I don't know. Have you tried viewing the alignment in freeview to see if it is an fslview issue?
On 2/17/2020 4:50 PM, Austin Patrick wrote:
External Email - Use Caution
Dear FreeSurfer Community,
I have used the CVS and BBR registration methods to spatially align T1 and diffusion images to an ideal subject’s T1. I have noticed some discrepancies when viewing the aligned images in FSLview. If I toggle between subjects in FSLview the alignment looks quite good; however, when all subjects’ diffusion images are merged into a single 4D volume, the alignment is quite poor and variable. The same is true for subjects’ T1s. Is this a known issue and, if so, is it a problem with FSLview or my implementation of FreeSurfer?
Thanks,
-Austin
--
Austin M. Bazydlo, MS
PhD Candidate
Dept. of Medical Physics
University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer