diff --git a/probtrackxOptions.h b/probtrackxOptions.h index 4e2ed692e1294df0ca374ced8fd81da47125e9ff..f3e6f6e0b4de7a198cf08d110823d82a0b166979 100644 --- a/probtrackxOptions.h +++ b/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(""), diff --git a/streamlines.cc b/streamlines.cc index 910bcac5596e01a482ecfc44d58a7271cd20ba62..e7fd8de00efcfbf2311cb0da49ff1137c6e7e4d4 100644 --- a/streamlines.cc +++ b/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++ ){