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[[Category:Registration]]
 
[[Projects:ARRASuplements|Back to ARRA main page]]
 
[[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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*the organization of a use case hierarchy can be accomplished in several ways. The main categories are listed below. Not all combinations exist or are equally common occurrences. For example, a different-timepoint/contrast distinction is not necessary for inter-subject registration.
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*[[Projects:RegistrationDocumentation:UseCaseInventoryNotes|Notes & concepts about the Registration Case Library]]
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**'''ORGAN''': Brain, Head&Neck, Thorax, Abdomen&Pelvis, Limbs, WholeBody
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**'''SUBJECT''': intra-subject, inter-subject
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== Development Efforts ==
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**'''CONTENT''': same_TimeOrContent, different_TimeOrContent
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*Slicer4: '''[[Projects:RegistrationDocumentation:Developer4|Notes & feedbacl for GUI and algorithm implementation. Testing Summaries]]'''
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**'''MODALITY''': intra-modality, inter-modality
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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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**'''CONTRAST''': same_Contrast, different_Contrast
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*[[Projects:RegistrationDocumentation:RegEval_Anisotropy|'''Effects of Voxel Anisotropy and Intensity-Inhomogeneity on Image-Based 3D Registration''' ]]
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***MR, CT, PET+SPECT, US
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*[[Projects:RegistrationDocumentation:Benchmarking|'''Benchmarking''']]
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***T1, T2, PD, T2s, DTI, MRPerfusion
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*[[Projects:RegistrationDocumentation:ParameterTesting|Parameter Exploration]]
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**'''VIEW''': same_View, different_View
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*[[Projects:RegistrationDocumentation:Evaluation|Result Evaluation & Visualization]]
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*the '''VIEW''' distinction arises from commonly occurring problems of co-registering sets acquired with different slice orientation. The basics of dealing with axis orientation is already integrated into the algorithm, but further details remain: basically different_view implies a possibly high voxel size ratio (i.e. different voxel sizes if one image acquired axial the other coronal). Actions/Parameter settings are with multi-resolution settings, blurring and special checking of the axis orientation (vox2ras) meta-data. If, for example,voxel size ratio is close to [1 1 1] we need not do anything different other than resample based on vox2ras.
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*[[Projects:RegistrationImprovement|Kitware Wiki on developer efforts]]
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*Depending on grouping this leads to trees with 80-360 entries. Two example hierarchies based on the above distinctions, formatted as directory trees are here: (download and browse using your file browser)
 
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*'''User-populated content''' The exploding # of combinations makes a successful top-down approach difficult. More effective to organize bottom-up, i.e. have user invited content, which we organize into a growing tree. We could make call to the user community for submitting datasets and registration problems: e.g.
 
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  "if you have an interesting registration problem and your case is not covered in our library,
 
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  send us your case: we will register it and post it.
 
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  You get a free registration, the user community get a new example case. Everybody wins."
 
  
 
==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 Developers ==
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== Contact ==
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This will contain lists of ideas for GUI and function addition/improvements.
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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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*'''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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**any questions/concerns are welcome on the slicer user mailing list: mailto:slicer-users@bwh.harvard.edu
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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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**particular questions/concerns re. these pages or Registration Documentation drop a line to mailto:meier@bwh.harvard.edu
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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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----
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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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== Links ==
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*[[Downloads|Data links]]
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*[https://www.predict-hd.net huntington data]
  
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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]
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*NAMIC registration:
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*Contact: Dominik Meier : mailto:meier@bwh.harvard.edu
  
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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: [http://www.slicer.org/slicerWiki/index.php/Documentation-3.5]
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* http://www.na-mic.org/Wiki/index.php/MeningiomaMRIRegistrationStudy#Limitations_of_the_Slicer_registration_tools
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*Slicer Bug Tracker: [http://na-mic.org/Mantis/my_view_page.php]
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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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*NAMIC 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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*Contact: Dominik Meier : meier@bwh.harvard.edu
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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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