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