External Email - Use Caution
Hi Freesurfer Devs,
I’m attempting to transform the Harvard-Oxford subcortical atlas (obtained from https://secure-web.cisco.com/1Tup0RI4qms0go1SEsu5ke-k7Cz5iL5tezC3TmgzZcvjKql...) to my subjects’ native anatomical space to create individualized versions of this atlas. To do so I used the line:
mri_label2vol --seg H-O_subcortical_parcellation_thr50.nii --temp rawavg.mgz --o HO-subcort.mgz --regheader H-O_subcortical_parcellation_thr50.nii
based on the recommendation from https://secure-web.cisco.com/1bcvHE7fWzSmfgBGxlww4NvvAmOJRlTofNlaCk_OCSbG9AN... However, when I load the rawavg.mgz and individualized atlas in freeview, the atlas is ~30 mm away from being aligned. Do you have any idea why this might be the case or recommendations to get a better alignment?
Thanks! Chris