Projects:RegistrationDocumentation:UseCaseInventory

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Source

Data is collected from a variety of sources. Because we want to focus on the registration problem and not be distracted by image format or other data management issues, the datasets listed here are copied and reformatted. As the data becomes available a download link is added.

• Options for the download location is a direct link to a download page from the main 3Dslicer user page or XNAT Central. The former seems preferable, since the general XNAT GUI appears too complex for a simple 1-case download. We expect most users to download only 1 or 2 files closest to their particular use case, not entire study sets. Such download should be acessible with 1-2 clicks, as with other slicer resources.
• Disk usage: Likely these example sets will grow no larger than 10GB. Estimating 50-80MB per case would allow 60-100 cases within a 5GB space.
• Since we post reformatted and preprocessed data, where possible the link to the original source is provided.
• Links here also from the NA-MIC resource page.To be updated when moving.

Formatting

We seek to have all datasets in a single-volume file format, most likely .nii or .nrrd
Once formatting, anonymization and description are complete, listing here will be replaced with a download link. Temporarily listed are links to source databases, where avail.

Case Inventory Brain

• Intra-subject T1-T2-DTI
• DTI baseline to T1 inter-subject with clipped FOV
• DTI affine & non-rigid alignment
• Intra-subject PD,T2, T1Gd (MS)
• Scan-rescan intra-subject. No change.
• UNC Midas Database of healthy volunteers
• fMRI: inter-subject structural scan to MNI atlas target

Case Inventory Non-Brain

• PET-CT whole body, 2 timepoints each -- see here
• Breast Cancer MRI: pre- and post-treatment
• 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
• knee registration for Simbios project -- http://slicer.spl.harvard.edu/slicerWiki/index.php/Stanford_Simbios_group
• liver MR to CT -- will make available
• kidney MR to CT -- will make available

Case Inventory Non-human

• Vervet Atlas

Self-validation Sets

These are datasets with artificial misalignment, i.e. the perfect alignment is known.

• Dual Echo PD/T2 intra subject different contrast self validation
• Isotropic Brain SPGR T1 with single axis rotation

First 10 cases:

1. Brain intra-subject, same contrast T1, change detection follow-up: tumor growth
2. Brain intra-subject, same contrast PD&T2, change detection follow-up: new MS lesions
3. Brain intra-subject, different contrast, co-register all series of same exam
4. Brain inter-subject, co-register T1 SPGR to atlas dataset (ICBM). Resample a label map.
5. Brain intra-subject, DTI to baseline, calculate Xform from B0 and realign 25-direction DTI tensor
6. Brain, intra-subject, example with clipped FOV, example of masking required
7. Prostate
8. Prostate with changed FOV. masking required
9. Breast Cancer: feasible with affine focus?
10. PET to CT Whole Body single timepoint
11. Knee inter-subject registration to initialize segmentation