So someone else may correct me... but to clarify..
dcm2nii actually exports the "angulation corrected" b-matrix....
It's been a while since I looked in great detail-- the easiest way to
do sanity checks is actually look at the generated "bvecs" file
produced by DMC2NII for 10 subjects scanned with the "same" scan
parameters..
If there is NO angulation applied... all the bvecs should be the same
across all of your subjects...
If instead you notice variations that vary from patient to patient (at
least among those with different slice angulations).... you can feel
confident it's giving you the "fixed" numbers.
In the simplest case... you may set the following gradients in the
scanner console
1 0 -1
0 0 1
0 0 -1
0 1 0
-1 -1 0
(or whatever)
IF you acquiring at an angulation... instead of getting "1"'s.. you'll
get 0.99 0 -0.99 (or whatever)...
Actually I think dcm2nii outputs the data so that X2+yz+z2 = 1 .... so
your numbers may appear slightly difference..
But long story short--- if you have 10 subjects with 10 angulations
using the same exact protocol... if there bvecs files all return
slightly different numbers (Which makes sense if you account for
angulation)... then you "know" it's likely exporting the right numbers
dg
On Thu, Oct 6, 2011 at 9:38 AM, West, John D. <[log in to unmask]> wrote:
> 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
>
--
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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