Hi Freesurfer Devs,

 

I’m attempting to transform the Harvard-Oxford subcortical atlas (obtained from https://neurovault.org/collections/262/) 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat.  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