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:
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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
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