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Stamatios Sotiropoulos authoredStamatios Sotiropoulos authored
probtrackxOptions.h 10.77 KiB
/* probtrackxOptions.h
Tim Behrens, FMRIB Image Analysis Group
Copyright (C) 2004 University of Oxford */
/* CCOPYRIGHT */
#if !defined(probtrackxOptions_h)
#define probtrackxOptions_h
#include <string>
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include <stdio.h>
#include "utils/options.h"
#include "utils/log.h"
#include "commonopts.h"
//#include "newmatall.h"
using namespace Utilities;
namespace TRACT {
class probtrackxOptions {
public:
static probtrackxOptions& getInstance();
~probtrackxOptions() { delete gopt; }
Option<int> verbose;
Option<bool> help;
Option<string> basename;
Option<string> maskfile;
Option<string> seedfile;
Option<string> mode;
Option<string> targetfile;
Option<bool> simpleout;
Option<bool> pathdist;
Option<bool> s2tout;
FmribOption<bool> matrix1out;
FmribOption<bool> matrix2out;
FmribOption<bool> matrix3out;
FmribOption<string> maskmatrix3;
FmribOption<bool> maskmatrixout;
Option<string> outfile;
Option<string> rubbishfile;
Option<string> stopfile;
FmribOption<string> prefdirfile;
Option<string> seeds_to_dti;
Option<string> dti_to_seeds;
FmribOption<string> skipmask;
Option<string> seedref;
Option<string> mask2;
Option<string> waypoints;
Option<bool> network;
Option<string> meshfile;
FmribOption<string> meshspace;
FmribOption<string> lrmask;
Option<string> logdir;
Option<bool> forcedir;
Option<int> nparticles;
Option<int> nsteps;
Option<float> distthresh;
FmribOption<float> distthresh3;
Option<float> c_thr;
Option<float> fibthresh;
Option<bool> sampvox;
Option<float> steplength;
Option<bool> loopcheck; Option<bool> usef;
Option<int> randfib;
Option<int> fibst;
Option<bool> modeuler;
Option<int> rseed;
Option<bool> seedcountastext;
FmribOption<bool> splitmatrix2;
void parse_command_line(int argc, char** argv,Log& logger);
void modecheck();
void modehelp();
void matrixmodehelp();
void status();
private:
probtrackxOptions();
const probtrackxOptions& operator=(probtrackxOptions&);
probtrackxOptions(probtrackxOptions&);
OptionParser options;
static probtrackxOptions* gopt;
};
inline probtrackxOptions& probtrackxOptions::getInstance(){
if(gopt == NULL)
gopt = new probtrackxOptions();
return *gopt;
}
inline probtrackxOptions::probtrackxOptions() :
verbose(string("-V,--verbose"), 0,
string("Verbose level, [0-2]"),
false, requires_argument),
help(string("-h,--help"), false,
string("Display this message"),
false, no_argument),
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, or ascii file with multiple volumes, or freesurfer label file"),
true, requires_argument),
mode(string("--mode"), string(""),
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("\tOutput path distribution"),
false, no_argument),
pathdist(string("--pd"), false,
string("\tCorrect path distribution for the length of the pathways"),
false, no_argument),
s2tout(string("--os2t"), false,
string("\tOutput seeds to targets"),
false, no_argument),
matrix1out(string("--omatrix1"), false,
string("Output matrix1"),
false, no_argument),
matrix2out(string("--omatrix2"), false,
string("Output matrix2"),
false, no_argument), matrix3out(string("--omatrix3"), false,
string("Output matrix3 (NxN connectivity matrix)"),
false, no_argument),
maskmatrix3(string("--mask3"), "",
string("Mask used for NxN connectivity matrix"),
false, requires_argument),
maskmatrixout(string("--omaskmatrix"), false,
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("\tReject pathways passing through locations given by this mask"),
false, requires_argument),
stopfile(string("--stop"), string(""),
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"),
false, requires_argument),
seeds_to_dti(string("--xfm"), string(""),
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)"),
false, requires_argument),
skipmask(string("--no_integrity"), string(""),
string("no explanation needed"),
false, requires_argument),
seedref(string("--seedref"), string(""),
string("Reference vol to define seed space in simple mode - diffusion space assumed if absent"),
false, requires_argument),
mask2(string("--mask2"), string(""),
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"),
false, requires_argument),
network(string("--network"), false,
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("\tFreesurfer-type surface descriptor (in ascii format)"),
false, requires_argument),
meshspace(string("--meshspace"), string("freesurfer"),
string("Mesh reference space - either 'freesurfer' (default) or 'caret' or 'first'"),
false, requires_argument),
lrmask(string("--lrmask"), string(""),
string("Low resolution binary brain mask for storing connectivity distribution in matrix2 mode"),
false, requires_argument),
logdir(string("--dir"), string("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"),
false, no_argument),
nparticles(string("-P,--nsamples"), 5000,
string("Number of samples - default=5000"),
false, requires_argument),
nsteps(string("-S,--nsteps"), 2000,
string("Number of steps per sample - default=2000"),
false, requires_argument),
distthresh(string("--distthresh"), 0,
string("Discards samples shorter than this threshold (in mm - default=0)"),
false, requires_argument),
distthresh3(string("--distthresh3"), 0,
string("Discards samples (in matrix3) shorter than this threshold (in voxels - default=0)"),
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"),
false, requires_argument),
sampvox(string("--sampvox"), false,
string("Sample random points within seed voxels"),
false, no_argument),
steplength(string("--steplength"), 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"),
false, no_argument),
usef(string("-f,--usef"), false,
string("Use anisotropy to constrain tracking"),
false, no_argument),
randfib(string("--randfib"), 0,
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("\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("\tRandom seed"),
false, requires_argument),
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)"),
false, no_argument),
options("probtrackx","probtrackx -s <basename> -m <maskname> -x <seedfile> -o <output> --targetmasks=<textfile>\n probtrackx --help\n")
{
try {
options.add(verbose);
options.add(help);
options.add(basename);
options.add(maskfile);
options.add(seedfile);
options.add(mode);
options.add(targetfile);
options.add(skipmask);
options.add(mask2);
options.add(waypoints);
options.add(network);
options.add(meshfile);
options.add(meshspace);
options.add(lrmask);
options.add(seedref);
options.add(logdir);
options.add(forcedir);
options.add(simpleout);
options.add(pathdist);
options.add(s2tout);
options.add(matrix1out);
options.add(matrix2out);
options.add(matrix3out);
options.add(maskmatrix3);
options.add(maskmatrixout);
options.add(outfile);
options.add(rubbishfile);
options.add(stopfile);
options.add(prefdirfile);
options.add(seeds_to_dti); options.add(dti_to_seeds);
options.add(nparticles);
options.add(nsteps);
options.add(distthresh);
options.add(distthresh3);
options.add(c_thr);
options.add(fibthresh);
options.add(sampvox);
options.add(steplength);
options.add(loopcheck);
options.add(usef);
options.add(randfib);
options.add(fibst);
options.add(modeuler);
options.add(rseed);
options.add(seedcountastext);
options.add(splitmatrix2);
}
catch(X_OptionError& e) {
options.usage();
cerr << endl << e.what() << endl;
}
catch(std::exception &e) {
cerr << e.what() << endl;
}
}
}
#endif