From a3640d51fd16de14c143d1cc7237aa0bc9e402d2 Mon Sep 17 00:00:00 2001
From: Mark Jenkinson <mark@fmrib.ox.ac.uk>
Date: Thu, 20 Dec 2007 12:13:51 +0000
Subject: [PATCH] Made changes for neurological fix - DO NOT MAKE STABLE YET
---
streamlines.cc | 23 +++++++++++++++++++++--
1 file changed, 21 insertions(+), 2 deletions(-)
diff --git a/streamlines.cc b/streamlines.cc
index 6ecbf8b..be581f3 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -606,18 +606,37 @@ namespace TRACT{
save_volume(m_seedcounts[m],logger.appendDir("seeds_to_"+tmpname));
}
}
-
+
+ // the following is a helper function for save_matrix*
+ // to convert between nifti coords (external) and newimage coord (internal)
+ void applycoordchange(volume<int>& coordvol, const Matrix& old2new_mat)
+ {
+ for (int n=0; n<=coordvol.maxx(); n++) {
+ ColumnVector v(4);
+ v << coordvol(n,0,0) << coordvol(n,1,0) << coordvol(n,2,0) << 1.0;
+ v = old2new_mat * v;
+ coordvol(n,0,0) = MISCMATHS::round(v(1));
+ coordvol(n,1,0) = MISCMATHS::round(v(2));
+ coordvol(n,2,0) = MISCMATHS::round(v(3));
+ }
+ }
+
void Counter::save_matrix1(){
save_volume(m_ConMat,logger.appendDir("fdt_matrix1"));
+ applycoordchange(m_CoordMat, m_seeds.niftivox2newimagevox_mat().i());
save_volume(m_CoordMat,logger.appendDir("coords_for_fdt_matrix1"));
+ applycoordchange(m_CoordMat, m_seeds.niftivox2newimagevox_mat());
}
void Counter::save_matrix2(){
save_volume(m_ConMat2,logger.appendDir("fdt_matrix2"));
+ applycoordchange(m_CoordMat2, m_seeds.niftivox2newimagevox_mat().i());
save_volume(m_CoordMat2,logger.appendDir("coords_for_fdt_matrix2"));
+ applycoordchange(m_CoordMat2, m_seeds.niftivox2newimagevox_mat());
+ applycoordchange(m_CoordMat_tract2, m_lrmask.niftivox2newimagevox_mat().i());
save_volume(m_CoordMat_tract2,logger.appendDir("tract_space_coords_for_fdt_matrix2"));
+ applycoordchange(m_CoordMat_tract2, m_lrmask.niftivox2newimagevox_mat());
save_volume4D(m_lookup2,logger.appendDir("lookup_tractspace_fdt_matrix2"));
-
}
int Seedmanager::run(const float& x,const float& y,const float& z,bool onewayonly, int fibst){
--
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