I ran the following Afni command:
3dAllineate -verb -1Dmatrix_save roi -prefix roi_hires+orig -input roi+tlrc -master anat_ns+orig -base anat_ns+orig
I have 15 separate roi files (I am just using roi in place of all the file names) that I ran the command on to try for one subject. The file produced is an abuc that seems to be orientated correctly and maintains the correct shape, but the spatial location is off. For example, Brodmann's 10 appears closer to the occipital cortex than the prefrontal cortex. I checked the 3dinfo and each roi file has the same data axes orientation and same geometry string. I'm wondering what I did wrong and how I can change it.
Thanks.