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Commit 6691da87 authored by Matthew Webster's avatar Matthew Webster
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This commit was manufactured by cvs2svn to create tag 'fsl-5_0_11'. 

Sprout from master 2017-07-05 14:45:27 UTC Saad Jbabdi <saad@fmrib.ox.ac.uk> 'small bug fix'
Cherrypick from master 2013-07-09 11:06:37 UTC Moises Fernandez <moisesf@fmrib.ox.ac.uk> 'Change FSLDEVDIR path with FSLDIR':
    CUDA/bedpostx_multigpu_LSF
Delete:
    CUDA/bedpostx_multigpu_PBS.sh
    RLR_MAP_routines.cpp
    RLR_MAP_routines.h
    doc/fdt_bedpostx.html
    doc/fdt_bedpostx_parallel.html
    doc/fdt_biggest.html
    doc/fdt_display.html
    doc/fdt_dtifit.html
    doc/fdt_eddy.html
    doc/fdt_images/eddy.gif
    doc/fdt_images/eddy.tif
    doc/fdt_images/eddy2.gif
    doc/fdt_images/fdt_bedpost.gif
    doc/fdt_images/fdt_bedpost.tiff
    doc/fdt_images/fdt_bedpostx.gif
    doc/fdt_images/fdt_fa.gif
    doc/fdt_images/fdt_fa_big.png
    doc/fdt_images/fdt_gui.gif
    doc/fdt_images/fdt_gui.tiff
    doc/fdt_images/fdt_l1.gif
    doc/fdt_images/fdt_lines.gif
    doc/fdt_images/fdt_lines_subs.gif
    doc/fdt_images/fdt_probtrackx.gif
    doc/fdt_images/fdt_rgb.gif
    doc/fdt_images/fdt_rgb_subs.gif
    doc/fdt_images/fdt_seeds2targets_quant_eg.gif
    doc/fdt_images/fdt_seeds2targets_thal.gif
    doc/fdt_images/fdt_simple_tract3.gif
    doc/fdt_images/fdt_spherical_polars.gif
    doc/fdt_images/fdt_twomasks_tracts.gif
    doc/fdt_images/fdt_vecreg.gif
    doc/fdt_images/fdt_vectors.jpg
    doc/fdt_images/fdt_vectorsx.jpg
    doc/fdt_images/fdt_xfibres_axial.png
    doc/fdt_images/fdt_xfibres_coronal.png
    doc/fdt_images/fsl-bg.jpg
    doc/fdt_images/fsl-logo.jpg
    doc/fdt_images/fslview_dti.gif
    doc/fdt_images/fslview_x.gif
    doc/fdt_images/gui_intro.gif
    doc/fdt_images/gui_intro.tif
    doc/fdt_images/qboot.gif
    doc/fdt_pipeline.html
    doc/fdt_probtrackx.html
    doc/fdt_reg.html
    doc/fdt_surface.html
    doc/fdt_thresh.html
    doc/fdt_top.html
    doc/fdt_utils.html
    doc/fdt_vecreg.html
    doc/index.html
    nldtifit.cpp
    nldtifit.h
    rubix.cc
    rubix.h
    rubix_parallel.sh
    rubix_postproc.sh
    rubix_preproc.sh
    rubixoptions.cc
    rubixoptions.h
    rubixvox.cc
    rubixvox.h
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/* rubixoptions.h
Stam Sotiropoulos, FMRIB Image Analysis Group
Copyright (C) 2012 University of Oxford */
/* CCOPYRIGHT */
#if !defined(rubixptions_h)
#define rubixptions_h
#include <string>
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include <stdio.h>
#include "utils/options.h"
#include "utils/log.h"
#include "utils/tracer_plus.h"
//#include "newmatall.h"
using namespace Utilities;
namespace RUBIX{
class rubixOptions {
public:
static rubixOptions& getInstance();
~rubixOptions() { delete gopt; }
Option<bool> verbose;
Option<bool> help;
Option<string> logdir;
Option<bool> forcedir;
Option<string> LRdatafile;
Option<string> LRmaskfile;
Option<string> LRbvecsfile;
Option<string> LRbvalsfile;
Option<string> HRdatafile;
// Option<string> HRmaskfile;
Option<string> HRbvecsfile;
Option<string> HRbvalsfile;
Option<int> nfibres;
Option<int> nmodes; //number of modes in the orientation prior
Option<int> modelnum;
Option<int> PVmodelnum;
Option<float> fudge;
Option<int> njumps;
Option<int> nburn;
Option<int> sampleevery;
Option<int> updateproposalevery;
Option<int> seed;
Option<bool> no_ard;
Option<bool> all_ard;
Option<bool> kappa_ard;
Option<bool> fsumPrior;
Option<bool> dPrior;
Option<bool> rician;
Option<bool> noS0jump;
Option<string> LRgrad_file;
Option<string> HRgrad_file;
Option<float> R_prior_mean; //setting the prior for model's 3 ratio of perp. to parallel diffusivity
Option<float> R_prior_std;
Option<float> R_prior_fudge; //if used (set to a positive number), an ARD for R is used for the high diffusivity regions with the requested fudge factor
void parse_command_line(int argc, char** argv, Log& logger);
private:
rubixOptions();
const rubixOptions& operator=(rubixOptions&);
rubixOptions(rubixOptions&);
OptionParser options;
static rubixOptions* gopt;
};
inline rubixOptions& rubixOptions::getInstance(){
if(gopt == NULL)
gopt = new rubixOptions();
return *gopt;
}
inline rubixOptions::rubixOptions() :
verbose(string("-V,--verbose"), false,
string("switch on diagnostic messages"),
false, no_argument),
help(string("-h,--help"), false,
string("display this message"),
false, no_argument),
logdir(string("--ld,--logdir"), string("logdir"),
string("log directory (default is 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),
LRdatafile(string("--dLR"), string("data_LR"),
string("Low-Res data file"),
true, requires_argument),
LRmaskfile(string("--mLR"), string("nodif_brain_mask_LR"),
string("Low-Res mask file"),
true, requires_argument),
LRbvecsfile(string("--rLR"), string("bvecs_LR"),
string("Low-Res b vectors file"),
true, requires_argument),
LRbvalsfile(string("--bLR"), string("bvals_LR"),
string("Low-Res b values file"),
true, requires_argument),
HRdatafile(string("--dHR"), string("data_HR"),
string("High-Res data file"),
true, requires_argument),
// HRmaskfile(string("--mHR"), string("nodif_brain_mask_HR"),
// string("High-Res mask file"),
// true, requires_argument),
HRbvecsfile(string("--rHR"), string("bvecs_HR"),
string("High-Res b vectors file"),
true, requires_argument),
HRbvalsfile(string("--bHR"), string("bvals_HR"),
string("High-Res b values file"),
true, requires_argument),
nfibres(string("--nf,--nfibres"),1,
string("Maximum number of fibres to fit in each HR voxel (default 1)"),
false,requires_argument),
nmodes(string("--nM,--nmodes"),2,
string("Number of modes for the orientation prior (default 2)"),
false,requires_argument),
modelnum(string("--model"),1,
string("\tWhich deconvolution model to use. 1:With sticks (default), 2:With sticks and a range of diffusivities, 3:With zeppelins"),
false,requires_argument),
PVmodelnum(string("--pvmodel"),1,
string("\tWhich partial volume model to use. 1:Sum of attenuations (default), 2:Attenuation of sums"),
false,requires_argument),
fudge(string("--fudge"),1,
string("\tARD fudge factor"),
false,requires_argument),
njumps(string("--nj,--njumps"),1500,
string("Num of jumps to be made by MCMC (default is 1500)"),
false,requires_argument),
nburn(string("--bi,--burnin"),0,
string("Total num of jumps at start of MCMC to be discarded (default is 0)"),
false,requires_argument),
sampleevery(string("--se"),30,
string("\tNum of jumps for each sample (MCMC) (default is 30)"),
false,requires_argument),
updateproposalevery(string("--upe"),40,
string("\tNum of jumps for each update to the proposal density std (MCMC) (default is 40)"),
false,requires_argument),
seed(string("--seed"),8665904,string("\tseed for pseudo random number generator"),
false,requires_argument),
no_ard(string("--noard"),false,string("\tTurn ARD off on all fibres"),
false,no_argument),
all_ard(string("--allard"),false,string("Turn ARD on for all fibres (default: on for all but first)"),
false,no_argument),
kappa_ard(string("--ard_kappa"),false,string("Turn ARD on for the dispersion of all orientation prior modes (default: off)"),
false,no_argument),
fsumPrior(string("--fsumPrior"),false,string("Turn on prior for the fsums across an LR voxel (default: off)"),
false,no_argument),
dPrior(string("--dPrior"),false,string("Turn on prior for the diffusivity across an LR voxel (default: off)"),
false,no_argument),
rician(string("--rician"),false,string("Use Rician Noise model (default is Gaussian)"),
false,no_argument),
noS0jump(string("--noS0jump"),false,string("Do not jump S0 parameters and keep them to their ML estimates (default: off)"),
false,no_argument),
LRgrad_file(string("--gLR"), string("grad_devLR"),
string("\tLR Gradient Nonlinearity Tensor"),
false, requires_argument),
HRgrad_file(string("--gHR"), string("grad_devHR"),
string("\tHR Gradient Nonlinearity Tensor"),
false, requires_argument),
R_prior_mean(string("--Rmean"),0.13,string("\tSet the prior mean for R of model3 (default:0.13- Must be<0.5))"),false, requires_argument),
R_prior_std(string("--Rstd"),0.03,string("\tSet the prior standard deviation for R of model3 (default:0.03)"),false, requires_argument),
R_prior_fudge(string("--Rfudge"),0,string("If set(>0), an ARD prior is used for R with the requested fudge factor"),false, requires_argument),
options("RubiX v1.0", "rubix --help (for list of options)\n")
{
try {
options.add(verbose);
options.add(help);
options.add(logdir);
options.add(forcedir);
options.add(LRdatafile);
options.add(LRmaskfile);
options.add(LRbvecsfile);
options.add(LRbvalsfile);
options.add(HRdatafile);
//options.add(HRmaskfile);
options.add(HRbvecsfile);
options.add(HRbvalsfile);
options.add(nfibres);
options.add(nmodes);
options.add(modelnum);
options.add(PVmodelnum);
options.add(fudge);
options.add(njumps);
options.add(nburn);
options.add(sampleevery);
options.add(updateproposalevery);
options.add(seed);
options.add(no_ard);
options.add(all_ard);
options.add(kappa_ard);
options.add(fsumPrior);
options.add(dPrior);
options.add(rician);
options.add(noS0jump);
options.add(LRgrad_file);
options.add(HRgrad_file);
options.add(R_prior_mean);
options.add(R_prior_std);
options.add(R_prior_fudge);
}
catch(X_OptionError& e) {
options.usage();
cerr << endl << e.what() << endl;
}
catch(std::exception &e) {
cerr << e.what() << endl;
}
}
}
#endif
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