Training:Events Update

2015.06.05 3D Slicer DTI tutorial

2014.10.23 Weidong Cai's work page

2014.10.15 Lung Segments Color Map ; http://labelpage.halle.us

2014.10.03 Slicer at RSNA portal

2014.09.23 Parth Amin's work

2014.09.18 Deep Brain Stimulation

2014.06.24 Python programming tutorial

2014.06.18 DWIConvert Training Resources

2014.10.11 Sidong's Liu work page

2012.06.19

git commit -a -m "ENH: changed xxx"

git push origin master

2012.06.18 How to build an extension

2012.04.06 Tract Lookup Table

2012.03.30 SimpleITK page

2012.03.27 Team Color Map

2012.02.21 MICCAI 2012 DTI Challenge website

2012.02.14 Slicer4 DTI issues

2012.10.11 Slicer4.0 binaries for SPIE2012

2011.10.12 DTI heart tractography

2011.09.22
Virtual Machine Configuration ( exploratory work)

2011.08.05
Training Events Portal (SPujol)
2011.06.28
DTI Import/Export (SPujol)
2010.05.12
Journal of Slicer Workshop Tests (S.Pujol)
2010.05.04
Slicer3.6 Training Portfolio Agenda (S.Pujol)
2010.01.25
Training Data Gallery (S.Pujol)
2010.01.04
Journal of Slicer Tests (S.Pujol)
2008.05.07 (S.Pujol)

• Slicer3 courses
  • Slicer3 Data Loading and Visualization: Introduction to the basics of loading, visualizing and interacting with data in 3D in the new Slicer3 release.
  • Slicer3 Course for Developers: Integration of an external program into the Slicer3 software environment using the new Execution Model.
• Slicer3 workshops
  • Organization and delivery of the UNC Slicer 3 Users and Plug-in Workshop, April 14, 2008, Chapel Hill, NC.
    • 8-hour course combining 4 hands-on sessions for users and developers and lectures on the architecture and software components of Slicer3.
    • 20 participants from UNC and Duke University.
  • Organization and delivery of the Spring 2008 Slicer3 User Training Workshop , February 20, 2008, SPL Boston, MA.
    • First Slicer3 hands-on training workshop for users covering the basics of loading, visualizing and saving data in Slicer3.
    • 11 participants from BWH and MGH.
  • Hands-on session on Slicer3 Plug-ins, January 8,2008, NA-MIC AHM 2008, Salt Lake City, Utah.
    • First Slicer3 course for developers covering the integration of external programs with Slicer3.
    • 18 participants from NA-MIC.
  • Slicer3 demonstration at the Biomedical Informatics Research Network AHM (BIRN AHM) 2007
• Thematic workshops submissions to international conferences
  • Submission of the workshop proposal 'Interfacing third-party software with the NA-MIC open-source toolkit' (Sonia Pujol, Randy Gollub, Steve Pieper, Jim Miller)' to the Medical Image Computing and Computer Assisted Intervention conference (MICCAI 2008), Sept 6-10, 2008, New-York, NY. Status: accepted.
  • Submission of the workshop proposal '3D Interactive Visualization of DICOM images with Slicer (Sonia Pujol, Randy Gollub, Steve Pieper, Kathryn Hayes)' to the Radiological Society of North America conference (RSNA 2008), Nov. 30- Dec. 5, 2008, Chicago, IL. Status: accepted.
• NA-MIC DTI Validation Study
  • Tractography breakout session, January 9, 2008, NA-MIC AHM 2008 Salt Lake City, Utah.
    • 6-hour session on tractography outputs for one subject and preliminary cross algorithm summary.
  • NA-MIC Contrasting Tractography Methods Conference, October 20,2007 Santa Fe, NM.
    • Two-days conference on preliminary tractography results on initial schizophrenia patients datasets, tracts of interest selection and pre-processing pipeline discussion.
  • Bi-weekly DTI validation project conference calls .

2007.09.05 (S.Pujol)

• New Slicer tutorial: Slicer Training 11 - Registration (71 slides)
  • Registration of MR data using a mutual information algorithm
  • Processing pipeline covering manual, semi-automatic and automatic registration functionalities
  • Intermediate results assessment based on neuroanatomical landmarks
• Organization and delivery of the OHBM DTI Training Workshop, June 9, 2007 - Chicago, IL
  • Satellite event of the 13th Annual Meeting of the Organization for Human Brain Mapping (OHBM2007)
  • 7 hour training integrating theoretical lectures with hands-on sessions on Diffusion Tensor Imaging
  • 45 international participants representing 38 Institutes from 8 countries
• Publication in Academic Radiology : Lowering the barriers inherent in translating advances in neuroimage analysis to clinical research applications. Pujol S, Kikinis R, Gollub RL (In Press). 'Through national collaborative effort supported by the NIH Roadmap, the integration of the most sophisticated algorithms into usable open-source systems enables clinical researchers to have access to a broad spectrum of cutting-edge analysis techniques. A critical step to maximize the long-term positive impact of this collaborative effort is to translate these techniques into new skills of clinical researchers. Our objective is to bridge the gap between scientific advances made by the biomedical imaging community and their widspread use in the clinical research community.'

2007.04.19 (R. Gollub)

• Preparations for the upcoming OHBM workshop are on-going.
• Final development of the Registration tutorial, the newest and final Slicer 2.6 tutorial, is nearly complete.
• Improvements to the exisiting segmentation tutorial will be compelted next.
• All future Slicer based tutorial development will be devoted to the Slicer 3 version, commensing with an introductory tutorial to train users to open, view and save image files.
• Parallel development of user targeted and software developer targetted tutorials will be planned during the upcoming Projects week in Boston.

2007.03.29 (S.Pujol)

• NA-MIC All Hands Meeting, January 10-12, 2007 - Salt Lake City
  • Training Core Update 2006 (Sonia Pujol)
  • EAB Meeting: Training Core Contributions 2006 (Sonia Pujol)
• Organization and delivery of the HCNR Slicer Training Workshop at the Surgical Planning Laboratory, November 1st, 2006 - Boston
  • 5 hour training organized in 3 hands-on sessions focused on Diffusion Tensor Imaging.
  • 28 participants from 20 different institute departments.

2007.01.16 (R. Gollub) Core 5 and Core 6 meeting held to discuss outcome of AHM and plan implemtation.

• See posted presentations on the AHM page for details of our progress to date.
• See 2007-01-16 Core 5, Core 6 Summit for brief synopsis of today's meeting and see Calendar.Slicer3.TrainingMaterials for proposed tutorial material development schedule
• Pending approval by the rest of Core 5 faculty and PI sign off, this constitutes the training plans for the first half of 2007
• Clean up of Training Core Wiki pages by Randy and Sonia ASAP

2006.08.22 (S.Pujol) Recently completed work

• Organization and delivery of the Slicer Training workshop at the National Library of Medicine - July 19, 2006
  • 8 hour training organized in 4 hands-on sessions guiding the participants through a logical progression from data loading and visualization to fiber tract clustering
  • 390 slides of hands-on exercises providing pratical experience on Diffusion Weighted Imaging analysis and visualization with Slicer
  • 24 participants from 11 different laboratories within the National Institutes of Health and 7 different universities and companies

This workshop was the NA-MIC Dissemination event at the National Centers for Biomedical Computing 2006 All Hands Meeting .

• New Slicer tutorial: Slicer Training 9 - DWI Dicom to Nrrd conversion within Slicer
  • Extraction of DWI acquisition parameters
  • DWI Nrrd header generation with the Tk Console
  • Validation using glyphs visualisation
• Upgrade of the DT-MRI Slicer tutorial
  • Slices interleaved vs volume interleaved visualisation
  • Selective seeding
  • Fiber tracts clustering

• Organisation and delivery of the NIH Slicer Training workshop - April 27, 2006"

4 hands-on sessions centered on tensor data conversion and analysis with 3D Slicer.

This event was hosted by the National Institutes of Health, Section on Tissue Biophysics and Biomimetics.

• New Slicer tutorial: Slicer Training 8 - Nrrd File Format
  • Nrrd terminology and requirements
  • Command line generation of DTI Nrrd headers from pre-computed tensor data
  • Validation using glyphs visualisation

2006.05.30 (R. Gollub / S.Pujol)

The UNC DTI Training workshop was well attended and well received. A number of suggestions for improvements were gathered based on discussion among faculty and web survey of participants.

For the June 2007 OHBM DTI Workshop:

1. consider adding MRI physicist faculty to give 30 min introductory lecture
2. consider moving the clinical correlation lecture to the first presentation as a way of providing focus, clarity and motivation for the workshop
3. add a 30 min Slicer introductory session prior to the DTI module
4. obtain permission to share slides from introductory lectures, clean-up slides and post on the wiki page of the workshop and Training core materials.

General improvements:

1. Make a new Nrrd tutorial for DWI DICOM data- use this one as the generic teaching
2. Determine whether there are normalization and registration tools for cross-subject analysis of DTI data within Slicer and if so add them to tutorial
3. Consider providing separate workshops for clinicians and computer scientists
4. Consider developping slides on file format history
5. Send follow-up e-mails to people who did not complete the web survey during the workshop
6. Enable tutorial delivery from Mac as well as PC

2006.05.05 (R. Gollub)

• Notes from T-con with Core 5 faculty May 5, 2006

2006.04.19 (S.Pujol)

• Slicer Advanced tutorial: EMAtlasBrainClassifier
• Performance and reliability testing of the vtkEMAtlasBrainClassifier module on Unix, Linux and Windows platforms
• Pre-processing and segmentation of the MIND Institute datasets with the EM algorithm
• Delivery of the April 10-11 NA-MIC Training workshop at the MIND Institute, New-Mexico: 4 hands-on sessions, 22 participants.

2006.01.31 (S.Pujol)

• NA-MIC All Hands Meeting, January 8-9, 2006 - Salt Lake City
  • Training Core Update 2005 (Sonia Pujol)
  • Training Core Plans 2006 (Randy Gollub)
    • Web-based training resources: Slicer 101
    • Neuroanatomy training seminar for NAMIC computer scientists
    • Additional NA-MIC kit tutorials
    • DTI Training Workshops
  • AHM 2006 Neuroanatomy seminar
• NA-MIC Programming Week, January 10-13, 2006 - Salt Lake City: Time-Series Navigation for fMRI Statistical Analysis based on a Client-Server architecture (Sonia Pujol)
• Delivery of the HCNR Slicer Training Workshop, January 24, 2006 - Surgical Planning Laboratory, Boston
• Creation of a new web-based NA-MIC Training survey

2005.12.08 (R. Gollub)

• Notes from T-con with Core 5 faculty December 8, 2005

2005.11.21 (R. Gollub)

• To be discussed on upcoming T-con with Core 5 faculty December 8, 2005

1. Development of training materials for UNC based open source analysis software
2. Delivery of Workshops at international meetings (OHBM, SFN for 2006?)
3. Delivery of Workshops at other venues (Spring Brain Conference, MIND institute, etc)
4. Participation in the validation/calibration efforts of NA-MIC

2005.11.03 (R. Gollub)

• Integrated update of www.slicer.org and www.na-mic.org and wiki pages for management of licensing, downloads, and supporting materials (together with Nicole Aucion, Mariana Jakob, Sonia, Randy G., Ron K. and Steve P.)
• Delivery of Slicer Training jointly sponsored by NA-MIC and HCNR (coordinated by Sonia and Sandy Wells)
• Continued development of fMRI data analysis tutorial client/server software. New deadline for completion of programming is December 2005.
• Joint NA-MIC and BIRN development and testing of the Quality Assurance and De-Identification Modules for Slicer continuing
• Wish List of new tutorial materials (work to begin after January 1, 2006):

1. New tutorial for visualizing co-registered statistical maps from PET and fMRI data in Slicer
2. Complete development of EM segmentor tutorial
3. Developer material tutorials (with Nicole A)
4. Documentation update for anticipated release of Slicer 2.6

• Establish new teleconf call date/time

2005.10.14 (R. Gollub)

• Development and delivery of the User Workshop SPL September 30, 2005 at SPL Boylston Lab
• Development and delivery of the Slicer/Freesurfer Workshop at UCSD in collaboration with the Morphometry BIRN project 2005 BIRN All Hands Metting 3D Slicer and FreesurferWorkshop
• Joint NA-MIC and BIRN development and testing of the Quality Assurance and De-Identification Modules for Slicer on going

2005.09.20 (S.Pujol)

• Organization of the September 16, 2005 Slicer Training Workshop at MGH Martinos Center
• Tests sessions of the vtkFreeSurferReaders module with Nicole Aucoin in preparation for the Slicer/FreeSurfer Training workshops
• New Slicer tutorial: Slicer Training 6 - vtkFreeSurferReaders
• New Slicer tutorial: Slicer Training 7 - Saving Data with Slicer

2005.08.12 (S.Pujol)

• Implementation and testing of an image reader in C for the fMRI datasets on the Server side of the Statistical Analysis tutorial
• Wish-list from the FreeSurfer users at MGH Martinos Center for the Sept.16 Slicer Training workshop
• Outcome of the Core 5 team TCON on 2005-2006 Training activities

2005.07.14 (S.Pujol)

• Intensity mapping in Java for visualization of the anatomical slices on the Client side of the Statistical Analysis tutorial
• New version of the Slicer DT-MRI module tutorial with non proprietary sample data
• Early objectives of the MGH Slicer Training workshop: loading and editing FreeSurfer volumes and surfaces within Slicer

2005.06.21 (S.Pujol)

• fMRI data resampling in Java for 2D visualization on the Client side of the Statistical Analysis tutorial
• New version of the Slicer tutorial for Loading and Viewing Data, based on experience gained in Dartmouth workshop.
• Documentation Template for the software developed by Core 1&2 during the Programming week

2005.04.29 (R. Gollub/S.Pujol)

• Focus of the fMRI tutorial development on data file format
• Wish-list from the Brain Imaging Laboratory for the May 26-27 Workshop at Dartmouth-Hitchcock Medical Center
  • File format management of Darmouth's datasets
  • 3D reconstruction of the hippocampus
  • Tractography within the memory system for further connectivity studies
  • Co-registration of different imaging modalities
• Joint effort with the Dissemination team to support the generation of external documentation during the June Programming Week

2005.04.12 (R. Gollub/S. Pujol)

Update

• fMRI Tutorial development continues to progress, both the software code and the html documentation are being improved
• We are also working out the details for what information to collect from new users when they access the tutorial
• beta testing planned in three phases,

1. among developers and fMRI statisticians (R. Gollub, D. Greve, R. Hoge, M. Vangel, W. Plesniack, N. White, C-F. Westin)
2. among NAMIC personnel (May 26-27 Dissemination event, end of June Programmers week)
3. among larger audience of fMRI statisticans (K. Worsely, T. Nichol, S. Smith, H. Stern, L. Friedman) July and August

• Still to be determined is the number and sites for server hosting. This will be addressed during the Programming Week.

2005.04.06 (S.Pujol)

Update of the current work

• Upgrade of the documentation of the fMRI Statistical Analysis tutorial to a learner-oriented guide,
• Centralization of the training materials disseminated on the wiki via cross-links to Core 5,
• Testing phase of the fMRI Client-Server application.

2005.03.17 (S.Pujol)

Update of the current work

• Update of the HST web-based fMRI Statistical Analysis tutorial with features from the interface of the new Client/Server application.
• Assist end-users in fMRI Analysis training by adding to the tutorial detailled answers to the questions of the HST web-based course.
• Planning and content of the Slicer Training workshop at MGH (June/July).
• Definition of evaluation tools for Training workshops.

The main goals are 1) the evaluation of the knowledge learned during the sessions, 2) the identification of further developments based on the feedback from the attendees. This can be done via a first web-based questionnaire using SurveyMonkey tool and workgroup/discussion sessions.

• Review of the litterature in education for possible publications of the results of Core 5 Training materials.

2005.03.16 (S.Pujol)

Outcome of the 2005.03.14 Training/Dissemination TCON

Team Discussions In attendance: Randy Gollub (MGH), Ron Kikinis (BWH), Tina Kapur (Epiphany Medical), Steve Pieper (BWH), Sonia Pujol (BWH).

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Core 5 and Core 6 joint efforts on key delivery to Core 3: Training sessions on Slicer3D

Please, visit the NAMIC TCON information http://www.na-mic.org/Wiki/index.php/TCON:Main to get the text summary of the discussion.

2005.03.05 (R. Gollub)

Updates below are based on the outcome of the 2005.03.4 Morphometry BIRN meeting held in Miami.

Team Discussions

In attendance: Randy Gollub (MGH)/ Jorge Jovicich (MGH)/ Susumu Mori (Johns Hopkins)/ Steve Pieper (BWH) and Allen Song (Duke).

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Susumu Mori of Johns Hopkins and Allen Song of Duke University are experts in DTI (and more), Allen is an MR physicist who have expertise in the acquisition and correction of DTI data, Susumu is focused on the analysis and visualization of the DTI data. Both of them have devoted considerable resources to the development of various training and educational software tools as they did their work and both would like to collaborate in one fashion or another.

Here is a complete list of ideas/information that were discussed:

1- They really liked the idea of the NAMIC Training Site becoming the Wiki Pedia for Medical Imaging Educational Resources and offered to help point us to materials they knew about.

2- We discussed having Sonia attend the ISMRM meeting to take the Educational Courses so she could bring those resources to bear- i.e. learn how to organize the material and get any additional web links, open source teaching materials to post. And get up to current speed with the state of the art in teaching this material. I have attended this in the past (1996 I believe) and it was great, but my materials will be very out of date.

3- We discussed having Sonia (and possibly me too) travel to NC after the fMRI tutorial is finished to visit not only Guido's, but also Allen's lab to show them the tutorial and to see the written material and software tools that they have developed. For MRI acquisition: Allen has a software tool that synthetically generates MRI data given a set of acquisition parameters (TE. TI, FOV, )- T1, T2, PD. Looks like a GE scanner. He imagines that it could be expanded to include DTI. He also has a simple visualization software tool that is written in ITK for 3D on the fly viewing of fMRI activation data that he thinks could readily be adapted for DTI results, perhaps even structural MRI. He also is going to explore the possibility that the publisher of his textbook might be willing to allow him to post some of the materials on our site, particularly the material on the included CD that is already in html. This includes a glossary and more.

4- Susumu has a BEAUTIFUL viewing software tool for visualizing DTI data, but he is not sure how he will share/distribute it. He already has a large database of DTI data on his web site that he is open to the scientific community for sharing along with other material there that we can investigate. We will stay in touch with him as we go.

5- Most importantly, they were both very enthusiastic about utilizing the M-BIRN calibration data set for educational purposes. They have no objection to working with us to make educational modules based on the lessons learned from this work. It is likely that this will be an on-going process that will take 1-3 years to fully implement.

6- They both agreed to be advisors to us in the overall planning for NAMIC MRI and DTI teaching. We could set a goal for Core 5 to have a draft "big picture" plan for what exactly we will teach and how to have a session at the October BIRN All Hands meeting in San Diego devoted to getting this group's input.

Steve P and Ron would like to add to our highest priority work list bringing Slicer training and dissemination for end users into final polished form. We, with Sonia's enthusiastic agreement, have approved her taking on a key role, together with Tina, in running the Slicer workshops being planned for the near future. We generated an initial action plan for this:

1- Steve P will be responsible (together with Alex Yarmakovic) for drafting a one page synopsis of Slicer 2.4 functionality

2- Steve P with Nicole, Marianna, and various SPL folk will gather together all currently available Slicer documentation, tutorials, presentations etc

3- Steve P or his designee will go through this and prepare a status report on Slicer training

4- Ron or his designee with organize a conference call to initiate "the NAMIC process" for training/dissemination development and support- the "how-to" for Cores 2, 5 and 6 to work together with Slicer as the initial software tool to get this treatment. The agenda for that meeting will be: -report on the status of Slicer (see 3 above) -plan for what deliverables we want (e.g. downloadable modular tutorials in pdf format, web based FAQ, moderated email users list, materials for Workshops, update log) and how they will be NAMIC branded -conceptual overview of division of responsibilities to implement the agreed upon plan.

2005.02.28 (S.Pujol)

Updates below are based on the outcome of the 2005.02.20-22 NAMIC AHM meeting.

Team Discussions In attendance: Guido Gerig (UNC)/ Greg Jones (Utah)/ Sonia Pujol (BWH) with input from Steve Pieper (BWH) and Carl-Fredrik Westin (BWH).

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Milestones and web-access of Core 5 tools were appreciated by NIH project managers as an excellent source of output material from NAMIC to the scientific community.

Key points

I) Identified need for multi-level training in DTI, with materials targeted for several audiences. From the most basic level to teach vocabulary and concepts to clinicians and novice learners to the most advanced to teach the applications engineers and algorithm developers about the relations among the analysis tools. Design of tutorial materials classified by the time required to complete (e.g. DTI in 10 minutes- designed for busy clinicians).

II) One goal of training is to improve DTI data quality for anyone who accesses our materials. Calibration of acquisition and analysis methods.

Suggested topics/domains for interactive educational material in this domain include: 1. Acquisition parameters: influence of the spatial resolution/ Scan Type (e.g. EPI vs spiral)/ Slice thickness, b-value, SNR, and gradient encoding directions, (One idea is a tutorial based on visualization of the same brain structure with different acquisition parameters), 2. Sources of geometric distortion, ways to minimize during acquisition and methods for correction during imaging processing, 3. Signal to Noise: 1.5 T vs 3T. III) Another goal of training is the understanding of the attributes of tissue that are revealed by DTI for anyone who accesses our materials: Visualization.

Suggested topics/domains for interactive educational material in this domain include 4. Tensors, 5. Glyphs , 6. Tractography.

Suggestion was made that for the Advanced Training we may need to help develop materials for training in the use of the NAMIC Image Analysis research tools (in coordination with the Core 1 developers, the Core 2 engineers and the Core 6 disseminators- see below). Tools for possible educational effort include 5. Clustering (C-F Westin – BWH), 6. Statistical Analysis (Guido Gerig – UNC), 7. QBall Imaging (David Tuch – MGH + Slicer3D).

Existing interactive tools that are available for use and additional development by the Training Core include Fiber Viewer (Guido Gerig, UNC) and Slicer3D DTI Module (C-F Westin, BWH). Another interesting software discussed was Diffusion Visualizer (Image Computing & Analysis Lab, Tokyo) used by David Tuch at MGH, but this is not open source.

Additional Ideas and Suggestions Collect material, make it available on NAMIC website (DTI library) Design of NAMIC format presentation to “brand” all our materials

Conclusion/Vision for how the Training Core fits into NAMIC efforts

Core1/Core 3 Communication issues --> Core 5 = interface between neuroscientists and computer scientists,

Teach the underlying fundamental medical imaging concepts/content through the tools; do not teach the tools, Open-Source oriented meeting (ITK), Software sharing for our community -> Image Analysis tools and all our training materials will be put in ITK when possible but will always be open source: NA-MIC toolkit.

Action Plans

1. Received positive endorsement to go forward with our overall plans as presented.
2. Need to develop overall framework for teaching DTI. Acquisition/calibration issues may be able to be partnered with Morphometry BIRN (Susumu Mori, Allen Song, Anders Dale, etc), update to come soon from Randy Gollub.
3. Need to develop an overall strategy for coordination with the Core 1 developers, the Core 2 engineers and the Core 6 Disseminators.
4. Organize upcoming immediate training/tele-teaching activities including NAMIC at MICCAI 2005, and workshops in Toronto and NIH.

• Training:Kickoff_Agenda