#!/usr/bin/env perl
#
# Compute the total cerebral volume by computing the volume of gray
# matter inside the gray surface.
#
# Copyright Alan C. Evans
# Professor of Neurology
# McGill University
#

use strict;
use warnings "all";
use File::Basename;
use File::Temp qw/ tempdir /;

use MNI::Startup;
use MNI::FileUtilities qw(check_output_dirs);

my $me = &basename($0);

my $Help = <<HELP;
| $me Compute the total cerebral volume by computing the volume 
| of gray matter inside the gray surface.
|
| Problems or comments should be sent to: claude\@bic.mni.mcgill.ca
HELP

my $Usage = "Usage: $me classify.mnc callosum_mask.mnc left_gray.obj righ_gray.obj\n".
            "       t1_to_tal.xfm output.dat\n\n";

die $Usage if(! ($#ARGV == 5) );

# define input variables:

my $cls=$ARGV[0];
my $callosum_mask=$ARGV[1];
my $gray_surface_left=$ARGV[2];
my $gray_surface_right=$ARGV[3];
my $t1_tal_xfm=$ARGV[4];
my $output=$ARGV[5];

# Directory for temporary files.

my $TmpDir = &tempdir( "$me-XXXXXXXX", TMPDIR => 1, CLEANUP => 1 );

# combine left/right gray surfaces

my $gray_surface_full = "${TmpDir}/gray_surface_full.obj";
&run( "objconcat", $gray_surface_left, $gray_surface_right, "none", "none",
      $gray_surface_full, "none" );

# mask out internal gray matter through the cut of the corpus callosum.

my $cls_fixed = "${TmpDir}/cls_fixed.mnc";
&run( "minccalc", "-clobber", "-expression", 'if(A[1]>0.5){out=3}else{out=A[0]}',
      $cls, $callosum_mask, $cls_fixed );

# compute gray volume of the cortex only.

&run( "compute_icbm_vols", "-clobber", "-transform", $t1_tal_xfm,
      "-invert", "-surface_mask", $gray_surface_full, $cls_fixed, 
      $output );


#Execute a system call.

sub run {
  print "@_\n";
  system(@_)==0 or die "Command @_ failed with status: $?";
}