small changes

probtrackxOptions.h

@@ -94,22 +94,22 @@ class probtrackxOptions {
    help(string("-h,--help"), false,
 	string("display this message"),
 	false, no_argument),
-   basename(string("-s,--samples"), string("DTI"),
+   basename(string("-s,--samples"), string("merged"),
 	       string("basename for samples files"),
 	       true, requires_argument),  
    maskfile(string("-m,--mask"), string("mask"),
 	    string("Bet binary mask file in diffusion space"),
 	    true, requires_argument),
    seedfile(string("-x,--seed"), string("Seed"),
-	    string("Seed volume or voxel depending on mode"),
+	    string("Seed volume, or voxel, or ascii file with multiple volumes"),
 	    true, requires_argument),
    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"),
+	    string("File containing a list of target masks - required for seeds_to_targets classification"),
 	    false, requires_argument),
-  simpleout(string("--opd"), false,
+  simpleout(string("--opd"), true,
 	    string("output path distribution"),
 	    false, no_argument), 
   pathdist(string("--pd"), false,
@@ -151,7 +151,7 @@ class probtrackxOptions {
 	 string("Waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks"),
        false, requires_argument),
  network(string("--network"), false,
-	 string("Only keep paths going through at least one waypoint mask, or another seed in multiple seeds mode"),
+	 string("Activate network mode - only keep paths going through at least one seed mask (required if multiple seed masks)"),
        false, no_argument),
    meshfile(string("--mesh"), string(""),
 	 string(""),

streamlines.cc

@@ -129,6 +129,7 @@ namespace TRACT{
 	int x_s =(int)round((float)xyz_seeds(1));
 	int y_s =(int)round((float)xyz_seeds(2));
 	int z_s =(int)round((float)xyz_seeds(3));
+	
 	  
 	//update every passed_flag
 	for( unsigned int wm=0;wm<m_waymasks.size();wm++ ){