Projects:RegistrationDocumentation:UseCaseList

---

Case Inventory Brain

• Case 01: Inter-subject Brain MRI (Tumor growth assessment): sagittal T1 with meningioma
• Case 02: Intra-subject Brain MRI (Multiple Sclerosis): T2 FLAIR to (defaced) T1 SPGR
• Intra-subject T1-T2-DTI-fMRI
• 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
• cases with defacing applied with mask avail.
• cases with defacing w/o mask
• example of half-way registration: 2 sets
• BIRN dataset ELUDE: longitudinal study of late-life depression at Duke University. There are 281 depressed subjects and 154 controls included. An MR scan of each subject was obtained every 2 years for up to 8 years (total of 1093 scans). ELUDE link (XNAT)
• BIRN dataset MIRIAD: cross-sectional depression. MIRIAD link (XNAT)
• BIRN dataset OASIS (XNAT)
• AC-PC alignment: can I do this with Slicer? -> fiducial-based alignment as separate module
• Registration comparison w & w.o bias field correction. When it does make a difference.
• defacing algorithm: Hum Brain Mapp. 2007 Sep;28(9):892-903.

Case Inventory Non-Brain

• PET-CT whole body, 2 timepoints each -- see here
• breast Cancer MRI: pre- and post-treatment
  • 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 tumor ablation: pre-procedural MRI to intra-procedural CT --> Dr. Stuart Silverman's IGT group: manuscript
• kidney tumor ablation: pre-procedural MRI to intra-procedural CT --> Dr. Stuart Silverman's IGT group
• kidney tumor ablation: intra-procedural CT - CT
• liver CT, intra-subject, contrast enhanced manuscript
• temporal bone (ear) intra-subject CT to MRI of the collab with Soenke in 2005
• tibia CT, Model-based surface registration

Case Inventory Non-human

• Vervet Atlas

Self-validation Sets

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

• testing PET-CT-MRI on the Vanderbuild database: RIRE
• Dual Echo PD/T2 intra subject different contrast self validation
• Isotropic Brain SPGR T1 with single axis rotation
• Parameter Sensitivity Analysis

First 10 cases (not in sequential order)

• Brain intra-subject, same contrast T1, change detection follow-up: tumor growth
• Brain MRI, intra-subject, same contrast PD&T2, change detection follow-up: new MS lesions
• Brain MRI, intra-subject, different contrast, co-register all series of the same exam: T1 SPGR, FLAIR, T2
• Brain MRI, intra-subject, DTI to reference, apply Xform to 25-direction DTI tensor
• Brain MRI, intra-subject, example with clipped FOV, example of masking required
• Brain MRI, inter-subject, co-register T1 SPGR to atlas dataset (ICBM). Resample a label map.
• Liver intra-subject, pre-procedural MRI to intra-procedural CT
• Prostate MRI, intra-subject
• Knee inter-subject registration to initialize segmentation
• PET to CT Whole Body single timepoint
• Breast Cancer: feasible with affine focus?