[Freesurfer] Longitudinal hippocampal subfield registered to base

Hi All,

I have applied the hippocampal subfield segmentation algorithm to each of my time points that have been longitudinally processed. I am now trying to register these back into base space using:

mri_convert -T BASE/mri/transforms/TP_to_base.lta -rl BASE/mri/norm.mgz -rt nearest --out_type mgz TP.long/mri/lh.hippoSfLabels-T1.v10.mgz TP.long/lh.hipp.base.mgz

Firstly, when I try to overlay lh.hipp.base.mgz for each timepoint onto BASE/mri/T1.mgz they do not align. Do you have any idea why this is?

Secondly, the output seems to be for the whole hippocampus, is there a way to do this for each subfield individually?

Any advice would be much appreciated,

Amanda