fsl_glm.cc

/*  fsl_glm - 

    Christian F. Beckmann, FMRIB Image Analysis Group

    Copyright (C) 2006-2008 University of Oxford  */

/*  CCOPYRIGHT  */

#include "libvis/miscplot.h"
#include "miscmaths/miscmaths.h"
#include "miscmaths/miscprob.h"
#include "utils/options.h"
#include <vector>
#include "newimage/newimageall.h"
#include "melhlprfns.h"

using namespace MISCPLOT;
using namespace MISCMATHS;
using namespace Utilities;
using namespace std;

// The two strings below specify the title and example usage that is
// printed out as the help or usage message

  string title=string("fsl_glm")+
		string("\nCopyright(c) 2004-2009, University of Oxford (Christian F. Beckmann)\n")+
    string(" \n Simple GLM allowing temporal or spatial regression on either text data or images\n");
  string examples="fsl_glm -i <input> -d <design> -o <output> [options]";

//Command line Options {
  Option<string> fnin(string("-i,--in"), string(""),
		string("        input file name (text matrix or 3D/4D image file)"),
		true, requires_argument);
  Option<string> fnout(string("-o,--out"), string(""),
		string("output file name for GLM parameter estimates (GLM betas)"),
		false, requires_argument);
  Option<string> fndesign(string("-d,--design"), string(""),
		string("file name of the GLM design matrix (text time courses for temporal regression or an image file for spatial regression )"),
		false, requires_argument);
  Option<string> fnmask(string("-m,--mask"), string(""),
		string("mask image file name if input is image"),
		false, requires_argument);
  Option<string> fncontrasts(string("-c,--contrasts"), string(""),
		string("matrix of t-statistics contrasts"),
		false, requires_argument);
  Option<string> fnftest(string("-f,--ftests"), string(""),
		string("matrix of F-tests on contrasts"),
		false, requires_argument,false);
	Option<int> dofset(string("--dof"),-1,
		string("        set degrees-of-freedom explicitly"),
		false, requires_argument);
	Option<bool> normdes(string("--des_norm"),FALSE,
		string("switch on normalisation of the design matrix columns to unit std. deviation"),
		false, no_argument);
	Option<bool> normdat(string("--dat_norm"),FALSE,
		string("switch on normalisation of the data time series to unit std. deviation"),
		false, no_argument);
	Option<bool> perfvn(string("--vn"),FALSE,
		string("        perform MELODIC variance-normalisation on data"),
		false, no_argument);
	Option<bool> perf_demean(string("--demean"),FALSE,
		string("switch on de-meaning of design and data"),
		false, no_argument);
	Option<int> help(string("-h,--help"), 0,
		string("display this help text"),
		false,no_argument);
	Option<bool> debug(string("--debug"), FALSE,
		string("display debug information"),
		false,no_argument,false);
	// Output options	
	Option<string> outcope(string("--out_cope"),string(""),
		string("output file name for COPEs (either as text file or image)"),
		false, requires_argument);
	Option<string> outz(string("--out_z"),string(""),
		string("        output file name for Z-stats (either as text file or image)"),
		false, requires_argument);
	Option<string> outt(string("--out_t"),string(""),
		string("        output file name for t-stats (either as text file or image)"),
		false, requires_argument);
	Option<string> outp(string("--out_p"),string(""),
		string("        output file name for p-values of Z-stats (either as text file or image)"),
		false, requires_argument);
	Option<string> outf(string("--out_f"),string(""),
		string("        output file name for F-value of full model fit"),
		false, requires_argument);
	Option<string> outpf(string("--out_pf"),string(""),
		string("output file name for p-value for full model fit"),
		false, requires_argument);
	Option<string> outres(string("--out_res"),string(""),
		string("output file name for residuals"),
		false, requires_argument);
	Option<string> outvarcb(string("--out_varcb"),string(""),
		string("output file name for variance of COPEs"),
		false, requires_argument);
	Option<string> outsigsq(string("--out_sigsq"),string(""),
		string("output file name for residual noise variance sigma-square"),
		false, requires_argument);
	Option<string> outdata(string("--out_data"),string(""),
		string("output file name for pre-processed data"),
		false, requires_argument);
	Option<string> outvnscales(string("--out_vnscales"),string(""),
		string("output file name for scaling factors for variance normalisation"),
		false, requires_argument);
        Option<vector<string> > textConfounds(string("--vxt"), vector<string>(), 
         string("\tlist of text files containing text matrix confounds. caution BETA option."), 
         false, requires_argument);
        Option<vector<string> > voxelwiseConfounds(string("--vxf"), vector<string>(), 
         string("\tlist of 4D images containing voxelwise confounds. caution BETA option."), 
         false, requires_argument);
		/*
}
*/
//Globals 
	Melodic::basicGLM glm;
	int voxels = 0;
	Matrix data;
	Matrix design;
	Matrix contrasts;
	Matrix fcontrasts;
	Matrix meanR;
	RowVector vnscales;
	volume<float> mask;  

////////////////////////////////////////////////////////////////////////////

// Local functions
void save4D(Matrix what, string fname){
		if(what.Ncols()==data.Ncols()||what.Nrows()==data.Nrows()){
			volume4D<float> tempVol;
			if(what.Nrows()>what.Ncols())
				tempVol.setmatrix(what.t(),mask);
			else
				tempVol.setmatrix(what,mask);
			save_volume4D(tempVol,fname);
		}
}

bool isimage(Matrix what){
	if((voxels > 0)&&(what.Ncols()==voxels || what.Nrows()==voxels))
		return TRUE;
	else
		return FALSE;
}

void saveit(Matrix what, string fname){
	if(isimage(what))
		save4D(what,fname);
	else if(fsl_imageexists(fndesign.value()))
		write_ascii_matrix(what.t(),fname);
	else
		write_ascii_matrix(what,fname);
}

int setup(int &dof){
	if(fsl_imageexists(fnin.value())){//read data
		//input is 3D/4D vol
		volume4D<float> tmpdata;
		read_volume4D(tmpdata,fnin.value());
		
		// create mask
		if(fnmask.value()>""){
			if(debug.value())
				cout << "Reading mask file " << fnmask.value() << endl;
			read_volume(mask,fnmask.value());
			if(!samesize(tmpdata[0],mask)){
				cerr << "ERROR: Mask image does not match input image" << endl;
				return 1;
 			};
		}else{
			if(debug.value())
				cout << "Creating mask image" << endl;
			mask=tmpdata[0]*0.0+1.0;
			data=tmpdata.matrix(mask);
			Melodic::update_mask(mask,data);
		}	
		data = tmpdata.matrix(mask);
		voxels = data.Ncols();
			
		if(perfvn.value()){
			if(debug.value())
				cout << "Perform MELODIC variance normalisation (and demeaning)" << endl;			
			data = remmean(data,1);
			vnscales = Melodic::varnorm(data);		
		}
	}
	else
	data = read_ascii_matrix(fnin.value());	

	if(fsl_imageexists(fndesign.value())){//read design
		if(debug.value())
			cout << "Reading design file "<< fndesign.value()<< endl;
		volume4D<float> tmpdata;
		read_volume4D(tmpdata,fndesign.value());
		if(!samesize(tmpdata[0],mask)){
			cerr << "ERROR: GLM design does not match input image in size" << endl;
			return 1;
		}
		if(debug.value())
			cout << "Transposing data" << endl;
		design = tmpdata.matrix(mask).t();
		data = data.t();
	}else{
		design = read_ascii_matrix(fndesign.value());
	}

	if (perf_demean.value() ) {
		if(debug.value())
			cout << "De-meaning the data matrix" << endl;
		data = remmean(data,1);
	}

	dof=ols_dof(design);
	Matrix baseConfounds;

	if ( textConfounds.set() ) {
	  baseConfounds=read_ascii_matrix( textConfounds.value().at(0) );
	  for(unsigned int i=1; i< textConfounds.value().size(); i++) 
		baseConfounds|=read_ascii_matrix( textConfounds.value().at(i) );
	  dof-=textConfounds.value().size();
	  if ( !voxelwiseConfounds.set() )
	    data=(IdentityMatrix(baseConfounds.Nrows())-baseConfounds*pinv(baseConfounds))*data;
	    }

	if ( voxelwiseConfounds.set() ) {
	  vector<Matrix> confounds;
	  confounds.resize(voxelwiseConfounds.value().size());
	  volume4D<float> input;
	  for(unsigned int i=0; i< confounds.size(); i++) {
	    read_volume4D(input,voxelwiseConfounds.value().at(i));
	    if ( mask.nvoxels() )	  
	      confounds.at(i)=input.matrix(mask);
	    else
	    confounds.at(i)=input.matrix();
	  }
	  for(int voxel=1;voxel<=data.Ncols();voxel++) {
	    Matrix confound(confounds.at(0).Column(voxel) );
	    for(unsigned int i=1; i< confounds.size(); i++) 
	    confound|=confounds.at(i).Column(voxel);
	    if ( textConfounds.set() )
	      confound=baseConfounds | confound;
	    data.Column(voxel)=(IdentityMatrix(confound.Nrows())-confound*pinv(confound))*data.Column(voxel);	  
	  }
	  dof-=confounds.size();
	}

	if(normdat.value()){
		if(debug.value())
			cout << "Normalising data matrix to unit std-deviation" << endl;
		data =  SP(data,ones(data.Nrows(),1)*pow(stdev(data,1),-1));
	}

	meanR=mean(data,1);

	if(perf_demean.value()){
		if(debug.value())
			cout << "De-meaning design matrix" << endl;	
		design = remmean(design,1);
		dof-=1;
	}

	if(normdes.value()){
		if(debug.value())
			cout << "Normalising design matrix to unit std-deviation" << endl;
		design =  SP(design,ones(design.Nrows(),1)*pow(stdev(design,1),-1));
	}
	if(fncontrasts.value()>""){//read contrast		
		contrasts = read_ascii_matrix(fncontrasts.value());
		if(!(contrasts.Ncols()==design.Ncols())){
			cerr << "ERROR: contrast matrix GLM design does not match GLM design" << endl;
			return 1;
		}
	}else{
		contrasts = IdentityMatrix(design.Ncols());
		contrasts &= -1.0 * contrasts;
	}
	return 0;	
}

void write_res(){	
	if(fnout.value()>"")
		saveit(glm.get_beta(),fnout.value());
	if(outcope.value()>"")
		saveit(glm.get_cbeta(),outcope.value());
	if(outz.value()>"")
		saveit(glm.get_z(),outz.value());
	if(outt.value()>"")
		saveit(glm.get_t(),outt.value());
	if(outp.value()>"")
		saveit(glm.get_p(),outp.value());
	if(outf.value()>"")
		saveit(glm.get_f_fmf(),outf.value());
	if(outpf.value()>"")
		saveit(glm.get_pf_fmf(),outpf.value());
	if(outres.value()>"")
		saveit(glm.get_residu(),outres.value());
	if(outvarcb.value()>"")
		saveit(glm.get_varcb(),outvarcb.value());
	if(outsigsq.value()>"")
		saveit(glm.get_sigsq(),outsigsq.value());
	if(outdata.value()>"")
		saveit(data,outdata.value());
	if(outvnscales.value()>"")
		saveit(vnscales,outvnscales.value());
}

int do_work(int argc, char* argv[]) {
  int dof(-1);
  if(setup(dof))
    exit(1);
  glm.olsfit(data,design,contrasts,dof);
  write_res();
  return 0;
}

////////////////////////////////////////////////////////////////////////////

int main(int argc,char *argv[]){
	  Tracer tr("main");
	  OptionParser options(title, examples);
	  try{
	    // must include all wanted options here (the order determines how
	    //  the help message is printed)
			options.add(fnin);
			options.add(fnout);
			options.add(fndesign);
			options.add(fncontrasts);
			options.add(fnmask);
			options.add(fnftest);
			options.add(dofset);
			options.add(normdes);
			options.add(normdat);
			options.add(perfvn);
			options.add(perf_demean);
			options.add(help);
			options.add(debug);
			options.add(outcope);
			options.add(outz);
			options.add(outt);
			options.add(outp);
			options.add(outf);
			options.add(outpf);
			options.add(outres);
			options.add(outvarcb);
			options.add(outsigsq);
			options.add(outdata);
			options.add(outvnscales);
			options.add(textConfounds);
			options.add(voxelwiseConfounds);
	    options.parse_command_line(argc, argv);

	    // line below stops the program if the help was requested or 
	    //  a compulsory option was not set
	    if ( (help.value()) || (!options.check_compulsory_arguments(true)) ){
				options.usage();
				exit(EXIT_FAILURE);
	    }else{
	  		// Call the local functions
	  		return do_work(argc,argv);
			}
		}catch(X_OptionError& e) {
			options.usage();
	  	cerr << endl << e.what() << endl;
	    exit(EXIT_FAILURE);
	  }catch(std::exception &e) {
	    cerr << e.what() << endl;
	  } 
	}