From e14cc15eebb89916fc889de61a88b4314d57339f Mon Sep 17 00:00:00 2001
From: Matthijs van Eede <matthijsvaneede@gmail.com>
Date: Fri, 6 Jan 2017 17:47:57 -0500
Subject: [PATCH] script to generate an xfm file for some input vector field

---
 perl/make_xfm_for_grid.pl | 47 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100755 perl/make_xfm_for_grid.pl

diff --git a/perl/make_xfm_for_grid.pl b/perl/make_xfm_for_grid.pl
new file mode 100755
index 0000000..d777d55
--- /dev/null
+++ b/perl/make_xfm_for_grid.pl
@@ -0,0 +1,47 @@
+#!/usr/bin/perl
+
+# generates an xfm file for a provided grid file
+
+use strict;
+use warnings;
+
+use File::Spec;
+use MNI::Startup;
+use Getopt::Tabular;
+use MNI::Spawn;
+use MNI::FileUtilities qw(test_file check_output_dirs);
+
+my $usage = "
+
+$0 [options] deformation_grid.mnc output_xfm_for_grid.xfm\n";
+
+
+# handle arguments
+my @left_over_args;
+my @arg_table = 
+    ( @DefaultArgs,
+    );
+
+GetOptions(\@arg_table, \@ARGV, \@left_over_args) or die "\n";
+
+
+my $deformation_grid = shift @left_over_args or die $usage;
+my $output_xfm = shift @left_over_args or die $usage;
+
+if(-f $output_xfm and not $Clobber) {
+  die "Error: output xfm file already exists and -clobber not specified: $output_xfm.\n";
+}
+
+if(not -f $deformation_grid){
+  die "Error: deformation grid does not exist: $deformation_grid.\n";
+}
+
+# save the realpath to the grid, otherwise it won't necessarily work
+my $deformation_grid_abs_path = File::Spec->rel2abs( $deformation_grid );
+
+# write to the output
+open(OUTPUT, "> $output_xfm");
+print OUTPUT "MNI Transform File\n";
+print OUTPUT "% created by $0 with grid $deformation_grid\n";
+print OUTPUT "Transform_Type = Grid_Transform;\n";
+print OUTPUT "Displacement_Volume = $deformation_grid_abs_path;\n";