Were your dMRI scans acquired in a strictly transverse plane (relative to the gradient axes), or were they angled in some fashion?  If the latter, it is possible that MRIconvert is rotating the bvecs into the space of the dMRI scans, which is what FSL expects.  The converter 'dcm2nii' definitely does this (if used with default options), so you could compare the bvecs from MRIconvert against those returned by 'dcm2nii'.

cheers,

-MH

-- 

Michael Harms, Ph.D.

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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: [log in to unmask]

From: Rotem Saar <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Sunday, July 20, 2014 5:28 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: [FSL] Diffusion analysis - difference between gradients tables

Dear FSL experts,

I'm currently trying to analyze Diffusion data in FSL. I'm working with dicoms from a 3T Philips scanner, 33 directions*60 slices, Bvalue = 800.

I used MRIconvert and transformed the dicoms into FSL-NIFTI format. It created all the necessary files.

At the first step, I'm interested in extracting the FA & MD maps.

The thing is - when I look at the gradient matrix created using MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert looks different.

So my question is which table should I use for diffusion analysis in FSL? The one that was created from the dicom header or the one created for FSL-NIFTI format ? Do u have any idea as to why is there a difference ?

I will really appreciate your help,

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 

Israel

 

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