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FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Rotem Saar <saar.ro...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Monday, July 21, 2014 1:54 PM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Diffusion analysis qs - gradient matrix Dear freesurfer experts,
For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects.
The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for
converting dicoms to nifti) looks different.
This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix.
So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ?
Thanks
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work
Ashkelon Academic College, Ashkelon, 78211
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