Dr. Gutman,
Thanks very much for the reply. We actually typically use dcm2nii for all our DTI processing, but since the developer recommended using the b-matrix, we wanted to try that out. However, from what you say below it may actually be less accurate is that right?
Since you have experience with dcm2nii, do you know if it also corrects the bvecs for scans acquired with oblique slices?
Thanks for all the help!
-John
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of David Gutman
Sent: Wednesday, October 05, 2011 5:39 PM
To: [log in to unmask]
Subject: Re: [FSL] Using b-matrix for dtifit
Have you tried MRICONVERT or dcm2nii (part of Mricron)....
http://lcni.uoregon.edu/~jolinda/MRIConvert/
http://www.cabiatl.com/mricro/
Both of those have the ability to extract these bvals/bvecs directory
from the siemens private tag--- presuming your WIP DTI sequence isn't
much different from the ones we've used, it should be able to pull the
bvecs/bvals directly to text files in an FSL friendly format. The
"theoretical" b-matrix that is implemented in the scanner console can
get affected based on scan angulation and other factors, so these tags
generally support the ACTUAL b-matrix applied as opposed to the one
specified in the WIP itself (which the scanner may not be able to
actually obtain)....
On Wed, Oct 5, 2011 at 5:23 PM, West, John D. <[log in to unmask]> wrote:
> Hello.
>
> We are currently running a WIP DTI sequence on our Siemens systems for which the developer recommends using the b-matrix located in the dicom header for calculating the diffusion tensor. Is there a way to run dtifit using this matrix rather than the bval and bvec files? Thanks for your help.
>
> -John West
>
--
David A Gutman, M.D. Ph.D.
Assistant Professor of Biomedical Informatics
Senior Research Scientist, Center for Comprehensive Informatics
Emory University School of Medicine
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