Dear freesurfer users,

I have a problem regarding to how to map the electrode coordinates to a common template.

After running mri_cvs_register, I got a cvs subfolder, and then I run

applyMorph --template /autofs/cluster/freesurfer/centos7_x86_64/dev/subjects/cvs_avg35_inMNI152/mri/orig.mgz --transform $SUBJECTS_DIR/$subid/cvs/combined_tocvs_avg35_inMNI152_elreg_aseg.tm3d point_list $SUBJECTS_DIR/$subid/cvs/coord_xyz.txt $SUBJECTS_DIR/$subid/cvs/transformed_coord.txt linear

where coord_xyz.txt contains all the original coordinates information, but after that I did a visualization using freeview, and the transformed coordinates looks outside of the brain.

Anyone knows how to fix this problem? Or what is the cause of this problem. The original RAS coordinates align well for the brain of each subject. I searched a lot of email archives, but didn't find a good answer.

Thanks.

Best regards,

Feng