I am trying to use the Thomas (thalamus optimized multi-atlas segmentation v2.1) thalamic atlas to extract 7T fMRI data processed in AFNI. I used the anatomical dataset created with @sswarper (anat_final) for the thalamic segmentation. I then run the thomas_csh_mv script The alignment of the final ROIs with anat_final are excellent when I view the overlays with MRIcroGL or FSLeyes.
However, when I try to overlay the thalamic ROIs on the anat_final within the afni gui, they won’t align and I get the following warning: Forced switch from 'Original View' to 'Talairach View'. It then substitutes the anat+orig file as the underlay, which is way off. The fact that the alignment looks fine when viewed with a a different viewer suggests the alignment is fine, but I don't want to assume that when extracting ROI data. Is there something written into the header of the anat_final that afni is reading and changing the alignment?
I apologize if my ignorance is showing. Thanks for any help!
