fsl_regfilt.cc

/*  fsl_regfilt - 

    Christian F. Beckmann, FMRIB Image Analysis Group

    Copyright (C) 2006-2011 University of Oxford / Christian F. Beckmann */
 
/*  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
    
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    University").
    
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    makes clear that no condition is made or to be implied, nor is any
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#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_regfilt (Version 1.2)")+
		string("\n\n Copyright(c) 2011, University of Oxford (Christian F. Beckmann)\n")+
		string(" Data de-noising by regressing out part of a design matrix\n")+
		string(" using simple OLS regression on 4D images");
  string examples="fsl_regfilt -i <input> -d <design> -f <component numbers or filter threshold> -o <out> [options]";

//Command line Options {
  Option<string> fnin(string("-i,--in"), string(""),
		string("        input file name (4D image)"),
		true, requires_argument);
  Option<string> fnout(string("-o,--out"), string(""),
		string("output file name for the filtered data"),
		true, requires_argument);
  Option<string> fndesign(string("-d,--design"), string(""),
		string("file name of the matrix with time courses (e.g. GLM design or MELODIC mixing matrix)"),
		true, requires_argument);
  Option<string> fnmask(string("-m,--mask"), string(""),
		string("mask image file name"),
		false, requires_argument);		
   Option<string> filter(string("-f,--filter"),string(""),
		string("filter out part of the regression model, e.g. -f \"1,2,3\" "),
		false, requires_argument);
	Option<bool> freqfilt(string("-F,--freqfilt"),false,
		string("filter out components based on high vs. low frequency content "),
		false, no_argument);
	Option<bool> freq_ic(string("--freq_ic"),true,
		string("switch off IC Z-stats filtering as part of frequency filtering"),
		false, no_argument);		
	Option<float> freq_ic_smooth(string("--freq_ic_smooth"),5.0,
		string("smoothing width for IC Z-stats filtering as part of frequency filtering"),
		false, no_argument);		
	Option<float> freqthresh(string("--fthresh"),0.15,
		string("frequency threshold ratio - default: 0.15"),
		false,requires_argument);		
	Option<float> freqthresh2(string("--fthresh2"),0.02,
		string("frequency filter score threshold - default: 0.02"),
		false,requires_argument);		
	Option<bool> verbose(string("-v"),FALSE,
		string("        switch on diagnostic messages"),
		false, no_argument);
	Option<bool> aggressive(string("-a"),FALSE,
		string("        switch on aggressive filtering (full instead of partial regression)"),
		false, no_argument);
	Option<bool> perfvn(string("--vn"),FALSE,
		string("        perfrom variance-normalisation on 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("switch on debug messages"),
		false,no_argument,false);
	// Output options	
	Option<string> outdata(string("--out_data"),string(""),
		string("output file name for pre-processed data (prior to denoising)"),
		false, requires_argument);
	Option<string> outmix(string("--out_mix"),string(""),
		string("output file name for new mixing matrix"),
		false, requires_argument);
	Option<string> outvnscales(string("--out_vnscales"),string(""),
		string("output file name for scaling factors from variance normalisation"),
		false, requires_argument);
		/*
}
*/
//Globals {
	int voxels = 0;
	float TR;
	Matrix data;
	Matrix design;
	Matrix fdesign;
	Matrix meanR, meanC;
	Matrix newData, newMix;
	RowVector vnscales;
	volume<float> mask;
	volume<float> Mean;
	vector<int> comps, ind;
	vector<int>::iterator it;
	  /*
}
*/
////////////////////////////////////////////////////////////////////////////

// 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
		write_ascii_matrix(what,fname);
}

Matrix smooth_map(Matrix what, float howmuch){
	volume4D<float> tempVol;
	tempVol.setmatrix(what,mask);
    tempVol= smooth(tempVol,howmuch);
	Matrix out;
	out = tempVol.matrix(mask);
	return out;
}

int parse_filterstring(){
	int ctr=0;    
	char *p;
	char t[1024];
	const char *discard = ", [];{(})abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ~!@#$%^&*_-=+|\':><./?";

	strcpy(t, filter.value().c_str());
	p=strtok(t,discard);
	ctr = atoi(p);
	if(ctr>0 && ctr<=design.Ncols())
		comps.push_back(ctr);
	do{
	  	p=strtok(NULL,discard);
	  	if(p){
			ctr = atoi(p);
	    	if(ctr>0 && ctr<=design.Ncols())
				comps.push_back(ctr);
	    }
	}while(p);
	return 0;
}

int calc_freqindex(){
	if(debug.value()) cerr << " In calc_freqindex " << endl;
	
	fdesign = Melodic::calc_FFT(design);
	if(debug.value()) cerr << " fdesign: " << fdesign.Nrows() << " x " << fdesign.Ncols() << endl;	
	
	int Nps = fdesign.Nrows();
	float MAXf = 1/(2*TR);
	float Nthresh = ceil(Nps * freqthresh.value()/MAXf);	
	if(debug.value()) cerr << " Nps: " << Nps << " MAXf: " << MAXf << " Nthresh: " << Nthresh << endl;	
	
	Matrix sum_ratio;	
	sum_ratio = SP(sum(fdesign.Rows(1,Nthresh),1),pow(sum(sum(fdesign.Rows(Nthresh+1,Nps))),-1));
	sum_ratio /= (float)sum_ratio.MaximumAbsoluteValue();
	if(debug.value()) cerr << " sum_ratio: " << sum_ratio << endl;		

	if(freq_ic.value()){		
		Matrix scores = zeros(1,design.Ncols());
		{
			Matrix ICs, noisestddev, stdNoisei,unmixMatrix;
	
			unmixMatrix = pinv(design);
			ICs = unmixMatrix * data;
			noisestddev = stdev(data-design*ICs);	
			stdNoisei = pow(noisestddev*
				std::sqrt((float)(data.Nrows()-1))/
				std::sqrt((float)(data.Nrows()-ICs.Nrows())),-1);
			
			ColumnVector diagvals;
			diagvals = pow(diag( unmixMatrix*unmixMatrix.t()),-0.5);
			
			ICs=smooth_map(SP(ICs,diagvals*stdNoisei),freq_ic_smooth.value());
			ICs= SP(ICs,ones(ICs.Nrows(),1)*meanR);
			volume4D<float> tempVol;
			tempVol.setmatrix(ICs,mask);
			tempVol.threshold(0.0);
			for(int ctr = 0; ctr < design.Ncols(); ctr++ )
				scores(1,ctr+1) = tempVol[ctr].percentile(0.99,mask);
			scores/=scores.MaximumAbsoluteValue();
			scores-=scores.MinimumAbsoluteValue();
			if(debug.value()) cerr << " initial scores: " << scores << endl;
		}
		scores = SP(scores,sum_ratio);
		scores /= scores.Maximum();
		if(debug.value()) cerr << " scores: " << scores << endl;
		for(int ctr = 1; ctr <= design.Ncols(); ctr++ )
			if(scores(1,ctr) < freqthresh2.value())	
			comps.push_back(ctr);
	}	
	return 0;
}

int get_comp(){
	if(filter.value().length()>0 && parse_filterstring())
		return 1;

	if(freqfilt.value() && calc_freqindex())
		return 1;
		
	//sort and remove duplicates 
	sort (comps.begin(), comps.end());
	it = unique (comps.begin(), comps.end());
	comps.resize( it - comps.begin() );
	
	if(debug.value()){
		for (it=comps.begin(); it!=comps.end(); ++it)
	    	cout << " " << *it;
	  	cout << endl; 
	}
	
	return 0;
}

int dofilter(){

	if(verbose.value())
		cout << "  Calculating maps " << endl;  

  	Matrix unmixMatrix = pinv(design);
  	Matrix maps = unmixMatrix * data;

	Matrix noisedes;
 	Matrix noisemaps;

   	noisedes = design.Column(comps.at(0));
    noisemaps  = maps.Row(comps.at(0)).t();    
 	
  	for(int ctr = 1; ctr < (int)comps.size();++ctr){
    	noisedes  |= design.Column(comps.at(ctr));
  		noisemaps |= maps.Row(comps.at(ctr)).t();
	}
	if(debug.value()) cerr << " noisedes " << noisedes.Nrows() << " x " << noisedes.Ncols() << endl;	

	if(verbose.value())
		cout << "  Calculating filtered data " << endl;

  	if(aggressive.value())
		newData = data - noisedes * (pinv(noisedes)*data);
	else
		newData = data - noisedes * noisemaps.t();
		
	if(perfvn.value())
		newData = SP(newData,ones(newData.Nrows(),1)*vnscales);	
  	newData = newData + ones(newData.Nrows(),1)*meanR;

	for(int ctr = 1; ctr <= design.Ncols();++ctr)
		ind.push_back(ctr);
	for(int ctr = 0; ctr < (int)comps.size();++ctr)
		it=remove(ind.begin(),ind.end(),comps.at(ctr));
	ind.resize(design.Ncols()-comps.size());
	if(debug.value()){
		for (it=ind.begin(); it!=ind.end(); ++it)
	    	cout << " " << *it;
	  	cout << endl; 
	}	
	
	if(ind.size()>0){
		newMix=design.Column(ind.at(0));
		for(int ctr = 1; ctr < (int)ind.size();++ctr)
			newMix |= design.Column(ind.at(ctr));
		newMix = newMix - noisedes * (pinv(noisedes)*newMix);
		
		if(debug.value())
			cerr << " newMix " << newMix.Nrows() << " x " << newMix.Ncols() << endl;
	}
		
  	return 0;	
}

int setup(){
	if(fsl_imageexists(fnin.value())){//read data
		//input is 3D/4D vol
		volume4D<float> tmpdata;
		read_volume4D(tmpdata,fnin.value());
		TR=tmpdata.TR();
		
		// create mask
		if(fnmask.value()>""){
			read_volume(mask,fnmask.value());
			if(!samesize(tmpdata[0],mask)){
				cerr << "ERROR: Mask image does not match input image" << endl;
				return 1;
			};
		}else{
			if(verbose.value())
				cout << "  Creating mask image "  << endl;
			Mean = meanvol(tmpdata);
			float Mmin, Mmax;
			Mmin = Mean.min(); Mmax = Mean.max();
			mask = binarise(Mean,float(Mmin + 0.01* (Mmax-Mmin)),Mmax);
		}
		
		data = tmpdata.matrix(mask);
		voxels = data.Ncols();
		if(verbose.value())
			cout << " Data matrix size : " << data.Nrows() << " x " << voxels << endl;
		
	}else{
		cerr << "ERROR: cannot read input image " << fnin.value()<<endl;
		return 1;
	}
	
	design = read_ascii_matrix(fndesign.value());

	if(!isimage(data)){
		cerr << "ERROR: need to specify 4D input to use filtering" << endl;
		return 1;
	}
	
	meanR=mean(data,1);
	data = remmean(data,1);
	meanC=mean(design,1);
	design = remmean(design,1);
	if(perfvn.value())
		vnscales = Melodic::varnorm(data);
		
	if(debug.value()) cerr << " data: " << data.Nrows() << " x " << data.Ncols() << endl;	
    if(debug.value()) cerr << " design: " << design.Nrows() << " x " << design.Ncols() << endl;	
				
	return 0;	
}

void write_res(){	
	saveit(newData,fnout.value());
	if(outdata.value()>"")
		saveit(data,outdata.value());
	if(outvnscales.value()>"")
		saveit(vnscales,outvnscales.value());
	if(outmix.value()>"" && newMix.Storage()>0)
		saveit(newMix,outmix.value());
}

int do_work(int argc, char* argv[]) {
  	if(setup())
		exit(1);
	if(get_comp())
		exit(1);
	if(dofilter())
		exit(1);	
	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(fnmask);
			options.add(filter);
			options.add(freqfilt);
			options.add(freq_ic);
			options.add(freq_ic_smooth);
			options.add(freqthresh);
			options.add(freqthresh2);
			options.add(perfvn);
			options.add(verbose);
			options.add(aggressive);
			options.add(help);
			options.add(debug);
			options.add(outdata);
			options.add(outmix);
			options.add(outvnscales);
	    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;
	  } 
}