From cc0a8f3bdc462adef376709b47a749da553585cc Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Thu, 23 May 2013 14:17:05 +0000
Subject: [PATCH] Added GD mask code
---
fslcc.cc | 21 ++++++++++++++++++++-
1 file changed, 20 insertions(+), 1 deletion(-)
diff --git a/fslcc.cc b/fslcc.cc
index 1bd2731..3e8b803 100755
--- a/fslcc.cc
+++ b/fslcc.cc
@@ -11,7 +11,9 @@
using namespace NEWIMAGE;
using namespace Utilities;
-
+Option<string> fnmask(string("-m"), string(""),
+ string("mask file name "),
+ false, requires_argument);
Option<bool> noabs(string("--noabs"), false,
string("\tDon't return absolute values (keep sign)"),
false, no_argument);
@@ -44,6 +46,22 @@ int fmrib_main(int argc, char *argv[])
input_volume1-=input_volume1.mean();
input_volume2-=input_volume2.mean();
}
+
+
+ volume<T> theMask;
+ if( fnmask.value().length() > 0 ) {
+ read_volume(theMask,fnmask.value());
+ if(!samesize(input_volume1[0],theMask)){
+ cerr << "Error: Mismatch in mask dimensions" << endl;
+ return 1;
+ }
+ for(int t1=0;t1<=input_volume1.maxt();t1++)
+ input_volume1[t1] *= theMask;
+ for(int t2=0;t2<=input_volume2.maxt();t2++)
+ input_volume2[t2] *= theMask;
+ }
+
+
for(int t1=0;t1<input_volume1.tsize();t1++)
{
double ss1=sqrt(input_volume1.constantSubVolume(t1).sumsquares());
@@ -73,6 +91,7 @@ int main(int argc,char *argv[])
string examples("fslcc [options] <first_input> <second_input> ");
OptionParser options(title, examples);
+ options.add(fnmask);
options.add(noabs);
options.add(nodemean);
options.add(thresh);
--
GitLab