#/bin/tcsh
#########################################################
# super-recon
#
# This script will run all of the recon-all -all options
#
# Version 1.02  - Daniel Goldenholz
#
#
# Examples:
# super_recon all $SUBJECTS_DIR $SUBJECT /space/dicom/file1 /space/dicom/file2 my_email@wherever.nmr.com
# super_recon 1 $SUBJECTS_DIR $SUBJECT /space/dicom/file1 /space/dicom/file2
# super_recon 2 $SUBJECTS_DIR $SUBJECT lh &
# super_recon 2 $SUBJECTS_DIR $SUBJECT rh &
# super_recon 3 $SUBJECTS_DIR $SUBJECT
########################################################

source /usr/local/freesurfer/nmr-std-env

######################################################
# EDIT THIS STUFF
#

######################################################

setenv SUPER_RECON "`pwd`/$0"
setenv SUPER_STEP $1
setenv SUBJECTS_DIR $2
setenv SUBJECT $3
setenv OPT1 $4
setenv OPT2 $5
setenv OPT3 $6
setenv DIR $SUBJECTS_DIR/$SUBJECT/scripts/
cd $SUBJECTS_DIR
set nWaitsMax  = 1000;
set WaitSleep =  1m;

switch ( $SUPER_STEP )
	case "all":
		# This is the all  case, where we run everything
		setenv MYMAIL $OPT3
		$SUPER_RECON 1 $SUBJECTS_DIR $SUBJECT $OPT1 $OPT2
		$SUPER_RECON 2 $SUBJECTS_DIR $SUBJECT lh &
		$SUPER_RECON 2 $SUBJECTS_DIR $SUBJECT rh &
		@ nWaits = 1;
		while(! -e $DIR/super_recon2lh.status && ! -e $DIR/super_recon2rh.status && $nWaits < $nWaitsMax)
			sleep $WaitSleep;
			@ nWaits = $nWaits + 1;
		end
		if( $nWaits == $nWaitsMax ) then
			echo "ERROR: timed out waiting for hemispheres to finish."
			exit 1
		endif
		$SUPER_RECON 3 $SUBJECTS_DIR $SUBJECT
		echo "super-recon $SUBJECT finished without error at `date`" | \
			mail -s "$SUBJECT DONE `date`" $MYMAIL
		breaksw
	case 1:
		# This is the whole head stage
		setenv invol1 $OPT1
		setenv invol2 $OPT2
		setenv LOG $DIR/recon-all.log
		setenv STAT $DIR/recon-all-status.log
		recon-all -s $SUBJECT -log $LOG -status $STAT -i $invol1 -i $invol2
		recon-all -s $SUBJECT -log $LOG -status $STAT -motioncor
		recon-all -s $SUBJECT -log $LOG -status $STAT -nuintensitycor
		recon-all -s $SUBJECT -log $LOG -status $STAT -talairach
		recon-all -s $SUBJECT -log $LOG -status $STAT -normalization
		recon-all -s $SUBJECT -log $LOG -status $STAT -skullstrip
		recon-all -s $SUBJECT -log $LOG -status $STAT -gcareg
		recon-all -s $SUBJECT -log $LOG -status $STAT -canorm
		recon-all -s $SUBJECT -log $LOG -status $STAT -careg
		recon-all -s $SUBJECT -log $LOG -status $STAT -rmneck
		recon-all -s $SUBJECT -log $LOG -status $STAT -skull-lta
		recon-all -s $SUBJECT -log $LOG -status $STAT -calabel
		recon-all -s $SUBJECT -log $LOG -status $STAT -segstats
		recon-all -s $SUBJECT -log $LOG -status $STAT -normalization2
		recon-all -s $SUBJECT -log $LOG -status $STAT -segmentation
		recon-all -s $SUBJECT -log $LOG -status $STAT -fill
		echo "Done. `date`" > $DIR/super_recon1.status
		breaksw
	case 2:
		# These are the hemisphere dependent stages
		setenv hemi $OPT1
		setenv LOG $DIR/recon-all-${hemi}.log
		setenv STAT $DIR/recon-all-status-${hemi}.log
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -tessellate
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -smooth1
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -inflate1 
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -qsphere 
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -fix 
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -finalsurfs
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -smooth2
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -inflate2 
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -cortribbon 
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -sphere
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -surfreg
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -contrasurfreg
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -avgcurv
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -cortparc
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -parcstats
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -cortparc2
		recon-all -s $SUBJECT -log $LOG -status $STAT -hemi $hemi -parcstats2
		echo "Done. `date`" > $DIR/super_recon2${hemi}.status
		breaksw
	case 3:
		# This stage is not hemisphere dependent
		setenv LOG $DIR/recon-all.log
		setenv STAT $DIR/recon-all-status.log
		recon-all -s $SUBJECT -log $LOG -status $STAT -aparc2aseg
		echo "Done. `date`" > $DIR/super_recon3.status
		breaksw
	default
		echo "Unrecognized input"
endsw

echo "super-recon is done dude! `date`"