remove temp changes that sneaked in

probtrackxOptions.h

@@ -62,6 +62,7 @@ class probtrackxOptions {
   Option<int> nparticles;
   Option<int> nsteps;
   Option<float> distthresh;
+  FmribOption<float> distthresh3;
   Option<float> c_thr;
   FmribOption<float> fibthresh;
   Option<bool> sampvox;
@@ -75,6 +76,7 @@ class probtrackxOptions {
   Option<bool> seedcountastext;
   FmribOption<bool> splitmatrix2;
 
+
   void parse_command_line(int argc, char** argv,Log& logger);
   void modecheck();
   void modehelp();
@@ -182,7 +184,7 @@ class probtrackxOptions {
 	 string("\tFreesurfer-type surface descriptor (in ascii format)"),
        false, requires_argument),
    meshspace(string("--meshspace"), string("freesurfer"),
-	 string("Mesh reference space - either 'freesurfer' (default) or 'caret'"),
+	 string("Mesh reference space - either 'freesurfer' (default) or 'caret' or 'first'"),
        false, requires_argument),
   lrmask(string("--lrmask"), string(""),
 	 string("Low resolution binary brain mask for storing connectivity distribution in matrix2 mode"),
@@ -202,6 +204,9 @@ class probtrackxOptions {
    distthresh(string("--distthresh"), 0,
 	    string("Discards samples shorter than this threshold (in mm - default=0)"),
 	    false, requires_argument),
+   distthresh3(string("--distthresh3"), 0,
+	    string("Discards samples (in matrix3) shorter than this threshold (in voxels - default=0)"),
+	    false, requires_argument),
    c_thr(string("-c,--cthr"), 0.2, 
 	 string("Curvature threshold - default=0.2"), 
 	 false, requires_argument),
@@ -277,6 +282,7 @@ class probtrackxOptions {
        options.add(nparticles);
        options.add(nsteps);
        options.add(distthresh);
+       options.add(distthresh3);
        options.add(c_thr);
        options.add(fibthresh);
        options.add(sampvox);

streamlines.cc

@@ -483,13 +483,6 @@ namespace TRACT{
     m_SeedRow=1;
     
 
-    // where we initialise the vector that stores average path lengths
-    // (maybe in the future, we shouldn't need --os2t to do this...)
-    if(opts.pathlengths.value()){
-      m_pathlengths.ReSize(m_numseeds,opts.nparticles.value());
-      m_pathlengths = -1.0;
-      m_nsamp=1;
-    }
   }
   
 
@@ -638,9 +631,8 @@ namespace TRACT{
     if(opts.matrix2out.value()){
       next_matrix2_row();
     }
-    if(opts.seedcountastext.value() || opts.pathlengths.value()){
+    if(opts.seedcountastext.value()){
       m_SeedRow++;
-      m_nsamp=1;
     }
   }
   
@@ -690,15 +682,6 @@ namespace TRACT{
       }
     }
 
-    if(opts.pathlengths.value()){
-      float pathlength=0.0;
-      for(unsigned int i=0;i<m_path.size();i++){
-	pathlength+=opts.steplength.value();
-      }
-      m_pathlengths(m_SeedRow,m_nsamp)=pathlength;
-      m_nsamp++;
-    }
-
     
   }
 
@@ -905,10 +888,6 @@ namespace TRACT{
   void Counter::save_pathdist(){  
     m_prob.setDisplayMaximumMinimum(m_prob.max(),m_prob.min());
     save_volume(m_prob,logger.appendDir(opts.outfile.value()));
-
-    if(opts.pathlengths.value()){
-      write_ascii_matrix(m_pathlengths,logger.appendDir("pathlengths"));
-    }
   }
   
   void Counter::save_pathdist(string add){  //for simple mode