Hi Daniel - You can confirm if the orientation is different from your other
scans by running mri_info directly on the dicom. If these two subjects were
scanned in a completely different orientation than the rest of the subjects in
your study, e.g. coronal vs. axial, if does raise the question of whether it's
a good idea to include them. Even if the resolution is isotropic, the EPI
distortions in the images will be different depending on the phase-encode
direction.
As far as the gradient vectors are concerned, mri_convert will save them in the
voxel space of the individual scan, regardless of orientation. It doesn't hurt
to look at the principal eigenvectors of the tensors (dmri/dtifit_V1) just as a
sanity check. If those lines are oriented correctly in all 3 views, then the
gradient table was read correctly.
Best,
a.y
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow
<ddcc2...@gmail.com>
Sent: Thursday, August 15, 2019 8:35 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA - OrientLAS issue for a subject
External Email - Use Caution
For reference, I think the issue had to do with the orientation of these two
subjects. I added tome code to use 3dwarp -deoblique to the dwi_orig.nii.gz and
then ran orientLAS and it worked this time.
The only thing I am unsure about is if this will nulify the bvals and bvecs I
have and ruin later preprocessing steps? This is the only solution to the
problem I have found thus far though.
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
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