From 3437bfb86d71efd079858a079c05a778cabb26a1 Mon Sep 17 00:00:00 2001
From: Jason <jason@darth-mac.uoregon.edu>
Date: Thu, 3 Sep 2015 12:23:49 -0700
Subject: [PATCH] copying ref to output directory in nii2dt.pl

---
 nii2dt/nii2dt.pl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nii2dt/nii2dt.pl b/nii2dt/nii2dt.pl
index 46787d9..a5d9457 100644
--- a/nii2dt/nii2dt.pl
+++ b/nii2dt/nii2dt.pl
@@ -273,6 +273,8 @@
 system("$antsDir/ImageMath 3 ${outputDir}/${outputFileRoot}rd.nii.gz TensorRadialDiffusion ${outputDir}/${outputFileRoot}dt.nii.gz");
 system("$antsDir/ImageMath 3 ${outputDir}/${outputFileRoot}rgb.nii.gz TensorColor ${outputDir}/${outputFileRoot}dt.nii.gz");
 
+# Copy ref image to output directory
+system("cp $ref ${outputDir}/${outputFileRoot}ref.nii.gz");
 
 # cleanup
 if ($cleanup) {