diff --git a/probtrackxOptions.h b/probtrackxOptions.h index 5c28f2b5810fea1aa01d65e872542272e0e18eef..4e2ed692e1294df0ca374ced8fd81da47125e9ff 100644 --- a/probtrackxOptions.h +++ b/probtrackxOptions.h @@ -48,7 +48,7 @@ class probtrackxOptions { Option<string> seedref; Option<string> mask2; Option<string> waypoints; - Option<bool> waypoints_and; + Option<bool> network; Option<string> meshfile; FmribOption<string> lrmask; Option<string> logdir; @@ -148,12 +148,12 @@ class probtrackxOptions { string("second mask in twomask_symm mode."), false, requires_argument), waypoints(string("--waypoints"), string(""), - string("Waypoint mask or ascii list of waypoint masks"), + string("Waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks"), false, requires_argument), - waypoints_and(string("--network"), true, - string("Searches for pathways connecting every seed to at least one waypoint"), - false, no_argument), - meshfile(string("--mesh"), string(""), + network(string("--network"), false, + string("Only keep paths going through at least one waypoint mask, or another seed in multiple seeds mode"), + false, no_argument), + meshfile(string("--mesh"), string(""), string(""), false, requires_argument), lrmask(string("--lrmask"), string(""), @@ -195,7 +195,7 @@ class probtrackxOptions { rseed(string("--rseed"), 12345, string("Random seed"), false, requires_argument), - options("probtrack","probtrack -s <basename> -m <maskname> -x <seedfile> -o <output> --targetmasks=<textfile>\n probtrack --help\n") + options("probtrackx","probtrackx -s <basename> -m <maskname> -x <seedfile> -o <output> --targetmasks=<textfile>\n probtrackx --help\n") { @@ -210,7 +210,7 @@ class probtrackxOptions { options.add(skipmask); options.add(mask2); options.add(waypoints); - options.add(waypoints_and); + options.add(network); options.add(meshfile); options.add(lrmask); options.add(seedref); diff --git a/streamlines.cc b/streamlines.cc index 71ea3b74cb6c68ee4b046a2192247ed2986e4e86..a35e3d7bd926f0643d024c207bc7dc070c88702d 100644 --- a/streamlines.cc +++ b/streamlines.cc @@ -200,7 +200,7 @@ namespace TRACT{ bool accept_path=true; if(m_passed_flags.size()!=0){ - if(opts.waypoints_and.value()){ + if(!opts.network.value()){ for(unsigned int i=0; i<m_passed_flags.size();i++) if(!m_passed_flags[i]) accept_path=false;