Hi Steven,
Thanks a lot for your input, I appreciate it.
One follow-up question: I have executed the following processing steps
flirt -in T1_coreg.nii -ref MCALT_atlas.nii -out T1_to_atlas.nii -omat T1_to_atlas.mat -interp nearestneighbour -dof 12
convert_xfm -inverse T1_to_atlas.mat -omat atlas_to_T1.mat
flirt -in MCALT_atlas.nii -ref T1_coreg.nii -applyxfm -init atlas_to_T1.mat -out atlas_to_T1.nii -interp nearestneighbour -dof 12
But my output is unsatisfactory, as you can see in the image below!
I get the sense that you and others (as described here) that this can be common with FSL, and that it is generally harder to get everything right compared to ANTs. So, thanks again for your advice, I will try using ANTs and see how this performs.
Bastiaan
