I've been working on a series of spm scripts for working with the Multi
Voxel Pattern Analysis software package from Princeton university.
However I've run into a snag. specifically this warning:
Warning: Cant get default Analyze orientation - assuming flipped
Appears to be shooting me in the foot. If I load a file then save it to
a new file it doesn't compare properly as the file has been flipped left
to right. I didn't discover the issue until I compared the file to a
afni BRIK/HEAD version of the same file which appears to not have this
issue in matlab. Overall the issue isn't a huge problem so long as it's
kept in mind and i could probably just code a patch into our opening
command but I'd rather nail down the actual issue at hand and fix it
To note, the command 'nifti' generates the same error and appears to
create the same issues as our opening scripts (which simply utilize spm5).