The warp.anat.Xat.1D file was generated when I run uber_subject.py for resting state data. I assumed that that warp.anat.Xat.1D file was the matrix that resulted from the alignment of the tlrc template and the anatomical image, but I don't know for sure.
In any case, I just noticed what could be the main issue: The ROI was created in the same subject that I'm using in afni now, however, the T1 that I was using in freesurfer to create the ROI doesn't have the same dimensions as the anatomical that I'm using in afni (the one I used for uber_subject.py). In this case, I assume I need to resample the ROI first (3dresample?) and then run 3dAllineate to transform the resampled ROI to tlrc space?
Thanks for any input!
