#!/bin/bash

procnum=$1 #enter in full subject directory name without trailing '/'

#The command below will open the brainmask.mgz and T1.mgz volumes and the surfaces for both hemispheres. This will be used to determine if pial and white boundaries have been drawn properly. 

freeview -v $procnum/mri/T1.mgz \
$procnum/mri/brainmask.mgz \
$procnum/mri/wm.mgz:colormap=heat:opacity=0.4 \
-f $procnum/surf/lh.white:edgecolor=yellow \
$procnum/surf/lh.pial:edgecolor=red \
$procnum/surf/rh.white:edgecolor=yellow \
$procnum/surf/rh.pial:edgecolor=red