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dcm2nii issues an error "DTI vector error: Position is not head first supine" in this particular situation and I have no data to confirm.

In order to understand things better my question actually is (independent of any nifti conversion tool):

What coordinate system does the fsl tool "dtifit" expect from the b-vectors?

After conversion to nifti the coordinate system of the nifti-DWI volumes is +RAS,

so "dtifit" will expect that the b-vecs also follow +RAS , is this assumption correct ?

Any confirmation greatly appreciated!

Andreas

Gesendet: Donnerstag, 21. November 2013 um 18:48 Uhr
Von: "Harms, Michael" <[log in to unmask]>
An: [log in to unmask]
Betreff: Re: [FSL] dtifit: bvecs - expected coordinate system

You should be fine using the output of 'dcm2nii' as is. (As long as you subsequently don't manually alter the orientation of the images from the default that it gives you). You can confirm this by running dtifit and verify that the V1 vectors point in the proper directions.

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: [log in to unmask]

From: Andreas Werner <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Thursday, November 21, 2013 2:50 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: [FSL] dtifit: bvecs - expected coordinate system

Dear FSL list and experts,

thank you for dtifit, it is a very useful tool.

I have one question: What coordinate system of the b-vectors does dtifit expect ?

Is it e.g. +LPS ? (i.e. the coordiante value increases from right to left (x), from anterior to posterior (y) and from inferior to superior (z)).

As I understand, one can normally just take the bvec-output from "dcm2nii" after DICOM conversion, but I am not sure if I can trust

dcm2nii in my case due to our rather unconventional patient positoning (Head first prone, rather than head first supine).

The bvec output of dcm2nii seems to follow +LPS convention in this particular situation, so I may need to make some asjustments.

Therefore my question above.

Thanks in advance !

Andreas

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