From 516eff9629a241ea67d49c145d0c3e3eb27b827d Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Sun, 29 Jul 2007 16:19:34 +0000
Subject: [PATCH] cleaning

---
 Makefile      | 2 +-
 maskdyads     | 4 ++--
 probtrackx.cc | 5 ++++-
 pt_simple.cc  | 6 ++++--
 ptx_simple.cc | 1 -
 streamlines.h | 2 +-
 vecreg.cc     | 4 ++--
 7 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/Makefile b/Makefile
index f7c2593..990faa5 100644
--- a/Makefile
+++ b/Makefile
@@ -50,7 +50,7 @@ VECREGOBJS=vecreg.o
 SGEBEDPOST = bedpost bedpost_datacheck
 SGEBEDPOSTX = bedpostX bedpostX_postproc.sh bedpostX_preproc.sh bedpostX_single_slice.sh
 
-SCRIPTS = eddy_correct zeropad ${SGEBEDPOST} ${SGEBEDPOSTX}
+SCRIPTS = eddy_correct zeropad maskdyads ${SGEBEDPOST} ${SGEBEDPOSTX}
 FSCRIPTS = correct_and_average ocmr_preproc
 
 XFILES = dtifit ccops probtrack find_the_biggest medianfilter diff_pvm make_dyadic_vectors proj_thresh vecreg xfibres
diff --git a/maskdyads b/maskdyads
index de80def..d2dd2d0 100755
--- a/maskdyads
+++ b/maskdyads
@@ -22,7 +22,7 @@ if [ "$3" != "" ] ; then
 fi
 
 
-$FSLDIR/bin/avwmaths++ $f -thr $t -bin /tmp/grot
-$FSLDIR/bin/avwmaths++ $d -mul /tmp/grot ${d}_thr$t
+$FSLDIR/bin/fslmaths $f -thr $t -bin /tmp/grot
+$FSLDIR/bin/fslmaths $d -mul /tmp/grot ${d}_thr$t
 $FSLDIR/bin/imrm /tmp/grot
 
diff --git a/probtrackx.cc b/probtrackx.cc
index 4150d57..816381a 100644
--- a/probtrackx.cc
+++ b/probtrackx.cc
@@ -32,8 +32,11 @@ int main ( int argc, char **argv ){
   if(opts.verbose.value()>0){
     opts.status();
   }
-  if(opts.mode.value()=="simple")
+  if(opts.mode.value()=="simple"){
     track();
+    return 0;
+  }
+
   string tmpin=opts.seedfile.value();
   if(fsl_imageexists(opts.seedfile.value())){ 
     if(fsl_imageexists(opts.mask2.value())){ twomasks();}
diff --git a/pt_simple.cc b/pt_simple.cc
index 8ba9858..ea90070 100644
--- a/pt_simple.cc
+++ b/pt_simple.cc
@@ -201,7 +201,9 @@ void track(){
       
     } // Close Particle Number Loop    
     string thisout=opts.outfile.value()+num2str(Seeds(SN,1))+(string)"_"+num2str(Seeds(SN,2))+(string)"_"+num2str(Seeds(SN,3));
-    save_volume(prob,logger.appendDir(thisout));
-    //save_volume(prob,thisout);
+
+    save_volume(prob,thisout);
+  
   } //Close Seed number Loop
+
 }
diff --git a/ptx_simple.cc b/ptx_simple.cc
index 418c252..8c79bfb 100644
--- a/ptx_simple.cc
+++ b/ptx_simple.cc
@@ -50,5 +50,4 @@ void track(){
     counter.reset_prob();
   } //Close Seed number Loop
 
-  //counter.save_total(keeptot);
 }
diff --git a/streamlines.h b/streamlines.h
index e908d20..050937f 100644
--- a/streamlines.h
+++ b/streamlines.h
@@ -93,7 +93,7 @@ namespace TRACT{
     Matrix m_I;
     vector<ColumnVector> m_path;
     
-    vector<volume<float> > m_seedcounts;
+    vector<volume<int> > m_seedcounts;
     vector<volume<int> > m_targetmasks;
     vector<string> m_targetmasknames;
     vector<int> m_targflags;
diff --git a/vecreg.cc b/vecreg.cc
index 5dd4ae6..7507fc3 100755
--- a/vecreg.cc
+++ b/vecreg.cc
@@ -11,8 +11,8 @@
 
 using namespace Utilities;
 
-string title="vector_flirt (Version 1.0)\nVector Affine/non linear Tranformation with Orientation Preservation";
-string examples="vector_flirt -i <input4Dvector> -o <output4D> -t <transformation>";
+string title="vecreg (Version 1.0)\nVector Affine/non linear Tranformation with Orientation Preservation";
+string examples="vecreg -i <input4Dvector> -o <output4D> -t <transformation>";
 
 Option<bool> verbose(string("-v,--verbose"),false,
 		       string("switch on diagnostic messages"),
-- 
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