Hi Matthew,
Just gave your suggestion a try - looks like it may have solved things.
The "Parcels_combo" label image was originally aligned to MNI standard space, so I substituted a standard brain in to to generate the “parc2anat.mat” transform, i.e.,
flirt -in /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -ref struc.nii -out results/parc2anat -omat results/parc2anat.mat
I then followed the same steps I outlined before, with the "Parcels_combo" only being used in the final command. Hopefully this is in keeping with what you suggested. Looks to have successfully generated the "Parcels_combo_reor.nii.gz" image I was looking for that has the parcels successfully registered to the subject's scan.
Let me know if any of this sounds problematic, otherwise thanks very much for your help.
Best,
Claire
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