Meier at 21:55, 21 January 2010

2010-01-21T21:55:35Z

Meier: Created page with '---- ==Case Inventory Brain== *'''Case 01: Inter-subject Brain MRI (Tumor growth assessment): sagittal T1 with meningioma…'

2010-01-21T21:54:09Z

Created page with '---- ==Case Inventory Brain== *'''Case 01: Inter-subject Brain MRI (Tumor growth assessment): sagittal T1 with meningioma…'

New page

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==Case Inventory Brain==
*'''Case 01: [[Projects:RegistrationDocumentation:UseCaseExample1b|Inter-subject Brain MRI (Tumor growth assessment): sagittal T1 with meningioma]]'''
*'''Case 02: [[Projects:RegistrationDocumentation:UseCaseExample1|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-non-rigid|DTI affine & non-rigid alignment]]
*Intra-subject PD,T2, T1Gd (MS)
**Scan-rescan intra-subject. No change.
**[http://ij.itk.org/midas/community/view/21 UNC Midas Database of healthy volunteers]
**[[FMRI-to-hires|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). [http://nirlarc.duhs.duke.edu/nirle/ ELUDE link (XNAT)]
*BIRN dataset MIRIAD: cross-sectional depression. [http://nirlarc.duhs.duke.edu/nirle/ MIRIAD link (XNAT)]
* [http://central.xnat.org/app/template/XDATScreen_report_xnat_projectData.vm/search_element/xnat:projectData/search_field/xnat:projectData.ID/search_value/CENTRAL_OASIS_CS 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: [http://www.ncbi.nlm.nih.gov/pubmed/17295313| Hum Brain Mapp. 2007 Sep;28(9):892-903.]

==Case Inventory Non-Brain==
*PET-CT whole body, 2 timepoints each -- [[media:2009-08-PETCT.zip|see here]]
*breast Cancer MRI: pre- and post-treatment
**[[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
* 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: [http://www.na-mic.org/publications/item/view/567 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 [http://www.na-mic.org/publications/item/view/1702 manuscript]
* temporal bone (ear) intra-subject CT to MRI of the [http://www.na-mic.org/publications/item/view/257 collab with Soenke in 2005]
* tibia CT, [http://www.na-mic.org/publications/item/view/339 Model-based surface registration]

==Case Inventory Non-human==
*[http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php 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: [http://www.insight-journal.org/RIRE/ RIRE]
*Dual Echo PD/T2 intra subject different contrast self validation
*Isotropic Brain SPGR T1 with single axis rotation
*[[Projects:RegistrationDocumentation:ParameterTesting|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?

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	==Case Inventory Brain==		==Case Inventory Brain==

Projects:RegistrationDocumentation:UseCaseList - Revision history

Meier at 21:55, 21 January 2010

Meier: Created page with '---- ==Case Inventory Brain== *'''Case 01: Inter-subject Brain MRI (Tumor growth assessment): sagittal T1 with meningioma…'