Visualization with freesurfer

21 sec read

Assume CON14 is our subject ID and it is inside directory $SUBJECTS_DIR.

After the display window and the control panel pops up, try playing with the menus and buttons.

tkmedit for volume

tkmedit CON14 rawavg.mgz
tkmedit CON14 rawavg.mgz lh.pial -aux-surface rh.pial
File > Load Segmentation > (for "Load Volume") aparc+aseg.mgz (for "Load Color Table") FreeSurferColorLUT.txt

tksurfer for surface

tksurfer CON14 lh inflated
tksurfer CON14 lh pial
tksurfer CON14 rh pial
File > Label > Import Annotation > (browse to) lh.aparc.annot

tkregister2 for check registration

tkregister2 --s CON14 --fstal


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