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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@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 ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298