Problems viewing Thomas thalamic atlas with anatomy following alignment

AFNI Message Board
1

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!

2

The view and space of the dataset are not being interpreted in the way you expect. This command will show what view the AFNI GUI and other commands will assume from the header of the dataset:

3dinfo -av_space mydset.nii.gz

In some cases, the header of the dataset shows an ambiguous code that can either be in a standard template space or in a native space. You can set AFNI_NIFTI_VIEW to be either orig or tlrc.

You can enforce a particular space, like MNI, on a dataset with

3drefit -space MNI mydset.nii.gz

3

Thanks Daniel - that worked!