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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==Reference Manual==
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*[[Projects:RegistrationDocumentation:UseCaseInventoryNotes|Notes & concepts about the Registration Case Library]]
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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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*Preferred formats: Slicer Wiki, maybe PDF
 
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==User Manuals==
 
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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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formats: Slicer Wiki, PowerPoint.
 
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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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== Development Efforts ==
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*These movies contain step by step instructions, running through each of the use-cases described above.
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*Slicer4: '''[[Projects:RegistrationDocumentation:Developer4|Notes & feedbacl for GUI and algorithm implementation. Testing Summaries]]'''
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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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*Slicer3: [[Projects:RegistrationDocumentation:Developer|Notes & ideas for GUI and algorithm implementation. Discussion platform with the developer group]]
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*video tutorials have become a popular and widespread form to document GUI interactions, particularly tutorials
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*[[Projects:RegistrationDocumentation:RegEval_Anisotropy|'''Effects of Voxel Anisotropy and Intensity-Inhomogeneity on Image-Based 3D Registration''' ]]
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* they can have almost  the quality of direct tutoring
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*[[Projects:RegistrationDocumentation:Benchmarking|'''Benchmarking''']]
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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:ParameterTesting|Parameter Exploration]]
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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:Evaluation|Result Evaluation & Visualization]]
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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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*[[Projects:RegistrationImprovement|Kitware Wiki on developer efforts]]
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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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*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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*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 Developers ==
 
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This will contain lists of ideas for GUI and function addition/improvements.
 
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*'''Parameter Presets:''' To navigate the jungle of parameter settings and avoid complex GUI design efforts, all parameters are listed and controllable via a preset dropdown menu. The menu can then be labeled by use cases i.e. combinations of MR-MR, same contrast, inter-subject, inter-modality, fast, precise etc. Parameter sets can be saved to files and shared. Each preset becomes a menu entry. This will enable building a library of presets that can be shared among users also.
 
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*'''Recursive DOF hierarchy:''' Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is  here: [[Projects:RegistrationImprovement:RecursiveScheme]]
 
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:The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. [[Media:DOFHierarchy_GUI.jpg‎ ]]
 
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*'''Tooltip link:'''direct links to Reference Manual from Widget tooltips? Can the static text or widget itself launch a link to the Reference manual entry on the Documentation Wiki? That would enable a one-click answer to "What does this button do?"
 
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*'''Affine SVD:''' decomposition of affine into the 4 3DOF components: translation, rotation, scaling, shearing. Can an SVD do this for 12DOF vs. 3 DOF? Having values that relate directly to geometry can help greatly in evaluating and adjusting results. E.g. user can tell visually which of the 3 rotations is most out of alignment. Checking the result rotation angles already provides a quick check and valuable info about where things went awry if solution is suboptimal. Also enables to decouple individual elements, i.e. extract the shear component etc. The current "Transforms" module already does this for translation & rotation, but the scale and shear portions are missing.
 
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*'''Offline WIKI''': can the documentation WIKI be downloaded and used offline, e.g. for laptop users?
 
  
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==Reference Manual==
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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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* Each entry will have one short description (that could also serve as tooltip) and one longer, more technical explanation.
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* links to journal articles for in depth algorithm info
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*Preferred formats:  Slicer Wiki, maybe PDF, cross-linking required
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*'''[[Projects:RegistrationDocumentation:ReferenceManual|Draft Registration Reference Manual]]'''
  
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==User Manuals & Tutorials==
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*[https://www.slicer.org/wiki/Slicer3:Registration#Registration_in_3D_Slicer|'''Main Registration Portal Page''']
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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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*[https://www.slicer.org/wiki/Slicer-3-6-FAQ '''FAQ & Cookbooks''']
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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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**[[Projects:RegistrationDocumentation:UserManual|Draft Registration User Manual]]
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**[[Projects:RegistrationDocumentation:DocumentationResources|notes and documentation resources]]
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*Tutorials will be case oriented and always demonstrate a particular task or feature
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**[[Projects:RegistrationDocumentation:VideoTutorials|Video Tutorials: showcase of specific workflow]]
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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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== Contact ==
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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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**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 ==
 
== Links ==
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*Developer efforts (Kitware): [[Projects:RegistrationImprovement]]
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*[[Downloads|Data links]]
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*Slicer Wiki: [http://www.slicer.org/slicerWiki/index.php/Documentation-3.5]
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*[https://www.predict-hd.net huntington data]
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*Slicer Bug Tracker: [http://na-mic.org/Mantis/my_view_page.php]
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*[[ITK_Registration_Optimization|Register Images Reference Material]]
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*[[Events:Registration_Summit_August_2009|Registration Summit Aug'09]]
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*[[2009_Summer_Project_Week_Slicer3_registration]]
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*[https://www.slicer.org/wiki/Documentation-3.5 Slicer Documentation 3.5]
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*[http://na-mic.org/Mantis/my_view_page.php|Slicer Bug Tracker]
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*[[AHM_2010]]
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*[[2010_Winter_Project_Week_RegistrationCaseLibrary|AHM 2010 Project Week: Registration Case Library Project Page]]
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*[https://www.slicer.org/wiki/Slicer3:Slicer3Brand#3D_Slicer_Visual_Communication_Guide Slicer Logo & Communication Guide]
 
*NAMIC registration:
 
*NAMIC registration:
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*Contact: Dominik Meier : meier@bwh.harvard.edu
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*Contact: Dominik Meier : mailto:meier@bwh.harvard.edu
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=== Bundled Registration and Tests ===
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* http://www.na-mic.org/Wiki/index.php/Projects:DBP2:Harvard:Registration_Documentation
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* http://www.na-mic.org/Wiki/index.php/MeningiomaMRIRegistrationStudy#Limitations_of_the_Slicer_registration_tools
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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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* [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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