Difference between revisions of "Events:Registration Summit August 2009"
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=Agenda= | =Agenda= | ||
− | *Attendees: Casey Goodlett, Steve Pieper, Dominik Meier, Andriy Fedorov, Ron Kikinis | + | *Attendees: Casey Goodlett, Steve Pieper, Dominik Meier, Andriy Fedorov, Ron Kikinis, Sylvain Jaume |
*Date and place: Friday, August 21, 1249 Boylston, 2nd floor conference room | *Date and place: Friday, August 21, 1249 Boylston, 2nd floor conference room | ||
*Schedule | *Schedule | ||
− | #09:00-12:00 Review of registration in Slicer | + | #09:00-12:00 Review of registration in Slicer: |
+ | ##What input is the user asked to provide and in what form. | ||
+ | ##Does a standard user understand what they are supposed to provide? | ||
+ | ##What does the user expect registration results to look like? | ||
+ | ##Bias correction | ||
+ | ##histogram normalization | ||
+ | ##handling image distortion (EPI) | ||
+ | ##capture range and start pose | ||
+ | ##ROI/VOI | ||
+ | ##greyscale versus segmentation (binaries, surface models) | ||
+ | ##inter subject versus intrasubject | ||
+ | ##[http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.4#Registration List of modules]: | ||
+ | ###transformation module | ||
+ | ###linear registration | ||
+ | ###rigid registration | ||
+ | ###affine registration | ||
+ | ###b-spline registration | ||
+ | ###register images | ||
+ | ###Utah b-spline | ||
+ | ###VMTK/Python ICP | ||
+ | ###ACPC registration | ||
#12:00-01:00 Lunch | #12:00-01:00 Lunch | ||
− | #01:00-05:00 Making plans, use case scenarios, sample data sets | + | #01:00-05:00 Making plans, use case scenarios, sample data sets, plan larger registration summit |
+ | ##Action Items | ||
+ | ### User specified ROI - mask image and/or box | ||
+ | ### Test transform is correctly inverted | ||
+ | ### Prototype user-version RegisterImages (up to affine) (2 organ regions) | ||
+ | #### Same subject - same subject different modality (grayscale) | ||
+ | #### same subject different timepoints (grayscale) (user knows nothing about algorithms!) | ||
+ | ### Try datasets that are now available on this page | ||
+ | ### document RegisterImages | ||
+ | ### automated testing | ||
+ | ### non-rigid once affine is working | ||
+ | Other items: | ||
+ | |||
+ | * Workflow with Wendy | ||
+ | * CUDA Implementation with Yogesh | ||
+ | |||
+ | =Needs= | ||
+ | |||
+ | * Robust solutions | ||
+ | * Clinical APIs as opposed to engineering APIs | ||
+ | * Good default parameters | ||
+ | * Modality recorded in the image class to automate use case and parameter selection | ||
+ | * Fast techniques for interactive investigations | ||
+ | * Non-interactive techniques can run longer | ||
+ | * Transform IO to all modules (mapping RAS to LPS as needed) | ||
+ | * Ability to apply estimated transforms to other types of data | ||
+ | * Region of interest registration (anything from a brain mask to a structure segmentation) | ||
+ | * Validation datasets | ||
+ | * Regression testing of registration accuracy | ||
=References= | =References= | ||
== Bundled Registration and Tests == | == Bundled Registration and Tests == | ||
− | * | + | * https://www.slicer.org/wiki/Documentation-3.4#Registration |
* http://www.na-mic.org/Wiki/index.php/Projects:DBP2:Harvard:Registration_Documentation | * 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 | * http://www.na-mic.org/Wiki/index.php/MeningiomaMRIRegistrationStudy#Limitations_of_the_Slicer_registration_tools | ||
+ | |||
+ | == Some Sample data == | ||
+ | * Breast Cancer - [[media:bcData.zip|original data]], [[media:4jim.zip|two time points after some registration and processing]] | ||
+ | * Prostate image database (intra- and inter-subject registration use cases) http://prostatemrimagedatabase.com/index.html | ||
+ | * liver MR to CT -- will make available | ||
+ | * kidney MR to CT -- will make available | ||
+ | * pet CT to Pet CT -- [[media:2009-08-PETCT.zip|see here]] question: what changed between the two time points. Load scene and move the slider in slice views panel. | ||
+ | * knee registration for Simbios project -- http://slicer.spl.harvard.edu/slicerWiki/index.php/Stanford_Simbios_group | ||
+ | * Vervet MRI -- made available to Kitware for testing, will go public once the project is over | ||
== Slicer-compatible add-on registration modules == | == Slicer-compatible add-on registration modules == | ||
Line 22: | Line 79: | ||
* http://www.nitrc.org/projects/brainsmush/ | * http://www.nitrc.org/projects/brainsmush/ | ||
* http://www.nitrc.org/projects/brainsdemonwarp/ | * http://www.nitrc.org/projects/brainsdemonwarp/ | ||
+ | * http://www.nitrc.org/projects/cmtk/ | ||
+ | |||
+ | == Comprehensive evaluations of registration tools == | ||
+ | * http://mindboggle.info/papers/index.php | ||
+ | |||
+ | == In-house evaluations of registration tools == | ||
+ | * [http://www.na-mic.org/Wiki/index.php/Projects:DBP2:Harvard:Registration_Documentation Sophisticated end-user without computer vision background using Slicer modules] | ||
+ | * [http://www.na-mic.org/Wiki/index.php/Vervet_MRI_registration Vervet head MRI atlas-to-subject registration] | ||
+ | * [http://www.na-mic.org/Wiki/index.php/MeningiomaMRIRegistrationStudy Head MRI registration between different timepoints (human subjects, changing pathology present)] | ||
+ | * [https://www.slicer.org/wiki/Slicer3:Registration Side by side comparisons in slicer2 and slicer3 with data and images] |
Latest revision as of 17:45, 10 July 2017
Home < Events:Registration Summit August 2009Contents
Agenda
- Attendees: Casey Goodlett, Steve Pieper, Dominik Meier, Andriy Fedorov, Ron Kikinis, Sylvain Jaume
- Date and place: Friday, August 21, 1249 Boylston, 2nd floor conference room
- Schedule
- 09:00-12:00 Review of registration in Slicer:
- What input is the user asked to provide and in what form.
- Does a standard user understand what they are supposed to provide?
- What does the user expect registration results to look like?
- Bias correction
- histogram normalization
- handling image distortion (EPI)
- capture range and start pose
- ROI/VOI
- greyscale versus segmentation (binaries, surface models)
- inter subject versus intrasubject
- List of modules:
- transformation module
- linear registration
- rigid registration
- affine registration
- b-spline registration
- register images
- Utah b-spline
- VMTK/Python ICP
- ACPC registration
- 12:00-01:00 Lunch
- 01:00-05:00 Making plans, use case scenarios, sample data sets, plan larger registration summit
- Action Items
- User specified ROI - mask image and/or box
- Test transform is correctly inverted
- Prototype user-version RegisterImages (up to affine) (2 organ regions)
- Same subject - same subject different modality (grayscale)
- same subject different timepoints (grayscale) (user knows nothing about algorithms!)
- Try datasets that are now available on this page
- document RegisterImages
- automated testing
- non-rigid once affine is working
- Action Items
Other items:
- Workflow with Wendy
- CUDA Implementation with Yogesh
Needs
- Robust solutions
- Clinical APIs as opposed to engineering APIs
- Good default parameters
- Modality recorded in the image class to automate use case and parameter selection
- Fast techniques for interactive investigations
- Non-interactive techniques can run longer
- Transform IO to all modules (mapping RAS to LPS as needed)
- Ability to apply estimated transforms to other types of data
- Region of interest registration (anything from a brain mask to a structure segmentation)
- Validation datasets
- Regression testing of registration accuracy
References
Bundled Registration and Tests
- https://www.slicer.org/wiki/Documentation-3.4#Registration
- 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
Some Sample data
- Breast Cancer - original data, two time points after some registration and processing
- Prostate image database (intra- and inter-subject registration use cases) http://prostatemrimagedatabase.com/index.html
- liver MR to CT -- will make available
- kidney MR to CT -- will make available
- pet CT to Pet CT -- see here question: what changed between the two time points. Load scene and move the slider in slice views panel.
- knee registration for Simbios project -- http://slicer.spl.harvard.edu/slicerWiki/index.php/Stanford_Simbios_group
- Vervet MRI -- made available to Kitware for testing, will go public once the project is over
Slicer-compatible add-on registration modules
- http://www.bioimagesuite.org/
- http://www.nitrc.org/frs/shownotes.php?release_id=575
- http://www.nitrc.org/projects/multimodereg/
- http://www.nitrc.org/projects/brainsmush/
- http://www.nitrc.org/projects/brainsdemonwarp/
- http://www.nitrc.org/projects/cmtk/