Hi Daniel

Unfortunately the atlases by the Zilles group does not have ROIs for the thalamic subregions that I need.

So, I am trying to warp the TT_Daemon atlases into MNI space to get MNI ROIs that way.

My plan is to warp from the afni directory the TT_avg152T1+tlrc.BRIK.gz to the MNI_avg152T1+tlrc.BRIK.gz template. Then I will use the resulting transformation matrix to transform the atlas. However I am getting an error I was hoping you could help me with.

My command was set up like this:
3dAllineate -input /opt/afni/TT_avg152T1+tlrc.BRIK.gz -prefix warped152_mniHopefully -1Dparam_save ParametersSaved.1D -master /opt/afni/MNI_avg152T1+tlrc.BRIK.gz

But the error says: ** FATAL ERROR: No base dataset AND source dataset has only 1 sub-brick
I figure there is something special I have to do to let it know it is anatomical to anatomical and not epis, but I can't find from the documentation how?

I tried using the .py script in case but it also doesn't work.

align_epi_anat.py -anat /opt/afni/MNI_avg152T1+tlrc.BRIK.gz -epi /opt/afni/TT_avg152T1+tlrc.BRIK.gz -epi_base 1
AttributeError: 'NoneType' object has no attribute 'input'


Thanks for any tips you can offer!
Best
Kirk