clarified default options

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")
    {