Difference between revisions of "Projects:RegistrationDocumentation"

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[[Category:Registration]]
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[[Projects:ARRASuplements|Back to ARRA main page]]
 
==Use Case Library==
 
==Use Case Library==
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*this will contain a list of the most common scenarios encountered for Slicer Registration. Each case will contain a dataset, a parameter set, a guided tutorial with example result. The hierarchy will be represented graphically as a tree and as a list with links to the abovementioned data. The library will be as exhaustive as possible, containin brain and non-brain, different modalities (MRI, CT, PET/SPECT).
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*'''[[Projects:RegistrationDocumentation:UseCaseInventory| Registration Case Library ]]'''
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*considered is also a list of troubleshooting cases, i.e. a list of the most common sources of registration failure, again complete with dataset, tutorial and remedy.
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*'''[[Projects:RegistrationDocumentation:UseCaseAdvertisement|Use Case Sharing Advertisment Page]]'''
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*[[Projects:RegistrationDocumentation:UseCaseInventoryNotes|Notes & concepts about the Registration Case Library]]
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== Development Efforts ==
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*Slicer4: '''[[Projects:RegistrationDocumentation:Developer4|Notes & feedbacl for GUI and algorithm implementation. Testing Summaries]]'''
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*Slicer3: [[Projects:RegistrationDocumentation:Developer|Notes & ideas for GUI and algorithm implementation. Discussion platform with the developer group]]
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*[[Projects:RegistrationDocumentation:RegEval_Anisotropy|'''Effects of Voxel Anisotropy and Intensity-Inhomogeneity on Image-Based 3D Registration''' ]]
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*[[Projects:RegistrationDocumentation:Benchmarking|'''Benchmarking''']]
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*[[Projects:RegistrationDocumentation:ParameterTesting|Parameter Exploration]]
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*[[Projects:RegistrationDocumentation:Evaluation|Result Evaluation & Visualization]]
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*[[Projects:RegistrationImprovement|Kitware Wiki on developer efforts]]
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==Reference Manual==
 
==Reference Manual==
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*This will contain detailed descriptions of each parameter and each control element within the slicer registration module. The description should help the user understand what exactly that function/parameter does and if/how useful it will be for their specific registration problem
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*The reference manual will be organized by submodules and contain detailed descriptions of each parameter and each control element within the slicer registration module. The description should help the user understand what exactly that function/parameter does and if/how useful it will be for their specific registration problem.
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*Preferred formats:  Slicer Wiki, maybe PDF
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* Each entry will have one short description (that could also serve as tooltip) and one longer, more technical explanation.
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==User Manuals==
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* links to journal articles for in depth algorithm info
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*this documentation will discussing the main registration module functionality as a whole, focusing not on the individual controls but the main workflow.
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*Preferred formats:  Slicer Wiki, maybe PDF, cross-linking required
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formats: Slicer Wiki, PowerPoint.
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*'''[[Projects:RegistrationDocumentation:ReferenceManual|Draft Registration Reference Manual]]'''
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*Also included in this category are Background Tutorials, explaining the basics of registration, formats: PowerPoint. Minimal understanding of the inner workings of a registration optimization algorithm is essential to understand and judge the results obtained and obtainable.
 
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==Training Video Tutorials==
 
  
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[[Image:TrainingMovieThumbnail.jpg|thumb|frame| [[Media:VideoTutorialDemo_v1_0.mov|Training Movie Demo (1min)]]]]
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==User Manuals & Tutorials==
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*These movies contain step by step instructions, running through each of the use-cases described above.  
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*[https://www.slicer.org/wiki/Slicer3:Registration#Registration_in_3D_Slicer|'''Main Registration Portal Page''']
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*An example of the features/character of a video tutorial is here: [[Media:VideoTutorialDemo_v1_0.mov]]
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*[[Media:NCIGT2010_RegistrBreakout_Slides_v3_1.ppt|'''Registration Basics, Registration Tools & User Support in Slicer''' (Powerpoint, 14MB)]]
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*video tutorials have become a popular and widespread form to document GUI interactions, particularly tutorials
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*[https://www.slicer.org/wiki/Slicer-3-6-FAQ '''FAQ & Cookbooks''']
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* they can have almost  the quality of direct tutoring
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*The user manual will contain a systematic overview of registration functionality within 3DSlicer. formats: Slicer Wiki, PowerPoint.  
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*they are compact in length and filesize (because the changes are local and small over time, MPEG compression is very effective with little quality loss), which makes them ideal for online distribution
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**[[Projects:RegistrationDocumentation:UserManual|Draft Registration User Manual]]
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*movie viewing capability is mainstream, i.e. all OS will have this capability, viewers can be downloaded for free
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**[[Projects:RegistrationDocumentation:DocumentationResources|notes and documentation resources]]
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*the audio track can provide main instructions, motivation, commentary and an abundance of detail information at the right juncture, something very difficult to provide in other formats without overloading a tutorial
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*Tutorials will be case oriented and always demonstrate a particular task or feature
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*the step by step interaction is captured unambiguously. We do not spend a lot of time and space in showing slides with screen captures.
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**[[Projects:RegistrationDocumentation:VideoTutorials|Video Tutorials: showcase of specific workflow]]
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*since they are easy to make and great software is inexpensive, potential use even for developer communication can be considered, e.g. to document complex bugs
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**Background Tutorials, explaining the basics of registration, formats: PowerPoint. Minimal understanding of the inner workings of a registration optimization algorithm is essential to understand and judge the results obtained and obtainable.
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*they have a low usage threshold, i.e. users are more inclined to watch a video than to dig through a power point presentation
 
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*they are not all that useful for reference or main documentation material, e.g. a tutorial on main registration concepts is probably still better in PPT.
 
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*formats: video files (quicktime, WMV, mp4 , Flash), optimized for streaming or download
 
  
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== Ideas for Developent Efforts ==
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== Contact ==
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*This will contain lists on function improvements that require develoment effort, e.g. new GUI features, but also strategic notes on data and algorithm structure
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*if there is anything you think would be of help to the 3DSlicer registration user, be that documentation, examples or features, we'd love to hear about it:
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*direct links to Reference Manual from Widget tooltips?
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**any questions/concerns are welcome on the slicer user mailing list: mailto:slicer-users@bwh.harvard.edu
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**particular questions/concerns re. these pages or Registration Documentation drop a line to mailto:meier@bwh.harvard.edu
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== Links ==
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*[[Downloads|Data links]]
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*[https://www.predict-hd.net huntington data]
  
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----
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*[[ITK_Registration_Optimization|Register Images Reference Material]]
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==Meeting Minutes==
 
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*action items & notes from meetings, TCONs and reviews
 
  
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<showhide>
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*[[Events:Registration_Summit_August_2009|Registration Summit Aug'09]]
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* Meeting 2009-09-30 __HIDER__
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*[[2009_Summer_Project_Week_Slicer3_registration]]
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<hide>
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*[https://www.slicer.org/wiki/Documentation-3.5 Slicer Documentation 3.5]
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**main effort in first few months will be building of a use case library: starting with a tree of use case scenarios (brain-non-brain, inter- vs. intramodality, MR-MR inter-contrast, inter-subject vs. intra-subject, DTI to structural. Emphasis is on applications/cases, not technology, i.e. no distinction between implementation (e.g. fiducials, cost function etc.). Whole body scenarios: PET-CT, PET-CT with follow-up to track tumor growth, image-guided therapy applications
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*[http://na-mic.org/Mantis/my_view_page.php|Slicer Bug Tracker]
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**aside/along with a graphic representation of this tree is a table with links to 1) the dataset, 2) the parameter settings, 3) the tutorial running the example set
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*[[AHM_2010]]
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**setup a weekly meeting. Current: Wed. 9.30am . ca. 30min
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*[[2010_Winter_Project_Week_RegistrationCaseLibrary|AHM 2010 Project Week: Registration Case Library Project Page]]
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**include considerations of precision vs. speed and vs. robustness. The interactive nature of Slicer sets a ~10minute effort limit per case as a guideline
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*[https://www.slicer.org/wiki/Slicer3:Slicer3Brand#3D_Slicer_Visual_Communication_Guide Slicer Logo & Communication Guide]
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**write up a brief spec.aim for Stuart Silverman for sharing his intra-operative data: for the NAC supplement we plan to establish a library of use cases to guide segmentation efforts. This library an associated registration strategies will be shared on the Web.
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*NAMIC registration:
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**documentation for ARRA via a NAC website, which follows a wiki2web self-service structure. Marianna is contact for details
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*Contact: Dominik Meier : mailto:meier@bwh.harvard.edu
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**day-to-day documentation on the NAMIC wiki. Create my own Regsitration page.
 
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**support personnel: Casey as developer, Andy as "super-user". Twice weekly interaction with Casey is recommended.
 
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**Ron supports the single module/tab with all parameters + presets menu option. It is a clean design and highly expandable.
 
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**Ron suggests Casey touch base with J.C. (Jean Christophe Fillion Robin) also @ Kitware, who works on the QT widget issue, so that he's aware of new capabilities such as Webkit that enable displaying "live" online documentation directly in the program.
 
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</hide>
 
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</showhide>
 
  
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== Links ==
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=== Bundled Registration and Tests ===
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*Developer efforts (Kitware): [[Projects:RegistrationImprovement]]
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* http://www.na-mic.org/Wiki/index.php/Projects:DBP2:Harvard:Registration_Documentation
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*Slicer Wiki:  
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* http://www.na-mic.org/Wiki/index.php/MeningiomaMRIRegistrationStudy#Limitations_of_the_Slicer_registration_tools
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*NAMIC registration
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* [http://www.na-mic.org/Wiki/index.php/Vervet_MRI_registration Vervet head MRI atlas-to-subject registration]
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*
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* [http://www.na-mic.org/Wiki/index.php/MeningiomaMRIRegistrationStudy Head MRI registration between different timepoints (human subjects, changing pathology present)]
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* [https://www.slicer.org/wiki/Slicer3:Registration Side by side comparisons in slicer2 and slicer3 with data and images]
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* http://mindboggle.info/papers/index.php
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*testing on the Vanderbuild database: [http://www.insight-journal.org/RIRE/ RIRE]
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* [[ITK_Registration_Optimization#Algorithmic_Requirements_and_Use_Cases|ITK Registration Optimization Sets]]
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*[[DTI-non-rigid]]
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*[[Projects:DBP2:Harvard:Registration_Documentation:Compare#Case_to_case_registration]]

Latest revision as of 17:41, 10 July 2017

Home < Projects:RegistrationDocumentation

Back to ARRA main page

Use Case Library

Development Efforts

Reference Manual

  • The reference manual will be organized by submodules and contain detailed descriptions of each parameter and each control element within the slicer registration module. The description should help the user understand what exactly that function/parameter does and if/how useful it will be for their specific registration problem.
  • Each entry will have one short description (that could also serve as tooltip) and one longer, more technical explanation.
  • links to journal articles for in depth algorithm info
  • Preferred formats: Slicer Wiki, maybe PDF, cross-linking required
  • Draft Registration Reference Manual

User Manuals & Tutorials

Contact

  • if there is anything you think would be of help to the 3DSlicer registration user, be that documentation, examples or features, we'd love to hear about it:

Links

Bundled Registration and Tests

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