I'm trying to run mcflirt on 4 functional runs of a subject and I'm
trying to realign them to the first volume of the first run using FSL
3.3.11
mcflirt -in run1 -refvol 0
mcflirt -in run2 -reffile run1_mcf_meanvol
However, when I load the meanvol (or the mcf files) written by mcflirt
from run1 and run2 they have different orientation matrices (similar
but different). I would like these to be identical.
Any help would be much appreciated.
Thanks,
Satra
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