Newer
Older
/* MELODIC - Multivariate exploratory linear optimized decomposition into
independent components
meloptions.h - class for command line options
Christian F. Beckmann, FMRIB Image Analysis Group
/* CCOPYRIGHT */
#ifndef __MELODICOPTIONS_h
#define __MELODICOPTIONS_h
#include <iostream>
#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;
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
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<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<float> tr;
Option<bool> logPower;
Option<string> fn_Tdesign;
Option<string> fn_Tcon;
Option<string> fn_TconF;
Option<string> fn_Sdesign;
Option<string> fn_Scon;
Option<string> fn_SconF;
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
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<int> dummy;
Option<int> repeats;
Option<float> nlconst1;
Option<float> nlconst2;
Option<float> smooth_probmap;
Option<bool> remove_meanvol;
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() :
logdir(string("-o,--outdir"), string("melodic.log"),
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),
threshold(string("--bgthreshold"), 0.00000001,
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("--separate_whiten"), true,
string("switch on separate whitening"),
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 off conversion to percent BOLD signal change"),
false, no_argument),
pspec(string("--pspec"), false,
string("switch on conversion to powerspectra"),
false, no_argument),
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),
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),
mmthresh(string("--mmthresh"), string("0.5"),
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),
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),
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),
fn_TconF(string("--Tconf"), string(""),
string("F-contrast matrix across time-domain"),
false, requires_argument),
fn_Sdesign(string("--Sdes"), string(""),
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),
output_all(string("--Oall"), false,
string("output everything"),
false, no_argument),
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
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),
debug(string("--debug"), false,
string("switch on debug messages"),
false, no_argument),
guessfname(string("-g,--guess"), string(""),
string("file name of guess of mixing matrix"),
false, requires_argument, false),
paradigmfname(string("-p,--paradigm"), string(""),
string("file name of FEAT paradigm file"),
false, requires_argument, false),
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),
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("--keepmeanvol"), true,
string("do not subtract mean volume"),
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),
guess_remderiv(string("--remderiv"), false,
string("removes every second entry in paradigm file (EV derivatives)"),
false, no_argument, false),
temporal(string("--temporal"), false,
string("perform temporal ICA"),
false, no_argument, false),
retrystep(3),
options(string(""),
string(" melodic -i <filename> <options>")+
string("\n \t \t to run melodic")+
string("\n melodic -i <filename> --mix=melodic_mix")+
string(" --filter=\"string of component numbers\"")+
string("\n \t \t to remove estimated ICs from input")+
string("\n melodic -i <filename> --ICs=melodic_IC")+
string(" --mix=melodic_mix <options>")+
string("\n \t \t to run Mixture Model based inference on estimated ICs")+
string("\n melodic --help "))
{
try {
options.add(logdir);
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(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(maxNumItt);
options.add(maxRestart);
options.add(mmthresh);
options.add(perf_mm);
options.add(ICsfname);
options.add(filtermix);
options.add(filter);
options.add(genreport);
options.add(tr);
options.add(logPower);
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(dummy);
options.add(repeats);
options.add(nlconst1);
options.add(nlconst2);
options.add(remove_meanvol);
options.add(remove_endslices);
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