All Hands Meeting 2005 Morphometry BIRN Tool Dissemination.

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Presentation transcript:

All Hands Meeting 2005 Morphometry BIRN Tool Dissemination

Recommendation for MRI acquisition protocols Software Processing and Visualization Tools MRI data Tutorials Morphometry BIRN: Tool Dissemination Domains for public dissemination

Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools: Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

Uncorrected ImagesCorrected Images Siemens Sonata (1.5T) Siemens AC88 (7T) Morphometry BIRN: gradient unwarping code

Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

Distortion corrections with phase-maps for each diffusion-encoding direction Morphometry BIRN: DTI correction code

Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

Morphometry BIRN: defacing code

Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

Freesurfer (MGH) (surfer.nmr.mgh.harvard.edu) 3D Slicer (BWH) ( ) LDMM JHU ( ) LONI Pipeline (UCLA) ( ) Morphometry BIRN: supported tools

Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

Open Access Structural Imaging Series project Rich structural & functional MRI dataset (WashU) Open access user agreement means free & unrestricted use of data Part I (November, 2005): 400 cross-sectional acquisitions across lifespan, including 100 demented individuals Extensions throughout 2006: longitudinal, DTI, fMRI, calibration…

The OASIS project Data set includes 3-4 raw T1- weighted scan, averaged, atlas- registered, and FSL- segmented. Data can be searched, downloaded, and viewed via the web site.

Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination