Hi Qi - Are those two images in the same space, or in different spaces (the aparc+aseg_mask in T1 space and the FA map in diffusion space)? If the latter is true, there is no reason to expect them to have the same orientation. Checking the registration between T1 and diffusion space is a sensible thing to do, but then you should compare the FA map to the aparc+aseg files in the dlabel/diff/ directory. The latter have been mapped from T1 to diffusion space, so they should have the same orientation as the FA map.
Best, Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu Sent: Tuesday, August 25, 2020 11:07 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] missing one tract but differently for a few subjects
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Hi,
When I examined the 18 tracts of /dpath results, a few subjects were found missing one tract but differently, for example, fmajor were missing for one subject and the other one was missing lh.slfp and rh.slfp. I was thinking could it be that AP-PA was flipped. Attached screenshots of dtifit_FA.nii, aparc+seg_mask.nii, and bvec. Can you provide some information about the flip so that I can examine it for the rest of the subjects?
Best, Qi