We have had similar problems. Following to Karsten Specht´s JUELICHIAN
advice (thanks again, Karsten!) I have been able to cope with the issue
in most situations: You need to set the MPRAGE´s into an axial
orientation via DISPLAY by pitching & rolling with - pi / 2 and than
REORIENTING IMAGES. It generates a .mat-file to reorient the images
before any of the calculations. You might wanna refrain from reslicing
(doable but may end up in a mess) and just go for coregister to match
functional with anatomical images. Sometimes I have found the YAWing of
use, too.
Problems may arise if you have just a few thin MPRAGE slices as we had
in one of our studies. Reslicing and segmentation trials failed. I am
still in the process to figure that one out...
many regards-
andreas
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