From eda42f54dded88d78f59aee1881f57955d27fdcd Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Mon, 23 Nov 2009 10:45:50 +0000
Subject: [PATCH] cleanup commandline help
---
probtrackxOptions.h | 67 ++++++++++++++++++++++++---------------------
1 file changed, 36 insertions(+), 31 deletions(-)
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index eefa5e6..33beaf4 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -39,14 +39,14 @@ class probtrackxOptions {
Option<bool> pathdist;
Option<bool> s2tout;
FmribOption<bool> matrix1out;
- Option<bool> matrix2out;
+ FmribOption<bool> matrix2out;
FmribOption<bool> matrix3out;
FmribOption<string> maskmatrix3;
FmribOption<bool> maskmatrixout;
Option<string> outfile;
Option<string> rubbishfile;
Option<string> stopfile;
- Option<string> prefdirfile;
+ FmribOption<string> prefdirfile;
Option<string> seeds_to_dti;
Option<string> dti_to_seeds;
FmribOption<string> skipmask;
@@ -55,7 +55,8 @@ class probtrackxOptions {
Option<string> waypoints;
Option<bool> network;
Option<string> meshfile;
- Option<string> lrmask;
+ FmribOption<string> meshspace;
+ FmribOption<string> lrmask;
Option<string> logdir;
Option<bool> forcedir;
Option<int> nparticles;
@@ -71,7 +72,7 @@ class probtrackxOptions {
Option<bool> modeuler;
Option<int> rseed;
Option<bool> seedcountastext;
- Option<bool> splitmatrix2;
+ FmribOption<bool> splitmatrix2;
void parse_command_line(int argc, char** argv,Log& logger);
void modecheck();
@@ -99,13 +100,13 @@ class probtrackxOptions {
inline probtrackxOptions::probtrackxOptions() :
verbose(string("-V,--verbose"), 0,
- string("verbose level, [0-2]"),
+ string("Verbose level, [0-2]"),
false, requires_argument),
help(string("-h,--help"), false,
- string("display this message"),
+ string("Display this message"),
false, no_argument),
basename(string("-s,--samples"), string("merged"),
- string("basename for samples files"),
+ string("Basename for samples files"),
true, requires_argument),
maskfile(string("-m,--mask"), string("mask"),
string("Bet binary mask file in diffusion space"),
@@ -114,49 +115,49 @@ class probtrackxOptions {
string("Seed volume, or voxel, or ascii file with multiple volumes, or freesurfer label file"),
true, requires_argument),
mode(string("--mode"), string(""),
- string("use --mode=simple for single seed voxel"),
+ string("\tUse --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 classification"),
false, requires_argument),
simpleout(string("--opd"), false,
- string("output path distribution"),
+ string("\tOutput path distribution"),
false, no_argument),
pathdist(string("--pd"), false,
- string("Correct path distribution for the length of the pathways"),
+ string("\tCorrect path distribution for the length of the pathways"),
false, no_argument),
s2tout(string("--os2t"), false,
- string("output seeds to targets"),
+ string("\tOutput seeds to targets"),
false, no_argument),
matrix1out(string("--omatrix1"), false,
- string("output matrix1"),
+ string("Output matrix1"),
false, no_argument),
matrix2out(string("--omatrix2"), false,
- string("output matrix2"),
+ string("Output matrix2"),
false, no_argument),
matrix3out(string("--omatrix3"), false,
- string("output matrix3 (NxN connectivity matrix)"),
+ string("Output matrix3 (NxN connectivity matrix)"),
false, no_argument),
maskmatrix3(string("--mask3"), "",
- string("mask used for NxN connectivity matrix"),
+ string("Mask used for NxN connectivity matrix"),
false, requires_argument),
maskmatrixout(string("--omaskmatrix"), false,
- string("output maskmatrix"),
+ string("Output maskmatrix"),
false, no_argument),
outfile(string("-o,--out"), string("fdt_paths"),
string("Output file (default='fdt_paths')"),
false, requires_argument),
rubbishfile(string("--avoid"), string(""),
- string("Reject pathways passing through locations given by this mask"),
+ string("\tReject pathways passing through locations given by this mask"),
false, requires_argument),
stopfile(string("--stop"), string(""),
- string("Stop tracking at locations given by this mask file"),
+ string("\tStop tracking at locations given by this mask file"),
false, requires_argument),
prefdirfile(string("--prefdir"), string(""),
- string("prefered orientation preset in a 4D mask"),
+ string("Prefered orientation preset in a 4D mask"),
false, requires_argument),
seeds_to_dti(string("--xfm"), string(""),
- string("Transform taking seed space to DTI space (either FLIRT matrix or FNIRT warpfield) - default is identity"),
+ string("\tTransform taking seed space to DTI space (either FLIRT matrix or FNIRT warpfield) - default is identity"),
false, requires_argument),
dti_to_seeds(string("--invxfm"), string(""),
string("Transform taking DTI space to seed space (compulsory when using a warpfield for seeds_to_dti)"),
@@ -168,7 +169,7 @@ class probtrackxOptions {
string("Reference vol to define seed space in simple mode - diffusion space assumed if absent"),
false, requires_argument),
mask2(string("--mask2"), string(""),
- string("second mask in twomask_symm mode."),
+ string("\tSecond mask in twomask_symm mode."),
false, requires_argument),
waypoints(string("--waypoints"), string(""),
string("Waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks"),
@@ -177,13 +178,16 @@ 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("Freesurfer-type surface descriptor (in ascii format)"),
+ string("\tFreesurfer-type surface descriptor (in ascii format)"),
+ false, requires_argument),
+ meshspace(string("--meshspace"), string("freesurfer"),
+ string("Mesh reference space - either 'freesurfer' (default) or 'caret'"),
false, requires_argument),
lrmask(string("--lrmask"), string(""),
- string("low resolution binary brain mask for stroring connectivity distribution in matrix2 mode"),
+ string("Low resolution binary brain mask for storing connectivity distribution in matrix2 mode"),
false, requires_argument),
logdir(string("--dir"), string("logdir"),
- string("Directory to put the final volumes in - code makes this directory - default='logdir'"),
+ string("\tDirectory to put the final volumes in - code makes this directory - default='logdir'"),
false, requires_argument),
forcedir(string("--forcedir"), false,
string("Use the actual directory name given - i.e. don't add + to make a new directory"),
@@ -201,13 +205,13 @@ class probtrackxOptions {
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 in mm - default=0.5"),
+ 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"),
+ string("Perform loopchecks on paths - slower, but allows lower curvature threshold"),
false, no_argument),
usef(string("-f,--usef"), false,
string("Use anisotropy to constrain tracking"),
@@ -216,19 +220,19 @@ class probtrackxOptions {
string("Default 0. Set to 1 to randomly sample initial fibres (with f > fibthresh). \n Set to 2 to sample in proportion fibres (with f>fibthresh) to f. \n Set to 3 to sample ALL populations at random (even if f<fibthresh)"),
false, requires_argument),
fibst(string("--fibst"),1,
- string("Force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0"),
+ string("\tForce a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0"),
false, requires_argument),
modeuler(string("--modeuler"), false,
string("Use modified euler streamlining"),
false, no_argument),
rseed(string("--rseed"), 12345,
- string("Random seed"),
+ string("\tRandom seed"),
false, requires_argument),
- seedcountastext(string("--seedcountastext"), false,
+ seedcountastext(string("--s2tastext"), false,
string("Output seed-to-target counts as a text file (useful when seeding from a mesh)"),
false, no_argument),
splitmatrix2(string("--splitmatrix2"), false,
- string("split matrix 2 along seed dimension (in case it is too large)"),
+ string("Split matrix 2 along seed dimension (in case it is too large)"),
false, no_argument),
options("probtrackx","probtrackx -s <basename> -m <maskname> -x <seedfile> -o <output> --targetmasks=<textfile>\n probtrackx --help\n")
{
@@ -247,6 +251,7 @@ class probtrackxOptions {
options.add(waypoints);
options.add(network);
options.add(meshfile);
+ options.add(meshspace);
options.add(lrmask);
options.add(seedref);
options.add(logdir);
--
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