Projects:RegistrationDocumentation

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Use Case Library

• Registration Case Library
• Use Case Sharing Advertisment Page
• Notes & concepts about the Registration Case Library

Development Efforts

• Notes & ideas for GUI and algorithm implementation. Discussion platform with the developer group
• Developer efforts (Kitware)

Reference Manual

• The reference manual 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.
• Each entry will have one short description (that could also serve as tooltip) and one longer, more technical explanation.
• Preferred formats: Slicer Wiki, maybe PDF, cross-linking required
• Draft Registration Reference Manual

User Manuals & Tutorials

• The user manual will contain a systematic overview of registration functionality within 3DSlicer. formats: Slicer Wiki, PowerPoint.
• Turtorials will be case oriented and always demonstrate a particular task or feature
• Video Tutorials: showcase of specific workflow
• 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.
• Topics for background tutorials:
  • the main components: transform, similarity function, optimization, interpolation
  • coordinate systems: physical vs. image space, RAS vs. LPI etc.
  • relevant image meta-data: image/axis orientation, image/CS origin, voxel size, dynamic range
  • overview of scenarios and their different challenges: image pairings, DOF, multi-modal, intra/inter-subject etc.
  • how to evaluate a match: tools & concepts
  • common mistakes to avoid: inappropriate DOF, overly flat similarity metric, CS inconsistencies, FOV discrepancies, wrong interpolation, insufficient search (sample points, multi-scale, DOF scale-space)
  • Troubleshooting guide: insufficient match - what next? Parameter modification, DOF change, initial alignment assist, fiducial help, ROI masking (e.g. skull stripping)
• Tutorial Resources
  • Coordinate Systems / Image Orientation
    • http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/NA-MIC_Kit/Coordinate_Systems
    • http://www.na-mic.org/Wiki/index.php/Execution_Model_Reference_Systems
    • http://mail.scipy.org/pipermail/nipy-devel/2009-July/001699.html
    • http://www.itk.org/ITK/applications/MutualInfo.html

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Links

• Registration Summit Aug'09
• Slicer Documentation 3.5
• Bug Tracker
• AHM_2010
• Slicer Logo & Communication Guide
• NAMIC registration:
• Contact: Dominik Meier : mailto:meier@bwh.harvard.edu

Bundled Registration and Tests

• http://www.na-mic.org/Wiki/index.php/Projects:DBP2:Harvard:Registration_Documentation
• http://www.na-mic.org/Wiki/index.php/MeningiomaMRIRegistrationStudy#Limitations_of_the_Slicer_registration_tools
• Vervet head MRI atlas-to-subject registration
• Head MRI registration between different timepoints (human subjects, changing pathology present)
• Side by side comparisons in slicer2 and slicer3 with data and images
• http://mindboggle.info/papers/index.php
• testing on the Vanderbuild database: RIRE
• ITK Registration Optimization Sets