probtrackx.cc

/*  Copyright (C) 2004 University of Oxford  */

/*  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


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 University").

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 Software or the sale of any products based on the Software.

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 You are not permitted under this Licence to use this Software
 commercially. Use for which any financial return is received shall be
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#include <iostream>
#include <fstream>
#include "newimage/newimageall.h"
#include "utils/log.h"
#include "probtrackx.h"
#include "utils/tracer_plus.h"
#include "stdlib.h"

using namespace std;
using namespace NEWIMAGE;
using namespace Utilities;
using namespace TRACT;

int main(int argc, char **argv) {

	//Tracer_Plus::settimingon();

	probtrackxOptions& opts = probtrackxOptions::getInstance();
	Log& logger = LogSingleton::getInstance();
	opts.parse_command_line(argc, argv, logger);
	srand(opts.rseed.value());

	if (opts.verbose.value() > 0) {
		opts.status();
	}

	//Check the correct use of matrices
	if (opts.matrix2out.value() && opts.lrmask.value() == "") {
		cerr
				<< "Error: --target2 must be specified when --omatrix2 is requested"
				<< endl;
		exit(1);
	}

	if (opts.matrix3out.value() && opts.mask3.value() == "") {
		cerr
				<< "Error: --target3 (or --target3 and --lrtarget3) must be specified when --omatrix3 is requested"
				<< endl;
		exit(1);
	}

	if (opts.matrix4out.value() && opts.dtimask.value() == "") {
		cerr
				<< "Error: --target4 (or --target4 and --colmask4) must be specified when --omatrix4 is requested"
				<< endl;
		exit(1);
	}

	if (opts.simple.value()) {
		if (opts.matrix1out.value() || opts.matrix3out.value()) {
			cerr << "Error: cannot use matrix1 and matrix3 in simple mode"
					<< endl;
			exit(1);
		}
		cout << "Running in simple mode" << endl;
		track();
	} else {

		// KE
		// if want to force beginning direction, check that
		// angle, inner, and outer surfaces are supplied
		if (opts.forceangle.value()) {
			if (opts.initdir.value() == "" || opts.innersurf.value() == "" || opts.outersurf.value() == "") {
				cerr << "Error: initdir, innersurf, and outersurf flags must ALL be provided." << endl;
				exit(1);
			}
		}

		if (opts.matrix5out.value() && opts.matrix5_mask.value() == "") {
			cerr << "Error: --matrix1.5 and --matrix1.5_mask must both be supplied." << endl;
			exit(1);
		}

		/*
		 * End KE
		 */

		if (!opts.network.value()) {
			cout << "Running in seedmask mode" << endl;
			seedmask();
		} else {
			cout << "Running in network mode" << endl;
			nmasks();
		}
	}


	//Tracer_Plus::dump_times(logger.getDir());

	return 0;
}