />
<br />
===== Modifications =====<br />
* OpenIGTLink Slicer Module:<br />
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module<br />
# Search for "crc" in this file -> You hit find the following lines <br> <br> <code> // If you want to skip CRC check, call Unpack() without argument. </code> <br> <code> int c = imgMsg->Unpack(1); </code> <br> <br><br />
# Change the last line to: <code> int c = imgMsg->Unpack(); </code><br />
# Recompile the OpenIGTLink Module<br />
## Change to the <code> Slicer-build </code> directory and type <code> $make </code><br />
<br />
* OpenIGTLink:<br />
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink<br />
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code><br />
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code><br />
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code><br />
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code><br />
# Recompile OpenIGTLink<br />
## Change to the OpenIGTLink-build directory and type <code> $make </code><br />
<br />
==== Hardware ====<br />
<br />
[[Image:Drawing-System_Design_Hardware.png |600px]]<br />
<br />
''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''<br />
<br />
* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]<br />
** 2 * 6 DOF Sensors<br />
*** 1 Sensor attached to the ultrasound probe<br />
*** 1 Sensor can be used to simulate a tracked surgical instrument<br />
<br />
* Ultrasound machine with Analog video output<br />
<br />
* Frame Grabber Card<br />
The System has successfully been test with the following 2 frame grabber cards:<br />
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]<br />
** Kuroutoshikou KRDM-CX23883<br />
<br />
* Optional: nVidia Cuda compatible graphics card<br />
<br />
===== Hardware Setup =====<br />
<br />
Tracker attached to ultrasound transducer<br />
<br />
[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]<br />
<br />
===Build Instructions===<br />
<br />
<br />
<br />
<br />
<br />
It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.<br />
<br />
A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] <br> <br><br />
<br />
# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound <br> <br><br />
# '''Configure''' via ccmake (version > 2.6) in your build directory <br> <br> ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' <br> <br> If you know how to do this, skip the next steps and procede with ''Compile'' <br> <br> <br />
## Make a new directory in with the name "Build" in the 4DUltrasound dir: <br> <br> <em> .../4DUltrasound$ mkdir Build </em> <br> <br><br />
## Change into the Build directory <br> <br> <em> .../4DUltrasound$ cd Build </em> <br> <br><br />
## Execute ccmake in this directory with the parent directory as parameter <br> <br> <em> .../4DUltrasound/Build$ ccmake ../ </em> <br> <br> If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: <em> .../Slicer3-lib/CMAKE-build/bin/ccmake </em> <br> <br><br />
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message <br> <br><br />
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER <br> <br><br />
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: <em> .../Slicer3-lib/VTK-build </em>) <br> <br> ''(In Ubuntu you must provide the absolute path no relative path will work)'' <br> <br><br />
## Hit "c" to start the configuration <br> <br> -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again <br> <br><br />
## Hit "c" <br> <br><br />
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable <br> <br><br />
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable <br> <br><br />
## Hit "c" <br> <br><br />
## Set "BUILD_SHARED_LIBS" to OFF <br> <br><br />
## Hit "g" to generate the Make files <br> <br><br />
# '''Compile''' 4D Ultrasound: Type <em>$ make </em> in your build directory<br> <br> <em> .../4DUltrasound/Build$ make </em><br />
<br />
=== Preparation to use 4D Ultrasound===<br />
<br />
Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]<br />
<br />
===Running 4D Ultrasound===<br />
<br />
Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]<br />
<br />
You need a working version of Slicer with OpenIGTLink and you must<br />
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code><br />
# Run Slicer<br />
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944<br />
# Run 4DUltrasound on the same machine you run Slicer<br />
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu<br />
<br />
====Commandline Options====<br />
{|border="0" cellpadding="4"<br />
|- bgcolor="silver"<br />
! Command !! Alternative !! Description<br />
|-<br />
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)<br />
|-<br />
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board<br />
|-<br />
<!--| --reconstruct-volume || -rv || Enable volume reconstruction<br />
|-<br />
| --dynamic-volumesize || -dvs || Enable dynamic size of reconstruction volume<br />
|- --><br />
| --track-ultrasound || -tu || Enable ultrasound tracking<br />
|-<br />
| --track-instrument || -ti || Enable instrument tracking<br />
|-<br />
| --simulate-instrument || -si || Simulate instrument<br />
|-<br />
<!--| --oigtl-server xxx || -os xxx || Specify OpenIGTLink server (default: 'localhost')<br />
|-<br />
| --oigtl-port xxx || -op xxx || Specify OpenIGTLink port of server (default: 18944)<br />
|-<br />
| --frames-per-second xxx || -fps xxx || Number of frames per second for the ultrasound data collection (default: 30)<br />
|-<br />
| --video-source xxx || -vs xxx || Set video source (default: '/dev/video0') <br />
|-<br />
| --video-source-channel xxx || -vsc xxx || Set video source channel (default: 3)<br />
|-<br />
| --video-mode xxx || -vm xxx || Set video mode; Options: NTSC, PAL (default: NTSC)<br />
|-<br />
| --scan-depth xxx || -sd xxx || Set depth of ultrasound scan in Millimeter (default: 70mm)<br />
|-<br />
--><br />
| --get-calibration-data || -gcd || Get calibration data<br />
|-<br />
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file<br />
|-<br />
| --verbose || -v || Print more information<br />
|-<br />
|}<br />
<br />
==== TO DO ====<br />
{|border="0" cellpadding="5"<br />
|- bgcolor="silver"<br />
! Priority !! MUST<br />
|-<br />
| align="center" | || <br />
|-<br />
| align="center" | || <br />
|- bgcolor="silver"<br />
! Priority !! SHOULD<br />
|-<br />
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)<br />
|-<br />
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory<br />
|-<br />
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake<br />
|-<br />
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2<br />
|-<br />
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library<br />
|-<br />
|- bgcolor="silver"<br />
! Priority !! COULD<br />
|-<br />
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code<br />
|-<br />
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature<br />
|-<br />
| align="center", width="70px" | || width="600px"| Tracker test feature<br />
|-<br />
| align="center", width="70px" | || width="600px"| Ultrasound test feature<br />
|-<br />
|}<br />
<br />
=== Ultrasound device ===<br />
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.<br />
<br />
==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====<br />
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]<br />
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling<br />
===== Linux (Ubuntu 8.10 , Fedora 5)=====<br />
* The card is automatically correct detected. No further configuration needed.<br />
* Linux Driver: Video4Linux2 bt878<br />
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant<br />
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).<br />
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]<br />
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]<br />
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html<br />
** The Impact VCB has # 10<br />
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"<br />
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"<br />
* The card uses NTSC video interlacing per default<br />
===== Hardware Information =====<br />
* Channel 3 delivers the s-video signal<br />
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):<br />
<code> <br />
int channel = 3;<br />
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))<br />
errno_exit ("VIDIOC_S_INPUT"); <br />
</code><br />
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!<br />
<br />
==== Video4Linux2 ====<br />
Video4Linux is part of the Linux kernel since version 2.6.xx<br />
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]<br />
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]<br />
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver<br />
===== Old links may soon be dead =====<br />
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]<br />
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]<br />
* Link collection for V4L: [http://www.exploits.org/v4l]<br />
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore<br />
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore<br />
<br />
==== Contacts ====<br />
* Christoph Ruetz<br />
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]<br />
<br />
=== Tracking device ===<br />
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.<br />
<br />
=====Contacts=====<br />
* Haiying Liu<br />
<br />
=== Calibration ===<br />
Description: To get the correct information from the ultrasound device it has to be calibrated<br><br />
===== Contacts =====<br />
* Raul San Jose<br />
Information:<br />
* I have serval links and information from Raul on which I have to go through<br />
<br />
== Slicer ==<br />
I am using the Slicer development version, i.e. Slicer trunk. <br />
<br />
=== Python Synchrograb Module ===<br />
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.<br />
<br />
=== Volume Rendering ===<br />
Module '''VolumeRenderingCuda''' was used in Slicer for volume rendering. This module has been moved out of Slicer3 trunk and saved in NAMICSandBox/CUDAForVolumeRendering, and is not actively being developed. Now, we should use '''VolumeRendering''' module. Updated by Haiying Liu on Oct 30, 2009.<br />
<!-- === 3D CUDA ===<br />
I might not use Cuda acceleration since there is no real performance advantage at this point<br />
<br />
==== TO DO ====<br />
* Nothing<br />
<br />
==== Contacts ====<br />
* Ben Grauer: [https://www.slicer.org/wiki/Slicer3:Volume_Rendering_With_Cuda Volume Rendering with CUDA]<br />
* Nicholas Harlambang: CUDA Guru<br />
<br />
==== Documentation: VolumeRenderingCuda Module ====<br />
<br />
* Adjust the '''threshold''' (scroll bar below 'Component Weights Scrollbars') to correct values. Especially the lower value. Normally > 0<br />
* '''Scalar Opacity Mapping''': Shows a histogram of the used values an their transparence. Low transparent, high solid<br />
* '''Scalar Color Mapping''': You can click into and than in the color circle above and select certain colors for a specific value<br />
* '''Composite''': Here you can select different rendering modes<br />
* '''Volume''': You can also select just to display a slice instead of the whole volume. You can transform the slice in the ''Transforms Module'' and than select the ~ transformation matrix in '''Slice Matrix'''<br />
* '''Plus/Minus''': Select if you want to see everything or just the volume on one side of the slice and on the other<br />
--><br />
<br />
=== Links ===<br />
<br />
* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]<br />
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]<br />
<br />
* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]<br />
<br />
* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]<br />
<br />
<br />
<br />
=== Infos on loadable Modules ===<br />
<br />
<br />
<br />
[https://www.slicer.org/wiki/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] <br><br />
<br />
[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI]<br><br />
<br />
[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] <br><br />
<br />
<br />
<br />
=== Subscribe to different meetings ===<br />
<br />
* Journal Club<br />
<br />
* 1st Monday Seminar<br />
<br />
* Office OPRC<br />
<br />
* Radiology Grand Rounds<br />
<br />
* Cimit Forum<br />
<br />
<!--<br />
=== How to "Enable CUDA 2.0 in Fedora 8 for use with Slicer 3.3 Alpha" ===<br />
Date: Sept. 26th 2008<br />
<br />
Fedora 8 is the newest Fedora version for which CUDA is available. The available CUDA Version is 2.0. <br><br />
To enable CUDA 2.0 in Fedora 8 for Slicer 3.3 Alpha follow the steps below:<br />
<br />
==== Installation of Drivers ====<br />
<br />
* Download the CUDA installation files (Driver, Toolkit, SDK) here [http://www.nvidia.com/object/cuda_get.html] and remember the directory in which you downloaded them. I used<br />
for the driver installation binary<br />
~/Download/CUDA/Driver/ <br />
for the tool kit installation binary<br />
~/Download/CUDA/Toolkit/<br />
and for the SDK installation binary<br />
~/Download/CUDA/SDK/<br />
* For the installation there must not run a X-Server. Therefore we have to restart the computer. When you see the GRUB Bootscreen after the reboot press any key to enter the GRUB menu. Highlight the Fedora Version you want to boot and press <br />
a<br />
Then type <br />
Type 3<br />
and hit the 'Enter' key. Fedora will boot up without X Server and drop you at Command Line Login prompt.<br />
* Login and change into root mode via:<br />
su<br />
* Then switch to the directory where you downloaded the driver. For me this means: <br />
cd ~/Download/CUDA/Driver/<br />
* Now we have to change the permissions for the driver-binary and make it executable. This works with <br />
chmod +x BINARY-NAME<br />
(Replace 'BINARY-NAME' with the name of the driver binary)<br />
* Now start the installation with:<br />
./BINARY-NAME<br />
I changed none of the default values during the installation<br />
<br />
* For the sdk compilation follow this reference guide: [http://developer.download.nvidia.com/compute/cuda/2.0-Beta2/docs/SDK_Rel_Notes_Linux_2.0beta2.txt]<br> If you get the error message: "ld: cannot find -lglut", like I did, have a look at the reference under 'IV. Known Issues'<br />
<br />
* In the next step we do the same for the toolkit and for the sdk, e.g chance to the according directory, change the permissions and run the installation with the default values<br />
<br />
<br />
==== Enable CUDA in Slicer 3.3 Alpha ====<br />
<br />
* Start with the installation manual of Ben Grauer. You find it here [http://www.slicer.org/slicerWiki/images/a/ae/Cuda2slicer3.pdf]<br> Below you find corrections to certains points that did not work for me the way it was explained in the manual<br />
<br />
* In 1.1.2 Check out the following slicer branch instead and build it:<br />
<br />
svn co http://svn.slicer.org/Slicer3/trunk Slicer3<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
* Before you can go on with step 1.2.2 you have to Uncomment: <br />
**''CudaSupport'' in Slicer3/Libs/CMakeLists.txt<br />
**''VolumeRenderingCuda'' in Slicer3/Modules/CMakeLists.txt<br />
<br />
* In step 1.2.2 <br />
**you have to use your build directory (Slicer-build) as parameter for ccmake<br />
**for CUDA_INSTALL_PREFIX use /usr/local/cuda<br />
**for FOUND_CUT use $HOME/NVIDIA_CUDA_SDK/common/lib/linux/libcudpp.a<br />
**for FOUND_CUT_INCLUDE use $HOME/NVIDIA_CUDA_SDK/common/inc<br />
<br />
* Step 1.2.3 was not necessary for me<br />
<br />
* Just do a rebuild (run Slicer3/Scripts/getbuildtest.tcl) and the VolumeRenderingCUDA module is available<br />
<br />
This installation worked for me on a DELL machine with XEON Dual Core and a Nvidia G8800. For fast rendering make sure not enable compiz(Desktop Effects).<br />
--></div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Technical_Information&diff=98917Technical Information2023-04-11T20:00:47Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>=Technical information of 4D Ultrasound=<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]<br />
<br />
<br />
You have to understand the following steps to use 4DUltrasound<br />
<br />
# Fullfill the requirements<br />
# Check out code and build<br />
# Prepare for use<br />
# Understand how to use 4DUltrasound Tutorial<br />
<br />
===Requirement===<br />
In this section you will find requirements to run the software<br />
<br />
==== Software ====<br />
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [https://www.slicer.org/wiki/Slicer3:Build_Instructions here] )''<br />
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''<br />
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''<br />
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''<br />
<br />
===== Modifications =====<br />
* OpenIGTLink Slicer Module:<br />
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module<br />
# Search for "crc" in this file -> You hit find the following lines <br> <br> <code> // If you want to skip CRC check, call Unpack() without argument. </code> <br> <code> int c = imgMsg->Unpack(1); </code> <br> <br><br />
# Change the last line to: <code> int c = imgMsg->Unpack(); </code><br />
# Recompile the OpenIGTLink Module<br />
## Change to the <code> Slicer-build </code> directory and type <code> $make </code><br />
<br />
* OpenIGTLink:<br />
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink<br />
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code><br />
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code><br />
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code><br />
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code><br />
# Recompile OpenIGTLink<br />
## Change to the OpenIGTLink-build directory and type <code> $make </code><br />
<br />
==== Hardware ====<br />
<br />
[[Image:Drawing-System_Design_Hardware.png |600px]]<br />
<br />
''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''<br />
<br />
* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]<br />
** 2 * 6 DOF Sensors<br />
*** 1 Sensor attached to the ultrasound probe<br />
*** 1 Sensor can be used to simulate a tracked surgical instrument<br />
<br />
* Ultrasound machine with Analog video output<br />
<br />
* Frame Grabber Card<br />
The System has successfully been test with the following 2 frame grabber cards:<br />
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]<br />
** Kuroutoshikou KRDM-CX23883<br />
<br />
* Optional: nVidia Cuda compatible graphics card<br />
<br />
===== Hardware Setup =====<br />
<br />
Tracker attached to ultrasound transducer<br />
<br />
[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]<br />
<br />
===Build Instructions===<br />
<br />
<br />
<br />
<br />
<br />
It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.<br />
<br />
A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] <br> <br><br />
<br />
# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound <br> <br><br />
# '''Configure''' via ccmake (version > 2.6) in your build directory <br> <br> ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' <br> <br> If you know how to do this, skip the next steps and procede with ''Compile'' <br> <br> <br />
## Make a new directory in with the name "Build" in the 4DUltrasound dir: <br> <br> <em> .../4DUltrasound$ mkdir Build </em> <br> <br><br />
## Change into the Build directory <br> <br> <em> .../4DUltrasound$ cd Build </em> <br> <br><br />
## Execute ccmake in this directory with the parent directory as parameter <br> <br> <em> .../4DUltrasound/Build$ ccmake ../ </em> <br> <br> If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: <em> .../Slicer3-lib/CMAKE-build/bin/ccmake </em> <br> <br><br />
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message <br> <br><br />
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER <br> <br><br />
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: <em> .../Slicer3-lib/VTK-build </em>) <br> <br> ''(In Ubuntu you must provide the absolute path no relative path will work)'' <br> <br><br />
## Hit "c" to start the configuration <br> <br> -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again <br> <br><br />
## Hit "c" <br> <br><br />
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable <br> <br><br />
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable <br> <br><br />
## Hit "c" <br> <br><br />
## Set "BUILD_SHARED_LIBS" to OFF <br> <br><br />
## Hit "g" to generate the Make files <br> <br><br />
# '''Compile''' 4D Ultrasound: Type <em>$ make </em> in your build directory<br> <br> <em> .../4DUltrasound/Build$ make </em><br />
<br />
=== Preparation to use 4D Ultrasound===<br />
<br />
Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]<br />
<br />
===Running 4D Ultrasound===<br />
<br />
Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]<br />
<br />
You need a working version of Slicer with OpenIGTLink and you must<br />
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code><br />
# Run Slicer<br />
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944<br />
# Run 4DUltrasound on the same machine you run Slicer<br />
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu<br />
<br />
====Commandline Options====<br />
{|border="0" cellpadding="4"<br />
|- bgcolor="silver"<br />
! Command !! Alternative !! Description<br />
|-<br />
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)<br />
|-<br />
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board<br />
|-<br />
<!--| --reconstruct-volume || -rv || Enable volume reconstruction<br />
|-<br />
| --dynamic-volumesize || -dvs || Enable dynamic size of reconstruction volume<br />
|- --><br />
| --track-ultrasound || -tu || Enable ultrasound tracking<br />
|-<br />
| --track-instrument || -ti || Enable instrument tracking<br />
|-<br />
| --simulate-instrument || -si || Simulate instrument<br />
|-<br />
<!--| --oigtl-server xxx || -os xxx || Specify OpenIGTLink server (default: 'localhost')<br />
|-<br />
| --oigtl-port xxx || -op xxx || Specify OpenIGTLink port of server (default: 18944)<br />
|-<br />
| --frames-per-second xxx || -fps xxx || Number of frames per second for the ultrasound data collection (default: 30)<br />
|-<br />
| --video-source xxx || -vs xxx || Set video source (default: '/dev/video0') <br />
|-<br />
| --video-source-channel xxx || -vsc xxx || Set video source channel (default: 3)<br />
|-<br />
| --video-mode xxx || -vm xxx || Set video mode; Options: NTSC, PAL (default: NTSC)<br />
|-<br />
| --scan-depth xxx || -sd xxx || Set depth of ultrasound scan in Millimeter (default: 70mm)<br />
|-<br />
--><br />
| --get-calibration-data || -gcd || Get calibration data<br />
|-<br />
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file<br />
|-<br />
| --verbose || -v || Print more information<br />
|-<br />
|}<br />
<br />
==== TO DO ====<br />
{|border="0", cellpadding="5"<br />
|- bgcolor="silver"<br />
! Priority !! MUST<br />
|-<br />
| align="center" | || <br />
|-<br />
| align="center" | || <br />
|- bgcolor="silver"<br />
! Priority !! SHOULD<br />
|-<br />
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)<br />
|-<br />
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory<br />
|-<br />
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake<br />
|-<br />
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2<br />
|-<br />
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library<br />
|-<br />
|- bgcolor="silver"<br />
! Priority !! COULD<br />
|-<br />
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code<br />
|-<br />
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature<br />
|-<br />
| align="center", width="70px" | || width="600px"| Tracker test feature<br />
|-<br />
| align="center", width="70px" | || width="600px"| Ultrasound test feature<br />
|-<br />
|}<br />
<br />
=== Ultrasound device ===<br />
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.<br />
<br />
==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====<br />
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]<br />
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling<br />
===== Linux (Ubuntu 8.10 , Fedora 5)=====<br />
* The card is automatically correct detected. No further configuration needed.<br />
* Linux Driver: Video4Linux2 bt878<br />
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant<br />
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).<br />
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]<br />
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]<br />
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html<br />
** The Impact VCB has # 10<br />
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"<br />
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"<br />
* The card uses NTSC video interlacing per default<br />
===== Hardware Information =====<br />
* Channel 3 delivers the s-video signal<br />
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):<br />
<code> <br />
int channel = 3;<br />
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))<br />
errno_exit ("VIDIOC_S_INPUT"); <br />
</code><br />
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!<br />
<br />
==== Video4Linux2 ====<br />
Video4Linux is part of the Linux kernel since version 2.6.xx<br />
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]<br />
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]<br />
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver<br />
===== Old links may soon be dead =====<br />
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]<br />
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]<br />
* Link collection for V4L: [http://www.exploits.org/v4l]<br />
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore<br />
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore<br />
<br />
==== Contacts ====<br />
* Christoph Ruetz<br />
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]<br />
<br />
=== Tracking device ===<br />
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.<br />
<br />
=====Contacts=====<br />
* Haiying Liu<br />
<br />
=== Calibration ===<br />
Description: To get the correct information from the ultrasound device it has to be calibrated<br><br />
===== Contacts =====<br />
* Raul San Jose<br />
Information:<br />
* I have serval links and information from Raul on which I have to go through<br />
<br />
== Slicer ==<br />
I am using the Slicer development version, i.e. Slicer trunk. <br />
<br />
=== Python Synchrograb Module ===<br />
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.<br />
<br />
=== Volume Rendering ===<br />
Module '''VolumeRenderingCuda''' was used in Slicer for volume rendering. This module has been moved out of Slicer3 trunk and saved in NAMICSandBox/CUDAForVolumeRendering, and is not actively being developed. Now, we should use '''VolumeRendering''' module. Updated by Haiying Liu on Oct 30, 2009.<br />
<!-- === 3D CUDA ===<br />
I might not use Cuda acceleration since there is no real performance advantage at this point<br />
<br />
==== TO DO ====<br />
* Nothing<br />
<br />
==== Contacts ====<br />
* Ben Grauer: [https://www.slicer.org/wiki/Slicer3:Volume_Rendering_With_Cuda Volume Rendering with CUDA]<br />
* Nicholas Harlambang: CUDA Guru<br />
<br />
==== Documentation: VolumeRenderingCuda Module ====<br />
<br />
* Adjust the '''threshold''' (scroll bar below 'Component Weights Scrollbars') to correct values. Especially the lower value. Normally > 0<br />
* '''Scalar Opacity Mapping''': Shows a histogram of the used values an their transparence. Low transparent, high solid<br />
* '''Scalar Color Mapping''': You can click into and than in the color circle above and select certain colors for a specific value<br />
* '''Composite''': Here you can select different rendering modes<br />
* '''Volume''': You can also select just to display a slice instead of the whole volume. You can transform the slice in the ''Transforms Module'' and than select the ~ transformation matrix in '''Slice Matrix'''<br />
* '''Plus/Minus''': Select if you want to see everything or just the volume on one side of the slice and on the other<br />
--><br />
<br />
=== Links ===<br />
<br />
* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]<br />
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]<br />
<br />
* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]<br />
<br />
* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]<br />
<br />
<br />
<br />
=== Infos on loadable Modules ===<br />
<br />
<br />
<br />
[https://www.slicer.org/wiki/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] <br><br />
<br />
[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI]<br><br />
<br />
[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] <br><br />
<br />
<br />
<br />
=== Subscribe to different meetings ===<br />
<br />
* Journal Club<br />
<br />
* 1st Monday Seminar<br />
<br />
* Office OPRC<br />
<br />
* Radiology Grand Rounds<br />
<br />
* Cimit Forum<br />
<br />
<!--<br />
=== How to "Enable CUDA 2.0 in Fedora 8 for use with Slicer 3.3 Alpha" ===<br />
Date: Sept. 26th 2008<br />
<br />
Fedora 8 is the newest Fedora version for which CUDA is available. The available CUDA Version is 2.0. <br><br />
To enable CUDA 2.0 in Fedora 8 for Slicer 3.3 Alpha follow the steps below:<br />
<br />
==== Installation of Drivers ====<br />
<br />
* Download the CUDA installation files (Driver, Toolkit, SDK) here [http://www.nvidia.com/object/cuda_get.html] and remember the directory in which you downloaded them. I used<br />
for the driver installation binary<br />
~/Download/CUDA/Driver/ <br />
for the tool kit installation binary<br />
~/Download/CUDA/Toolkit/<br />
and for the SDK installation binary<br />
~/Download/CUDA/SDK/<br />
* For the installation there must not run a X-Server. Therefore we have to restart the computer. When you see the GRUB Bootscreen after the reboot press any key to enter the GRUB menu. Highlight the Fedora Version you want to boot and press <br />
a<br />
Then type <br />
Type 3<br />
and hit the 'Enter' key. Fedora will boot up without X Server and drop you at Command Line Login prompt.<br />
* Login and change into root mode via:<br />
su<br />
* Then switch to the directory where you downloaded the driver. For me this means: <br />
cd ~/Download/CUDA/Driver/<br />
* Now we have to change the permissions for the driver-binary and make it executable. This works with <br />
chmod +x BINARY-NAME<br />
(Replace 'BINARY-NAME' with the name of the driver binary)<br />
* Now start the installation with:<br />
./BINARY-NAME<br />
I changed none of the default values during the installation<br />
<br />
* For the sdk compilation follow this reference guide: [http://developer.download.nvidia.com/compute/cuda/2.0-Beta2/docs/SDK_Rel_Notes_Linux_2.0beta2.txt]<br> If you get the error message: "ld: cannot find -lglut", like I did, have a look at the reference under 'IV. Known Issues'<br />
<br />
* In the next step we do the same for the toolkit and for the sdk, e.g chance to the according directory, change the permissions and run the installation with the default values<br />
<br />
<br />
==== Enable CUDA in Slicer 3.3 Alpha ====<br />
<br />
* Start with the installation manual of Ben Grauer. You find it here [http://www.slicer.org/slicerWiki/images/a/ae/Cuda2slicer3.pdf]<br> Below you find corrections to certains points that did not work for me the way it was explained in the manual<br />
<br />
* In 1.1.2 Check out the following slicer branch instead and build it:<br />
<br />
svn co http://svn.slicer.org/Slicer3/trunk Slicer3<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
* Before you can go on with step 1.2.2 you have to Uncomment: <br />
**''CudaSupport'' in Slicer3/Libs/CMakeLists.txt<br />
**''VolumeRenderingCuda'' in Slicer3/Modules/CMakeLists.txt<br />
<br />
* In step 1.2.2 <br />
**you have to use your build directory (Slicer-build) as parameter for ccmake<br />
**for CUDA_INSTALL_PREFIX use /usr/local/cuda<br />
**for FOUND_CUT use $HOME/NVIDIA_CUDA_SDK/common/lib/linux/libcudpp.a<br />
**for FOUND_CUT_INCLUDE use $HOME/NVIDIA_CUDA_SDK/common/inc<br />
<br />
* Step 1.2.3 was not necessary for me<br />
<br />
* Just do a rebuild (run Slicer3/Scripts/getbuildtest.tcl) and the VolumeRenderingCUDA module is available<br />
<br />
This installation worked for me on a DELL machine with XEON Dual Core and a Nvidia G8800. For fast rendering make sure not enable compiz(Desktop Effects).<br />
--></div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=4D_Ultrasound_Progress&diff=989164D Ultrasound Progress2023-04-11T19:59:20Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]<br />
<br />
<br />
----<br />
<span style="color:#FF0000"> '''The project is finished. I am documenting the results in my diploma thesis at the moment.''' <span style="color:#FF0000"><br />
----<br />
<br />
== Steps to go ==<br />
<br />
{|border="0" cellpadding="5"<br />
<br />
|- bgcolor="silver"<br />
<br />
! colspan="2" | Slicer<br />
<br />
|-<br />
<br />
| align="center" bgcolor="#009900" | DONE || Implement slicer module to start Synchrograb from within Slicer<br />
<br />
|- bgcolor="silver"<br />
<br />
! colspan="2" | Create 3D volume with Synchrograb<br />
<br />
|-<br />
<br />
| align="center" width="70px" | || width="600px"|Create ultrasound calibration matrix<br />
<br />
|-<br />
<br />
| align="center" width="70px", bgcolor="#009900" | DONE || width="600px"|Create 3D volume with data from the ultrasound device and the tracker<br />
<br />
|-<br />
<br />
| align="center" bgcolor="#009900" | DONE || Include options for turning on and off US/Tracker device in cmake<br />
<br />
|-<br />
<br />
| align="center" bgcolor="#009900" | DONE || Create 3D volume with mockup images and tracking information from the tracker<br />
<br />
|-<br />
<br />
| bgcolor="#009900" align="center" | DONE || Create 3D volume with mockup images and mockup tracking information<br />
<br />
|- bgcolor="silver"<br />
<br />
! colspan="2" | Synchrograb<br />
<br />
|-<br />
<br />
| bgcolor="#009900" align="center" | DONE || Send 3D volume data via OpenIGTLink to Slicer and display data in Slicer<br />
<br />
|-<br />
<br />
| bgcolor="#009900" align="center" | DONE || Compile Synchrograb core i.d. uncomment unnecessary parts (Ultrasound, Tracker)<br />
<br />
|- bgcolor="silver"<br />
<br />
! colspan="2" | Preparation<br />
<br />
|-<br />
<br />
| bgcolor="#009900" align="center" | DONE || Display 3D volume data received via OpenIGTLink with the volume rendering module<br />
<br />
|-<br />
<br />
| bgcolor="#009900" align="center" | DONE || Create stand alone software to send volume data to Slicer via OpenIGTLink<br />
<br />
|-<br />
<br />
| bgcolor="#009900" align="center" | DONE || Compile and run Slicer with OpenIGTLink and volume rendering<br />
<br />
|-<br />
<br />
|}<br />
<br />
== Progress - i.e. what I have done so far==<br />
<br />
<br />
<br />
<br />
<br />
{| border="0" cellpadding="3" cellspacing=0<br />
<br />
|- bgcolor="#abcdef"<br />
<br />
! Month !! Week # !! Start Date - End Date !! Done !! Date Done<br />
<br />
|-<br />
<br />
|height=5|<br />
<br />
|- bgcolor="#D0D0D0"<br />
<br />
!| February !! Week 05 !! 27.01 - 01.02 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | Slices and tracker matrices are sended to Slicer in real-time ||align="center" | x || Fri Jan, 16th<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
!bgcolor="#FFFFFF"| !! Week 04 !! 19.01 - 26.01 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | Literature research complete ||align="center" | x || Thu Jan, 22th<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
!bgcolor="#FFFFFF"| !! Week 03 !! 12.01 - 18.01 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | - ||align="center" | ||<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
!bgcolor="#FFFFFF"| !! Week 02 !! 05.01 - 11.01 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | - ||align="center" | ||<br />
<br />
|- bgcolor="#D0D0D0"<br />
<br />
!| January !! Week 01 !! 29.12 - 04.01 || ||<br />
<br />
|-<br />
<br />
|height="20px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | - ||align="center" | ||<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
!bgcolor="#FFFFFF"| !! Week 52 !! 22.12 - 28.12 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | Trilinear Interpolation works ||align="center" | x || Wed Dec, 17th<br />
<br />
|-<br />
<br />
| || colspan="2" | Reconstructed Volume has correct depth ||align="center" | x || Tue Dec, 16th<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
!bgcolor="#FFFFFF"| !! Week 51 !! 15.12 - 21.12 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | Created Slicer Module to start Synchrograb within Slicer ||align="center" | x || Wed Dec, 10th<br />
<br />
|-<br />
<br />
| || colspan="2" | Ultrasound device module works ||align="center" | x || Tue Dec, 9th<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
!bgcolor="#FFFFFF"| !! Week 50 !! 08.12 - 14.12 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | Fixed vtk3DPanoramicReconstructor together with Noby ||align="center" | x || Fri Dec, 5th<br />
<br />
|-<br />
<br />
| || colspan="2" | NDI Tracker module works ||align="center" | x || Wed Dec, 3rd<br />
<br />
|- bgcolor="#D0D0D0"<br />
<br />
!| December !! Week 49 !! 01.12 - 07.12 || ||<br />
<br />
|-<br />
<br />
| height="20px"|<br />
<br />
|-<br />
<br />
| || colspan="2" | - ||align="center" | ||<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
!bgcolor="#FFFFFF"| !! Week 48 !! 24.11 - 30.11 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | vtkVideoSource works ||align="center" | x || Mon Nov, 24th<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
!bgcolor="#FFFFFF"| !! Week 47 !! 17.11 - 23.11 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | 3D Volume generated with mock-up images and mock-up tracking data ||align="center" | x || Mon Nov, 17th<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
!bgcolor="#FFFFFF"| !! Week 46 !! 10.11 - 16.11 || ||<br />
<br />
|-<br />
<br />
| height="10px"|<br />
<br />
|-<br />
<br />
| || colspan="2" | Tracker Simulator works ||align="center" | x || Thu Nov, 13th<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
! bgcolor="#FFFFFF"| !! Week 45 || 03.11 - 09.11 || ||<br />
<br />
|-<br />
<br />
|height="10px" |<br />
<br />
|-<br />
<br />
| || colspan="2" | Ultrasound Simulator works ||align="center" | x || Tue Nov, 4th<br />
<br />
|- bgcolor="#D0D0D0"<br />
<br />
! November !! | Week 44 || 27.10 - 02.11 || ||<br />
<br />
|-<br />
<br />
| height="20px"|<br />
<br />
|-<br />
<br />
| || colspan="2" | Starting work on "Creating a 3D-Volume with Synchrograb"||align="center" | ||<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
! bgcolor="#FFFFFF"| !! Week 43 || 20.10 - 26.10 || ||<br />
<br />
|-<br />
<br />
| height="10px"|<br />
<br />
|-<br />
<br />
| || colspan="2" |Send Volume Data via OpenIGTLink from SynchroGrab to Slicer ||align="center" | x || Tue Oct, 14th<br />
<br />
|-<br />
<br />
| || colspan="2" |Compile SynchroGrab (using latest OpenIGTLink Library) ||align="center" | x || Tue Oct, 14th<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
! bgcolor="#FFFFFF"| !! Week 42 || 13.10 - 19.10 || ||<br />
<br />
|-<br />
<br />
| height="10px"|<br />
<br />
|-<br />
<br />
| || colspan="2" | Understand and Use OpenIGTLink || align="center" | x || Tue Oct, 7th<br />
<br />
|- bgcolor="#E8E8E8"<br />
<br />
! bgcolor="#FFFFFF"| !! Week 41 || 06.10 - 12.10 || ||<br />
<br />
|-<br />
<br />
|height=10|<br />
<br />
|-<br />
<br />
| || colspan="2" |Get CUDA Rendering Volume working in Slicer || align="center" |x || Wed Oct, 2nd<br />
<br />
|-<br />
<br />
| || colspan="2" |Set up CUDA driver on th303_d4_6 || align="center" | x || Tue Sep, 30th<br />
<br />
|- bgcolor="#D0D0D0"<br />
<br />
! October !! Week 40 || 29.09 - 5.10 || ||<br />
<br />
|-<br />
<br />
| height="20px"|<br />
<br />
|-<br />
<br />
| || colspan="2" | Set up Fedora 8 on th303_d4_6 || align="center" | x || Fri Sep, 26th<br />
<br />
|-<br />
<br />
| || colspan="2" | Totally Understand GradientDiffusion Filter Module || align="center" | x || Thu Sep, 25th<br />
<br />
|- bgcolor="#D0D0D0" <br />
<br />
! September !! Week 39 || 22.09 - 28.09 || ||<br />
<br />
|-<br />
<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images&diff=989152009 Summer Project Week Project Segmentation of Muscoskeletal Images2023-04-11T19:54:37Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
<gallery widths="400px" perrow="6"><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]<br />
Image:Knee.jpg| Knee MRI Image<br />
Image:LabelMap Femur.jpg|Filled Femur Label Map<br />
Image:Femur Patella Tibia.jpg|EM Segmented Output<br />
Image:Logo_simbios.gif<br />
Image:64 58 Affine 350 Iterations.jpeg | 64 Affine Registered on 58<br />
Image:64 58 PipeLinedAffine Registration 200 Iterations.JPG | 64 Pipeline Affine Registered on 58<br />
Image:64 58 BSpline 210 Iterations.JPG | 64 Bspline Registered on 58<br />
Image:42 Masked.jpg | Masked 42 MRI<br />
Image:64 Masked.jpg | Masked 64 MRI<br />
Image:42 BSpline To 64 DifferenceAfter.jpg | Registered Image Difference of 42 and 64<br />
Image:42 Registered To 64.jpg | BSpline Registered Output of 42 and 64<br />
</gallery><br />
<br />
<br />
==Key Investigators==<br />
* Stanford: Harish Doddi, Saikat Pal, Scott Delp<br />
* Harvard: Ron Kikinis<br />
* Steve Pieper, Isomics, Inc. <br />
* Luis Ibanez, Kitware, Inc.<br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The aim of this project is to develop an automatic/semi-automatic methodology to convert whole body imaging datasets into three-dimensional models for neuromuscular biomechanics and finite element simulations. <br />
<br />
Specific Aims<br />
* Explore the segmentation techniques for knee MRI datasets with special focus on patella, femur and tibia bones.<br />
<br />
</div><br />
<br />
<div style="width: 30%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
We are working on understanding the capabilities of RegisterImage module in Slicer to apply image-to-image registration on knee datasets. We are implementing masking algorithms to isolate specific knee bones, and perform parameter exploration to evaluate the sensitivity of registered images to input parameters. We are exploring the feasibility of applying python ICP-based registration algorithms to directly morph a surface model to a target image geometry.<br />
<br />
Our goals for the project week are: <br />
* Implement an algorithm to acquire masked regions of interest from MR datasets.<br />
* Perform and evaluate results from a parameter space exploration study of RegisterImages Batchmake module on knee dataset.<br />
* Resolve issues in building Python modules from slicer source code.<br />
* Explore possibility of model-to-image registration using existing atlas (.vtk, .stl) to a target image using Python ICP Registration module.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Investigated the masking algorithm and completed the module to mask and register images. Need to explore the parameters technique for this code.<br />
* Resolved issues in building Python<br />
* Cluster set up completed<br />
* Converted Model to masked label map volume to further a masked label volume. Now we have the problem of registering label map volume to an MRI image.<br />
<br />
<br />
</div></div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=2012_Progress_Report_Science_Wiki_Version&diff=989142012 Progress Report Science Wiki Version2023-04-11T19:49:17Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]<br><br />
Back to [[2012_Progress_Report|NAMIC_2012_Progress_Report]]<br><br />
<br />
This is where the outline for the 2012 scientific report for NA-MIC goes in. Ann will provide this outline by 4/1.<br />
=Assignments: Short version=<br />
Reporting Interval: 7/1/2011- 6/30/2012<br />
{| class="wikitable sortable labelpage labelpagetable" border="1" width="100%" cellpadding="5"<br />
|- style="background:#c2c2c2; color:black" align="left" <br />
| style="width:20%" | Task<br />
| style="width:20%" | Owner<br />
| style="width:60%" | Title, comments <br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|1. INTRODUCTION<br />
| style="background:#c4f4af; color:black"|Ron<br />
| style="background:#fff6a6; color:black"|Update Figure 1-1. Geo-anatomical Map of NA-MIC Collaborations, Recent changes and Center (administrative) highlights<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|2. [[2012_Progress_Report_HIGHLIGHTS | HIGHLIGHTS]]<br />
| style="background:#c4f4af; color:black"|Will Schroeder, Kitware<br />
| style="background:#b4e4d4; color:black"|2.1 Algorithms, 2.2 Engineering, 2.3 NA-MIC Kit.<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/23/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|3. [[2012_Progress_Report_IMPACT | IMPACT AND VALUE TO BIOCOMPUTING]]<br />
| style="background:#c4f4af; color:black"|Jim Miller, GE<br />
| style="background:#b4e4d4; color:black"|3.1 Impact within the Center, 3.2 Impact within NIH-Funded Research, 3.3 National and International Impact<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4. RESEARCH PROGRESS SUMMARIES<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#fff6a6; color:black"| <br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1 DRIVING BIOLOGICAL PROJECTS<br />
| style="background:#c4f4af; color:black"|DBP PIs<br />
| style="background:#fff6a6; color:black"| <br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1.1 [[2012_Progress_Report_DBP Atrial_Fibrillation | Atrial Fibrillation]]<br />
| style="background:#c4f4af; color:black"|Rob MacLeod, Utah<br />
| style="background:#b4ebd4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1.2 [[2012_Progress_Report_DBP Huntington's Disease | Huntington's Disease]]<br />
| style="background:#c4f4af; color:black"|Hans Johnson, Iowa<br />
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/18/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1.3 [[2012_Progress_Report_DBP Adaptive Radiotherapy | Adaptive Radiotherapy for Head and Neck Cancer]]<br />
| style="background:#c4f4af; color:black"|Gregory C. Sharp, MGH<br />
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/17/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|4.1.4 [[2012_Progress_Report_DBP_TBI | Traumatic Brain Injury]]<br />
| style="background:#c4f4af; color:black"|Jack Van Horn, UCLA<br />
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|5. COMPUTER SCIENCE CORE<br />
| style="background:#c4f4af; color:black"|Ross Whitaker<br />
| style="background:#fff6a6; color:black"|Brief Introduction: Algorithms, Engineering, NA-MIC Kit<br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|5.1 Algorithms<br />
| style="background:#c4f4af; color:black"|Polina Golland, Guido Gerig, Allen Tannenbaum, Martin Styner<br />
| style="background:#b4e4d4; color:black"|5.1.1 Statistical Models of Anatomy and Pathology, Polina Golland<br>A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black"|5.1.2. Geometric Correspondence, Guido Gerig<br>A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br><br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black"|5.1.3. User Interactive Segmentation, Allen Tannenbaum<br>A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br><br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black"|5.1.4. Longitudinal and Time Series Analysis, Martin Styner<br>A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br><br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|5.2 <br />
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller<br />
| style="background:#b4e4d4; color:black"|5.2.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | End-user Platform, Steve Pieper]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black" align="center"|5.2.2. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Computational Platform, Jim Miller]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black" align="center"|5.2.3. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Data Management Platform, Dan Marcus]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|<br />
| style="background:#c4f4af; color:black"|<br />
| style="background:#b4e4d4; color:black" align="center"|5.2.4.[[2012_Progress_Report_Science_Wiki_Version_Engineering | Software Process, Stephen R. Aylward ]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|5.3 [[2012_Progress_Report_Science_Wiki_Version_Engineering | NA-MIC Kit]]<br />
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller<br />
| style="background:#b4e4d4; color:black"|5.3.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Expansion<br>5.3.2. Release<br>]]<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/21/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|6. [[2012_Progress_Report_ARRA_Supplement| ARRA SUPPLEMENT]]<br />
| style="background:#c4f4af; color:black"|Steve Aylward<br />
| style="background:#b4e4d4; color:black"|6.1 Summary of Funded Activity<br />
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|7. [[2012_Progress_Report_Outreach| OUTREACH]]<br />
| style="background:#c4f4af; color:black"|Sonia Pujol<br />
| style="background:#b4e4d4; color:black"|7.1 Summary of Outreach Activities<br><br />
| style="background:#b4e4d4; color:black"|Submitted on 4/13/2012<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|8. NA-MIC PUBLICATIONS <br />
| style="background:#c4f4af; color:black"|Marianna <br />
| style="background:#fff6a6; color:black"|8.1 Papers that Acknowledge NA-MIC, 8.2. Conference Reports [[2012_Progress_Report#Dissemination|Go to All Papers List]]<br />
|<br />
|-<br />
| style="background:#ffffdd; color:black" align="center"|9. External Advisory Board (EAB) Report<br />
| style="background:#c4f4af; color:black"|Bill Lorensen<br />
| style="background:#fff6a6; color:black"|<br />
|<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=2007_Programming/Project_Week_MIT&diff=989132007 Programming/Project Week MIT2023-04-11T19:47:12Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
Back to [[Events]]<br />
<br />
[[Image:ProjectWeek-2007.png|200px]]<br />
<br />
=Welcome to the web page for the 5th Project Week!=<br />
<br />
[[Image:Mit.jpg|thumb|right|400px|Photo taken by Jeffrey Hawley. More [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=3945 photos ] taken by Jeffrey Hawley.]]<br />
<br />
==Summary==<br />
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 48 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.<br />
<br />
Statistics at a glance:<br />
* 85 Registered Attendees: 35 NA-MIC participants, 48 collaborators, 2 EAB+NIH<br />
** 35 NA-MIC Participants breakdown by cores: Core 1 (7), Core 2 (14), Core 3 (10), Core 4-5-6-7 (4)<br />
** 46 Collaborators: Acoustic Med (2), BWH (19), Caltech (2), GE (1), Harvard IIC (1), JHU (1), Kitware (1), Knowledge Vis (1), Mario Negri (1), MGH (2), NWU (4), University of Iowa(12), Virginia Tech (1)<br />
* 41 Projects: DBP-II(6), Structural Analysis (2), Diffusion Image Analysis (7), NA-MIC Kit (14), External Collaborations (12)<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past_Project_Weeks|here]].<br />
<br />
== Logistics ==<br />
*Dates: June 25-29, 2007.<br />
*Location: MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
<br />
'''Registration Fee:''' $200 (this will cover the cost of breakfast, lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to: <br />
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139<br />
<br />
If you are attending for one day only, the registration fee is not required.<br />
<br />
'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br />
<br />
([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br />
<br />
===Introduction to NA-MIC Project Week===<br />
<br />
NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br />
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br />
<br />
* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br />
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br />
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br />
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br />
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br />
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br />
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br />
* Everyone should '''bring a laptop'''. We will have four projectors.<br />
* About half the time will be spent working on projects and the other half in project related discussions.<br />
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br />
<br />
=== Agenda===<br />
* Monday June 25<br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br />
** 3:30-5:30pm Start project work<br />
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]<br />
* Tuesday June 26<br />
** 8:30am breakfast<br />
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])<br />
*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]<br />
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br />
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)<br />
** 11-12pm: [[Special topic breakout: IGT for Prostate]] <br />
** noon lunch<br />
** 1:30-2:30pm: [[Special topic breakout: KWWidgets]] <br />
** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]] <br />
** 3:30-4:30pm: [[Special topic breakout: Atlases]] <br />
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]] <br />
** 5:30pm adjourn for day<br />
* Wednesday June 27<br />
** 8:30am breakfast<br />
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]<br />
** 5:30pm adjourn for day<br />
* Thursday June 28<br />
** 8:30am breakfast<br />
** noon lunch<br />
** 5:30pm adjourn for day<br />
* Friday June 29<br />
** 8:30am breakfast<br />
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br />
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])<br />
<br />
=== Preparation ===<br />
<br />
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week NA-MIC Project Week mailing list].<br />
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engineer Core Projects and Assign/Verify Teams]]<br />
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]<br />
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]<br />
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)<br />
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)<br />
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
<br />
<br />
== A History in Wiki Links ==<br />
A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br />
<br />
== Projects ==<br />
===DBP II===<br />
These are projects by the new set of DBPS:<br />
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br />
#* [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)<br />
#*[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (Nicole Aucoin, John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).<br />
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br />
#*[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)<br />
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br />
#*[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)<br />
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):<br />
#*[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration<br />
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)<br />
<br />
===Structural Analysis===<br />
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)<br />
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)<br />
<br />
===Diffusion Image Analysis===<br />
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose BWH)<br />
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)<br />
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)<br />
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)<br />
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)<br />
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)<br />
# [[Projects/Diffusion/2007_Project_Week_Glyphed_Visualization_For_Volume_Data|Sliced Multiple Glyphed Visualization for Volume Data]] (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)<br />
<br />
===Calibration/Validation===<br />
This is a new category of projects jointly led by team members in Core 1, Core 3 and Core 5<br />
#[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Ross Whitaker, Guido Gerig, Randy Gollub)<br />
<br />
===NA-MIC Kit - Slicer 3===<br />
#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)<br />
#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)<br />
# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)<br />
# [[Projects/Slicer3/2007_Project_Week_Lightbox|Lightbox]] (James, Jim, Wendy, Alex)<br />
# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Curt, Nicole, Alex, Steve, Will, Vince)<br />
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)<br />
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Katie, Steve, Bill Hoffman)<br />
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)<br />
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)<br />
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)<br />
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)<br />
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)<br />
# [[Projects/Slicer3/2007_Project_Week_Lego Mindstorms dissemination for IGT | Lego Mindstorms Dissemination for IGT]] (Danielle Pace)<br />
# [[Projects/Slicer3/2007_Project_Week_EdgeDetection | Edge Detection in Slicer3]] (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)<br />
<br />
===External Collaborations===<br />
# Meshing<br />
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)<br />
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)<br />
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)<br />
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)<br />
# Registration<br />
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)<br />
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)<br />
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)<br />
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)<br />
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)<br />
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)<br />
# MIND Clinical Imaging Study: [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)<br />
<br />
===Non-Medical Collaborations===<br />
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)<br />
<br />
==Attendee List==<br />
===Core1===<br />
#John Melonakos, Georgia Tech, Core 1 <br />
#Tauseef Rehman, Georgia Tech, Core 1 <br />
#Casey Goodlett, UNC, Core 1 <br />
#Serdar K Balci, MIT, Core 1 <br />
#Elliot Uvero, MIT, Core 1 <br />
#Ran Tao, Utah, Core 1 <br />
#Kevin Teich, MGH, Core 1 <br />
===Core2===<br />
#W. Bryan Smith, UCSD/NCMIR, Core 2 <br />
#Jeffrey Grethe, UCSD, Core 2 <br />
#Marco Ruiz, UCSD, Core 2 <br />
#Neil Jones, UCSD, Core 2 <br />
#Jim Miller, GE Core 2 <br />
#Dan Blezek, GE Core 2 <br />
#Steve Pieper, Isomics, Core 2 <br />
#Alex Yarmarkovich, Isomics, Core 2 <br />
#Will Schroeder, Kitware, Core 2 <br />
#Yumin Yuan, Kitware, Core 2 <br />
#Brad Davis, Kitware, Core 2 <br />
#Luis Ibanez, Kitware, Core 2 <br />
#Bill Hoffman, Kitware, Core 2 (Mon, Tue) <br />
#Nathan Hageman, UCLA, Core 2 (Tue, Wed)<br />
<br />
===Core3-I&II===<br />
#Sylvain Bouix, BWH, Core 3 <br />
#Katharina Quintus, BWH, Core 3 <br />
#Marc Niethammer, BWH. Core 3 <br />
#Marek Kubicki, BWH, Core 3 (II) (One-day)<br />
#Clement Vachet, UNC Core 3 (II) <br />
#David Gobbi, Queen's University, Core 3 (II) <br />
#Csaba Csoma, Johns Hopkins University, Core 3 (II) <br />
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II) <br />
#Mark Scully, The MIND Institute, Core 3 (II) <br />
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01 <br />
===Core 4,5,6,7===<br />
#Zack Galbreath, Kitware, Core 4 (Mon, Tue) <br />
#Randy Gollub, MGH, COre 5<br />
#Tina Kapur, BWH, Core 6 <br />
#Ron Kikinis, Core 7, PI <br />
===Collaborators===<br />
#Chris Wyatt, Virginia Tech, Collaborator R01 <br />
#Vincent Magnotta, University of Iowa, Collaborator R01 <br />
#Kiran Shivanna, University of Iowa, Collaborator R01 <br />
#Hans Johnson, University of Iowa, Collaborator <br />
#Gary E. Christensen, University of Iowa, Collaborator <br />
#Joo Hyun (Paul) Song, University of Iowa, Gary's student <br />
#Xiujuan Geng, University of Iowa, Gary's student <br />
#Jake Nickel, University of Iowa, Gary's student <br />
#Nick Kiguta, University of Iowa, Gary's student <br />
#Kunlin Cao, University of Iowa, Gary's student <br />
#James Harris, University of Iowa, Gary's student <br />
#Kai Ding, University of Iowa, Gary's student <br />
#Jeffrey Hawley, University of Iowa, Gary's student <br />
#Luca Antiga, Mario Negri Institute, Collaborator <br />
#Stephen Aylward, Kitware, Collaborator <br />
#Peter Kazanzides, JHU, Collaborator (One-day)<br />
#Skip Talbot, Northwestern University, Collaborator <br />
#Alex Kogan, Northwestern University, Collaborator<br />
#Vladimir Kleper, Northwestern University, Collaborator <br />
#Pat Mongkolwat, Northwestern University, Collaborator <br />
#Greg Sharp, MGH, Collaborator <br />
#Lilla Zollei, MGH, Collaborator (One-day)<br />
#James Ross, GE, Collaborator <br />
#Alex Gouaillard, CEGS Caltech, Collaborator <br />
#Sean Megason, CEGS caltech, Collaborator <br />
#Clif Burdette, Acousticmed, Collaborator <br />
#Jack Blevins, Acousticmed, Collaborator <br />
#Curtis Lisle, KnowledgeVis, Collaborator<br />
#Douglas Alan, Harvard IIC, Collaborator <br />
#Michael Halle, BWH/IIC, Collaborator <br />
#Katie Hayes, BWH, Core 2 <br />
#Nicole Aucoin, BWH, Core 2 <br />
#Wendy Plesniak, BWH, Collaborator <br />
#Kilian Pohl, BWH Collaborator <br />
#Raimundo Sierra, BWH, Collaborator <br />
#Lauren O'Donnell, BWH, Collaborator <br />
#Raul San Jose, BWH, Collaborator <br />
#C-F Westin, BWH, Collaborator <br />
#Demian Wassermann, BWH/INRIA , Collaborator <br />
#Danielle Pace, BWH , Summer Intern <br />
#Sandy Wells, BWH, Collaborator <br />
#Haiying Liu, BWH Collaborator <br />
#Clare Tempany, BWH Collaborator (One-day) <br />
#Noby Hata, BWH Collaborator (One-day)<br />
#Hong Xiang, BWH Collaborator (One-day)<br />
#Kim Lawson, BWH Collaborator (One-day)<br />
#Junichi Tokuda, BWH Collaborator (One-day)<br />
#Robert Cormack, BWH Collaborator (One-day)<br />
<br />
===NIH, EAB===<br />
#Zohara Cohen, NIH (One-day)<br />
#Bill Lorensen, EAB (One-day)<br />
<br />
'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''<br />
<br />
==Pictures==<br />
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=3945 PICTURES!] taken by Jeffrey Hawley</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=2007_December_Slicer_IGT_Programming&diff=989122007 December Slicer IGT Programming2023-04-11T19:45:22Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
<br />
=Introduction=<br />
<gallery Caption="Sponsored by"><br />
image:NAMIC_380x463.jpg|[http://www.na-mic.org NA-MIC]<br />
image:NCIGTlogo.gif|[http://www.ncigt.org NCIGT]<br />
image:Logo_CIMIT.png|IGT program of [http://www.cimit.org CIMIT]<br />
Image:Logo_nac.gif|[http://nac.spl.harvard.edu/ NAC]<br />
</gallery><br />
<br />
This was a working meeting for research groups with funding to work on the IGT extensions of the NA-MIC kit. There will be a follow up meeting during the NA-MIC AHM in SLC.<br />
<br />
=Summery=<br />
Over 20 researchers attended this meeting. <br />
<br />
{|<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo.jpg|200px]]<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo01.jpg|200px]]<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo02.jpg|200px]]<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo03.jpg|200px]]<br />
|-<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo05.jpg|200px]]<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo06.jpg|200px]]<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo08.jpg|200px]]<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo09.jpg|200px]]<br />
|-<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo04.jpg|200px]]<br />
|[[Image:2007_December_Slicer_IGT_Programming_photo07.jpg|200px]]<br />
|}<br />
<br />
<br />
=Dates.Location.Hotels=<br />
<br />
Date: December 12-14, 2007<br />
<br />
SPL at 1249 Boylston Street, Boston MA. ([http://www.spl.harvard.edu/Directions#Getting_to_1249_Boylston_Street Directions])<br />
<br />
Area hotels: [[Boston_Hotels]]<br />
<br />
=Goal=<br />
*Continued [[Leadership:SlicerIGT_2007|'''discussion''']] of Slicer IGT infrastructure, applications, and timelines<br />
*Introduce each team's effort in Slicer in the context of IGT<br />
*Find unmet needs<br />
*Identify high-priority working items<br />
*Identify each team's potential contribution to the high-priority tasks<br />
<br />
=Meeting summery=<br />
Twenty three investigators using Slicer for their IGT research supported by NIH gathered in Brigham and Women's Hospital from December 12 to 14, 2007. <br />
We discussed current status, unmet needs, future direction, and resource sharing in Slicer engineering. Four live demonstrations using real tracking device <br />
and phantoms were performed to facilitate the discussion. In summery, we concluded that the 3D Slicer, which currently centers around medical image <br />
processing and visualization, definitely has proven to be also useful for IGT and has potential to become enabling tool for new domain of research in IGT. <br />
However, we also agreed that Slier still has gap in its in feature list to meet requirements of the investigators goals in their own clinical targets as well as innovative IGT applications. These unmet needs are<br />
*Plug-in mechanism to develop a high-performance software specifically tailored to a target clinical application<br />
*Controlled and fast Data/communication/event management<br />
*Inter-device communication mechanism to/from Slicer<br />
*Fast Volume rendering for 4D IGT<br />
*Flexible GUI design<br />
Objective evidence for existence of these needs derives from our own assessment as well as our extensive discussion during the meeting. Continued existence of these need represents an important problem because, until the needs are met, new and innovative IGT procedures using state-of-art imaging and treatment device may not be available due to lack of guiding and navigation software. <br />
As the next step in IGT research using Slicer, we decided to collaboratively develop the above mentioned mechanism through resource sharing, frequent communication, and if necessary additional funding support.<br />
<br />
=Agenda=<br />
==Wednesday, December 12 ==<br />
'''Theme: Where are we?'''<br />
===12noon: Lunch===<br />
===12:55pm: Welcome (Ron Kikinis)===<br />
===1-2pm:Slicer and IGSTK presentation===<br />
*Slicer: overview of architecture, current status, and future plans (Pieper, Hata)<br />
**History<br />
**Clinical applications<br />
**transition from 2.6 to 3<br />
**resource<br />
**[[media:Pieper-IGT-retreat-2007-12-12.ppt | Slicer Core]] + [https://www.slicer.org/wiki/Slicer3:Loadable_Modules Loadable Modules]<br />
*IGSTK<br />
** [[Media:IGSTK-Architecture-IGT-Meeting-Dec-12-2007.ppt|Architecture Overview]] (Ibanez)<br />
** Current status, and future plans (Cheng) [http://public.kitware.com/IGSTKWIKI/index.php/Design_Discussion Refactoring Design Discussion]<br />
**IGSTK has time stamping for tracker and event.<br />
**Monitors to ensure the minimal latency between display and data acquisition (possible take away from IGSTK to Slicer).<br />
**GUI tools for sample programs are FLTK and Qt<br />
<br />
===215-330pm: Presentation by Slicer Developers===<br />
<br />
*2:30-3:00pm - [[Media:2007_Slicer_programming_meeting-CIMIT.ppt|NCIGT CIGL Stoll]] and Demo<br />
**Issues for Slicer<br />
#Move toward multi-process model, keep idea of GPU capability in mind for future<br />
#online/unsupervised segmentation, online/fast registration (almost like tracking); can trade some accuracy for speed<br />
#flexibility in registration techniques - data collection is not perfectly constrained (patient positions vary, image quality varies, fiducials sometimes/not) - tools for anatomy-based registration<br />
*3:00-3:15 - NA-MIC Collaborator Georgetown Cleary/Yaniv<br />
*3:15-3:30 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides<br />
*3:30pm-3:45pm: Review of today's progress<br />
<br />
===400pm: Adjourn===<br />
===4-6pm (optional) MRI Demonstration ===<br />
*Use of Slicer for control and display with MRI (prostate module) presented by Junichi Tokuda. Location: Advanced MRI center, 221 Longwood, Boston<br />
**See [[2007_December_Slicer_IGT_Programming_MRI_DEMO| slicer-MRI demo]]<br />
<br />
==Thursday, December 13==<br />
'''Theme: Where are we?'''<br />
===9-10:00am Demos:===<br />
*Hata (Tracking at BWH)<br />
*Freudling (Pieper) (Volume rendering)<br />
<br />
===1000-10:30am Demonstrations===<br />
**[[Media:Neuro-Dec07.pdf|Robot-assisted neurosurgery with Slicer ]] (Kazanzides)<br />
**Robot connected to Slicer via Robot control unit (with Real time OS)<br />
**Slicer CT coords != Stealthstation CT coords<br />
**Needs rasToIjk matrix from xml file<br />
**Inter-computer communication<br />
<br />
*Slicer 3 IGT update<br />
<br />
===10:30am: Identifying the unmet needs===<br />
(At this point, representatives from each site should start thinking which part of the unment needs they can take primary responsibility, and take home as homework.)<br />
<br />
#Queens: NA-MIC DBP<br />
#JHU: BRP<br />
#BWH: NCIGT etc.<br />
#Georgetown: Liver RF<br />
#Kitware-BWH<br />
<br />
*Identify the unique needs in IGT<br />
*Identify commonality among the projects<br />
*which one is to be covered by actively funded project?<br />
*Identity and prioritize unmet needs <br />
*Find commonality among the needs, consolidate if necessary<br />
<br />
<br />
<br />
===Unmet needs #1: Plug-in mechanism===<br />
Related wiki page -> [https://www.slicer.org/wiki/Slicer/Features/Events_and_communication Plug-in mechanism / Modules]<br />
*Currently we use CMake + Slicer3<br />
*Compile vs. Run-time -> run-time is current choice for Steve<br />
*Slicer Base version 3.0<br />
*Binary distributed againg Base version<br />
*Firefox extension<br />
*'''How do you balance testing and flexibility.'''<br />
*Version control necessary<br />
*'''effort underway in NA-MIC/NAC'''<br />
*Module/function dependency<br />
<br />
*Common functions to be implemented in Base<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
*Module/function dependency<br />
{| border="1" cellpadding="5" cellspacing="0" align="center"<br />
|-<br />
| align="left" | Features <br />
| align="left" | Base<br />
| align="left" | Module<br />
|-<br />
| align="left" | Visualization<br />
| align="left" | MRML, Arbitary ViewPoint (Pre-defined)<br />
| align="left" | Liver RF<br />
|-<br />
| align="left" | Filtering <br />
| align="left" | None<br />
| align="left" | Command Line Module<br />
|-<br />
| align="left" | IGT <br />
| align="left" | <br />
*Tracker I/O (BWH Hata)<br />
**Tracker On/Off<br />
*Real-Image I/O (BWH Hata)<br />
**'''Video capturing'''<br />
**Simple loading image<br />
**Imager control for each modality<br />
***MRI (NCIGT Tokuda)<br />
<br />
*Image re-slicing based on tracker (BWH Hata Liu)<br />
<br />
*GUI configuration control (XXX)<br />
<br />
*Human interface control<br />
**Foot pedal (BWH Liu)<br />
<br />
*Stereo<br />
*Output to outside display<br />
<br />
*Logging replay and saving<br />
**IGSTK has fast version<br />
**MRML scene recorder (Georgetown)<br />
| align="left" | BWH, Georgetown, JHU, Queens applications<br />
|-<br />
| align="left" | Registration <br />
| align="left" | Transform Display, Edit and Save/Resotre<br />
| align="left" | Calculae Transforms, Resample Data<br />
|-<br />
| align="left" | Segmentation <br />
| align="left" | Label Maps, Parcellated Surface<br />
| align="left" | Segmentation Algorighms<br />
|-<br />
| align="left" | Quantification<br />
| align="left" | Label, Image, Volume Statistics; Numpy access to MRML<br />
| align="left" | Applications in Python or MATLAB<br />
|-<br />
| align="left" | Real-time Integration<br />
| align="left" | VTK Rendering, KWWidgets framework, Tracker Support (as Transforms)<br />
| align="left" | Direct Manipulation of the MRL Scene; 2D/3D Widgets; Device Interface<br />
|-<br />
| align="left" | Diffusion Imaging<br />
| align="left" | DWI, DTI, Fiber Bundles<br />
| align="left" | Tractography, Clustering, Atlases<br />
|-<br />
| align="left" | Application<br />
| align="left" | Bundles of Modules in Distribution: Registration Editor, some Filters<br />
| align="left" | Customized Extensions, Domain specific code, optimized Interface<br />
|-<br />
|}<br />
<br />
<br />
<br />
<br />
===Unmet needs #2 Data/communication/event ===<br />
Related wiki page [https://www.slicer.org/wiki/Slicer/Features/Events_and_communication Events / Data transfer]<br />
<br />
* Data Workflow I/O<br />
* ticking and latency management<br />
* Threads to read-in tracker info<br />
* Special DICOM and PACS<br />
* Priority control of events? -> Event Manager<br />
* Realtime needs<br />
* Inter-communication mechanism to/from Slicer<br />
<br />
* '''Socket mechanism in SlicerDaemon'''<br />
* Steve's presentation of small programming sending coords to SlicerDaemon and updating MRML<br />
* Scenesnapshot can be used as logging. Replay. Crash recovery<br />
* State machines may be useful mechanism in Slicer<br />
** follow up activities in the related wiki page [https://www.slicer.org/wiki/Slicer/Features/Events_and_communication Events / Data transfer] '''<br />
*Connection with commercial navigation system<br />
**MR/T BWH<br />
**Brainlab <br />
**Neuromate<br />
**Medtronics <br />
<br />
<br />
===Unmet needs #4: Inter-device communication mechanism to/from Slicer ===<br />
** [https://www.slicer.org/wiki/Slicer/Features/Middleware Inter-device communication mechanism to/from Slicer]<br />
*** Tracker Image<br />
*** Publish subscribe ORB/ACE [Peter]<br />
*** Socket IGSTK [Junichi Patrick]<br />
<br />
===Unmet needs #5: Volume rendering===<br />
** Volume rendering<br />
*** Performance and speed continue to be upgraded<br />
*** GPU, fastere volume rendering<br />
*** 4D IGT<br />
*** Real I/O<br />
*** New MRML? Time-series MRML volume?<br />
<br />
** (Regulartory approval) (Legal issue/ form / guideline)<br />
<br />
*[[2007_December_Slicer_IGT_Programming_IGSTK_Slicer_Integration|December 12-14, 2007, Slicer IGT Programming - IGSTK Slicer Integration]]<br />
<br />
<br />
===Unmet needs #3: GUI ===<br />
<br />
* [https://www.slicer.org/wiki/Slicer/Features/GUI GUI]<br />
** GUI-Workflow (David)<br />
** David's opening statement from Queens' perspective<br />
** How can we add additional windows?<br />
** KWWidgets has workflow mechanism<br />
** Compacting GUI - necessary<br />
** Single screen? Two screen setup? Two screen setup to be tried by David<br />
** [http://www.kwwidgets.org/Wiki/KWWidgets/Wizard_Workflow KWWidgets Wizard Workflow] [http://www.kwwidgets.org/Wiki/images/5/53/KWWidgets_-_Wizard_Workflow_-_IGT_-_07%2C_Dec.ppt Powerpoint presentation].<br />
<br />
<br />
** Observing events (convenience) <br />
** Status window is nice<br />
** short cut<br />
*** pre-defined view point<br />
*** lower left (two complicated)<br />
** GUI Layout to be stored in MRML (as log)<br />
** Turning off lower left<br />
** Status (window) part<br />
** human interface--<br />
*** '''configurable GUI using current XML mechanism'''<br />
<br />
*5pm: Review day and plan for Friday (Hata)<br />
<br />
*5:30pm: adjourn<br />
<br />
==Friday, December 14==<br />
===9:00am: breakfast, work===<br />
===9:30-11:00am Review of the meeting===<br />
*Discuss how we can continue this effort in what way<br />
**Hands on IGT Week<br />
**Outreaching to animal research community<br />
**Training and simulation<br />
<br />
<br />
*Action Items<br />
**[[2007_Slier_IGTWS_homework_NCIGT| NCIGT]]<br />
**[[2007_Slier_IGTWS_homework_GT| Georgetown]]<br />
**[[2007_Slier_IGTWS_homework_Kitware | Kitware ]]<br />
**[[2007_Slicer_IGTWS_homework_Queens| Queens ]]<br />
**[[2007_Slicer_IGTWS_homework_JHU| JHU ]]<br />
*11:00am-noon: Wrapup/Suggestion to NAC, NCIGT, NAC, and ultimately NIH(Hata) <br />
*noon: adjourn and head out to group lunch<br />
<br />
==Confirmed Attendees==<br />
#Noby Hata, BWH (NCIGT)<br />
#Steve Pieper, Isomics - (All Days) (NAMIC, NAC)<br />
#Patrick Cheng, Georgetown (NAMIC Collab)<br />
#Ziv Yaniv, Georgetown (NAMIC Collab)<br />
#Kevin Cleary, Georgetown (Wed only) (NAMIC Collab)<br />
#Luis Ibanez, Kitware (NAMIC)<br />
#Sebastien Barre, Kitware (NCIGT)<br />
#Stephen Aylward, Kitware (NCIGT)<br />
#Jeff Stoll (except Thursday), BWH/CIMIT (NCIGT) <br />
#Haiying Liu, BWH (NCIGT)<br />
#Katie Hayes, BWH (NAC)<br />
#Peter Kazanzides (except Friday), JHU (NAMIC Collab) <br />
#Csaba Csoma, JHU (NAMIC/NCIGT Collab)<br />
#David Gobbi, Queens (NAMIC/NCIGT Collab)<br />
#Tina Kapur,BWH (NAMIC/NCIGT)<br />
#Ron Kikinis, BWH (NAMIC/NCIGT)<br />
#Junichi Tokuda, BWH (NCIGT)<br />
#Raul San Jose, BWH (NAC)<br />
#Neculai Archip, BWH (Wed only) (NCIGT)<br />
#Nicholas Ayache (NCIGT) (Wed only)<br />
#Andy Freudling, (NAMIC)<br />
#Henrik Keller (NCIGT)<br />
#Benjamin Grauer (NCIGT)</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=WebGLExport_TutorialContestSummer2012&diff=98911WebGLExport TutorialContestSummer20122023-04-11T19:39:49Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>= Overview =<br />
Export data from Slicer to visualize it in a web browser<br />
<br />
'''Audience:''' End-users<br />
<br />
= Testing =<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| WebGL Export || Mac OS - Lion || 4.1 || 06-15-2012 || Nicolas Rannou || OK<br />
|-<br />
| WebGL Export || Windows XP 64 bit || 4.1 || 06-15-2012 || Nicolas Rannou || OK<br />
|-<br />
| WebGL Export || Linux Ubuntu 64 bit || 4.1 || 06-15-2012 || Nicolas Rannou || OK<br />
|-<br />
|}<br />
<br />
= Resources =<br />
*Download the slides [[File:WebGLExport_TutorialContestSummer2012.pdf]]<br />
*Download the data [http://www.spl.harvard.edu/publications/bitstream/download/5276 here]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=UKF-Tractography_TutorialContestWinter2016&diff=98910UKF-Tractography TutorialContestWinter20162023-04-11T19:38:56Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>[[2016_Winter_Project_Week#Agenda|Back to Winter project week Agenda]]<br />
<br />
This tutorial, helps you to load diffusion data, run the tensor estimation, calculate scalar measurements, and define ROIs to finally be able to run UKF tractography.<br />
<br />
*Tutorial [[Media:UKF-Tractography_TutorialContestWinter2016.pdf]] <br />
*Dataset [[Media:UKF-Tractography_TutorialContestWinter2016.zip]]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| UKF-Tractography || Mac OS || 4.5.0-1 release || January-06-2016 || Pegah Kahali<br />
| Pass<br />
|-<br />
| || Windows || || || <br />
| <br />
|-<br />
| || Linux || || || <br />
| <br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=TutorialContestJanuray2016Review&diff=98909TutorialContestJanuray2016Review2023-04-11T19:37:57Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>=Submissions=<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''1) Slicer Version'''||'''2) Platforms'''||'''3) Slicer License'''||'''4) Data anonymized'''||'''5) Contact Info'''||'''6) Tutorial Template followed'''|||'''7) Tutorial Template format followed'''||'''8) Additional Instructions'''||'''Test Windows'''|| '''Test Linux'''||'''Test Mac||Total'''<br />
|-<br />
| Fiber Bundle Selection And Scalar Measurement (http://wiki.na-mic.org/Wiki/index.php/FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016) ||4.5.0-1 release (1) || Mac, Windows, Linux(3) ||Yes (1)||Yes(1) || <br />
|| No ||Yes(1)|| No || Yes(1) ||Yes(1)||Yes(1)||10<br />
|-<br />
| Plastimatch Tutorial Update Winter 2016 (http://wiki.na-mic.org/Wiki/index.php/Plastimatch_TutorialContestWinter2016) ||4.5.0-1 release (1)|| Linux (1)|| Yes(1) ||Yes(1) || GCSHARP@PARTNERS.ORG (1) || No ||Yes(1)|| No ||No ||Yes(1) ||No|| 7<br />
|-<br />
|UKF-Tractography (http://wiki.na-mic.org/Wiki/index.php/UKF-Tractography_TutorialContestWinter2016) ||4.5.0-1 release(1) || Mac (1)|| Yes(1) || Yes(1) || yogesh@bwh.harvard.edu (1) ||No(0) ||Yes(1)||No ||No || No || Yes(1)||7<br />
|-<br />
|Subject Hierarchy (http://wiki.na-mic.org/Wiki/index.php/SubjectHierarchyTutorial2016Winter) ||4.5.0-1 release(1) ||Mac, Windows, Linux(3) ||Yes(1)|| Yes(1) ||csaba.pinter@queensu.ca (1) || Yes(1) ||Yes(1)|| No || Yes(1) || Yes(1) || Yes(1)||12<br />
|}<br />
<br />
=Rules=<br />
<br />
The evaluation criteria for the 2016 tutorial contest are below:<br />
*Tutorial must be based on the Slicer 4.5 nightly build available at the link below:<br />
**[http://slicer.cdash.org/viewFiles.php?buildid=726991 2015.12.15 Slicer4.5 (Linux)]<br />
**[http://slicer.cdash.org/viewFiles.php?buildid=726992 2015.12.15 Slicer4.5 (Windows)]<br />
**[http://slicer.cdash.org/viewFiles.php?buildid=726990 2015.12.15 Slicer4.5 (MacOSX)]<br />
*To enter the contest, you must provide a self-test that can be run in Slicer and '''a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)+'''.<br />
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [https://www.slicer.org/wiki/Slicer:license Slicer license]<br />
*Tutorial data must be anonymized<br />
*Tutorial must include contact information of the primary author (e-mail and phone number) <br />
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2016.ppt | Winter 2016 contest tutorial template]].<br />
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules <br><br />
+Applicants will work with the NAC Training Core in advance to do the multi-platform testing.<br />
<br />
<br />
==Judges==<br />
*Parshin Unadkat<br />
*Utsav Soni<br />
*Ye Cheng<br />
*Valentin Demeusy</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Training:Winter_2017_Contest_Table&diff=98908Training:Winter 2017 Contest Table2023-04-11T19:36:34Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || || ||<br />
|<br />
|-<br />
| || Windows || || || <br />
|<br />
|-<br />
| || Linux || || || <br />
|<br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Training:Winter_2016_Contest_Table&diff=98907Training:Winter 2016 Contest Table2023-04-11T19:35:33Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div><br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || || ||<br />
|<br />
|-<br />
| || Windows || || || <br />
|<br />
|-<br />
| || Linux || || || <br />
|<br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Training:Summer_2014_Contest_Table&diff=98906Training:Summer 2014 Contest Table2023-04-11T19:32:19Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || || || <br />
|<br />
|-<br />
| || Windows 7 32 bit || || || <br />
|<br />
|-<br />
| || Windows 7 64 bit || || || <br />
|<br />
|-<br />
| || Linux 64 bit || || || <br />
|<br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Training:Summer_2013_Contest_Table&diff=98905Training:Summer 2013 Contest Table2023-04-11T19:32:02Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || || || <br />
|<br />
|-<br />
| || Windows 7 32 bit || || || <br />
|<br />
|-<br />
| || Windows 7 64 bit || || || <br />
|<br />
|-<br />
| || Linux 64 bit || || || <br />
|<br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Training:Summer_2012_Contest_Table&diff=98904Training:Summer 2012 Contest Table2023-04-11T19:31:42Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || || || <br />
|<br />
|-<br />
| || Windows 7 32 bit || || || <br />
|<br />
|-<br />
| || Windows 7 64 bit || || || <br />
|<br />
|-<br />
| || Linux 64 bit || || || <br />
|<br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Training:Summer_2011_Contest_Table&diff=98903Training:Summer 2011 Contest Table2023-04-11T19:31:20Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>This table contains all the tests of the Summer 2011 tutorial contest submissions. <br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date '''|| ''' Test Author''' ||'''Comments/Mantis Links'''<br />
|-<br />
|-<br />
| EMSegmenter_TutorialContestSummer2011 ||| 3.6 || Linux 32 || 2011-06-10|| Dominique Belhachemi || success <br />
|-<br />
| EMSegmenter_TutorialContestSummer2011 ||| 3.6 || Linux 64 || 2011-06-10|| Dominique Belhachemi || success <br />
|-<br />
| EMSegmenter_TutorialContestSummer2011 ||| 3.6 || Mac Snow Leopard || 2011-06-10|| Dominique Belhachemi || success <br />
|-<br />
| TBISegmentation_TutorialContestSummer2011 ||| 3.6 || Windows XP || 2011-05-25|| Andrei Irimia || success <br />
|-<br />
| TBISegmentation_TutorialContestSummer2011 ||| 3.6 || Windows 7 || 2011-05-20 || Andrei Irimia || success<br />
|-<br />
| TBISegmentation_TutorialContestSummer2011 ||| 3.6 || Linux 64 || 2011-05-26 || Andrei Irimia || success<br />
|-<br />
| TBISegmentation_TutorialContestSummer2011 ||| 3.6 || Linux 32 || 2011-05-28 || Andrei Irimia || success<br />
|-<br />
| TBISegmentation_TutorialContestSummer2011 ||| 3.6 || Mac Darwin || 2011-06-01 || Andrei Irimia || success<br />
|-<br />
| ShapeAnalysisModule || Slicer 3.6.3 || Linux 64 || 06/03/2011 || Lucile Bompard|| success<br />
|-<br />
| shapeAnalysisMANCOVA_Wizard || Slicer 3.6.3 || Linux 64 || 06/03/2011 || Lucile Bompard|| sucess<br />
|-<br />
| Non-rigid MR-CT Image Registration_TutorialContestSummer2011 || Slicer 3.6.3 (built from source code) || Linux 32 || 06/13/2011 || Atsushi Yamada|| success<br />
|-<br />
| Non-rigid MR-CT Image Registration_TutorialContestSummer2011 || Slicer 3.6.3 (built from source code) || Linux 64 || 06/13/2011 || Atsushi Yamada|| success<br />
|-<br />
| Non-rigid MR-CT Image Registration_TutorialContestSummer2011 || Slicer 3.6.3 (built from source code)|| Mac Darwin || 06/03/2011 || Atsushi Yamada|| success<br />
|-<br />
| Plastimatch Dose Warping || Slicer 3.6.3 || Windows 7 || 06/07/2011 || Nadya Shusharina || success<br />
|-<br />
| Plastimatch Dose Warping || Slicer 3.6.3 || Linux 64 || 06/07/2011 || Greg Sharp || success<br />
|}<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Summer_2011_Tutorial_Contest Summer 2011 tutorial contest]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Training:Slicer3.6_101_Test_Table&diff=98902Training:Slicer3.6 101 Test Table2023-04-11T19:30:03Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>This table contains all the tests of the Slicer3.6 101 page tutorials.<br />
<br />
*For Training Workshop specific module testing results, please refer to the [http://www.na-mic.org/Wiki/index.php/Journal_of_Slicer_Workshop_Tests Journal of Slicer Workshop Tests ]<br />
*For previous module testing results for Slicer versions 3.6 and older, please refer to the [http://wiki.na-mic.org/Wiki/index.php/Journal_of_Slicer_Tests#Concept Journal of Slicer Tests]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|-<br />
| |[http://wiki.na-mic.org/Wiki/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf Centerline Extraction of Coronary Arteries]||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]<br />
|Mac Darwin|| 11-10-11 || OK (Tested by Daniel)<br />
|-<br />
| |[http://wiki.na-mic.org/Wiki/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf Centerline Extraction of Coronary Arteries]||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe '''Release ''' Slicer3-3.6.3-2011-03-04-win32.exe]<br />
|Windows|| 11-10-11 || OK (Tested by Daniel)<br />
|-<br />
| |[http://wiki.na-mic.org/Wiki/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf Centerline Extraction of Coronary Arteries]||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]<br />
|Linux 64|| 11-10-11 || OK (Tested by Daniel)<br />
|-<br />
| |[https://na-mic.org/w/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)]||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]<br />
|Mac Darwin|| 06-10-11 || OK (Tested by Dominique)<br />
|-<br />
| |[https://na-mic.org/w/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)]||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe '''Release ''' Slicer3-3.6.3-2011-03-04-win32.exe]<br />
|Windows|| 06-10-11 || OK (Tested by Dominique)<br />
|-<br />
| |[https://na-mic.org/w/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)]||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]<br />
|Linux 64|| 06-10-11 || OK (Tested by Dominique)<br />
|-<br />
|[https://na-mic.org/w/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)] ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]<br />
|Linux 32|| 06-10-11 || OK (Tested by Dominique)<br />
|-<br />
| |[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)]||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]<br />
|Mac Darwin|| 05-20-11 || OK (Tested by Dominique)<br />
|-<br />
| |[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)]||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe '''Release ''' Slicer3-3.6.3-2011-03-04-win32.exe]<br />
|Windows|| 05-13-11 || OK<br />
|-<br />
| |[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)]||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]<br />
|Linux 64|| 05-17-11 || OK (Tested by Dominique)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)] ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz '''Release ''' (Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz)]<br />
|Linux 32|| 03-23-2011 || OK (Tested by Dominique)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/e/e3/EMSegmenterTutorialSimpleMode-Slicer-3.6.3-1.pdf EM Segmenter (Simple Mode)] ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz '''Release ''' (Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz)]<br />
|Linux 32|| 03-23-2011 || OK (Tested by Dominique)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.slicer.org/download_files/Release/darwin-x86/Slicer3-3.6.2-2010-11-03-darwin-x86.tar.gz '''Release ''' (Slicer3-3.6.2-2010-11-03-darwin-x86.tar.gz)]<br />
|Mac Darwin|| 12-30-2010 || OK (Tested by Daniel)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.slicer.org/download_files/Release/linux-x86/Slicer3-3.6.2-2010-11-03-linux-x86_64.tar.gz '''Release ''' (Slicer3-3.6.2-2010-11-03-linux-x86_64.tar.gz)]<br />
|Linux 64|| 12-29-2010 || OK (Tested by Dominique)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.slicer.org/download_files/Release/linux-x86/Slicer3-3.6.2-2010-11-03-linux-x86.tar.gz '''Release ''' (Slicer3-3.6.2-2010-11-03-linux-x86.tar.gz)]<br />
|Linux 32|| 12-29-2010 || OK (Tested by Dominique)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]<br />
|Windows XP || 12-07-2010 || OK (Tested by SPujol)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86.tar.gz | '''Linux 32''' (Slicer3-3.6.2-2010-12-03-linux-x86.tar.gz Linux-x32)]]<br />
|Linux 32|| 12-07-2010 || OK (Tested by Junichi)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]<br />
|Windows XP || 12-04-2010 || OK (Tested by Junichi)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] |||[[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]<br />
|Mac Darwin || 12-04-2010 || OK (Tested by Junichi)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]<br />
|Linux 64|| 12-04-2010 || OK (Tested by Junichi)<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-darwin-x86.tar.gz ||Mac ||11-2-2010 || All OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86.tar.gz||Linux 32||11-2-2010|| All OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86_64.tar.gz||Linux 64|| 11-2-2010|| All OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-win32.exe|| Win XP&7|| 11-2-2010|| All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/6/67/PerkStationModule_TutorialContestSummer2010.pdf PERK Station Tutorial]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-25-2010||All OK<br />
|-<br />
|VMTK Centrelines Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-25-2010||All OK<br />
|-<br />
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-25-2010||All OK<br />
|-<br />
|EM Fibre Clustering||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-23-2010||All OK<br />
|-<br />
|EM Fibre Clustering||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-23-2010||All OK<br />
|-<br />
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-23-2010||All OK<br />
|-<br />
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-23-2010||All OK<br />
|-<br />
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-22-2010||All OK<br />
|-<br />
|VMTK Centrelines Tutorial||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-22-2010||All OK<br />
|-<br />
|EM Fibre Clustering||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-22-2010||All OK<br />
|-<br />
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-21-2010||All OK<br />
|-<br />
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-21-2010||All OK<br />
|-<br />
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-21-2010||All OK<br />
|-<br />
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-21-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-21-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-20-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-12-2010||All OK<br />
|-<br />
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-12-2010||All OK<br />
|-<br />
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-12-2010||All OK<br />
|-<br />
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-12-2010||All OK<br />
|-<br />
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow Tutorial][https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-12-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow Tutorial][https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-12-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-11-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-11-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-11-2010||All OK<br />
|-<br />
|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal Lesion Comparison] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-10-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK<br />
|-<br />
|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal Lesion Comparison] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow Tutorial][https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK<br />
|-<br />
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-06-2010||All OK<br />
|-<br />
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-06-2010||All OK<br />
|-<br />
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-06-2010||All OK<br />
|-<br />
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-06-2010||All OK<br />
|-<br />
|Robust Statistics Segmentation [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-29-2010||All OK; tutorial slide edits in progress<br />
|-<br />
|Robust Statistics Segmentation [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||09-29-2010||All OK; tutorial slide edits in progress<br />
|-<br />
|Robust Statistics Segmentation [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-29-2010||All OK; tutorial slide edits in progress<br />
|-<br />
|Atlas Label Merging & Surface Based Registration Tutorial [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||09-29-2010||All OK; tutorial slide edits in progress<br />
|-<br />
|Atlas Label Merging & Surface Based Registration Tutorial [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-27-2010||All OK; tutorial slide edits in progress<br />
|-<br />
|Atlas Label Merging & Surface Based Registration Tutorial [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||09-22-2010||All OK; tutorial slide edits in progress<br />
|-<br />
|Atlas Label Merging & Surface Based Registration Tutorial [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-22-2010||All OK; tutorial slide edits in progress<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-09-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||09-09-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||09-09-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-09-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute][https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 |||09-01-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-01-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 |||09-01-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin |||09-01-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
||[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.12010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
||[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
||[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|}<br />
<br />
<br />
Questions, comments, and feedback can be sent to Sonia Pujol (spujol@bwh.harvard.edu)</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Training:Slicer3.6.3_101_Test_Table&diff=98901Training:Slicer3.6.3 101 Test Table2023-04-11T19:28:36Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>This table contains all the tests of the Slicer3.6.3 101 page tutorials.<br />
<br />
*For Training Workshop specific module testing results, please refer to the [http://www.na-mic.org/Wiki/index.php/Journal_of_Slicer_Workshop_Tests Journal of Slicer Workshop Tests ]<br />
*For previous module testing results for Slicer versions 3.6.2 and older, please refer to the [http://wiki.na-mic.org/Wiki/index.php/Journal_of_Slicer_Tests#Concept Journal of Slicer Tests]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]<br />
|Windows|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]<br />
|Linux 64|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]<br />
|Linux 32|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]<br />
|Mac Darwin|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]<br />
|Windows|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]<br />
|Linux 64|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]<br />
|Linux 32|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]<br />
|Mac Darwin|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]<br />
|Windows|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]<br />
|Linux 64|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]<br />
|Linux 32|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]<br />
|Mac Darwin|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]<br />
|Windows|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]<br />
|Linux 64|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]<br />
|Linux 32|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]<br />
|Mac Darwin|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]<br />
|Windows|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]<br />
|Linux 64|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]<br />
|Linux 32|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]<br />
|Mac Darwin|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]<br />
|Windows|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]<br />
|Linux 64|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]<br />
|Linux 32|| || <br />
|-<br />
| ||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]<br />
|Mac Darwin|| || <br />
|}<br />
<br />
Questions, comments, and feedback can be sent to Kathryn Hayes (hayes@nmr.mgh.harvard.edu)</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Training:2010tutorialcontest&diff=98900Training:2010tutorialcontest2023-04-11T19:27:25Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>== Summer 2010 Project Week Panel ==<br />
[[2010_Summer_Project_Week|Back to Project Week Page]]<br />
<br />
[http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials Link to tutorials]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer 3.6'''||'''Platform'''||'''Slicer License'''||'''Contact Info'''||'''Tutorial Template followed'''||'''Additional Directions Clear?'''||'''QA Windows XP'''||'''QA Linux 64'''||'''QA Linux 32'''||'''QA mac'''<br />
|-<br />
|'''Fiducials'''||yes||linux64, windows (linux32, mac)||yes||yes||yes||yes||6-25-2010||7-6-2010||7-6-2010||6-21-2010<br />
|-<br />
|'''RSS (Robust Statistics Segmenter)'''||yes||linux64&32, windows, mac||yes||yes||yes||yes||6-20-2010||6-20-2010||6-20-2010||6-20-2010<br />
|-<br />
|'''Automatic SPHARM Shape Analysis in 3D Slicer'''<ref>currently undergoing debugging; please see Mantis report for details http://www.na-mic.org/Bug/view.php?id=908</ref>||yes||linux||yes||yes||yes||yes||N/A||In Progress||In Progress||N/A<br />
|-<br />
|'''Atlas Label Fusion & Surface Registration'''||yes||linux64(&32), mac, (windows)||yes||yes||yes||yes||7-15-2010||6-22-2010||7-15-2010||6-22-2010<br />
|- <br />
|'''Stochastic Tractography'''||yes||linux64, (mac)||yes||yes||yes||yes||N/A||6-21-2010||6-25-2010||6-21-2010<br />
|-<br />
|'''Robot-assisted MRI-guided prostate biopsy'''||yes||windows, (mac), (linux64&32)||yes||yes||yes||yes|||6-22-2010||7-15-2010||7-15-2010||6-22-2010<br />
|-<br />
|'''GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness'''<ref>currently undergoing debugging; please see Mantis report for details http://www.na-mic.org/Bug/view.php?id=908</ref>||yes||linux||yes||yes||yes||yes||N/A||In Progress||In Progress||N/A<br />
|-<br />
|'''White Matter Lesion Segmentation'''<ref>currently undergoing debugging; please see Mantis report for details http://www.na-mic.org/Bug/view.php?id=908</ref>||yes||linux64&32||yes||yes||yes||yes||N/A||In Progress||In Progress||N/A<br />
|-<br />
|'''Image-overlay Guided Needle Insertion'''||yes||windows||yes||yes||yes||yes||6-21-2010||N/A||N/A||N/A<br />
|-<br />
|'''Fluid Mechanics Tractography'''<ref>currently undergoing debugging due to problems with CMakelists.txt file</ref>||yes, but as a trunk build in NAMIC sandbox||mac||yes||yes||yes||yes||N/A||N/A||N/A||In Progress<br />
|-<br />
|'''End to End Meshing Workflow'''||yes||linux64&32, mac||yes||yes||yes||yes||N/A||6-20-2010||6-20-2010||6-20-2010<br />
|-<br />
|'''Longitudinal Lesion Comparison'''||yes||linux64&32, mac, (windows)||yes||yes||yes||yes||7-15-2010||6-25-2010||6-25-2010||6-23-2010<br />
|}<br />
<br />
*'''N/A''' means that tutorial is not working on the corresponding platform.<br />
<br />
-----</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Tests_of_Iowa_Workshop_tutorials&diff=98899Tests of Iowa Workshop tutorials2023-04-11T19:23:01Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>[[Iowa 2012 Workshop Materials]]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Tutorial Data'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Test Author & Comments/Mantis Links'''<br />
|-<br />
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OS Lion || || ||<br />
|-<br />
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OS Snow Leopard || 2012/03/18 ||2012-03-18 (r19639) || Sonia. OK.<br />
|-<br />
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 32 || || ||<br />
|-<br />
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP || 2012-03-17 || 3/18.12 || Steve<br>Everything works except turning on glyphs after label map seeding, which results in a crash due to lack of memory. Suggestion is to skip this step of the tutorial for users on win32. Another option is to only segment a single slice of the corpus in order to generate fewer tracts. Also it might help to delete the dwi volume after tensor estimation. When I did these steps I was able to complete all steps of the tutorial.<br />
|-<br />
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux Unbuntu 64 || || ||<br />
|-<br />
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux 64 (debug) || || ||<br />
|-<br />
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux 64 (debug)|| r19517 || 03/07/2012 || <br />
Nicole: <s>[http://na-mic.org/Bug/view.php?id=1793 1793]</s>. <s>[http://na-mic.org/Bug/view.php?id=1795 1795]</s><br />
|-<br />
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 64b (package)|| r19577 || 03/13/2012 || <br />
Julien <br>pdf is 95MB !?!?<br>Page 22, Popup look is now different<br>Page 23, in red slice only the popup should still be up (didn't unpin)<br>Page 25: Diffusion Tensor Estimation has been renamed into DWI to DTI estimation<br>Page 25: dwi is already selected as Input DWI<br>Page 25: Minor Bug ! It stays "scheduled" for >5secs, not sure why<br>Page 26: Popup looks different now<br>Page 30: shouldn't labda1~labda2 >> lambda3 look more like a smarties ?<br>Page 32: typo connect ->connects<br>Page 36: Need to click on ">>" button first<br>Page 41: Bug ! After apply, the foreground image is reset to none, need to manually set it back to dti<br>Page 46: After selecting FractionalAnisotropy, Auto WL is automatically selected<br>Page 48: You might want to include screenshot of Link button again<br>Page 51: No need to move the mouse in 3D view, it automatically refreshes. If not, then a bug must be reported<br>Page 57: 1 bullet point has no . at the end(for information, there is no . in the other slides.<br>Page 60: Advice to use the right/left arrow keys to slice through?<br>Page 65: No axial slice displayed in 3D<br>Page 74: explain how to rename?<br>Page 78: explain to go to Annotation module again ?<br>Page 79: no need to turn off and on, it automatically refreshed when I placed the fiducial. If not, then a bug must be reported.<br>Page 81: explain where to place fiducial.<br>Page 82: Bug, it doesn't recompute automatically <br />
|-<br />
|-<br />
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 64b (package) || 4.1.0-rc1-2012-03-17 <br> r19637 || 03/19/2012 || <br />
Benjamin - Work as expected <br> Setting a low (<4) scpacing value, in Glyphs, can turn your computer out of memories <br />
|-<br />
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux Unbuntu 64 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 || Benjamin - Work as expected <br> Setting a low (<4) scpacing value, in Glyphs, can turn your computer out of memories<br />
|-<br />
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OSX 10.7 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 || Jc - Work as expected<br />
|-<br />
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP 32b || Slicer 4.1.0 rc1 (r19609) || 03/15/2012 ||<br />
Julien <br>no link for the data mentioned in the tutorial<br>No mention to what Slicer version the tutorial is compatible with<br>Page1: Slicer Logo is 4.0, does it mean it's compatible with 4.0 ? no<br>Page 10: I have 100modules (from log messages dialog CTRL+0)<br>Page 19: typo: appears in the 2D viewer'''s'''<br>Page 22: Add "fit image to window" icon<br>Page 41: Odd black pixels in fa volume (see email)<br>Page 58: Add arrow to indicates how to change to yellow layout ?<br>Page 60: icon of the draw tool ? I first used the paint tool instead<br>Page 64: no "Minimum Length", only "Minimum Path Length". Bug ? why "Maximum Length" is not also "Maximum Path Length" ?<br>Page 64: Bug: why only Integration Step Length is (mm) but not others?<br>Page 66: Click on "Glyph" -> Crash (Slicer= 690Mo)<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]<br />
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Mac OS Lion || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]<br />
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Windows 7 64 || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]<br />
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset]|| Windows XP 32 || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]<br />
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Linux Ubuntu 64|| Slicer4.1rc1 || 03/19/2012 ||<br />
Benjamin <br> p3 : Image has no link with this tutorial <br> p16 : The Directory HelloPython has two sub directories "code" and "data". Wrong path. <br> p21 : Add comment to warn the user about the indentation <br> p17 : Slicer layout change compare to the previous screenshot <br> p31 : We are not able to copy properly the text <br> p35 : helloPython sript path is ".../helloPython/code/" <br> p36: word "can" is written twice, and I already have 3 items in the sub menu "Exemples" <br> p48: The Directory HelloPython has two sub directories "code" and "data". Wrong path. <br> p50: Slicer layout change compare to the previous screenshot <br> p55: The last line should be on 1 line, or warn the user who may not know how work Python. <br> p59: Same as p48 and p16 <br> p61: Slicer layout change compare to the previous screenshot <br> p62: More explanation maybe - Up/Down - Left/Right - ?<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]<br />
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Linux Ubuntu 64 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 ||<br />
Benjamin - Work as expected<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]<br />
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Windows 7 64b (package) || 4.1.0-rc1-2012-03-17 <br> r19637 || 03/19/2012 ||<br />
Benjamin - Work as expected<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]<br />
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || MacOSX 10.7 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 ||<br />
Jc - Work as expected<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]<br />
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || linux 64 (debug) || || ||<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]<br />
||[[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]] || Mac OS SnowLeopard || 2012.03.18|| 2012.03.18 || Sonia. OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]<br />
||[[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]] || Mac OS Lion || || ||<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]<br />
||[[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]] || Windows 7 64|| 4.1.0-rc1-2012-03-17 r19637 || March 19 || Julien<br>Page 13: Background is already correctly set<br>Page 14: circle on screenshot where to change current volume to "BaselineVolume" (DTIVolume selected by default) (+ typo, it's "BaselineVolume" not "Baseline Volume")<br>Page 24: You might want to mention that Grow Cut works in 3D<br>Page 31: grow cut button circle is off<br>Page 39: I don't have the axial slice visible in 3D view<br>Page 40: Didn't understand why positioning the mouse in the cystic part<br>Page 46: Give description for "Output Fiber Bundle"<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]<br />
||[[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]] || Windows XP 32|| version from tutorial page || March 19 || Steve<br>Worked as expected<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]<br />
||[[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]] || Linux Ubuntu 64 || 4.1rc1 || March 15 || Steve - worked great - few content comments sent to Sonia<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]<br />
||[[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]] || Linux 64 (debug) || || ||<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]<br />
||[[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]] || Linux Ubuntu 64 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 || Benjamin - worked as expected<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]<br />
||[[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]] || Windows 7 (package) || 4.1.0-rc1-2012-03-17 <br> r19637 || 03/19/2012 || Benjamin - worked as expected<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]<br />
||[[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]] || Mac OSX 10.7 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 || Jc - worked as expected<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization ]<br />
||[[media:3DVisualizationData.zip| 3D Visualization dataset]] || Mac OS SnowLeopard || 2012-03-18 || 2012-03-18 (r19639) || Sonia. OK. Note: The Save Scene doesn't save the scene with the correction orientation e.g. if the user saves the scene with 3D viewer showing the 3D models in Superior orientation, the scene gets restore in Anterior orientation.<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]<br />
||[[media:3DVisualizationData.zip|3D Visualization dataset]] || Mac OS Lion || || ||<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]<br />
||[[media:3DVisualizationData.zip| 3D Visualization dataset]] || Windows 7 64 || || || Julien<br>Page 47: Opacity could have been set from the tree view directly (last column)<br>Page 55 is a double<br>Page 56: no mention to check the Slice Intersection checkbox<br>Page 67 is a doublon<br><br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]<br />
||[[media:3DVisualizationData.zip| 3D Visualization dataset]] || Windows XP 32 || 2012-03-17 || 3/18/12 || Steve<br> Everything worked as expected (32 bit windows build)<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]<br />
||[[media:3DVisualizationData.zip| 3D Visualization dataset]] || Linux 64 (debug) || || ||<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]<br />
||[[media:3DVisualizationData.zip| 3D Visualization dataset]] || Linux Ubuntu 64 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 ||<br />
Benjamin - No Crash <br> Loading Scene - Image are not scaled all the time in the Slice views (random)- <br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]<br />
||[[media:3DVisualizationData.zip| 3D Visualization dataset]] || Windows 7 64b (package) || 4.1.0-rc1-2012-03-17 <br> r19637 || 03/19/2012 ||<br />
Benjamin - No Crash <br> Loading Scene - Image are not scaled all the time in the Slice views (random)-<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]<br />
||[[media:3DVisualizationData.zip| 3D Visualization dataset]] || Mac OSX 10.7 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 ||<br />
Jc - <br> Crash at exit during the first part but can't reproduce <br> Loading Scene - Image are not scaled all the time in the Slice views (random)- <br />
|-<br />
|}<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/Slicer-4.1 Back to Slicer4.1 Feb 27 page]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Summer2014_Tutorial_Contest&diff=98898Summer2014 Tutorial Contest2023-04-11T19:20:23Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div><br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial must be based on the [Slicer nightly build of May 25]'''||'''Works on all supported platforms (Mac,Windows,Linux)'''||'''Tutorial and all of its components must be released under the Slicer license'''||'''Anonymized tutorial data'''||'''Contact information of the primary author (e-mail)'''||'''Tutorial must follow the guidelines specified and use the [[Media:TutorialContest_Template_2014.ppt | Summer 2014 contest tutorial template]]'''||'''If applicable, tutorial must provide clear directions for downloading and installing additional modules'''<br />
|-<br />
| Tutorial #1||Yes||Yes||Yes||Yes||Yes|||Yes<br />
|-<br />
| Tutorial #2||Yes||Yes||Yes||Yes||Yes||Yes<br />
|}<br />
<br />
Comments for Tutorial 1:<br />
<br />
* Better to talk about what is the motivation of this software/tutorial. <br />
* Need to specify that this module is created for the trained physicians, assuming the users already know what are the plaques, Hounsfield Unit (HU), Agatston score. It would be good to mention that the cardiovascular disease is caused by plaques in arteries. <br />
* It would be great to talk about the advantages of this software, such like it allows the users to select 80 KEV or 120 KEV, while other softwares don't; this software takes only 3 minutes, but the other software may take 18 minutes.<br />
* Should mention SimpleITK and other tools they used to develop this software. <br />
* Better to show a case study with both 80 KEV and 120 KEV.<br />
<br />
Comments for Tutorial 2:<br />
<br />
* It could be enhanced by providing the clinical background and motivation.<br />
* Need to explain what are the input images and LGE-MRI?<br />
* It would be better to explain how to download or built this software. <br />
* Should provide the test data and specify what type of data are required if using own data, because there are so many different sequences, such like resolution, format, parameter. <br />
* It would be good to give more details about what are the buttons do, e.g., 'registration', 'next', and where the results are saved? <br />
* If the images need to be registered first, the authors should clearly specify it.<br />
* 'CarreraSlice' is a new tool, so it would be better to briefly describe how to use it for segmentation.</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Summer2011_Tutorial_Contest_Review&diff=98897Summer2011 Tutorial Contest Review2023-04-11T19:17:34Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>== Summer 2011 Project Week Panel ==<br />
[[2011_Summer_Project_Week|Back to Project Week Page]]<br />
<br />
[http://www.na-mic.org/Wiki/index.php/Summer_2011_Tutorial_Contest#List_of_submitted_tutorials Link to tutorials]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/Training:Summer_2011_Contest_Table Summer 2011 test table ]<br />
<br />
=Rules of the Summer 2011 Contest=<br />
#Tutorial must be based on the '''March 2011 Slicer3.6.3 release''' or on '''Slicer4'''.<br />
#To enter the contest, you must provide '''a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)+'''.<br />
#Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [https://www.slicer.org/wiki/Slicer:license Slicer license]<br />
#Tutorial data must be anonymized<br />
#Tutorial must include contact information of the primary author (e-mail and phone number) <br />
#Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2011.ppt | tutorial template]].<br />
#If applicable, the tutorial must provide clear directions for downloading and installing additional modules <br><br />
<br />
<br />
=Submissions=<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''1) Slicer Version'''||'''2) Platforms'''||'''3) Slicer License'''||'''4)Data anonymized'''||'''5) Contact Info'''||'''6) Tutorial Template followed'''|||'''7) Additional Instructions'''||'''Test Windows XP'''||'''Test Windows 7''|| '''Test Linux 64'''||'''Test Linux 32'''||'''Test mac'''<br />
|-<br />
|[[TBISegmentation_TutorialContestSummer2011| UCLA Automatic Segmentation of Traumatic Brain Injury Using ABC]] ||March 2011 Slicer3.6.3 release||Linux 64 only||yes||yes||yes||yes||yes||yes||yes||yes||yes||yes<br />
|-<br />
|[[UNC ShapeAnalysisModule| UNC ShapeAnalysisModule]] ||March 2011 Slicer3.6.3 release||Linux 64 only||yes||yes||yes||yes||no||no||no||yes||no||no<br />
|-<br />
|[[UNC shapeAnalysisMANCOVA_Wizard| UNC shapeAnalysisMANCOVA_Wizard]] ||March 2011 Slicer3.6.3 release||Linux 64 only||yes||yes||yes||yes||no||no||no||yes||no||no<br />
|-<br />
|[[Plastimatch Dose Warping| Plastimatch Dose Warping]] ||March 2011 Slicer3.6.3 release||Windows7||yes||yes||yes||yes||yes||no||yes||yes||no||failed w/fix suggested by Steve & Tina<br />
|-<br />
|[[BRAINSCut Tutorial for human brain sub-cortical segmentation| BRAINSCut Tutorial for human brain sub-cortical segmentation]] ||March 2011 Slicer3.6.3 release||Mac & Linux 64 & Linux 32||?||?||?||?||?||no||no||yes||no||yes<br />
|-<br />
|[[Non-rigid registration of pre-procedural MRI and intra-procedural CT for CT-guided cryoablation therapy| Non-rigid registration of pre-procedural MRI and intra-procedural CT for CT-guided cryoablation therapy]] ||?||?||?||?||?||?||?||no||no||yes||yes||yes<br />
|-<br />
|[[DTIPrep Tutorial| DTIPrep Tutorial]] ||March 2011 Slicer3.6.3 release||Mac & Linux 64||?||?||?||?||?||?||?||?||?||?<br />
|-<br />
|[[EMSegmenter_End_User_Tasks| EMSegmenter_End_User_Tasks]] ||?||?||?||?||?||?||?||no||no||yes||yes||yes<br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=SubjectHierarchyTutorial2016Winter&diff=98896SubjectHierarchyTutorial2016Winter2023-04-11T19:15:14Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>[[2016_Winter_Project_Week#Agenda|Back to Winter project week Agenda]]<br />
<br />
This tutorial demonstrates the basic usage and potential of Slicer’s data manager module Subject Hierarchy using a two-timepoint radiotherapy phantom dataset. It shows how to explore loaded data, may it be from DICOM or research formats, how to organize the data, and how to access the data type specific actions. It is also emphasized that data type support and offered actions can be easily extended.<br />
<br />
*Tutorial [[Media:SubjectHierarchy.TutorialContestWinter2016.pdf]]<br />
*Dataset [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip SlicerRT_WorldCongress_TutorialIGRT_Dataset]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| Subject Hierarchy || Mac OS || 4.5.0-1 || Every night || Csaba Pinter || Passed<br />
|-<br />
| Subject Hierarchy || Windows || 4.5.0-1 || Every night || Csaba Pinter || Passed<br />
|-<br />
| Subject Hierarchy || Linux || 4.5.0-1 || Every night || Csaba Pinter || Passed<br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=SlicerRT_TutorialContestSummer2013&diff=98895SlicerRT TutorialContestSummer20132023-04-11T19:13:45Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
<br />
===SlicerRT Tutorial===<br />
<br />
Material for the Slicer 4.3 SlicerRT tutorial, Project Week Summer 2013:<br />
<br />
[http://wiki.na-mic.org/Wiki/images/b/b0/SlicerRT_TutorialContestSummer2013.pdf SlicerRT tutorial contest presentation]<br />
<br />
[http://slicer.kitware.com/midas3/download/folder/1345/SlicerRtTutorial_Namic2013June.zip SlicerRT tutorial contest test data on MIDAS]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| SlicerRT || Mac OS || Nightly || 06.19. || Csaba Pinter<br />
| Passed<br />
|-<br />
| SlicerRT || Windows 7 32 bit || Nightly || ||<br />
| <br />
|-<br />
| SlicerRT || Windows 7 64 bit || Nightly || || Csaba Pinter<br />
| Passed<br />
|-<br />
| SlicerRT || Linux 64 bit || Nightly || || Csaba Pinter<br />
| Passed<br />
|-<br />
|}<br />
<br />
[http://www.na-mic.org/Wiki/index.php/2013_Tutorial_Contest Back to tutorial contest]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Slicer4_Automated_Tests_Table_Slicer4_automated_test_table&diff=98894Slicer4 Automated Tests Table Slicer4 automated test table2023-04-11T19:12:49Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date & author'''||'''Test results ||'''Mantis Links (if tests failed)'''<br />
|-<br />
|Data Loading and 3D Visualization || Mac OS SnowLeopard || nightly-build 2012-06-05|| Sonia 06/08/12 || automated [[media:Macro1_SlicerDataLoadingVisualization_part1.zip |macro1_slicerDataLoading3DVisualization_part1_MacOSX]] Description: Slide 24 to Slice35 of tutorial + File-->Save Scene|| Not reproducible. I played the test three times: 1) first run: the red slice view was not set to 6x6 in the 'red Slice viewer only' mode, and then the 6x6 view showed up in the green slice viewer in conventional mode. 2) second run: worked fine 3) third run: same error as in 1). Bug report: http://www.na-mic.org/Bug/view.php?id=2177<br />
|-<br />
|Data Loading and 3D Visualization || Mac OS Lion|| nightly-build 2012-06-12|| Tatsushi 06-15-2012 || automated [[media:Macro1_SlicerDataLoadingVisualization_part2_MacOSX.zip|macro1_slicerDataLoading3DVisualization_part2_MacOSX]]|| reproducible.<br />
|-<br />
|Data Diffusion MRI Analysis || Mac OS Lion|| nightly-build 2012-06-12|| Tatsushi 06-15-2012 || automated [[media:Macro1_DTI_test_part1.zip|macro1_slicerDiffusion MRI analysis_part1_MacOSX ]]||reproducible<br />
|-<br />
|Data Diffusion MRI Analysis || Mac OS Lion|| nightly-build 2012-06-12|| Tatsushi 06-15-2012 || automated [[media:Macro1_SlicerDiffusion MRI analysis_part2_MacOSX.zip|macro1_slicerDiffusion MRI analysis_part2_MacOSX ]]||Not reproducible. Opacity did not change<br />
|-<br />
|Data Diffusion MRI Analysis || Mac OS Lion|| nightly-build 2012-06-12|| Tatsushi 06-15-2012 || automated [[media:Macro1_SlicerDiffusion MRI analysis_part3_MacOSX.zip|macro1_slicerDiffusion MRI analysis_part3_MacOSX ]]||Not reproducible. Color maps not shown<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Plastimatch_TutorialContestWinter2016&diff=98893Plastimatch TutorialContestWinter20162023-04-11T19:11:29Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>[[2016_Winter_Project_Week#Agenda|Back to Winter project week Agenda]]<br />
<br />
Please find below the tutorial entry for Plastimatch B-spline Registration.<br />
The tutorial is submitted under in category 5 "TUTORIAL UPGRADE/UPDATE".<br />
The most recent version of the tutorial was based on Slicer 3.5, and was last revised in 2010.<br />
It is now refreshed and renewed for Slicer 4.5.<br />
<br />
*Tutorial [[Media:Plastimatch_TutorialContestWinter2016.pdf]]<br />
*Dataset [[Media:Plastimatch_TutorialContestWinter2016.zip]]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || || || <br />
|<br />
|-<br />
| || Windows || || || <br />
|<br />
|-<br />
|Plastimatch_TutorialContestWinter2016 || Linux ||Slicer 4.5 Stable ||Dec 31, 2015 ||Greg Sharp <br />
||None<br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=PlastimatchDose_TutorialContestSummer2012&diff=98892PlastimatchDose TutorialContestSummer20122023-04-11T18:29:48Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>= Testing =<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| Plastimatch Dose|| Mac OS - Lion || 4.1 || 06-15-2012 || James Jackleford || OK<br />
|-<br />
| Plastimatch Dose || Windows 7 64 bit || 4.1 || 06-15-2012 || James Jackleford|| OK <br />
|-<br />
| Plastimatch Dose || Linux 64 bit || 4.1 || 06-15-2012 || James Jackleford|| OK <br />
|-<br />
|}<br />
<br />
= Resources = <br />
<br />
*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Download the slides]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=OpendIGTLinkIF_TutorialContestSummer2012&diff=98891OpendIGTLinkIF TutorialContestSummer20122023-04-11T18:28:59Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>= Testing =<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| OpenIGTLinkIF || Mac OS - Lion || 4.1 || 06-15-2012 || Junichi Tokuda || OK<br />
|-<br />
| OpenIGTLinkIF|| Windows XP 64 bit || 4.1 || 06-15-2012 || Junichi Tokuda|| OK<br />
|-<br />
| OpenIGTLinkIF || Linux Ubuntu 64 bit || 4.1 || 06-15-2012 || Junichi Tokuda || OK<br />
|-<br />
|}<br />
<br />
= Resources = <br />
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf Download the slides]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=OpenIGTLinkIF_TutorialContestSummer2012&diff=98890OpenIGTLinkIF TutorialContestSummer20122023-04-11T18:28:08Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div><table><br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || Slicer 4.1 || June 10 || Junichi Tokuda || OK<br />
|-<br />
| || Windows 7 32 bit || || ||<br />
|<br />
|-<br />
| || Windows 7 64 bit || Slicer 4.1 || June 19 || Junichi Tokuda || OK<br />
|-<br />
| || Linux 64 bit || Slicer 4.1 || June 19 || Junichi Tokuda || OK (with Ubuntu 10.10)<br />
|-<br />
|}<br />
<br />
<br />
=Presentation=<br />
*[http://www.na-mic.org/Wiki/index.php/OpendIGTLinkIF_TutorialContestSummer2012 OpenIGTLinkIF Junichi Tokuda, BWH]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=New_wiki_page&diff=98889New wiki page2023-04-11T18:27:09Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
===Hello CLI Tutorial===<br />
<br />
<br />
Material for the Slicer 4.2 Hello CLi tutorial, Project Week Summer 2013:<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:Cardiac_MRI_Toolkit_Tutorial_Summer2013.pptx Powerpoint Presentation: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pptx]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:Cardiac_MRI_Toolkit_Tutorial_Data.zip Data: Cardiac_MRI_Toolkit_Tutorial_Data.zip]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || || || <br />
|<br />
|-<br />
| || Windows 7 32 bit || || || <br />
|<br />
|-<br />
| || Windows 7 64 bit || || || <br />
|<br />
|-<br />
| || Linux 64 bit || || || <br />
|<br />
|-<br />
|}<br />
[[HelloCLI_TutorialContestSummer2013]]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Madrid_2012_Workshop_Preparation&diff=98888Madrid 2012 Workshop Preparation2023-04-11T18:24:54Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>The [http://www.na-mic.org/Wiki/index.php/Madrid-May-21-2012-Slicer-Workshop Madrid NA-MIC MIT-Vision Workshop] will be held on May 21-22, 2012. This page serves as a place holder for the training materials and associated cross-platform tests.<br />
<br />
==Tentative Agenda ==<br />
*Cross-Platform Testing<br />
**Start Date: Friday April 27, 2012<br />
**End Date: Friday May 11, 2012 <br />
*Final version of Slicer binaries for the workshop participants posted on the event page : Monday May 14, 2012<br />
*Workshop: Monday May 21 - Tuesday May 22<br />
<br />
==Workshop Tutorials ==<br />
<br />
The slides and datasets below are the ones that will be used at the Madrid event.<br />
<br />
*Tutorial 1: [[media:DataLoadingAndVisualizationSlicer4_Madrid2012_SoniaPujol.pdf | Data Loading and 3D Visualization Tutorial]]<br />
*Tutorial 2: [[media:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf | Hello Python Tutorial ]]<br />
*Tutorial 3: [[media:DTI Analysis Tutorial Slicer4.1 Madrid2012 SoniaPujol.pdf | Diffusion Tensor Imaging Tutorial]]<br />
*Tutorial 4: [[media:WhiteMatterExplorationNeurosurgicalPlanning_Madrid2012_SoniaPujol.pdf | Neurosurgical Planning Tutorial]]<br />
<br />
== Workshop Datasets ==<br />
*Dataset 1: [[media:3DVisualizationData.zip|Data Loading and 3D Visualization dataset]]<br />
*Dataset 2: [http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip Hello Python dataset]<br />
*Dataset 3: [http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Tensor Imaging dataset]<br />
*Dataset 4: [[media:WhiteMatterExplorationData.zip| Neurosurgical Planning dataset]]<br />
<br />
== Binaries ==<br />
* MacOSX [http://slicer.cdash.org/viewFiles.php?buildid=17794 Slicer4.1 MacOSX]<br />
* Linux 64 [http://slicer.cdash.org/viewFiles.php?buildid=17795 Slicer4.1 Linux 64]<br />
* Windows 7 64 [http://slicer.cdash.org/viewFiles.php?buildid=17820 Slicer4.1 Windows7 64]<br />
* Windows 7 32 [http://slicer.cdash.org/viewFiles.php?buildid=17796 Slicer4.1 Windows7 32]<br />
<br />
== Madrid Workshop Test Table == <br />
=== '''Tutorial1: Data Loading and 3D Visualization''' ===<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Test type (manual/automated)||'''Test Author and results (Mantis Links if tests failed)'''<br />
|-<br />
|Data Loading and 3D Visualization || Mac OS SnowLeopard || || Sonia - ok|| <br />
|<br />
|-<br />
|Data Loading and 3D Visualization || Mac OS Lion|| || Laurent - ok || <br />
|<br />
|-<br />
| Data Loading and 3D Visualization|| Windows 7 32 bit || || Marianna - ok || <br />
|<br />
|-<br />
|Data Loading and 3D Visualization || Windows 7 64 bit || || Christopher Mullins (Kitware) - ok || <br />
|<br />
|-<br />
|Data Loading and 3D Visualization || Windows XP 32 bit || || || <br />
|<br />
|-<br />
|Data Loading and 3D Visualization || Linux 64 bit || || Marianna - ok || <br />
|<br />
|-<br />
|}<br />
<br />
=== ''Tutorial2: Hello Python'' ===<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Test type (manual/automated)||'''Test Author and results (Mantis Links if tests failed)'''<br />
|-<br />
|Hello Python || Mac OS SnowLeopard || ||Sonia - ok || <br />
|<br />
|-<br />
|Hello Python || Mac OS Lion || || Laurent - ok|| <br />
|<br />
|-<br />
|Hello Python || Windows 7 32 bit || || Marianna || <br />
|<br />
|-<br />
|Hello Python || Windows 7 64 bit || || Jc (Kitware) - ok || <br />
|<br />
|-<br />
|Hello Python|| Windows XP 32 bit || || || <br />
|<br />
|-<br />
|Hello Python || Linux 64 bit || || Marianna - Part 1: Toggle Button did not show up || <br />
|<br />
|-<br />
|}<br />
<br />
=== ''Tutorial3: Diffusion Tensor Imaging '' ===<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Test type (manual/automated)||'''Test Author and results (Mantis Links if tests failed)'''<br />
|-<br />
|Diffusion Tensor Imaging || Mac OS SnowLeopard || || Sonia - ok || <br />
|<br />
|-<br />
|Diffusion Tensor Imaging || Mac OS Lion || ||Laurent - ok|| <br />
|<br />
|-<br />
|Diffusion Tensor Imaging || Windows 7 32 bit || || Marianna - ok || <br />
|<br />
|-<br />
|Diffusion Tensor Imaging || Windows 7 64 bit || || Jc (Kitware) - ok || <br />
|<br />
|-<br />
|Diffusion Tensor Imaging || Windows XP 32 bit || || || <br />
|<br />
|-<br />
|Diffusion Tensor Imaging || Linux 64 bit || || Marianna - ok (except for one non reproducible crash on slide #54|| <br />
|<br />
|-<br />
|}<br />
<br />
=== ''Tutorial4: Neurosurgical Planning '' ===<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Test type (manual/automated)||'''Test Author and results (Mantis Links if tests failed)'''<br />
|-<br />
|Neurosurgical Planning || Mac OS SnowLeopard || || Sonia -ok || <br />
|<br />
|-<br />
|Neurosurgical Planning || Mac OS Lion || || Laurent - ok|| <br />
|<br />
|-<br />
|Neurosurgical Planning || Windows 7 32 bit || || Marianna - ok|| <br />
|<br />
|-<br />
|Neurosurgical Planning || Windows 7 64 bit || || Michael Jeulin (Kitware) - ok || <br />
|<br />
|-<br />
|Neurosurgical Planning || Windows XP 32 bit || || || <br />
|<br />
|-<br />
|Neurosurgical Planning || Linux 64 bit || || Marianna -ok || <br />
|<br />
|-<br />
|}<br />
<br />
== Testing References ==<br />
<br />
'''Manual Tests'''<br />
<br />
The 4 tutorials have all been tested on Mac OS Lion, Mac OS Snow Leopard, Windows 7 32, Windows XP and Linux 64 Ubuntu using the Slicer4.1-2012-03-17-rc1 release candidate.<br />
** [http://slicer.cdash.org/viewFiles.php?buildid=12544 Mac OS X (64bit)]<br />
** [http://slicer.cdash.org/viewFiles.php?buildid=12545 Linux (64bit)]<br />
** [http://slicer.cdash.org/viewFiles.php?buildid=12546 Windows (32bit)]<br />
** [http://slicer.cdash.org/viewFiles.php?buildid=12554 Windows (64bit)]<br />
* The results of the manual tests have been posted on the [[Tests_of_Iowa_Workshop_tutorials | Iowa workshop test table ]].<br />
<br />
<br />
'''MIT Project week 2011 - Sikuli automated test'''<br />
<br />
http://www.na-mic.org/Wiki/index.php/2011_Summer_Project_Week_Automated_GUI_Testing</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=Journal_of_Slicer_Workshop_Tests&diff=98887Journal of Slicer Workshop Tests2023-04-11T18:20:15Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>== '''Concept''' ==<br />
<br />
This page will be used as a journal of tests for the Slicer workshops on four different platforms (Linux 32 and 64 bit, Mac Darwin, and Windows).<br />
<br />
* Event: [[http://www.na-mic.org/Wiki/index.php/RSNA_2011 RSNA 2011 ]]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| Slicer4.0gamma2011-11-21 || Mac OSX Lion ||11/22/2011 || slide 39: when downloading the label layer, the foreground <br />
disappeared, it needs to be reselected. slide 76: when using the compare viewer, I only have the option to <br />
compare 2 views so I end up with 4 windows on the screen instead of 3. Every time I tried to go from lightbox <br />
viewer to conventional viewer (last slide of the part 4), Slicer crashed. When I tried without data loaded to switch between the two I <br />
have no problem, it seems linked to the dataset. Closing the scene at the end of part4 or part 5 of the tutorial causes Slicer to crash. (Valerie Humblet)<br />
|-<br />
|[[Media:RSNA2010_OsirixPanoramixDataset.zip | Abdominal CT scan with AAA (Osirix Panoramix Dataset)]]||Slicer4.0gamma2011-11-21||Mac OSX Lion||11/22/2011||cropping, volume rendering and GPU: OK, did not test annotations. No problem when closing the scene (Valerie Humblet)<br />
|-<br />
|[https://na-mic.org/w/images/7/79/RSNA2010_Prostate.zip Prostate data]||Slicer4.0gamma2011-11-21||Mac OSX Lion||11/22/2011||<br />
|-<br />
|[https://na-mic.org/w/images/2/28/RSNA2011_Prostate.zip Prostate data RSNA 2011 in progress]||Slicer4.0gamma2011-11-21||Mac OSX Lion||11/22/2011||Unable to unzip the file. It shows as .zip.download (Valerie Humblet) <br />
|-<br />
|[https://na-mic.org/w/images/3/33/Slicer_data-RSNA2010-CTSA.zip Quantitative imaging]||Slicer4.0gamma2011-11-23||Mac OsX Lion||11/23/2011||Slicer3 minutes: OK; PET/CT (using volumes and SUV computation): OK; Change tracker: Need to use the volume rendering module to view VOI widget in 3D viewer, does not appear automatically, close scene causes Slicer to crash (Valerie Humblet)<br />
|-<br />
|[https://na-mic.org/w/images/3/33/Slicer_data-RSNA2010-CTSA.zip Quantitative imaging]||Slicer4.0gamma2011-11-23||Windows 2008 32 bits Vista||11/23/2011||Slicer3 minutes: OK; PET/CT (using volumes and SUV computation): OK; Change tracker: Need to use the volume rendering module to view VOI widget in 3D viewer, does not appear automatically, close scene causes Slicer to crash (Valerie Humblet)<br />
|}<br />
<br />
*'''Event''': [http://www.na-mic.org/Wiki/index.php/Events:2011-06-15-Robarts-Slicer-Workshop Robarts Institute workshop, Ontario, Canada]<br />
* Datasets:<br />
** [[media:Slicer3VisualizationDataset.zip | 3D Visualization dataset]]<br />
** [[media:WhiteMatterExplorationData.zip| White Matter Exploration dataset]] <br />
** [[media:HelloPython.zip | HelloPython dataset]]<br />
** [[media:Slicer3_BRAINSFITRegistration.zip | BRAINSFIT Registration dataset]]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]|| [http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz] || Linux 32 || 06-08-2011 || OK on Ubuntu 10.10 32-bit (Junichi Tokuda)<br />
|-<br />
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-08-2011 || OK on Fedora 14 64-bit (Atsushi)<br />
|-<br />
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || || OK (Sonia Pujol)<br />
|-<br />
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe]|| Windows XP || 06-09-2011 || OK (Junichi Tokuda)<br />
|-<br />
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe]|| Windows 7 || 06-07-2011 || Laurent Chauvin<br />
Slow on Windows 7 (64 bits).<br />
First two times, Slicer crashed (first time when window opened after clicking Add Volume, second time when I tried to switch to Data module)<br />
|-<br />
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf | Exploring peritumoral white matter fibers for neurosurgical planning ]]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz]|| Linux 32|| 06-08-2011 || OK on Ubuntu 10.10 (32-bit) (Junichi)<br />
|-<br />
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf | Exploring peritumoral white matter fibers for neurosurgical planning ]]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-08-2011 || Atsushi<br />
DTI volume was displayed with strange colors, or Slicer was crushed when I set Select the Scalar Mode to "Color By Orientation" on Fedora 14 64bit.<br />
|-<br />
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf | Exploring peritumoral white matter fibers for neurosurgical planning ]]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || 06-09-2011 || OK (Sonia Pujol)<br />
|-<br />
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf | Exploring peritumoral white matter fibers for neurosurgical planning ]]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe]|| Windows XP || 06-08-2011 || OK (Junichi Tokuda)<br />
|-<br />
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf | Exploring peritumoral white matter fibers for neurosurgical planning ]]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe]|| Windows 7 || 06-07-2011 || Laurent Chauvin<br />
Too slow to draw a line in grow cut mode (just points, but it's working.<br />
One crash: Uncaught exception: bad allocation.<br />
|-<br />
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython] <br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz] || Linux 32 || 06-08-2011 || OK on Ubuntu 10.10 (32-bit)(Junichi)<br />
|-<br />
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython ]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-09-2011 || Atsushi<br />
When adding "inputVolume = scene.GetNodeByID(HelloPythonInputVolume)" to the source code, "Python HelloPython" was disappeared from the module list. So, I was not able to execute this module on Fedora 14 64bit. The binary version are Slicer3-3.6.3-2011-06-07-linux-x86_64 and Slicer3-3.6.3-2011-03-04-linux-x86_64. <br />
|-<br />
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython ] <br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || 06-09-2011 || OK (Sonia Pujol)<br />
|-<br />
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython ] <br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows XP || 06-09-2011 || OK (Junichi Tokuda)<br />
|-<br />
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython ] <br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows 7 || 06-08-2011 || Laurent Chauvin<br />
Becareful when modifying HelloPython.py , Python is tab sensitive.<br />
|-<br />
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz] || Linux 32 || 06-07-2011 || OK on Ubuntu 10.10 (32-bit) (Junichi Tokuda)<br />
|-<br />
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-09-2011 || OK on Fedora 14 (64-bit) (Atsushi)<br />
|-<br />
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || || OK( Sonia Pujol)<br />
|-<br />
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows XP || 06-09-2011 || OK (Junichi Tokuda)<br />
|-<br />
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows 7 || 06-07-2011 || Laurent Chauvin<br />
|-<br />
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz] || Linux 32 || 06-09-2011 || OK (Junichi Tokuda)<br />
|-<br />
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-10-2011 || OK (Danielle Pace)<br />
|-<br />
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || || -when loading the scene, Slicer displays a warning that the users should ignore<br />
-for visualizing the glyphs, you need to tell the participants to put DTI_iso in Bg viewer <br />
- when select 'glyphs on display' with Scalar Mode 'Color by orientation', the glyphs are correctly displayed in the 3D viewer but all the 2D views are wrong <br />
-registration and resampling test work on MacBook Pro (8GB RAM) (Sonia Pujol)<br />
NOTE: Glyphs removed from tutorial (Danielle Pace)<br />
|-<br />
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows XP || 06-09-2011 || Error on final "Resample DTI Volume" step - Filed to allocat memory for image. (Junichi Tokuda)<br />
|-<br />
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]<br />
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows 7 || 06-09-2011 || Danielle Error on final "Resample DTI Volume" step - memory error, unable to allocate 77856768 elements of size 4 bytes<br />
Laurent Chauvin: Unable to complete last step. Message: Completed with errors, but no more informations about error.<br />
|}<br />
<br />
*[http://www.na-mic.org/Wiki/index.php/Events:_Johns_Hopkins_University_Seminar_April_2011#Introduction JHU workshop April 5, 2011]<br />
*[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Data Loading and 3D Visualization Data]<br />
*[http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Data]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]|| [http://na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz] || Linux 32||04/4/11 || OK (Hayes)<br />
|-<br />
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]||[http://na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]|| Linux 64 || 04/1/11|| OK (SPujol)<br />
|-<br />
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]||[http://na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]|| Mac Darwin || 04/1/11||OK (SPujol)<br />
|-<br />
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]||[http://na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]|| Windows XP&7 || 04/4/11 || OK (Hayes)<br />
|-<br />
|[https://na-mic.org/w/images/3/37/WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf Exploring peritumoral white matter fibers for neurosurgical planning ]<br />
||[http://na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]|| Linux 32|| 04/04/11|| OK (Hayes)<br />
|-<br />
|[https://na-mic.org/w/images/3/37/WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf Exploring peritumoral white matter fibers for neurosurgical planning ]<br />
||[http://na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]|| Linux 64 || 04/1/11 || OK (SPujol)<br />
|-<br />
|[https://na-mic.org/w/images/3/37/WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf Exploring peritumoral white matter fibers for neurosurgical planning ]<br />
||[http://na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]|| Mac Darwin || 04/1/11|| OK (SPujol)<br />
|-<br />
|[https://na-mic.org/w/images/3/37/WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf Exploring peritumoral white matter fibers for neurosurgical planning ]<br />
||[http://na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]|| Windows XP&7 || 04/04/11 || OK (Hayes)<br />
|-<br />
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz] || Linux 32 || 04/04/11|| OK (Hayes)<br />
|-<br />
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]|| Linux 64 || 04/1/11||OK (SPujol)<br />
|-<br />
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]|| Mac Darwin || 04/1/11||OK (SPujol)<br />
|-<br />
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe] || Windows XP&7 || 04/04/11|| OK (Hayes)<br />
|}<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 32|| 03/04/11 || Crashes when VTK models are rotated in 3D viewer (Hayes) (anago.nmr) [http://na-mic.org/Bug/view.php?id=1111 Bug Report]<br />
|-<br />
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || 03/04/11 || OK (Hayes) (panamint.nmr)<br />
|-<br />
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || 03/04/11 || Crashes when VTK models are rotated in 3D viewer (Hayes) (hima.nmr) [http://na-mic.org/Bug/view.php?id=1111 Bug Report]<br />
|-<br />
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A || Testing Slicer3-3.6.3-2011-03-04 instead<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ]|| Linux 32|| N/A|| Waiting on completed slides (Hayes)<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || N/A || Waiting on completed slides (Hayes)<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || N/A|| Waiting on completed slides (Hayes)<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 ||N/A || Waiting on completed slides (Hayes)<br />
|-<br />
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 32 || N/A || Testing Slicer3-3.6.3-2011-03-04 instead<br />
|-<br />
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || N/A ||Testing Slicer3-3.6.3-2011-03-04 instead<br />
|-<br />
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin ||N/A ||Testing Slicer3-3.6.3-2011-03-04 instead<br />
|-<br />
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A|| Testing Slicer3-3.6.3-2011-03-04 instead<br />
|}<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 32|| 03/03/11 || OK (Hayes) (anago.nmr)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || 02/28/11 || OK, slides need updating (Hayes) (panamint.nmr)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || 03/02/11 || Crashes when VTK models are rotated in 3D viewer (Hayes) (hima.nmr) [http://na-mic.org/Bug/view.php?id=1111 Bug Report]<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A || Testing UCSF slides instead<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ]|| Linux 32||N/A || Waiting on completed slides (Hayes)<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || N/A || Waiting on completed slides (Hayes)<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || N/A|| Waiting on completed slides (Hayes)<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A|| Waiting on completed slides (Hayes)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 32 || 03/03/11 || OK (Hayes) (anago.nmr)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || 02/28/11 || OK pending minor slide edits (Hayes) (panamint.nmr)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || 03/03/11 || OK (Hayes) (hima.nmr)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A || Testing UCSF slides instead<br />
|}<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 32|| 02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 64 || 02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Mac Darwin || N/A || Testing 3.6.3 RC2 instead (Hayes)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Windows XP&7 || N/A || Testing 3.6.3 RC2 instead (Hayes)<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ]|| Linux 32|| 02/24/11|| Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 64 || 02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Mac Darwin || N/A|| Testing 3.6.3 RC2 instead (Hayes)<br />
|-<br />
|Exploring peritumoral white matter fibers for neurosurgical planning <br />
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Windows XP&7 || N/A || Testing 3.6.3 RC2 instead (Hayes)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 32 ||02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 64 ||02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Mac Darwin || N/A || Testing 3.6.3 RC2 instead (Hayes)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Windows XP&7 || N/A || Testing 3.6.3 RC2 instead (Hayes)<br />
|}<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt CTSA Tutorial Slides] || [[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]<br />
||Mac ||12-03-2010 || OK (tested by SPujol)<br />
|-<br />
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt CTSA Tutorial Slides] ||[[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]<br />
||Linux 64|| 12-03-2010 || OK (tested by SPujol)<br />
|-<br />
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt CTSA Tutorial Slides] ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]<br />
|Windows XP & Windows 7|| 12-03-2010 || OK (tested by SPujol)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]<br />
|Windows XP || 12-04-2010 || OK (Tested by Junichi)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] |||[[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]<br />
|Mac Darwin || 12-04-2010 || OK (Tested by Junichi)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]<br />
|Linux 64|| 12-04-2010 || OK (Tested by Junichi)<br />
|-<br />
|[https://www.slicer.org/wiki/File:InteractiveEditorTutorial_Slicer3.6-SoniaPujol.pdf Interactive Editor Slides] || [[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]<br />
<br />
||Mac || 12-05-2010 || OK (Tested by Junichi)<br />
|-<br />
|[https://www.slicer.org/wiki/File:InteractiveEditorTutorial_Slicer3.6-SoniaPujol.pdf Interactive Editor Slides] ||[[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]<br />
||Linux 64|| 12-04-2010 || OK (tested by SPujol)<br />
<br />
|-<br />
|[https://www.slicer.org/wiki/File:InteractiveEditorTutorial_Slicer3.6-SoniaPujol.pdf Interactive Editor Slides] ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]<br />
|Windows XP & Windows 7|| 12-04-2010 || OK (tested by SPujol)<br />
<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/c/c7/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Dec2010.pdf Diffusion Tensor Imaging Slides] || [[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]] <br />
<br />
|| Mac || 12-06-2010 || OK (Tested by Junichi)<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/c/c7/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Dec2010.pdf Diffusion Tensor Imaging Slides] ||[[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]<br />
||Linux 64|| 12-04-2010 || OK (tested by SPujol)<br />
<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/c/c7/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Dec2010.pdf Diffusion Tensor Imaging Slides] ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]<br />
|Windows XP & Windows 7|| 12-04-2010 || OK (tested by SPujol)<br />
|}<br />
<br />
<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/RSNA2010.PlanningLog '''RSNA 2010''' NAMIC Workshop November 29, 2010 ]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-darwin-x86.tar.gz ||Mac ||11-2-2010 || All OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86.tar.gz||Linux 32||11-2-2010|| All OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86_64.tar.gz||Linux 64|| 11-2-2010|| All OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-win32.exe|| Win XP&7|| 11-2-2010|| All OK<br />
|}<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/RSNA2010.PlanningLog '''RSNA 2010''' Quantitative Medical Imaging for Clinical Research and Practice November 30, 2010 ]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[https://na-mic.org/w/images/4/4e/Combined-RSNA09-WJP.ppt draft target tutorial slides] ||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-darwin-x86.tar.gz ||Mac ||11-2-2010 || All OK<br />
|-<br />
|[https://na-mic.org/w/images/4/4e/Combined-RSNA09-WJP.ppt draft target tutorial slides] || http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86.tar.gz||Linux 32||11-2-2010|| All OK<br />
|-<br />
|[https://na-mic.org/w/images/4/4e/Combined-RSNA09-WJP.ppt draft target tutorial slides] ||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86_64.tar.gz||Linux 64|| 11-2-2010|| All OK<br />
|-<br />
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt Target tutorial slides] ||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-darwin-x86.tar.gz ||Mac ||- || -<br />
|-<br />
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt Target tutorial slides] || http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86.tar.gz||Linux 32||- || -<br />
|-<br />
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt Target tutorial slides] ||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86_64.tar.gz||Linux 64||- || -<br />
|}<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/RSNA2010.PlanningLog '''RSNA 2010''' Quantitative Imaging Reading Room November 27-December 3, 2010 ]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
| [http://www.na-mic.org/Wiki/index.php/File:RSNA2010QIRR-LoopSlides.ppt QIRR Presentation] (presentation only, no tutorial) ||-- ||-- ||-- ||-- <br />
|}<br />
<br />
<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/Events:UCLA-Slicer-Training-11-2010 - UCLA Workshop, Los Angeles, CA]<br />
**[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Data Loading and 3D Visualization Data]<br />
**[https://www.slicer.org/wiki/File:EditorTutorialDataset.zip Interactive Editor Data]<br />
**[http://www.slicer.org/slicerWiki/images/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Manual Registration Data]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editing]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editing]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editing]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editing]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.12010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|}<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/Events:UCSF-Slicer-Training-11-2010 - UCSF Workshop, San Francisco, CA]<br />
**[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Data Loading and 3D Visualization Data]<br />
**[https://www.slicer.org/wiki/File:EditorTutorialDataset.zip Interactive Editor Data]<br />
**[http://www.slicer.org/slicerWiki/images/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Manual Registration Data]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.12010-08-20] || Mac Darwin ||08-25-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|-<br />
|ABC module ?||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK<br />
|}<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/MICCAI_2010 - MICCAI 2010, Beijing, China]<br />
** [http://www.na-mic.org/Wiki/index.php/File:HelloPython.zip Python Tutorial Data]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:ProgrammingIntoSlicer3.6.1_Python_SoniaPujol.pdf Programming in Slicer3 with Python]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||08-27-2010||All OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:ProgrammingIntoSlicer3.6.1_Python_SoniaPujol.pdf Programming in Slicer3 with Python]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||08-27-2010||All OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:ProgrammingIntoSlicer3.6.1_Python_SoniaPujol.pdf Programming in Slicer3 with Python]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||08-30-2010||All OK<br />
|-<br />
|[http://www.na-mic.org/Wiki/index.php/File:ProgrammingIntoSlicer3.6.1_Python_SoniaPujol.pdf Programming in Slicer3 with Python]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-30-2010||All OK<br />
|}<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/Beijing_2010_NA-MIC_Workshop - PLA General Hospital Tutorial, Beijing China]<br />
**[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Data Loading and 3D Visualization Data]<br />
**[http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Tutorial Data]<br />
**[http://www.slicer.org/slicerWiki/images/d/d1/Slicer-tutorial-neurosurgery.zip Neurosurgical Tutorial Data]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64|| 08-27-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32|| 08-27-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7|| 08-30-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin|| 08-30-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||08-27-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||08-27-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||08-30-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-30-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/ba/SlicerNeurosurgeryTutorial-3.6.1.ppt Neurosurgical Planning]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-01-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/ba/SlicerNeurosurgeryTutorial-3.6.1.ppt Neurosurgical Planning]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-01-2010 ||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/ba/SlicerNeurosurgeryTutorial-3.6.1.ppt Neurosurgical Planning]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||09-01-2010||All OK<br />
|-<br />
|[http://www.slicer.org/slicerWiki/images/b/ba/SlicerNeurosurgeryTutorial-3.6.1.ppt Neurosurgical Planning]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-01-2010||All OK<br />
|}<br />
<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/2010-Slicer-UNCDuke August 11, 2010 - UNC Duke Workshop]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86_64.tar.gz Slicer3-3.6-2010-08-05] || Linux x64||08-08-2010 ||All OK<br />
|-<br />
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86.tar.gz Slicer3-3.6-2010-08-05] || Linux 32 ||08-08-2010||All OK<br />
|-<br />
|Data Loading and 3D Visualization||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-darwin-x86.tar.gz Slicer3-3.6-2010-08-05] ||Mac Darwin ||08-08-2010 ||All OK<br />
|-<br />
|Data Loading and 3D Visualization||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-win32.exe Slicer3-3.6-2010-08-05] || Windows XP ||08-08-2010 ||All OK<br />
|-<br />
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-win32.exe Slicer3-3.6-2010-08-05] || Windows 7 ||08-08-2010 ||All OK<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86_64.tar.gz Slicer3-3.6-2010-08-05] ||Linux x64 ||08-08-2010 ||All OK with Thresholding tweak<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86.tar.gz Slicer3-3.6-2010-08-05] || Linux 32 ||08-08-2010 ||All OK with Thresholding tweak<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-05] || Windows XP ||08-09-2010 ||All OK<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-05] ||Windows 7 ||08-09-2010 ||All OK<br />
|-<br />
|Interactive Editing ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-05] ||Mac Darwin||08-08-2010||All OK with Thresholding tweak <br />
|-<br />
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-05] ||Linux x64 || 08-08-2010||All OK<br />
|-<br />
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-05] ||Linux 32 ||08-08-2010||All OK<br />
|-<br />
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-05] ||Windows XP ||08-08-2010||All OK<br />
|-<br />
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-05] || Windows 7 ||08-08-2010|| All OK<br />
|-<br />
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-05] ||Mac Darwin || 08-08-2010||All OK<br />
|-<br />
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86_64.tar.gz Slicer3-3.6-2010-08-05] ||Linux x64 ||08-08-2010 ||All OK<br />
|-<br />
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86.tar.gz Slicer3-3.6-2010-08-05] ||Linux 32 ||08-08-2010 ||All OK <br />
|-<br />
|Manual Registration|| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-win32.exe Slicer3-3.6-2010-08-05]||Windows XP || 08-08-2010||All OK <br />
|-<br />
|Manual Registration|| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-win32.exe Slicer3-3.6-2010-08-05] || Windows 7 || 08-08-2010||All OK <br />
|-<br />
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-darwin-x86.tar.gz Slicer3-3.6-2010-08-05] ||Mac Darwin ||08-08-2010 ||All OK<br />
|-<br />
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-02] || Linux x64|| 08-07-2010|| All OK<br />
|-<br />
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-03] || Linux 32 ||08-07-2010 ||All OK<br />
|-<br />
|Data Loading and 3D Visualization||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-04] ||Mac Darwin || 08-04-2010|| All OK<br />
|-<br />
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows XP || 08-08-2010||All OK<br />
|-<br />
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows 7 || 08-08-2010||All OK<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-02] ||Linux x64 || 08-05-2010||All OK<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-03] || Linux 32 ||08-07-2010 ||All OK<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows XP ||08-08-2010 || All OK<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] ||Windows 7 ||08-08-2010 || All OK<br />
|-<br />
|Interactive Editing ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-04] ||Mac Darwin||08-04-2010 || All OK<br />
|-<br />
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-02] ||Linux x64 || 08-06-2010||All OK<br />
|-<br />
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-03] ||Linux 32 || 08-07-2010||All OK <br />
|-<br />
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] ||Windows XP ||08-08-2010 ||All OK<br />
|-<br />
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows 7 ||08-08-2010 ||All OK <br />
|-<br />
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-04] ||Mac Darwin || 08-04-2010|| All OK<br />
|-<br />
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-02] ||Linux x64 || 08-07-2010||All OK <br />
|-<br />
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-03] ||Linux 32 ||08-07-2010 || All OK<br />
|-<br />
|Manual Registration || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03]||Windows XP ||08-08-2010 || All OK<br />
|-<br />
|Manual Registration || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows 7 ||08-08-2010 || All OK <br />
|-<br />
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-04] ||Mac Darwin || 08-04-2010|| All OK<br />
|}<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/2010-Slicer-StLouis July 1st,2010- StLouis Workshop] Use Slicer3.6 release (under construction)<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6-2010-06-10-linux-x86_64.tar.gz Slicer3-3.6-2010-06-10] ||Linux x64 ||06-25-2010||All OK<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6-2010-06-10-win32.exe Slicer3-3.6-2010-06-10] ||Windows XP&7 || 06-25-2010||All OK<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6-2010-06-10-darwin-x86.tar.gz Slicer3-3.6-2010-06-10] ||Mac Darwin||06-25-2010||All OK<br />
|-<br />
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6-2010-06-10-linux-x86.tar.gz Slicer3-3.6-2010-06-10] || Linux x32|| 06-25-2010||All OK<br />
|-<br />
|Data Loading and 3D Visualization || [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6-2010-06-10-linux-x86_64.tar.gz Slicer3-3.6-2010-06-10] || Linux x64||06-11-2010||All OK<br />
|-<br />
|Data Loading and 3D Visualization || [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6-2010-06-10-win32.exe Slicer3-3.6-2010-06-10] ||Windows XP || 06-11-2010||All OK<br />
|-<br />
|Data Loading and 3D Visualization || [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6-2010-06-10-darwin-x86.tar.gz Slicer3-3.6-2010-06-10] ||Mac Darwin||06-11-2010||All OK<br />
|-<br />
|Data Loading and 3D Visualization || [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6-2010-06-10-linux-x86.tar.gz Slicer3-3.6-2010-06-10] || Linux x32] || 06-11-2010||All OK<br />
|-<br />
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6-2010-06-10-linux-x86_64.tar.gz Slicer3-3.6-2010-06-10] ||Linux x64 ||06-11-2010||All OK<br />
|-<br />
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6-2010-06-10-win32.exe Slicer3-3.6-2010-06-10] ||Windows XP || 06-11-2010 || All OK<br />
|-<br />
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6-2010-06-10-darwin-x86.tar.gz Slicer3-3.6-2010-06-10] ||Mac Darwin||06-11-2010||All OK<br />
|-<br />
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6-2010-06-10-linux-x86.tar.gz Slicer3-3.6-2010-06-10] || Linux x32 || 06-11-2010||All OK<br />
|-<br />
|Neurosurgical Planning|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6-2010-06-10-linux-x86_64.tar.gz Slicer3-3.6-2010-06-10] ||Linux x64 ||06-30-2010||All OK<br />
|-<br />
|Neurosurgical Planning|| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6-2010-06-10-win32.exe Slicer3-3.6-2010-06-10] ||Windows XP || 06-30-2010||All OK<br />
|-<br />
|Neurosurgical Planning|| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6-2010-06-10-darwin-x86.tar.gz Slicer3-3.6-2010-06-10] ||Mac Darwin||06-30-2010||All OK<br />
|-<br />
|Neurosurgical Planning|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6-2010-06-10-linux-x86.tar.gz Slicer3-3.6-2010-06-10] || Linux x32|| 06-30-2010||All OK<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=HelloCLI_TutorialContestSummer2013&diff=98886HelloCLI TutorialContestSummer20132023-04-11T18:15:20Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
===Hello CLI Tutorial===<br />
<br />
<br />
Material for the Slicer 4.2 Hello CLI tutorial, Project Week Summer 2013:<br />
<br />
[[File:Hello_CLI_TutorialContestSummer2013.pdf]]<br />
<br />
[[File:Hello_CLI_TutorialContestSummer2013.zip]]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| Hello CLI || Mac OS || Slicer 4.2.2 || ||<br />
|<br />
|-<br />
| Hello CLI || Windows 7 32 bit || Slicer 4.2.2 || ||<br />
| <br />
|-<br />
| Hello CLI || Windows 7 64 bit || Slicer 4.2.2 || ||<br />
| <br />
|-<br />
| Hello CLI || Linux 64 bit || Slicer 4.2.2 || || <br />
|<br />
|-<br />
|}<br />
<br />
[http://www.na-mic.org/Wiki/index.php/2012_Tutorial_Contest Back to tutorial contest]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016&diff=98885FiberBundleSelectionAndScalarMeasurement TutorialContestWinter20162023-04-11T18:14:28Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>[[2016_Winter_Project_Week#Agenda|Back to Winter project week Agenda]]<br />
<br />
This tutorial guided you through the fiber bundle label selection and fiber tract scalar measurements to select fiber bundles passing through region(s) of interest and calculate scalar measurements (such as FA and trace) from fiber bundles.<br />
<br />
*Tutorial [[Media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.pdf]] <br />
*Dataset [[Media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.zip]]<br />
*Image [[Media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016_Snapshot.png]]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| FiberBundleSelectionAndScalarMeasurement || Mac OS || 4.5.0-1 release || January-01-2016 || Fan Zhang<br />
| Pass<br />
|-<br />
| FiberBundleSelectionAndScalarMeasurement || Windows || 4.5.0-1 release || January-01-2016 || Fan Zhang<br />
| Pass<br />
|-<br />
| FiberBundleSelectionAndScalarMeasurement || Linux || 4.5.0-1 release || January-01-2016 || Fan Zhang<br />
| Pass<br />
|-<br />
|}</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012&diff=98884DoseAccumulationforAdaptiveRadiationTherapy TutorialContestSummer20122023-04-11T18:13:35Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>= Testing =<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| Dose Accumulation for Adaptive Radiation Therapy || Mac OS - Lion || 4.1 || 06-15-2012 || Kevin Wang, Csaba Pinter, Andras Lasso || <br />
|-<br />
| Dose Accumulation for Adaptive Radiation Therapy || Windows XP 64 bit || 4.1 || 06-15-2012 || Kevin Wang, Csaba Pinter, Andras Lasso || OK<br />
|-<br />
| Dose Accumulation for Adaptive Radiation Therapy || Linux Ubuntu 64 bit || 4.1 || 06-15-2012 || Kevin Wang, Csaba Pinter, Andras Lasso || <br />
|-<br />
|}<br />
<br />
= Resources =<br />
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Download the slides]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=DTIPrep_TutorialContestSummer2013&diff=98883DTIPrep TutorialContestSummer20132023-04-11T18:12:14Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div><br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || || || <br />
|<br />
|-<br />
| || Windows 7 32 bit || || || <br />
|<br />
|-<br />
| || Windows 7 64 bit || || || <br />
|<br />
|-<br />
| || Linux 64 bit || || || <br />
|<br />
|-<br />
|}<br />
<br />
----<br />
[[File:DTIPrep_TutorialContestSummer2013.pdf| Presentation]]<br />
<br />
[[File:DTIPrepData_TutorialContestSummer2013.zip| Data]]</div>JChris.FillionRhttps://www.na-mic.org/w/index.php?title=CardiacMRIToolkit_TutorialContestSummer2013&diff=98882CardiacMRIToolkit TutorialContestSummer20132023-04-11T18:10:44Z<p>JChris.FillionR: Fix MediaWiki formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)</p>
<hr />
<div>__NOTOC__<br />
===Cardiac MRI Toolkit Tutorial===<br />
<br />
<br />
Material for the Slicer 4.1 Cardiac MRI Toolkit tutorial, Project Week Summer 2013:<br />
<br />
[[File: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pdf]]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:Cardiac_MRI_Toolkit_Tutorial_Data.zip Data: Cardiac_MRI_Toolkit_Tutorial_Data.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part1.zip Videos Part 1: Tutorial_Videos_Part1.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part2.zip Videos Part 2: Tutorial_Videos_Part2.zip]<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| Cardiac MRI Toolkit Extension || Mac OS || Slicer 4.2.2 || 2013/06/07 || Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 32 bit || Slicer 4.2.2 || || <br />
| <br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 64 bit || Slicer 4.2.2 || 2013/06/07 || Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Linux 64 bit || Slicer 4.2.2 || 2013/06/19 || Salma Bengali<br />
| Worked<br />
|-<br />
|}<br />
<br />
[http://www.na-mic.org/Wiki/index.php/2012_Tutorial_Contest Back to tutorial contest]</div>JChris.FillionR