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All Hands Meeting 2005 Morphometry BIRN Tool Dissemination.

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Presentation on theme: "All Hands Meeting 2005 Morphometry BIRN Tool Dissemination."— Presentation transcript:

1 All Hands Meeting 2005 Morphometry BIRN Tool Dissemination

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

3 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

4 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

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

6 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

7 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

8 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

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

10 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

11 Freesurfer (MGH) (surfer.nmr.mgh.harvard.edu) 3D Slicer (BWH) (www.slicer.org )www.slicer.org LDMM JHU (www.cis.jhu.edu/software/ldmm )www.cis.jhu.edu/software/ldmm LONI Pipeline (UCLA) (www.loni.ucla.edu )www.loni.ucla.edu Morphometry BIRN: supported tools

12 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

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 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

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