Hi Mark,
So for 1 subject we acquired 46 EPI slices that cover the whole brain and a
set of 20 slices that cover the superior part of the brain.
Using FLIRT, I have applied the matrix outputted for the 46 slices to the 20
slices datasets but still cannot seem to warp these EPI into MNI space. The
data are not aligned with the anat, and are in a strange orientation.
I'm not sure I know what to do from here.
Thanks
Pat
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