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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
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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:
http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_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:
http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_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 Images Corrected Images
Siemens Sonata(1.5T)
Siemens AC88(7T)
Morphometry BIRN: gradient unwarping code
Recommendation for MRI acquisition protocols• Scanner Upgrade Calibration Protocol:
http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_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
http://wiki.na-mic.org/Wiki/index.php/Mbirn:_B0_and_eddy_current_correction_code_for_diffusion_MRI
Recommendation for MRI acquisition protocols• Scanner Upgrade Calibration Protocol:
http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_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
http://wiki.na-mic.org/Wiki/index.php/Mbirn:_Defacer_for_structural_MRI
Recommendation for MRI acquisition protocols• Scanner Upgrade Calibration Protocol:
http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_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)(www.slicer.org )
LDMM JHU(www.cis.jhu.edu/software/ldmm )
LONI Pipeline (UCLA)(www.loni.ucla.edu )
Morphometry BIRN: supported tools
Recommendation for MRI acquisition protocols• Scanner Upgrade Calibration Protocol:
http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_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
• www.oasis-brains.org
• 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:
http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_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
