meshes in probtrackx

Makefile

@@ -30,7 +30,7 @@ VECREG=vecreg
 DTIFITOBJS=dtifit.o dtifitOptions.o
 CCOPSOBJS=ccops.o ccopsOptions.o
 PTOBJS=probtrack.o probtrackOptions.o pt_alltracts.o pt_matrix.o pt_seeds_to_targets.o pt_simple.o pt_twomasks.o pt_matrix_mesh.o
-PTXOBJS=probtrackx.o probtrackxOptions.o streamlines.o ptx_simple.o ptx_seedmask.o ptx_twomasks.o ptx_nmasks.o
+PTXOBJS=probtrackx.o probtrackxOptions.o streamlines.o ptx_simple.o ptx_seedmask.o ptx_twomasks.o ptx_nmasks.o ptx_meshmask.o
 FTBOBJS=find_the_biggest.o
 PJOBJS=proj_thresh.o
 MEDOBJS=medianfilter.o 

probtrackx.cc

@@ -43,7 +43,8 @@ int main ( int argc, char **argv ){
     else{ seedmask(); }
   }
   else if(opts.network.value()){ nmasks(); }
-  else {};
+  else if(opts.meshfile.value()!=""){meshmask();}
+  else {cout << "exit without doing anything"<<endl;return 0;};
 
   //else if(fopen(tmpin.c_str(),"r")!=NULL ){ track();}
 

probtrackx.h

@@ -8,3 +8,4 @@
 #include "ptx_seedmask.h"
 #include "ptx_twomasks.h"
 #include "ptx_nmasks.h"
+#include "ptx_meshmask.h"

streamlines.h

@@ -69,7 +69,7 @@ namespace TRACT{
 	pop_waymasks();
     }
 
-
+    const Tractvolsx& get_vols() const {return vols;}
     inline int nfibres() const {return vols.nfibres();}
     inline const float get_x_seed() const {return m_x_s_init;}
     inline const float get_y_seed() const {return m_y_s_init;}

tractvolsx.h

@@ -204,7 +204,7 @@ namespace TRACTVOLSX{
 	return th_ph_f;
       }
 
-      ColumnVector dimensions(){
+      ColumnVector dimensions() const{
 	ColumnVector dims(3);
 	dims << (*thsamples[0]).xdim() <<(*thsamples[0]).ydim() << (*thsamples[0]).zdim();
 	return dims;