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Morphometry BIRN Tool Dissemination

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

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Morphometry BIRN Tool Dissemination

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  1. Morphometry BIRN Tool Dissemination

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

  3. 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)

  4. 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)

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

  6. 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)

  7. Morphometry BIRN:DTI correction code Distortion corrections with phase-maps for each diffusion-encoding direction http://wiki.na-mic.org/Wiki/index.php/Mbirn:_B0_and_eddy_current_correction_code_for_diffusion_MRI

  8. 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)

  9. Morphometry BIRN:defacing code http://wiki.na-mic.org/Wiki/index.php/Mbirn:_Defacer_for_structural_MRI

  10. 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)

  11. Morphometry BIRN:supported tools 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 )

  12. 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)

  13. 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…

  14. 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.

  15. 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)

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