Hello All,
I'm running level I FEAT, and am really new to using FSL. Some of the subject images give me particularly bad registration, whereas others are fine in spite of the same settings. What do you think I might be missing?
When I downloaded these data from our server, some of these images were flipped upside down. Our server admin said it happens sometimes with using dcm2nii. So I used a series of fslorient commands to get them oriented right (see below).
Also, it is not that only the images I used fslorient commands on are giving me these errors. Other images that I reoriented using the same commands are giving me fine registrations during the FEAT. Any insight in what I may be doing wrong?
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This was the series of commands I used to flip images:
fslorient -deleteorient File1Run1.nii
fslswapdim File1Run1.nii.gz -x y -z File1Run1Swapz.nii
fslorient -setqformcode 1 File1Run1Swapz.nii
fslview File1Run1Swapz.nii
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The problem with registration in FEAT I see is kind of similar to what's described here: the functional image is translated to the top of the red outlines..., which makes me think the problem's similar to what is described in this thread - but their solution doesn't work for me...
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;79056e6f.1412
I'd really appreciate any help/pointers...
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