From 9ef9c48484c2b58598ce5bb1e7411a45f1cce33f Mon Sep 17 00:00:00 2001
From: Mark Jenkinson <mark@fmrib.ox.ac.uk>
Date: Wed, 19 Dec 2007 18:29:20 +0000
Subject: [PATCH] Made changes for neurological fix - DO NOT MAKE STABLE YET
---
ptx_simple.cc | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/ptx_simple.cc b/ptx_simple.cc
index c96372a..798cf82 100644
--- a/ptx_simple.cc
+++ b/ptx_simple.cc
@@ -29,15 +29,23 @@ void track(){
else{
read_volume(seedref,opts.maskfile.value());
}
-
+
Streamliner stline;
Counter counter(seedref,stline);
counter.initialise();
Seedmanager seedmanager(counter);
-
-
+
Matrix Seeds = read_ascii_matrix(opts.seedfile.value());
+ // convert coordinates from nifti (external) to newimage (internal)
+ // conventions - Note: for radiological files this should do nothing
+ for (int n=1; n<=Seeds.Nrows(); n++) {
+ ColumnVector v(4);
+ v << Seeds(n,1) << Seeds(n,2) << Seeds(n,3) << 1.0;
+ v = seedref.niftivox2newimagevox_mat() * v;
+ Seeds(n,1) = v(1); Seeds(n,2) = v(2); Seeds(n,3) = v(3);
+ }
+
int keeptot=0;
for(int SN=1; SN<=Seeds.Nrows();SN++){
float xst=Seeds(SN,1);
--
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