From 7392e248f2bd645aaeb02b0990bb1025fa7211e0 Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Thu, 16 Nov 2000 19:54:52 +0000
Subject: [PATCH] *** empty log message ***
---
cluster.cc | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/cluster.cc b/cluster.cc
index cbbdb8e..08f27db 100644
--- a/cluster.cc
+++ b/cluster.cc
@@ -16,7 +16,7 @@
using namespace NEWIMAGE;
using std::vector;
-
+using namespace Opts;
string title="cluster (Version 1.0)\nCopyright(c) 2000, University of Oxford (Mark Jenkinson)";
string examples="cluster --in <filename> --thresh <value> [options]";
@@ -120,7 +120,7 @@ template <class S>
void vox2mmcoord(vector<triple<float> >& coords,
const volume<S>& vol)
{
- float vx = vol.xdim(), vy = vol.ydim(), vz = vol.zdim();
+ float vx = vol.xdim()*vol.xsign(), vy = vol.ydim()*vol.ysign(), vz = vol.zdim()*vol.zsign();
vox2mmcoord(coords,vx,vy,vz);
}
@@ -133,7 +133,7 @@ void addoriginoffset(vector<triple<T> >& coords, const volume<S>& vol)
if (orig.SumAbsoluteValue() < 0.1) return; // zero origin -> no work
for (unsigned int n=0; n<coords.size(); n++) {
coords[n].x -= (T) (orig(1) - 1.0); // -1.0 convert from SPM convention
- coords[n].y -= (T) (orig(2) - 1.0); // -1.0 convert from SPM convention
+ coords[n].y -= (T) (orig(2) - 2.0); // -2.0 convert from SPM convention (NFI)
coords[n].z -= (T) (orig(3) - 1.0); // -1.0 convert from SPM convention
}
}
@@ -415,7 +415,7 @@ int fmrib_main(int argc, char *argv[])
// and maintains the same values otherwise
volume<T> lcopy;
relabel_image(labelim,lcopy,threshidx);
- lcopy.threshold(0.5);
+ lcopy.threshold(1);
save_volume(zvol * lcopy,outthresh.value());
}
--
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