diff --git a/probtrackx.cc b/probtrackx.cc
index 03e7bbef679198f1fa125013d7b44eeb4fa68496..7a4b57570bded57772b469b80932ff74560ca66e 100644
--- a/probtrackx.cc
+++ b/probtrackx.cc
@@ -34,9 +34,11 @@ int main ( int argc, char **argv ){
}
if(opts.mode.value()=="simple")
track();
- else if(fsl_imageexists(opts.mask2.value())){ twomasks();}
+ string tmpin=opts.seedfile.value();
+ if(fsl_imageexists(opts.mask2.value())){ twomasks();}
else if(fsl_imageexists(opts.seedfile.value())){ seedmask();}
-
+ //else if(fopen(tmpin.c_str(),"r")!=NULL ){ track();}
+
// else if(opts.mode.value()=="seeds_to_targets")
// seeds_to_targets();
// else if(opts.mode.value()=="seedmask")
@@ -57,9 +59,9 @@ int main ( int argc, char **argv ){
// maskmatrix();
// else if(opts.mode.value()=="meshlengths")
// mesh_lengths();
- else{
- cout <<"Invalid setting for option mode -- try setting mode=help"<<endl;
- }
+ //else{
+ // cout <<"Invalid setting for option mode -- try setting mode=help"<<endl;
+ //}
return 0;
}
diff --git a/probtrackxOptions.cc b/probtrackxOptions.cc
index 682cd4797d2052a5a82c331041934d8be7a7599a..a7dbf1387a48237b1a8832db7be18427822a7a0d 100644
--- a/probtrackxOptions.cc
+++ b/probtrackxOptions.cc
@@ -80,7 +80,7 @@ probtrackxOptions* probtrackxOptions::gopt = NULL;
check=false;
}
}
- if(mode.value()=="seedmask"){
+ /* if(mode.value()=="seedmask"){
if(logdir.value()==""){
mesg+="You must set an output directory name in seedmask mode: --dir\n";
check=false;
@@ -163,7 +163,7 @@ probtrackxOptions* probtrackxOptions::gopt = NULL;
mesg+="You must set an output name in maskmatrix mode: -o\n";
check=false;
}
- }
+ } */
if(!check){
cerr<<mesg;
exit(2);
@@ -175,9 +175,10 @@ probtrackxOptions* probtrackxOptions::gopt = NULL;
void probtrackxOptions::modehelp()
{
- cout<<"tracking mode - Options are:\n\n simple (default)\n Input is text file defining start point.\n Output is dti space volume with connectivity values at each voxel.\n If your seed voxel is not in diffusion space\n you need to specify a volume in yuour input\n space (--seedref)\n and a matrix taking this space to diffusion space(--xfm).\n\n seeds_to_targets\n Inputs are a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n and a text file with the name of a single target mask\n on each new line (--targetmasks).\n Output is a single volume for each target mask where the value of each\n volume within the seed mask corresponds to the number of particles \n seeded from this voxel reaching this target mask.\n\n seedmask\n Input is a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n Output is seed space volume with connectivity values at each voxel\n summed from every seed.\n\n twomasks_symm\n Input is a binary volume for first mask (-x)\n also requires a binary volume for second mask (--mask2)\n (requires a matrix taking both seeds to DTI space (--xfm))\n Output is the sum of all paths the from first mask which pass\n through the second and vice-versa i.e. only paths\n which pass through both masks are retained.\n\n waypoints\n Input is a binary volume for seed mask (-x)\n also requires a binary waypoint mask or ascii list\n of waypoint masks (--mask2)\n (requires a matrix taking both seeds to DTI space (--xfm))\n Output is a volume containing all the paths from the\n seedmask which pass through ALL of the waypoint masks.\n"<<endl;
+ /* cout<<"tracking mode - Options are:\n\n simple (default)\n Input is text file defining start point.\n Output is dti space volume with connectivity values at each voxel.\n If your seed voxel is not in diffusion space\n you need to specify a volume in yuour input\n space (--seedref)\n and a matrix taking this space to diffusion space(--xfm).\n\n seeds_to_targets\n Inputs are a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n and a text file with the name of a single target mask\n on each new line (--targetmasks).\n Output is a single volume for each target mask where the value of each\n volume within the seed mask corresponds to the number of particles \n seeded from this voxel reaching this target mask.\n\n seedmask\n Input is a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n Output is seed space volume with connectivity values at each voxel\n summed from every seed.\n\n twomasks_symm\n Input is a binary volume for first mask (-x)\n also requires a binary volume for second mask (--mask2)\n (requires a matrix taking both seeds to DTI space (--xfm))\n Output is the sum of all paths the from first mask which pass\n through the second and vice-versa i.e. only paths\n which pass through both masks are retained.\n\n waypoints\n Input is a binary volume for seed mask (-x)\n also requires a binary waypoint mask or ascii list\n of waypoint masks (--mask2)\n (requires a matrix taking both seeds to DTI space (--xfm))\n Output is a volume containing all the paths from the\n seedmask which pass through ALL of the waypoint masks.\n"<<endl;
if ( getenv("FSLINFMRIB"))
matrixmodehelp();
+ */
}
void probtrackxOptions::matrixmodehelp(){
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index 6025418cc50faa53030517d6d8840c6edc1e45a3..32ad71cb123c38aca9d299c07e5b306dea46a703 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -100,10 +100,10 @@ class probtrackxOptions {
seedfile(string("-x,--seed"), string("Seed"),
string("Seed volume or voxel depending on mode"),
true, requires_argument),
- mode(string("--mode"), string("simple"),
- string("tracking mode - To see list of options and explanations, use --mode=help"),
- true, requires_argument),
- targetfile(string("--targetmasks"), string("cmasks"),
+ mode(string("--mode"), string(""),
+ string("use --mode=simple for single seed voxel"),
+ false, requires_argument),
+ targetfile(string("--targetmasks"), string("cmasks"),
string("File containing a list of target masks - required for seeds_to_targets mode"),
false, requires_argument),
simpleout(string("--opd"), false,
@@ -123,7 +123,7 @@ class probtrackxOptions {
false, no_argument),
outfile(string("-o,--out"), string(""),
- string("Output file"),
+ string("Output file (only for single seed voxel mode)"),
false, requires_argument),
rubbishfile(string("--rubbish"), string(""),
string("Rubbish file"),
diff --git a/ptx_twomasks.cc b/ptx_twomasks.cc
index a750178898beadd4491fb233cb7fe9009cf00861..a1190dfb269da9ca830f8fafc83ed6fa0c312e42 100644
--- a/ptx_twomasks.cc
+++ b/ptx_twomasks.cc
@@ -33,22 +33,20 @@ void twomasks()
for(int y=0;y<seeds.ysize();y++){
for(int x=0;x<seeds.xsize();x++){
if(seeds(x,y,z)>0){
- seedmanager.run(x,y,z);
+ seedmanager.run(x,y,z,false,-1);
}
}
}
}
- cout<<"finished a"<<endl;
stline.pop_waymasks();
- cout<<"popped"<<endl;
stline.add_waymask(seeds);
-
+ cout<<"added"<<endl;
for(int z=0;z<seeds2.zsize();z++){
for(int y=0;y<seeds2.ysize();y++){
for(int x=0;x<seeds2.xsize();x++){
if(seeds2(x,y,z)>0){
- seedmanager.run(x,y,z);
+ seedmanager.run(x,y,z,false,seeds2(x,y,z)-1);
}
}
}
diff --git a/streamlines.cc b/streamlines.cc
index 59738389d915dc7bd1cf87634545d68dacc610a8..f845479a8fd8cf901099bf73f2a9bf8aed009d10 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -493,7 +493,7 @@ namespace TRACT{
}
void Counter::save_pathdist(){
- save_volume(m_prob,logger.appendDir(opts.outfile.value()));
+ save_volume(m_prob,logger.appendDir("fdt_paths"));
}
void Counter::save_pathdist(string add){ //for simple mode
@@ -537,11 +537,12 @@ namespace TRACT{
}
- void Seedmanager::run(const float& x,const float& y,const float& z,bool onewayonly){
+ void Seedmanager::run(const float& x,const float& y,const float& z,bool onewayonly, int fibst){
//onewayonly for mesh things..
cout <<x<<" "<<y<<" "<<z<<endl;
- int fibst=m_seeds(int(round(x)),int(round(y)),int(round(z)))-1;//fibre to start with is taken from seed volume..
-
+ if(fibst == -1){
+ fibst=m_seeds(int(round(x)),int(round(y)),int(round(z)))-1;//fibre to start with is taken from seed volume..
+ }
if(opts.randfib.value()){
float tmp=rand()/RAND_MAX;
if(tmp>0.5)
diff --git a/streamlines.h b/streamlines.h
index 4316f1fb97f6a2d298519e0d9ce178734e69bfbe..b09fc3b5559854130f7d49463ec2700e31957dc3 100644
--- a/streamlines.h
+++ b/streamlines.h
@@ -196,7 +196,7 @@ namespace TRACT{
m_seeddims.ReSize(3);
m_seeddims<<m_seeds.xdim()<<m_seeds.ydim()<<m_seeds.zdim();
}
- void run(const float& x,const float& y,const float& z,bool onewayonly=false);
+ void run(const float& x,const float& y,const float& z,bool onewayonly=false, int fibst=-1);
};
}