diff --git a/probtrackxOptions.h b/probtrackxOptions.h index fa2f5f75093de7feb99d58938ccdaa990b1e71bd..80efc0ab3f106a625ca4e86b6eee180af42e3690 100644 --- a/probtrackxOptions.h +++ b/probtrackxOptions.h @@ -162,7 +162,7 @@ class probtrackxOptions { 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(""), + string("Freesurfer-type surface descriptor (in ascii format)"), false, requires_argument), lrmask(string("--lrmask"), string(""), string("low resolution binary brain mask for stroring connectivity distribution in matrix2 mode"), @@ -174,19 +174,19 @@ class probtrackxOptions { string("Use the actual directory name given - i.e. don't add + to make a new directory"), false, no_argument), nparticles(string("-P,--nsamples"), 5000, - string("Number of samples"), + string("Number of samples - default=5000"), false, requires_argument), nsteps(string("-S,--nsteps"), 2000, - string("Number of steps per sample"), + string("Number of steps per sample - default=2000"), false, requires_argument), c_thr(string("-c,--cthr"), 0.2, string("Curvature threshold - default=0.2"), false, requires_argument), fibthresh(string("--fibthresh"), 0.01, - string("volume fraction before subsidary fibre orientations are considered default=0.01"), + string("volume fraction before subsidary fibre orientations are considered - default=0.01"), false, requires_argument), steplength(string("--steplength"), 0.5, - string("steplength"), + string("steplength in mm - default=0.5"), false, requires_argument), loopcheck(string("-l,--loopcheck"), false, string("perform loopchecks on paths - slower, but allows lower curvature threshold"), @@ -198,7 +198,7 @@ class probtrackxOptions { string("Select randomly from one of the fibres"), false, no_argument), fibst(string("--fibst"),1, - string("Force a starting fibre for tracking (default=1)"), + string("Force a starting fibre for tracking - default=1, i.e. first fibre orientation"), false, requires_argument), modeuler(string("--modeuler"), false, string("Use modified euler streamlining"), @@ -207,7 +207,7 @@ class probtrackxOptions { string("Random seed"), false, requires_argument), seedcountastext(string("--seedcountastext"), false, - string("Output seed-to-target counts as a text file"), + string("Output seed-to-target counts as a text file (useful when seeding from a mesh)"), false, no_argument), options("probtrackx","probtrackx -s <basename> -m <maskname> -x <seedfile> -o <output> --targetmasks=<textfile>\n probtrackx --help\n") {