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/* MELODIC - Multivariate exploratory linear optimized decomposition into
independent components
meloptions.h - class for command line options
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2008 University of Oxford */
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/* Part of FSL - FMRIB's Software Library
http://www.fmrib.ox.ac.uk/fsl
fsl@fmrib.ox.ac.uk
Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
Imaging of the Brain), Department of Clinical Neurology, Oxford
University, Oxford, UK
LICENCE
FMRIB Software Library, Release 4.0 (c) 2007, The University of
Oxford (the "Software")
The Software remains the property of the University of Oxford ("the
University").
The Software is distributed "AS IS" under this Licence solely for
non-commercial use in the hope that it will be useful, but in order
that the University as a charitable foundation protects its assets for
the benefit of its educational and research purposes, the University
makes clear that no condition is made or to be implied, nor is any
warranty given or to be implied, as to the accuracy of the Software,
or that it will be suitable for any particular purpose or for use
under any specific conditions. Furthermore, the University disclaims
all responsibility for the use which is made of the Software. It
further disclaims any liability for the outcomes arising from using
the Software.
The Licensee agrees to indemnify the University and hold the
University harmless from and against any and all claims, damages and
liabilities asserted by third parties (including claims for
negligence) which arise directly or indirectly from the use of the
Software or the sale of any products based on the Software.
No part of the Software may be reproduced, modified, transmitted or
transferred in any form or by any means, electronic or mechanical,
without the express permission of the University. The permission of
the University is not required if the said reproduction, modification,
transmission or transference is done without financial return, the
conditions of this Licence are imposed upon the receiver of the
product, and all original and amended source code is included in any
transmitted product. You may be held legally responsible for any
copyright infringement that is caused or encouraged by your failure to
abide by these terms and conditions.
You are not permitted under this Licence to use this Software
commercially. Use for which any financial return is received shall be
defined as commercial use, and includes (1) integration of all or part
of the source code or the Software into a product for sale or license
by or on behalf of Licensee to third parties or (2) use of the
Software or any derivative of it for research with the final aim of
developing software products for sale or license to a third party or
(3) use of the Software or any derivative of it for research with the
final aim of developing non-software products for sale or license to a
third party, or (4) use of the Software to provide any service to an
external organisation for which payment is received. If you are
interested in using the Software commercially, please contact Isis
Innovation Limited ("Isis"), the technology transfer company of the
University, to negotiate a licence. Contact details are:
innovation@isis.ox.ac.uk quoting reference DE/1112. */
#ifndef __MELODICOPTIONS_h
#define __MELODICOPTIONS_h
#include <fstream>
#include <stdlib.h>
#include <stdio.h>
#include "utils/options.h"
#include "utils/log.h"
#include "melodic.h"
using namespace Utilities;
namespace Melodic {
class MelodicOptions {
public:
static MelodicOptions& getInstance();
~MelodicOptions() { delete gopt; }
string version;
string binpath;
string logfname;
bool filtermode;
bool explicitnums;
Option<string> logdir;
Option< std::vector<string> > inputfname;
Option<string> outputfname;
Option<string> maskfname;
Option<bool> use_mask;
Option<bool> update_mask;
Option<bool> perf_bet;
Option<float> threshold;
Option<int> pca_dim;
Option<string> pca_est;
Option<bool> joined_whiten;
Option<bool> dr_pca;
Option<float> vn_level;
Option<int> numICs;
Option<string> approach;
Option<string> nonlinearity;
Option<bool> varnorm;
Option<bool> pbsc;
Option<bool> pspec;
Option<string> segment;
Option<bool> tsmooth;
Option<float> epsilon;
Option<int> maxNumItt;
Option<int> maxRestart;
Option<int> rank1interval;
Option<string> mmthresh;
Option<bool> perf_mm;
Option<string> ICsfname;
Option<string> filtermix;
Option<string> smodename;
Option<string> filter;
Option<bool> genreport;
Option<string> fn_Tdesign;
Option<string> fn_Tcon;
Option<string> fn_TconF;
Option<string> fn_Sdesign;
Option<string> fn_Scon;
Option<string> fn_SconF;
Option<bool> output_all;
Option<bool> output_unmix;
Option<bool> output_MMstats;
Option<bool> output_pca;
Option<bool> output_white;
Option<bool> output_origIC;
Option<bool> output_mean;
Option<bool> verbose;
Option<bool> vers;
Option<bool> copyright;
Option<bool> help;
Option<bool> debug;
Option<string> guessfname;
Option<string> paradigmfname;
Option<float> nlconst1;
Option<float> nlconst2;
Option<float> smooth_probmap;
Option<bool> remove_meanvol;
Option<bool> remove_meantc;
Option<bool> remove_endslices;
Option<bool> rescale_nht;
Option<bool> guess_remderiv;
Option<bool> temporal;
int retrystep;
void parse_command_line(int argc, char** argv, Log& logger, const string &p_version);
private:
MelodicOptions();
const MelodicOptions& operator=(MelodicOptions&);
MelodicOptions(MelodicOptions&);
OptionParser options;
void print_usage(int argc, char *argv[]);
void print_version();
void print_copyright();
void status();
};
inline MelodicOptions& MelodicOptions::getInstance(){
if(gopt == NULL)
gopt = new MelodicOptions();
return *gopt;
}
inline MelodicOptions::MelodicOptions() :
string("output directory name\n"),
false, requires_argument),
inputfname(string("-i,--in"), std::vector<string>(),
string("input file names (either single file name or comma-separated list or text file)"),
true, requires_argument),
outputfname(string("-O,--out"), string("melodic"),
string("output file name"),
false, requires_argument,false),
maskfname(string("-m,--mask"), string(""),
string("file name of mask for thresholding"),
false, requires_argument),
use_mask(string("--nomask"), true,
string("switch off masking"),
false, no_argument),
update_mask(string("--update_mask"), true,
string("switch off mask updating"),
false, no_argument),
perf_bet(string("--nobet"), true,
string("\tswitch off BET"),
false, no_argument),
string("brain / non-brain threshold (only if --nobet selected)\n"),
false, requires_argument),
pca_dim(string("-d,--dim"), 0,
string("dimensionality reduction into #num dimensions (default: automatic estimation)"),
false, requires_argument),
pca_est(string("--dimest"), string("lap"),
string("use specific dim. estimation technique: lap, bic, mdl, aic, mean (default: lap)"),
false, requires_argument),
joined_whiten(string("--sep_whiten"), true,
joined_vn(string("--sep_vn"), true,
string("switch off joined variance nomalisation"),
false, no_argument),
dr_pca(string("--mod_pca"), true,
string("switch off modified PCA for concat ICA"),
false, no_argument, false),
vn_level(string("--vn_level"), float(2.3),
string("variance nomalisation threshold level (Z> value is ignored)"),
false, requires_argument, false),
numICs(string("-n,--numICs"), -1,
string("numer of IC's to extract (for deflation approach)"),
false, requires_argument),
approach(string("-a,--approach"), string("symm"),
string("approach for decomposition, 2D: defl, symm (default), 3D: tica (default), concat"),
false, requires_argument),
nonlinearity(string("--nl"), string("pow3"),
string("\tnonlinearity: gauss, tanh, pow3, pow4"),
false, requires_argument),
varnorm(string("--vn,--varnorm"), true,
string("switch off variance normalisation"),
false, no_argument),
string(" switch on conversion to percent BOLD signal change"),
false, no_argument, false),
string(" switch on conversion to powerspectra"),
segment(string("--covarweight"), string(""),
string("voxel-wise weights for the covariance matrix (e.g. segmentation information)"),
false, requires_argument),
tsmooth(string("--spca"), false,
string("smooth the eigenvectors prior to IC decomposition"),
false, no_argument, false),
epsilon(string("--eps,--epsilon"), 0.00005,
string("minimum error change"),
false, requires_argument),
epsilonS(string("--epsS,--epsilonS"), 0.03,
string("minimum error change for rank-1 approximation in TICA"),
false, requires_argument),
maxNumItt(string("--maxit"), 500,
string("\tmaximum number of iterations before restart"),
false, requires_argument),
maxRestart(string("--maxrestart"), 6,
string("maximum number of restarts\n"),
false, requires_argument),
string("number of iterations between rank-1 approximation (TICA)\n"),
false, requires_argument,false),
string("threshold for Mixture Model based inference"),
false, requires_argument),
perf_mm(string("--no_mm"), true,
string("\tswitch off mixture modelling on IC maps\n "),
false, no_argument),
ICsfname(string("--ICs"), string(""),
string("\tfilename of the IC components file for mixture modelling"),
false, requires_argument),
filtermix(string("--mix"), string(""),
string("\tmixing matrix for mixture modelling / filtering"),
false, requires_argument),
smodename(string("--smode"), string(""),
string("\tmatrix of session modes for report generation"),
false, requires_argument),
filter(string("-f,--filter"), string(""),
string("component numbers to remove\n "),
false, requires_argument),
genreport(string("--report"), false,
string("generate Melodic web report"),
false, no_argument),
guireport(string("--guireport"), string(""),
string("modify report for GUI use"),
false, requires_argument, false),
bgimage(string("--bgimage"), string(""),
string("specify background image for report (default: mean image)\n "),
false, requires_argument),
tr(string("--tr"), 0.0,
string("\tTR in seconds"),
false, requires_argument),
logPower(string("--logPower"), false,
string("calculate log of power for frequency spectrum\n"),
false, no_argument),
addsigchng(string("--sigchng"), false,
string("add signal change estimates to report pages\n"),
false, no_argument, false),
allPPCA(string("--allPPCA"), false,
string("add all PPCA plots\n"),
false, no_argument, false),
varplots(string("--varplots"), false,
string("add std error envelopes to time course plots\n"),
false, no_argument, false),
varvals(string("--varvals"), false,
string("add rank1 values after plots\n"),
false, no_argument, false),
fn_Tdesign(string("--Tdes"), string(""),
string(" design matrix across time-domain"),
false, requires_argument),
fn_Tcon(string("--Tcon"), string(""),
string(" t-contrast matrix across time-domain"),
false, requires_argument),
string(" F-contrast matrix across time-domain"),
false, requires_argument, false),
string(" design matrix across subject-domain"),
false, requires_argument),
fn_Scon(string("--Scon"), string(""),
string(" t-contrast matrix across subject-domain"),
false, requires_argument),
fn_SconF(string("--Sconf"), string(""),
string(" F-contrast matrix across subject-domain"),
false, requires_argument,false),
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output_unmix(string("--Ounmix"), false,
string("output unmixing matrix"),
false, no_argument),
output_MMstats(string("--Ostats"), false,
string("output thresholded maps and probability maps"),
false, no_argument),
output_pca(string("--Opca"), false,
string("\toutput PCA results"),
false, no_argument),
output_white(string("--Owhite"), false,
string("output whitening/dewhitening matrices"),
false, no_argument),
output_origIC(string("--Oorig"), false,
string("\toutput the original ICs"),
false, no_argument),
output_mean(string("--Omean"), false,
string("\toutput mean volume\n"),
false, no_argument),
verbose(string("-v,--verbose"), false,
string("switch on diagnostic messages"),
false, no_argument),
vers(string("-V,--version"), false,
string("prints version information"),
false, no_argument),
copyright(string("--copyright"), false,
string("prints copyright information"),
false, no_argument),
help(string("-h,--help"), false,
string("prints this help message"),
false, no_argument),
guessfname(string("--init_ica"), string(""),
string("file name of FEAT paradigm file (design.mat) for ICA initialisation"),
paradigmfname(string("--init_pca"), string(""),
string("file name of FEAT paradigm file (design.mat) for PCA initialisation"),
axials_str(string("--report_maps"), string(" -s 2 -A 950 "),
string("control string for spatial map images (see slicer)"),
false, requires_argument),
dummy(string("--dummy"), 0,
string("number of dummy volumes"),
false, requires_argument,false),
repeats(string("--repeats"), 1,
string("number of repeats (multistart)"),
false, requires_argument, false),
string("integer seed for random number generator within melodic"),
nlconst1(string("--nl1,--nlconst1"), 1.0,
string("nonlinear constant 1"),
false, requires_argument, false),
nlconst2(string("--nl2,--nlconst2"), 1.0,
string("nonlinear constant 2"),
false, requires_argument, false),
smooth_probmap(string("--smooth_pm"), 0.0,
string("width of smoothing kernel for probability maps"),
false, requires_argument, false),
remove_meanvol(string("--keep_meanvol"), true,
string("do not subtract mean volume"),
false, no_argument, false),
remove_meantc(string("--remove_meantc"), false,
string("remove mean time course"),
false, no_argument, false),
remove_endslices(string("--remEndslices"), false,
string("delete end slices (motion correction artefacts)"),
false, no_argument,false),
rescale_nht(string("--rescale_nht"), true,
string("switch off map rescaling after mixture-modelling"),
false, no_argument,false),
string("removes every second entry in paradigm file (EV derivatives)"),
false, no_argument, false),
temporal(string("--temporal"), false,
string("perform temporal ICA"),
options.add(inputfname);
options.add(outputfname);
options.add(guessfname);
options.add(maskfname);
options.add(use_mask);
options.add(perf_bet);
options.add(threshold);
options.add(pca_dim);
options.add(pca_est);
options.add(dr_pca);
options.add(numICs);
options.add(approach);
options.add(nonlinearity);
options.add(varnorm);
options.add(pbsc);
options.add(pspec);
options.add(segment);
options.add(tsmooth);
options.add(epsilon);
options.add(mmthresh);
options.add(perf_mm);
options.add(ICsfname);
options.add(filtermix);
options.add(fn_Tdesign);
options.add(fn_Tcon);
options.add(fn_TconF);
options.add(fn_Sdesign);
options.add(fn_Scon);
options.add(fn_SconF);
options.add(output_unmix);
options.add(output_MMstats);
options.add(output_pca);
options.add(output_white);
options.add(output_origIC);
options.add(output_mean);
options.add(verbose);
options.add(vers);
options.add(copyright);
options.add(help);
options.add(guessfname);
options.add(paradigmfname);
options.add(guess_remderiv);
options.add(temporal);
}
catch(X_OptionError& e) {
options.usage();
cerr << endl << e.what() << endl;
}
catch(std::exception &e) {
cerr << e.what() << endl;
}
}
}
#endif