diff --git a/Makefile b/Makefile index 23fefc357d2d4ed44aa95b764744ec73a68e68bb..10a6f7f6bae75a7562778c5a8de019b639b90dab 100644 --- a/Makefile +++ b/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 diff --git a/probtrackx.cc b/probtrackx.cc index 816381a2d6f7f1a9ea3764c7a3e691db7d4d7238..5a492546612341d753e5ec74c41137f7b39e34a9 100644 --- a/probtrackx.cc +++ b/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();} diff --git a/probtrackx.h b/probtrackx.h index 8610f9f046b6a5e8e72b27b6e725e34ebd4b60b2..41498fe5d54c00ca6911e1e8802e29d8b662aaaa 100644 --- a/probtrackx.h +++ b/probtrackx.h @@ -8,3 +8,4 @@ #include "ptx_seedmask.h" #include "ptx_twomasks.h" #include "ptx_nmasks.h" +#include "ptx_meshmask.h" diff --git a/streamlines.h b/streamlines.h index 37ce57a7a796548eeb2d8e1029c9421f983ed414..0558f573ff863da9836b156c86178041a1c81419 100644 --- a/streamlines.h +++ b/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;} diff --git a/tractvolsx.h b/tractvolsx.h index 5ca4dcb4beea9f807ee24c0194daa8ca16115834..c8b56a72eb820a580fa14312f700e20f4a5a48e1 100644 --- a/tractvolsx.h +++ b/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;