/*  run_mesh_utils.cc
    Brian Patenaude and Mark Jenkinson
    Copyright (C) 2006-2009 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
    
    
    LICENCE
    
    FMRIB Software Library, Release 5.0 (c) 2012, The University of
    Oxford (the "Software")
    
    The Software remains the property of the University of Oxford ("the
    University").
    
    The Software is distributed "AS IS" under this Licence solely for
    non-commercial use in the hope that it will be useful, but in order
    that the University as a charitable foundation protects its assets for
    the benefit of its educational and research purposes, the University
    makes clear that no condition is made or to be implied, nor is any
    warranty given or to be implied, as to the accuracy of the Software,
    or that it will be suitable for any particular purpose or for use
    under any specific conditions. Furthermore, the University disclaims
    all responsibility for the use which is made of the Software. It
    further disclaims any liability for the outcomes arising from using
    the Software.
    
    The Licensee agrees to indemnify the University and hold the
    University harmless from and against any and all claims, damages and
    liabilities asserted by third parties (including claims for
    negligence) which arise directly or indirectly from the use of the
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    No part of the Software may be reproduced, modified, transmitted or
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    the University is not required if the said reproduction, modification,
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    conditions of this Licence are imposed upon the receiver of the
    product, and all original and amended source code is included in any
    transmitted product. You may be held legally responsible for any
    copyright infringement that is caused or encouraged by your failure to
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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
    defined as commercial use, and includes (1) integration of all or part
    of the source code or the Software into a product for sale or license
    by or on behalf of Licensee to third parties or (2) use of the
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    (3) use of the Software or any derivative of it for research with the
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//#include <math.h>
#include <iostream>
#include <string>
#include <sstream>

#include <fstream>
#include <stdio.h>
#include <cmath>
#include <algorithm>
#include "math.h"


#include "miscmaths/f2z.h"
#include "libprob.h"


#include "meshUtils.h"
#include "first_lib/first_mesh.h"
#include "first_lib/first_newmat_vec.h"

#include "fslvtkio/fslvtkio.h"
// #include "shapeModel/shapeModel.h"
#include "miscmaths/miscprob.h"
#include "utils/options.h"
#include "newimage/newimageall.h"
#include "meshclass/meshclass.h"
#include "warpfns/fnirt_file_reader.h"
#include "basisfield/basisfield.h"
#include "MVdisc/MVdisc.h"
#include "shapeModel/shapeModel.h"

using namespace std;
using namespace NEWIMAGE;
using namespace MISCMATHS;
using namespace SHAPE_MODEL_NAME;
using namespace Utilities;
using namespace mesh;
using namespace fslvtkio;
using namespace meshutils;
// using namespace SHAPE_MODEL_NAME;
using namespace FIRST_LIB;
using namespace mvdisc;
string title="run_mesh_utils\nCopyright(c) 2009, University of Oxford (Brian Patenaude)";
string examples="run_mesh_utils [options] ";


Option<bool> verbose(string("-v,--verbose"), false, 
		     string("switch on diagnostic messages"), 
		     false, no_argument);
Option<bool> help(string("-h,--help"), false,
		  string("display this message"),
		  false, no_argument);
Option<bool> sampNN(string("--sampNN,--help"), false,
		    string("display this message"),
		    false, no_argument);
		  

Option<bool> toggle(string("--toggle,--toggle"), false,
		    string("toggle a feature"),
		    false, no_argument);
		  
		  
Option<int> myindex(string("-a,--myindex"), 0,
		    string("degrees of freedom"),
		    false, requires_argument);			  
Option<int> dof(string("-d,--dof"), 6,
		string("degrees of freedom (for fsl4.1.2 or before)"),
		false, requires_argument);
Option<int> dof2(string("-e,--dof2"), 6,
		 string("degrees of freedom2 (for fsl4.1.2 or before)"),
		 false, requires_argument);	
Option<string> inname(string("-i,--in"), string(""),
		      string("filename of input image"),
		      false, requires_argument);
Option<string> flirtmatname(string("-f"), string(""),
			    string("filename of flirt matrix"),
			    false, requires_argument);
Option<string> inname2(string("-j"), string(""),
		       string("filename ofsecond input image"),
		       false, requires_argument);		  


Option<int> label(string("-l,--label"),1,
		  string("mesh label"),
		  false, requires_argument);

Option<string> inmeshname(string("-m"), string(""),
			  string("filename of base mesh"),
			  true, requires_argument);
Option<string> inmeshname2(string("-n"), string(""),
			   string("filename of base mesh2"),
			   false, requires_argument);

Option<string> outname(string("-o,--out"), string(""),
		       string("filename of output image"),
		       true, requires_argument);

Option<float> thresh(string("-t,--thresh"), 0,
		     string("threshold"),
		     false, requires_argument);	

Option<float> shiftx(string("-x,--xshift"), 0,
		     string("filename of input image"),
		     false, requires_argument);
Option<float> shifty(string("-y,--yshift"), 0,
		     string("filename of input image"),
		     false, requires_argument);
Option<float> shiftz(string("-z,--zshift"), 0,
		     string("filename of input image"),
		     false, requires_argument);			  

Option<float> w_im(string("-p,--w_im"), 0.175,
		   string("weighting image force"),
		   false, requires_argument);		

Option<float> w_tan(string("-r,--w_tan"), 0,
		    string("weighting image force"),
		    false, requires_argument);		
					 
Option<float> w_tri(string("-q,--w_tri"), 0.01,
		    string("weighting image force"),
		    false, requires_argument);		
					 
Option<float> w_norm(string("-s,--w_norm"), 0,
		     string("weighting image force"),
		     false, requires_argument);		


Option<bool>  fullLDAoutput(string("--fullLDAoutput"), false,
			 string("output full classification information"),
			 false, no_argument);	

Option<bool> doMeshReg(string("--doMeshReg,--meshreg"), false,
		       string("display this message"),
		       false, no_argument);
Option<bool> doFillMesh(string("--doFillMesh,--fillmesh"), false,
			string("display this message"),
			false, no_argument);
Option<bool> doMeshToContours(string("--doMeshToContours,--meshToCont"), false,
			      string("convert mesh to a series of 2D contours"),
			      false, no_argument);
Option<bool> doCombineMeshes(string("--doCombineMeshes,--combMeshes"), false,
			     string("combine mesh results including vectors and scalars"),
			     false, no_argument);
Option<bool> doUnCentreMesh(string("--doUnCentreMesh,doUnCentreMesh"), false,
			    string("remove centre form ASCII vtk mesh (remove old IBIM format)"),
			    false, no_argument);
Option<bool>  doLabelAndCombineSB(string("--doLabelAndCombineSB, doLabelAndCombineSB"), false,
				  string("label shared vertices and combine meshes"),
				  false, no_argument);			  
							
Option<bool>  doAddMeshes(string("--doAddMeshes, doAddMeshes"), false,
			       string("doAddMeshes"),
			       false, no_argument);							  
								
Option<bool>  doSubtractMeshes(string("--doSubtractMeshes, doSubtractMeshes"), false,
			       string("doSubtractMeshes"),
			       false, no_argument);							  
								
Option<bool>  doAppendSBmask(string("--doAppendSBmask, doAppendSBmask"), false,
			     string("doAppendSBmask"),
			     false, no_argument);							    
			
Option<bool>  doAlterVertsBySBmask(string("--doAlterVertsBySBmask, doAlterVertsBySBmask"), false,
				   string("doAlterVertsBySBmask"),
				   false, no_argument);							 	  	
	
Option<bool>  doAppendIndexedSBmask(string("--doAppendIndexedSBmask, doAppendIndexedSBmask"), false,
				    string("doAppendIndexedSBmask"),
				    false, no_argument);	
		  
Option<bool>  useSc2(string("--useSc2, useSc2"), false,
		     string("useSc2"),
		     false, no_argument);	
		  
Option<bool>  inverse(string("--inverse, inverse"), false,
		      string("inverse"),
		      false, no_argument);	 
		  
		  		  
Option<bool>  doWarpMesh(string("--doWarpMesh,  doWarpMesh"), false,
			 string(" doWarpMesh"),
			 false, no_argument);	
		  
Option<bool>  doApplyFlirtThenSBmask(string("--doApplyFlirtThenSBmask, doApplyFlirtThenSBmask"), false,
				     string("doApplyFlirtThenSBmask"),
				     false, no_argument);		
Option<bool>  doSurfDistMap(string("--doSurfDistMap,  doSurfDistMap"), false,
			    string("doSurfDistMap"),
			    false, no_argument);	
		  
Option<bool>  doSurfMeanAndStDev(string("--doSurfMeanAndStDev,  doSurfMeanAndStDev"), false,
				 string("doSurfMeanAndStDev"),
				 false, no_argument);	
		  
Option<bool>  doLQSurfReg(string("--doLQSurfReg,  doLQSurfReg"), false,
			  string("doLQSurfReg"),
			  false, no_argument);												  
				
Option<bool>  doCartToSphere(string("--doCartToSphere,  doCartToSphere"), false,
			     string("doCartToSphere"),
			     false, no_argument);
				
Option<bool>  doSphereToCart(string("--doSphereToCart,  doSphereToCart"), false,
			     string("doSphereToCart"),
			     false, no_argument);		
		  	
Option<bool> doFindMidMidPoint(string("--doFindMidMidPoint, doFindMidMidPoint"), false,
			       string("doFindMidMidPoint"),
			       false, no_argument);			
				
Option<bool> doWarpGrid(string("--doWarpGrid, doWarpGrid"), false,
			string("doWarpGrid"),
			false, no_argument);		
Option<bool> doSampleGrid(string("--doSampleGrid, doSampleGrid"), false,
			  string("doSampleGrid"),
			  false, no_argument);
Option<bool> doSampleMesh(string("--doSampleMesh, doSampleMesh"), false,
			  string("doSampleMesh"),
			  false, no_argument);

Option<bool> doRandMesh(string("--doRandMesh, doRandMesh"), false,
			string("doRandMesh"),
			false, no_argument);								
					
Option<bool> doMeshToBvars(string("--doMeshToBvars, doMeshToBvars"), false,
			   string("doMeshToBvars"),
			   false, no_argument);	
										
Option<bool> doAddModesUsingScalars(string("--doAddModesUsingScalars, doAddModesUsingScalars"), false,
				    string("doAddModesUsingScalars"),
				    false, no_argument);	
				
Option<bool> doRandMatrices(string("--doRandMatrices, doRandMatrices"), false,
			    string("doRandMatrices"),
			    false, no_argument);	
				
Option<bool> doWriteConditionalIntensity(string("--doWriteConditionalIntensity, doWriteConditionalIntensity"), false,
					 string("doWriteConditionalIntensity"),
					 false, no_argument);	
			
Option<bool> doUgridToImage(string("--doUgridToImage, doUgridToImage"), false,
			    string("doUgridToImage"),
			    false, no_argument);	
			
Option<bool> doReplaceVertsWithCoef(string("--doReplaceVertsWithCoef, doReplaceVertsWithCoef"), false,
				    string("doReplaceVertsWithCoef"),
				    false, no_argument);

Option<bool> doCoefModelToImage(string("--doCoefModelToImage, doCoefModelToImage"), false,
				string("doCoefModelToImage"),
				false, no_argument);		
				
Option<bool> doFieldModelToImage(string("--doFieldModelToImage,doFieldModelToImage"), false,
				 string("doFieldModelToImage"),
				 false, no_argument);

Option<bool> doSubSampleGrid(string("--doSubSampleGrid,doSubSampleGrid"), false,
			     string("doSubSampleGrid"),
			     false, no_argument);

Option<bool> doScalarsToVolume(string("--doScalarsToVolume"), false,
			       string("doScalarsToVolume"),
			       false, no_argument);
Option<bool> doVertexScalarsToImageVolume(string("--doVertexScalarsToImageVolume"), false,
							   string("doVertexScalarsToImageVolume"),
							   false, no_argument);

Option<bool> doVectorsToVolume(string("--doVectorsToVolume"), false,
			       string("doVectorsToVolume"),
			       false, no_argument);

Option<bool> doPointsToVolume(string("--doPointsToVolume"), false,
			       string("doPointsToVolume"),
			       false, no_argument);

Option<bool> doVolumeToScalars(string("--doVolumeToScalars"), false,
			       string("doVolumeToScalars"),
			       false, no_argument);

Option<bool> doVolumeToVectors(string("--doVolumeToVectors"), false,
			       string("doVolumeToVectors"),
			       false, no_argument);

Option<bool> doFtoP(string("--doFtoP"), false,
		    string("doFtoP"),
		    false, no_argument);

Option<bool> doGetMeans(string("--doGetMeans"), false,
			string("doGetMeans"),
			false, no_argument);		

				
Option<bool> doFlipMesh(string("--doFlipMesh"), false,
			string("doFlipMesh"),
			false, no_argument);		
				
Option<bool> doAppendConstScalar(string("--doAppendConstScalar"), false,
				 string("doAppendConstScalar"),
				 false, no_argument);		
				
Option<bool> doShiftGrid(string("--doShiftGrid"), false,
			 string("doShiftGrid"),
			 false, no_argument);

Option<bool> doConcatIntensityGrid(string("--doConcatIntensityGrid"), false,
				   string("doConcatIntensityGrid"),
				   false, no_argument);

Option<bool> doDeMeanIntensities(string("--doDeMeanIntensities"), false,
				 string("doDeMeanIntensities"),
				 false, no_argument);
				
Option<bool> doConvert_ASCII_To_Binary(string("--doConvert_ASCII_To_Binary"), false,
				       string("doConvert_ASCII_To_Binary"),
				       false, no_argument);			
				
Option<bool> doConvert_Binary_To_ASCII(string("--doConvert_Binary_To_ASCII"), false,
				       string("doConvert_Binary_To_ASCII"),
				       false, no_argument);	
																		  
																	  		
Option<bool> doUnCentreModel(string("--doUnCentreModel"), false,
			     string(" doUnCentreModel"),
			     false, no_argument);	
		
//Option<bool> doSampleAndNormalizeIntensities(string("--doSampleAndNormalizeIntensities"), false,
//					     string(" doSampleAndNormalizeIntensities"),
//					     false, no_argument);
Option<bool> doSampleProfiles(string("--doSampleProfiles"), false,
							  string(" doSampleProfiles"),
							  false, no_argument);	
Option<bool> doDeformSurface(string("--doDeformSurface"), false,
			     string(" doDeformSurface"),
			     false, no_argument);

Option<bool> doMeshReg_LeastSq(string("--doMeshReg_LeastSq"), false,
			       string(" doMeshReg_LeastSq"),
			       false, no_argument);

Option<bool> doGetMeshFromModel(string("--doGetMeshFromModel"), false,
				string("doGetMeshFromModel"),
				false, no_argument);
							
Option<bool> doVertexLDA_LOO(string("--doVertexLDA_LOO"), false,
			     string("doVertexLDA_LOO"),
			     false, no_argument);

Option<bool> doVertexLDA_save(string("--doVertexLDA_save"), false,
			      string("doVertexLDA_save"),
			      false, no_argument);	
				
Option<bool> doVertexLDA_loadAndApply(string("--doVertexLDA_loadAndApply"), false,
				      string("doVertexLDA_loadAndApply"),
				      false, no_argument);	
				
Option<bool> doGetMaxScalar(string("--doGetMaxScalar"), false,
			    string("doGetMaxScalar"),
			    false, no_argument);	
				
Option<bool> doGetMeanScalar(string("--doGetMeanScalar"), false,
			     string("doGetMeanScalar"),
			     false, no_argument);	
				
Option<bool> doAddScalars(string("--doAddScalars"), false,
			  string("doAddScalars"),
			  false, no_argument);	
				
Option<bool> doDivideScalarsByScalar(string("--doDivideScalarsByScalar"), false,
				     string("doDivideScalarsByScalar"),
				     false, no_argument);	

Option<bool> doSubtractConstantFromScalars(string("--doSubtractConstantFromScalars"), false,
                                     string("doSubtractConstantFromScalars"),
                                     false, no_argument);
				
Option<bool> doDisplayNumericFieldNames(string("--doDisplayNumericFieldNames"), false,
				     string("doDisplayNumericFieldNames"),
				     false, no_argument);					 
		Option<bool> doDisplayNumericField(string("--doDisplayNumericField"), false,
				     string("doDisplayNumericField"),
				     false, no_argument);					 
		
Option<bool> doAddVertices(string("--doAddVertices"), false,
			   string("doAddVertices"),
			   false, no_argument); 
Option<bool> doDivideVerticesByScalar(string("--doDivideVerticesByScalar"), false,
				      string("doDivideVerticesByScalar"),
				      false, no_argument);

Option<bool> doReplaceScalarsByScalars(string("--doReplaceScalarsByScalars"), false,
				       string("doReplaceScalarsByScalars"),
				       false, no_argument);

Option<bool> doDrawMeshScalars(string("--doDrawMeshScalars"), false,
									   string("doDrawMeshScalars"),
									   false, no_argument);
Option<bool> doAverageSurfaces(string("--doAverageSurfaces"), false,
							   string("doAverageSurfaces"),
							   false, no_argument);

int nonoptarg;

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



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

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(doUnCentreModel);
    options.add(inname);
    options.add(inname2);
    options.add(doSubtractConstantFromScalars);
    options.add(w_im);

    options.add(w_tan);
    options.add(w_norm);
    options.add(w_tri);
	  options.add(doVertexScalarsToImageVolume);  
    options.add(inmeshname);
    options.add(inmeshname2);
    options.add(useSc2);
    options.add(flirtmatname);
    options.add(doMeshReg);
    options.add(doFillMesh);
    options.add(toggle);
    options.add(label);
    options.add(doMeshToContours);
    options.add(outname);
    options.add(sampNN);
    options.add(doCombineMeshes);
    options.add(doUnCentreMesh);
    options.add(doLabelAndCombineSB);
    options.add(doAddMeshes);
    options.add(doSubtractMeshes);
    options.add(doAppendSBmask);
    options.add(doAppendIndexedSBmask);
    options.add(doApplyFlirtThenSBmask);
    options.add(inverse);
    options.add(doWarpMesh);
    options.add(shiftx);
    options.add(shifty);
    options.add(shiftz);
    options.add(doSurfDistMap);
    options.add(doSurfMeanAndStDev);
    options.add(doLQSurfReg);
    options.add(doAlterVertsBySBmask);
    options.add(doSphereToCart);
    options.add(doCartToSphere);
    options.add(doFindMidMidPoint);
    options.add(doWarpGrid);
    options.add(doSampleGrid);
    options.add(doSampleMesh);
    options.add(doRandMesh);
    options.add(doMeshToBvars);
    options.add(doAddModesUsingScalars);
    options.add(doRandMatrices);
    options.add(thresh);
    options.add(doWriteConditionalIntensity);
    options.add(doUgridToImage);
    options.add(doReplaceVertsWithCoef);
    options.add(doCoefModelToImage);
    options.add(myindex);
    options.add(doFieldModelToImage);
    options.add(doSubSampleGrid);
    options.add(doScalarsToVolume);
    options.add(doVectorsToVolume);
    options.add(doPointsToVolume);
    options.add(doVolumeToScalars);
    options.add(doVolumeToVectors);
    options.add(doFtoP);
    options.add(doGetMeans);
    options.add(doFlipMesh);
    options.add(doAppendConstScalar);
    options.add(doShiftGrid);
    options.add(doConcatIntensityGrid);
    options.add(doDeMeanIntensities);
    options.add(doConvert_ASCII_To_Binary);
    options.add(doConvert_Binary_To_ASCII);
    options.add(doSampleProfiles);
    options.add(doDeformSurface);
    options.add(doMeshReg_LeastSq);
    options.add(doGetMeshFromModel);
    options.add(doVertexLDA_LOO);
    options.add(doVertexLDA_save);
    options.add(doVertexLDA_loadAndApply);
    options.add(fullLDAoutput);
    options.add(doGetMeanScalar);
    options.add(doGetMaxScalar);
    options.add(doAddScalars);
    options.add(doDivideScalarsByScalar);
    options.add(doDisplayNumericFieldNames);
    options.add(doDisplayNumericField);
    options.add(dof);
    options.add(dof2);
    options.add(doAddVertices);
    options.add(doDivideVerticesByScalar);
    options.add(doReplaceScalarsByScalars);
	  options.add(doDrawMeshScalars);
	  options.add(doAverageSurfaces);
    options.add(verbose);
    options.add(help);
    nonoptarg = 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);
		}
		// Call the local functions
		try{
		if (doConvert_ASCII_To_Binary.value())
		{
		//	meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
						fslvtkIO* m = new fslvtkIO();//inmeshname.value(),static_cast<fslvtkIO::DataType>(0));
		
						m->setSwitchRowsCols(toggle.value());
							m->readPolyData(inmeshname.value());

	cout<<"toggle "<<toggle.value()<<endl;
			m->setBinaryWrite(true);
			m->save(outname.value());

		
		}else if (doConvert_Binary_To_ASCII.value())
		{
		//	meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
						fslvtkIO* m = new fslvtkIO();//inmeshname.value(),static_cast<fslvtkIO::DataType>(0));
				m->setSwitchRowsCols(toggle.value());
							m->readPolyData(inmeshname.value());

	cout<<"toggle "<<toggle.value()<<endl;
			m->setBinaryWrite(false);
			m->save(outname.value());

		
		}else if (doUnCentreModel.value()){
			meshUtils* m = new meshUtils();
			m->setSwitchRowsCols(toggle.value());
			
			volume<float> im;
			read_volume(im,inname.value());//load label image
			float tx = (im.xsize()-1)/2.0*abs(im.xdim());
			float ty = (im.ysize()-1)/2.0*abs(im.ydim());
			float tz = (im.zsize()-1)/2.0*abs(im.zdim());
			cout<<"shift "<<tx<<" "<<ty<<" "<<tz<<endl;
			m->readPolyData(inmeshname.value());
						m->shiftPoints(tx,ty,tz );

			m->setBinaryWrite(true);
			m->save(outname.value());

		
		
		}else if (doFillMesh.value())
		{
			meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			volume<float> im;
			read_volume(im,inname.value());
			int bounds[6]={0,0,0,0,0,0};
			first_mesh::getBounds(m->getPointsAsVector<float>(),bounds,im.xdim(),im.ydim(),im.zdim());
			volume<short> mask=first_mesh::make_mask_from_mesh(im, m->getPointsAsVector<float>(), first_newmat_vector::matrixToVector<unsigned int>(m->getPolygons().t()), 1, bounds);
			save_volume(mask,outname.value());
			delete m;
		}else if (doSurfDistMap.value())
		{
			volume<short> imlb;
			read_volume(imlb,inname.value());//load label image
				meshUtils* m = new meshUtils;
		cout<<"load mesh"<<endl;
						m->loadMesh(inmeshname.value());
						cout<<"done load mesh"<<endl;

				vector<float> vdist;
				cout<<"surfdist"<<endl;
				m->SurfDistToLabels<float,short>(vdist,imlb,static_cast<short>(label.value()));
				m->setScalars(vdist);
				m->save(outname.value());
				delete m;
				
		}else if(doSurfMeanAndStDev.value())
		{
			meshUtils* m = new meshUtils;
			
			Matrix MeanPoints;
			Matrix MeanScalars;
			Matrix StDevScalars;
			m->SurfScalarsMeanAndStdev(meshUtils::fileToVector(inmeshname.value()),MeanPoints, MeanScalars,StDevScalars);
			m->setScalars(MeanScalars);
			m->addFieldData(StDevScalars,"std_dev","float");

			m->save(outname.value());
			delete m;
			
		}else if(doMeshReg.value())
		{
			meshUtils* m = new meshUtils;
			m->loadMesh(inmeshname.value());
			Matrix fmat=meshUtils::readFlirtMat(flirtmatname.value());
			if (inverse.value())
				fmat=fmat.i();
			m->meshReg(fmat);
			m->save(outname.value());
			delete m;
			
		}else if (doShiftGrid.value())
		{
			meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
			m->shiftPoints(shiftx.value(),shifty.value(),shiftz.value());
			m->save(outname.value());
			
			
		}else if (doLQSurfReg.value())
		{
			meshUtils* m = new meshUtils;
			m->loadMesh(inmeshname.value());
			
			meshUtils* mRef = new meshUtils;
			mRef->loadMesh(inmeshname2.value());
			
			Matrix fmat;
			m->LQSurfaceReg(mRef->getPointsAsMatrix(),fmat, dof.value());
			
			cout<<"final "<<fmat<<endl;
			
			meshUtils::writeFlirtMatrix(fmat, outname.value()+".mat");
			m->meshReg(fmat);
			m->save(outname.value()+".vtk");
			delete m;
			delete mRef;
		}else if (doCombineMeshes.value())
		{
			meshUtils m;
						
			m.combineMeshesWithVectorsAndScalars(meshUtils::fileToVector(inmeshname.value()));
			m.save(outname.value());
			//delete m;
		
		}else if (doMeshToContours.value())
		{
			meshUtils* m ;

			try
			{
				m=new meshUtils(inmeshname.value(),static_cast<fslvtkIO::DataType>(0));
				cout<<"load Mesh "<<inmeshname.value()<<endl;
			//	m.loadMesh(inmeshname.value());

			}catch (exception& e)
			{
				e.what();
				return 1;
			}
			
						
					vector< vector<float> > contours;
			
			cout<<"minmaxY "<<m->getMinY()<<" "<<m->getMaxY()<<endl;
			float res=thresh.value();
			
			
			unsigned int total=0;
			for (float y=m->getMinY()+res;y<=m->getMaxY();y+=res)
			{
				cout<<"slice "<<y<<endl;
				contours.push_back(m->sliceMesh(y));
				cout<<"end slice "<<endl;
				total+=contours.back().size()/3;
				cout<<"total "<<total<<endl;

			}
			cout<<"foudn verts "<<total<<endl;
			ofstream fout(outname.value().c_str());
			fout<<"# vtk DataFile Version 3.0"<<endl;
			fout<<"slices "<<endl;
			fout<<"ASCII"<<endl;
			fout<<"DATASET POLYDATA"<<endl;
			fout<<"POINTS "<<total<<" float"<<endl;
			
			short count=0;
			short count2=0;
//calculate volumes
			float volume=0;
			for (vector< vector<float> >::iterator verts=contours.begin();verts!=contours.end();verts++)
			{
				float area=0;
			//	for (vector<float>::iterator i=verts->begin();i!=verts->end();i=i)
			//	{
					for ( unsigned int j=0;j<verts->size()-3;j+=3)
					{
						//cout<<*verts<<" "<<*(verts+1)<<" "<<*(verts+2)<<" "<<*(verts+3)<<endl;
						//area+=(*verts) * (*(verts+5)) -  (*(verts+3)) * (*(verts+2));
						area+=verts->at(j)*verts->at(j+5) -verts->at(j+3)*verts->at(j+2);
					}
					area+=verts->at(verts->size()-3)*verts->at(2) - verts->at(verts->size()-1)*verts->at(0);
					
					area=abs(area)/2;
			//	}
				volume+=area*res;
				cout<<"area "<<area<<endl;
			}
			cout<<"volume "<<volume<<endl;

					
			for (vector< vector<float> >::iterator verts=contours.begin();verts!=contours.end();verts++)
			{
				for (vector<float>::iterator i=verts->begin();i!=verts->end();i++)
				{
					fout<<*i<<" ";
					if (count==2) { fout<<endl; count=0; }
					else count++;
				}
			}

					
			fout<<"LINES "<<total<<" "<<3*total<<endl;
			unsigned int cumSum=0;
			for (vector< vector<float> >::iterator verts=contours.begin();verts!=contours.end();verts++)
			{
				for (unsigned int i=0;i<verts->size()/3-1;i++)
				{
					fout<<"2 "<<cumSum+i<<" "<<cumSum+i+1<<endl;
				}
				fout<<"2 "<<cumSum+verts->size()/3-1<<" "<<cumSum<<endl;
				
				cumSum+=verts->size()/3;
			}
			
			
//			for (int i =0; i<total-1;i++){
//				fout<<"2 "<<i<<" "<<i+1<<endl;
//			}
//			fout<<"2 "<<verts.size()/3-1<<" "<<0<<endl;
			
					fout.close();

			delete m;

		}else if (doAppendSBmask.value())
		{
			meshUtils* m = new meshUtils;
			m->loadMesh(inmeshname.value());

			meshUtils* mRef = new meshUtils;
			mRef->loadMesh(inmeshname2.value());
			
			//replace the avgvertcies with the defored
			meshUtils* mnew = new meshUtils;
			mnew->loadMesh(inname.value());
			
			Matrix Sc=m->appendSharedBoundaryMask(mRef->getPointsAsMatrix());
			m->setPoints(mnew->getPointsAsMatrix());
			m->setScalars(Sc);
			m->save(outname.value());

			
			delete m;
			delete mRef;
			delete mnew;
		
		}else if (doAlterVertsBySBmask.value())
		{
			meshUtils* m = new meshUtils;
			m->loadMesh(inmeshname.value());

			meshUtils* mRef = new meshUtils;
			mRef->loadMesh(inmeshname2.value());
			
			m->sampleSharedBoundaryByMask(mRef->getPointsAsMatrix());
			m->save(outname.value());			
			delete m;

		}else if (doFindMidMidPoint.value())
		{
			meshUtils* m = new meshUtils;
			m->loadMesh(inmeshname.value());
	
			volume<char> im;
			read_volume(im,inname.value());
	
			float cx=0, cy=0, cz=0;
			m->findMidPointOfMidSlice(im,meshUtils::readFlirtMat(flirtmatname.value()),cx,cy,cz);
			cout<<"foudn verts"<<endl;
			ofstream fout;
			fout.open(outname.value().c_str());
			fout<<cx<<" "<<cy<<" "<<cz<<endl;
			fout.close();
			cout<<cx<<" "<<cy<<" "<<cz<<endl;
			delete m;

		}else if (doWarpGrid.value())
		{
			try
			{
			meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
			 
			 
			volume4D<float> warpField;
			read_volume4D(warpField,inname.value());
			m->warpGridWithDefField(warpField, shiftx.value(),shifty.value(),shiftz.value());
			m->save(outname.value());
			}catch(exception& e){
			
			cout<<e.what()<<endl;
			return 1;
			}
		
			
		}else if (doWarpMesh.value())
		{
			try
			{
			meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			 
			 
			volume4D<float> warpField;
			read_volume4D(warpField,inname.value());
			m->warpGridWithDefField(warpField, shiftx.value(),shifty.value(),shiftz.value());
			m->save(outname.value());
			}catch(exception& e){
			
			cout<<e.what()<<endl;
			return 1;
			}
		
			
		}else if (doSampleGrid.value())
		{
			cout<<"sample grid"<<endl;
			
			meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
			
		
		//	Matrix fmat=meshUtils::readFlirtMat(flirtmatname.value());
		//	m->meshReg(fmat.i());
			volume<float> image;
			vector<float> vsamples;
			read_volume(image,inname.value());
			m->sampleImageAtPoints<float>(image, vsamples);
			
				delete m;
			
			meshUtils* mout = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
			mout->setScalars<float>(vsamples);
			mout->save(outname.value());
			
			delete mout;
		}else if (doSampleMesh.value())
		{
			cout<<"sample grid"<<endl;
			
			meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			Matrix pts=m->getPointsAsMatrix();

			
			volume<float> image;
			vector<float> vsamples;
			read_volume(image,inname.value());
			m->sampleImageAtPoints<float>(image, vsamples);
			m->setScalars<float>(vsamples);
			m->save(outname.value());
			
			delete m;
		}else if (doRandMesh.value())
		{
			cout<<"sample grid"<<endl;
			
			meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			Matrix sc=m->getScalars();
			vector<bool> vsc;
			for (int i=0;i<sc.Nrows();i++)
			{
				if (sc.element(i,0)>thresh.value()){
				vsc.push_back(true);
				//						vsc.push_back(false);
			}else
					vsc.push_back(false);
			}
			
			Mesh m1;
			m1.load(inmeshname.value());
			Matrix points=m->getPointsAsMatrix();
			int count=0;
			for (vector<Mpoint*>::iterator i = m1._points.begin(); i!=m1._points.end(); i++ , count++)
			{
			(*i)->_update_coord = Pt(points.element(count,0), points.element(count,1),points.element(count,2)); 
				}	
				m1.update();
			meshUtils::generateRandomMeshUsingScalar(m1,outname.value(), vsc,40);
			delete m;
			
			
		}else if (doRandMatrices.value())
		{
			meshUtils::generateRandom6DOFMatrices( outname.value(), 40);

		}else if (doUgridToImage.value())
		{
				cout<<"convert grid to image"<<endl;
			
			meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
			
			volume<float> image;
			read_volume(image,inname.value());
			m->ugridToImage<float>(image);
		
			save_volume(image,outname.value());	
			delete m;
		
		}else if (doReplaceVertsWithCoef.value()){//used to play around 
				
				cout<<"replace verts"<<endl;
				
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));

				// MJ: WHAT IS GOING ON HERE?? APPARENTLY NOTHING, BUT WHY?
				
				
		//getcoefrep disappear		
		//		FnirtFileReader fr(inname.value());
				
		//		cout<<"number of ceofficient fields "<<fr.GetCoefRep().size()<<" "<<fr.GetCoefRep().at(0)->GetCoef()->Nrows()<<" "<<fr.GetCoefRep().at(1)->CoefSz()<<endl;
		//		Matrix Coefs=*(fr.GetCoefRep().at(0)->GetCoef()) & *(fr.GetCoefRep().at(1)->GetCoef()) & *(fr.GetCoefRep().at(2)->GetCoef());
		//		cout<<"Coefs "<<Coefs.Nrows()<<" "<<Coefs.Ncols()<<endl;
		//		m->setPoints(*(fr.GetCoefRep().at(0)->GetCoef()) | *(fr.GetCoefRep().at(1)->GetCoef()) | *(fr.GetCoefRep().at(2)->GetCoef()));
				
		//		m->save(outname.value());
		
			
		}else if (doScalarsToVolume.value()){
			meshUtils *m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			Matrix Msc=m->getScalars();
			volume<float> Scvol(Msc.Nrows(),1,1);
			for (unsigned int i=0; i<static_cast<unsigned int>(Msc.Nrows());i++)
						Scvol.value(i,0,0)=Msc.element(i,0);
			save_volume(Scvol,outname.value());
			
		}else if (doVertexScalarsToImageVolume.value()){
			meshUtils *m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			volume<float> image;
			read_volume(image,inname.value());
			image=0;
			// all vertices should be arranged along the x-axis
			int count=0;
			vector<float> pts=m->getPointsAsVector<float>();
			Matrix sc=m->getScalars();
			for (vector<float>::iterator i=pts.begin();i!=pts.end();i=i+3,count++)
			{
				cout<<"verts "<<*i<<" "<<*(i+1)<<" "<<*(i+2)<<endl;
				image.value(static_cast<int>(*i/image.xdim() + 0.5),static_cast<int>(*(i+1)/image.ydim() + 0.5),static_cast<int>(*(i+2)/image.zdim() + 0.5))=sc.element(count,0);

			}
			save_volume(image,outname.value());
		}else if (doVectorsToVolume.value()){
			meshUtils *m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			Matrix Msc=m->getVectors();
			volume4D<float> Scvol(Msc.Nrows(),1,1,Msc.Ncols());
			for (unsigned int i=0; i<static_cast<unsigned int>(Msc.Nrows());i++) {
			  for (unsigned int j=0; j<static_cast<unsigned int>(Msc.Ncols());j++) {
			    Scvol.value(i,0,0,j)=Msc.element(i,j);
			  }
			}
			save_volume4D(Scvol,outname.value());
			
		}else if (doVolumeToVectors.value()){
			meshUtils *m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			volume4D<float> Scvol;
			read_volume4D(Scvol,inname.value());
			// all vertices should be arranged along the x-axis
			Matrix Msc(Scvol.xsize(),Scvol.tsize());
			for (int i=0; i<Scvol.xsize();i++) {
			  for (int j=0; j<Scvol.tsize();j++) {
			    Msc.element(i,j)=Scvol.value(i,0,0,j);
			  }
			}
			m->setVectors(Msc);
			m->save(outname.value());
			
		}else if (doPointsToVolume.value()){
			meshUtils *m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			Matrix Msc=m->getPointsAsMatrix();
			volume<float> Scvol(Msc.Nrows(),3,1);
			for (unsigned int i=0; i<static_cast<unsigned int>(Msc.Nrows());i++) {
			  for (unsigned int j=0; j<3; j++) {
			    Scvol.value(i,j,0)=Msc.element(i,j);
			  }
			}
			save_volume(Scvol,outname.value());
			
		}else if (doFtoP.value()){
			meshUtils *m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			Matrix Msc=m->getScalars();
			m->readPolyData(inmeshname.value());
			if (verbose.value()) { cout<<"Msc "<<Msc<<endl; }
			F2z& ftz=F2z::getInstance();
			int df1, df2;
			if (verbose.value()) { m->displayNumericFieldDataNames(); }
			Matrix fdofs=m->getField("FStatDOFs");
			df1=MISCMATHS::round(fdofs(1,1));
			df2=MISCMATHS::round(fdofs(2,1));
			// override dofs with user-specified values (not generally needed)
			if (dof.set()) { df1=dof.value(); }
			if (dof2.set()) { df2=dof2.value(); }
			if (verbose.value()) { cout << "FStat DOFs = " << df1 << " and " << df2 << endl; }
			for (int i=0; i<Msc.Nrows();i++)
			  {
			    if (verbose.value()) {
			      if (abs(Msc.element(i,0))>3)
				cout<<"F "<<Msc.element(i,0)<<" z "<<1-MISCMATHS::fdtr(df1,df2,Msc.element(i,0))<<" p "<<erfc(ftz.convert(Msc.element(i,0),df1,df2))<<endl;
			    }
			    Msc.element(i,0)=1-MISCMATHS::fdtr(df1,df2,Msc.element(i,0));
			  }
			m->setScalars(Msc);
			m->save(outname.value());

			
		}else if (doGetMeans.value()){
			meshUtils *m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			Matrix pts=m->getPointsAsMatrix();
			Matrix Vecs=m->getVectors();
			ColumnVector labels(pts.Nrows());
			labels=0;
			
			meshUtils *mout = new meshUtils();
			mout->setPoints(pts);
			mout->setPolygons(m->getPolygons());

		
			Matrix dist=Vecs;
			for (int i =0;i<pts.Nrows();i++)
			{
				labels.element(i)=sqrt(dist.element(i,0)*dist.element(i,0)+dist.element(i,1)*dist.element(i,1)+dist.element(i,2)*dist.element(i,2));
				cout<<labels.element(i)<<endl;
			}

			mout->setScalars(labels);
			mout->save(outname.value()+"_mean0.vtk");
	
			
			labels=1;
				mout->setPoints(pts+Vecs);
			mout->setScalars(labels);
			mout->save(outname.value()+"_mean1.vtk");
		
		}else if (doCoefModelToImage.value()){//used to play around 
				int mode=myindex.value();

				cout<<"replace verts"<<endl;
				
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
				
				Matrix CoefMean=m->getPointsAsMatrix();
				cout<<"Smodes"<<endl;
				Matrix CoefModes=m->getField("Smodes");
				cout<<"SCondEigs"<<endl;
				ColumnVector se = m->getField("SCondEigs").t();
								ColumnVector ie = m->getField("ICondEigs").t();
				Matrix IModes=m->getField("Imodes");

				ColumnVector Vimean=m->getField("Imean");
				cout<<"i mean "<<Vimean.Nrows()<<" "<<IModes.Nrows()<<endl;
				
				
				
				FnirtFileReader fr(inname.value());
				
				cout<<"coef "<<CoefMean.Nrows()<<" "<<CoefMean.Ncols()<<" "<<CoefModes.Nrows()<<" "<<CoefModes.Ncols()<<" "<<endl;
				ColumnVector NewCoefX(CoefMean.Nrows());
				ColumnVector NewCoefY(CoefMean.Nrows());
				ColumnVector NewCoefZ(CoefMean.Nrows());
				
				volume4D<float> imean;
				volume4D<float> ivar;
				volume4D<float> fmean;
				
				volume<float> imtemp, imY,imZ;
				
				read_volume(imtemp,inname.value());
				imY=imtemp;
				imZ=imtemp;
				int count=0;
				for (int k=0;k<imtemp.zsize();k++)
					for (int j=0;j<imtemp.ysize();j++)
						for (int i=0;i<imtemp.xsize();i++)
						{
							imtemp.value(i,j,k)=CoefMean.element(count,0);
							imY.value(i,j,k)=CoefMean.element(count,1);
							imZ.value(i,j,k)=CoefMean.element(count,2);
							count++;
						}
				imean.addvolume(imtemp);
				imean.addvolume(imY);
				imean.addvolume(imZ);
				//save_volume4D(imean,outname.value());
				fmean=fr.FieldAsNewimageVolume4D();
				save_volume4D(fmean,"field_"+outname.value());
				
				//	meshUtils::getConditionalMeanAndVariance(model1, imean, ivar, imtemp, 0, -3, 3, 0.5, 210);
				
				//save_volume4D(imean, outname.value()+"_mean");
				//			save_volume4D(ivar, outname.value()+"_var");
				
				meshUtils* mout= new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(1));
				mout->warpGridWithDefField(fmean,0,0,0);
				//				mout->setPoints(CoefMean);
				mout->setScalars(Vimean);
				//cout<<"vimena "<<Vimean<<endl;
				mout->save("ugrid_int_mean.vtk");
				vector<float> vars;
				for (unsigned int i=0;i<=static_cast<unsigned int>(mode);i++)
							vars.push_back(0);
				
				volume4D<float> Vmode;
				volume4D<float> VmodeVar;
/*
				Matrix Mivar=m->getField("ICondMat");
				ColumnVector ieigs=m->getField("ICondEigs").t();
				ColumnVector Var(Mivar.Nrows());
				cout<<ieigs.Nrows()<<" "<<Mivar.Nrows()<<" "<<Mivar.Ncols()<<" "<<Var.Nrows()<<endl;
				for (unsigned int i=0;i<Var.Nrows();i++)
				{ 
					float vartemp=0;
					for (unsigned int j=0; j<Mivar.Ncols();j++)
						vartemp+=Mivar.element(i,j)*Mivar.element(i,j)*ieigs.element(j);
					
					Var.element(i)=vartemp;
				
				}
				*/
				for (float i=-3;i<=3;i+=0.5)
				{
				cout<<"Iter i "<<i<<endl;
	
				vars.at(mode)=i;
				Matrix inew=meshUtils::getDeformedVector(Vimean, IModes, se,vars);

				//*************Calculare variance**************//
				float n=336;//number of subjects
				float alpha=n-1/n; //degrees of freedom of joint distribution
				float k2=10584;//number of coefficients
				float den=(alpha+k2-2)*(n-1);
				float sc=(alpha+i*i)/den; //binner is i *i because only varying 1 mode
				cout<<"SCALE "<<sc<<endl;
				//Var*=sc;
				///******************//
				
				NewCoefX=CoefMean.Column(1);
				NewCoefY=CoefMean.Column(2);
				NewCoefZ=CoefMean.Column(3);
				//int mode=0;
				for (int i =0; i<CoefMean.Nrows();i++)
				{
					NewCoefX.element(i)+=CoefModes.element(3*i,mode)*sqrt(se.element(mode))*vars.at(mode);
					NewCoefY.element(i)+=CoefModes.element(3*i+1,mode)*sqrt(se.element(mode))*vars.at(mode);
					NewCoefZ.element(i)+=CoefModes.element(3*i+2,mode)*sqrt(se.element(mode))*vars.at(mode);
					
				}
				
				
				//////-------------------FUCNTION DISAAPPEARED NEED THEM TO WORK PROPERLY ------------------//////
//				fr.GetCoefRep().at(0)->SetCoef(NewCoefX);
//				fr.GetCoefRep().at(1)->SetCoef(NewCoefY);
//				fr.GetCoefRep().at(2)->SetCoef(NewCoefZ);
				volume4D<float> field=fr.FieldAsNewimageVolume4D();
				meshUtils* mout2= new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(1));
				mout2->warpGridWithDefField(field,0,0,0);
				mout2->setScalars(inew);
				cout<<"inew "<<inew.Nrows()<<endl;
				volume<float> image;
				read_volume(image,inname2.value());
				mout2->ugridToImage<float>(image);
				Vmode.addvolume(image);
			/*	
				mout2->setScalars(Var*sc);
				mout2->ugridToImage<float>(image);
				VmodeVar.addvolume(image);
*/
				
				
				//mout2->save("ugrid_int_min3mde0.vtk");
				delete mout2;
				cout<<"end of loop"<<endl;
				}
				cout<<"done looping"<<endl;
				save_volume4D(Vmode,outname.value());
				//				save_volume4D(VmodeVar,outname.value()+"_var");

				//	cout<<"number of ceofficient fields "<<fr.GetCoefRep().size()<<" "<<fr.GetCoefRep().at(0)->GetCoef()->Nrows()<<" "<<fr.GetCoefRep().at(1)->CoefSz()<<endl;
				//	Matrix Coefs=*(fr.GetCoefRep().at(0)->GetCoef()) & *(fr.GetCoefRep().at(1)->GetCoef()) & *(fr.GetCoefRep().at(2)->GetCoef());
				//	cout<<"Coefs "<<Coefs.Nrows()<<" "<<Coefs.Ncols()<<endl;
				//	m->setPoints(*(fr.GetCoefRep().at(0)->GetCoef()) | *(fr.GetCoefRep().at(1)->GetCoef()) | *(fr.GetCoefRep().at(2)->GetCoef()));
				
				//	m->save(outname.value());
			}else if (doFieldModelToImage.value()){//used to play around 
				int mode=myindex.value();

				cout<<"replace verts"<<endl;
				
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
				
				Matrix CoefMean=m->getPointsAsMatrix();
				cout<<"Smodes"<<endl;
				Matrix CoefModes=m->getField("Smodes");
				cout<<"SCondEigs"<<endl;
				ColumnVector se = m->getField("SCondEigs").t();
				ColumnVector ie = m->getField("ICondEigs").t();
				Matrix IModes=m->getField("Imodes");

				ColumnVector Vimean=m->getField("Imean");
				cout<<"i mean "<<Vimean.Nrows()<<endl;
	
							vector<float> vars;
				for (unsigned int i=0;i<=static_cast<unsigned int>(mode);i++)
							vars.push_back(0);
				
				volume4D<float> Vmode;
				volume4D<float> VmodeVar;

				Matrix Mivar=m->getField("ICondMat");
				ColumnVector ieigs=m->getField("ICondEigs").t();
				ColumnVector Var(Mivar.Nrows());
				cout<<ieigs.Nrows()<<" "<<Mivar.Nrows()<<" "<<Mivar.Ncols()<<" "<<Var.Nrows()<<endl;
				for (unsigned int i=0;i<static_cast<unsigned int>(Var.Nrows());i++)
				{ 
					float vartemp=0;
					for (unsigned int j=0; j<static_cast<unsigned int>(Mivar.Ncols());j++)
						vartemp+=Mivar.element(i,j)*Mivar.element(i,j)*ieigs.element(j);
					
					Var.element(i)=vartemp;
				
				}
			
				meshUtils* mout2= new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
				for (float i=-3;i<=3;i+=0.5)
		//					for (float i=-25;i<=59;i+=10)

					{
				cout<<"Iter i "<<i<<endl;
				vars.at(mode)=i;

				for (unsigned int q=0;q<vars.size();q++)
					cout<<vars.at(q)<<" ";
				cout<<endl;	
	
			//	Matrix snew=meshUtils::getDeformedVector(Vimean, IModes, se,vars);
				Matrix inew=meshUtils::getDeformedVector(Vimean, IModes, se,vars);

				//*************calculare variance**************//
				float n=336;//number of subjects
				float alpha=n-1/n; //degrees of freedom of joint distribution
				float k2=10584;//number of coefficients
				float den=(alpha+k2-2)*(n-1);
				float sc=(alpha+i*i)/den; //binner is i *i because only varying 1 mode
				cout<<"SCALE "<<sc<<endl;
				//Var*=sc;
				///******************//
			
				//int mode=0;
				CoefMean=m->getPointsAsMatrix();
				cout<<CoefMean.element(0,0)<<" "<<CoefMean.element(0,1)<<" "<<CoefMean.element(0,2)<<endl;
				for (int i =0; i<CoefMean.Nrows();i++)
				{
					CoefMean.element(i,0)+=CoefModes.element(3*i,mode)*sqrt(se.element(mode))*vars.at(mode);
					CoefMean.element(i,1)+=CoefModes.element(3*i+1,mode)*sqrt(se.element(mode))*vars.at(mode);
					CoefMean.element(i,2)+=CoefModes.element(3*i+2,mode)*sqrt(se.element(mode))*vars.at(mode);
					
				}
		
			//	meshUtils* mout2= new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(1));
				mout2->setPoints(CoefMean);
				mout2->setScalars(inew);
				
								cout<<"points set "<<endl;

				volume<float> image;
				read_volume(image,inname.value());
				mout2->ugridToImage<float>(image);
				Vmode.addvolume(image);
				
				
				cout<<"now do var "<<endl;
				mout2->setScalars(Var*sc);
								cout<<"now do var2 "<<endl;

				mout2->ugridToImage<float>(image);
				VmodeVar.addvolume(image);
				cout<<"now do var added "<<endl;

				
				
			//	mout2->save("ugrid_int_min3mde0.vtk");
			//	delete mout2;
				cout<<"end of loop"<<endl;
				}
				cout<<"done looping"<<endl;
				save_volume4D(Vmode,outname.value());
				save_volume4D(VmodeVar,outname.value()+"_var");

				//	cout<<"number of ceofficient fields "<<fr.GetCoefRep().size()<<" "<<fr.GetCoefRep().at(0)->GetCoef()->Nrows()<<" "<<fr.GetCoefRep().at(1)->CoefSz()<<endl;
				//	Matrix Coefs=*(fr.GetCoefRep().at(0)->GetCoef()) & *(fr.GetCoefRep().at(1)->GetCoef()) & *(fr.GetCoefRep().at(2)->GetCoef());
				//	cout<<"Coefs "<<Coefs.Nrows()<<" "<<Coefs.Ncols()<<endl;
				//	m->setPoints(*(fr.GetCoefRep().at(0)->GetCoef()) | *(fr.GetCoefRep().at(1)->GetCoef()) | *(fr.GetCoefRep().at(2)->GetCoef()));
				
				//	m->save(outname.value());
				
			}else if (doSubSampleGrid.value()){
				
				cout<<"sub sample grid"<<endl;
				
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
								cout<<"get Points"<<endl;

				Matrix Pts=m->getPointsAsMatrix();
								cout<<"opoints got "<<Pts.Nrows()<<" "<<Pts.Ncols()<<endl;

				//sample image at points
				volume<short> image;
				vector<short> vsamples;
				read_volume(image,inname.value());
				
				m->sampleImageAtPoints<short>(image, vsamples);
				cout<<"crreate mask"<<endl;
				vector<bool> vmask;
				int N=0;
				for (vector<short>::iterator i=vsamples.begin();i!=vsamples.end();i++)
				{
				
					if ((*i) >0 ) 
					{
						vmask.push_back(true);
						N++;
						cout<<"true "<<*i<<endl;
					}else
					{
						vmask.push_back(false);
												cout<<"false "<<*i<<endl;

					}
				}
				cout<<"set data "<<N<<endl;
				
				meshUtils* mout = new meshUtils();
				mout->setDataType(static_cast<meshUtils::DataType>(1));
								cout<<"Pointss"<<endl;
				mout->setPoints(meshUtils::subSampleMatrix(m->getPointsAsMatrix(),vmask));
								cout<<"Smodes"<<endl;

			//	mout->addFieldData(meshUtils::subSample_Nby1_3D_Matrix(m->getField("Smodes"),vmask),"Smodes","float");
			//	mout->addFieldData(meshUtils::subSampleMatrix(m->getField("Imodes"),vmask),"Imodes","float");
			/*	mout->addFieldData(meshUtils::subSampleMatrix(m->getField("Imean"),vmask),"Imean","float");
				mout->addFieldData(meshUtils::subSampleMatrix(m->getField("ICondMat"),vmask),"ICondMat","float");
			
				mout->addFieldData(m->getField("Errs"),"Errs","float");
				mout->addFieldData(m->getField("Labels"),"Labels","float");
				mout->addFieldData(m->getField("NumberOfSubjects"),"NumberOfSubjects","float");
				mout->addFieldData(m->getField("SCondEigs"),"SCondEigs","float");
				mout->addFieldData(m->getField("ICondEigs"),"ICondEigs","float");
*/
 cout<<"saving"<<endl;
				mout->save(outname.value());		
				delete m;
				delete mout;
				
			}else if (doFlipMesh.value()){
				volume<float> im;
				read_volume(im,inname.value());
				float tx=im.xsize()*im.xdim();

				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				m->shiftPoints(-tx,0,0);
				m->scalePoints(-1,1,1);
			//	m->shiftPoints(tx,ty,tz);
				m->save(outname.value());
			}else if (doAppendConstScalar.value()){
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				ColumnVector Sc(m->getPointsAsMatrix().Nrows());
				Sc=label.value();
				m->setScalars(Sc);
				m->save(outname.value());
			}else if (doConcatIntensityGrid.value()){
					meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
					meshUtils* m2 = new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(1));
				
					m->setPoints(m->getPointsAsMatrix() & m2->getPointsAsMatrix() );
					m->setScalars(m->getScalars() & m2->getScalars() );
					m->save(outname.value());
				
					delete m;
					delete m2;	
			}else if (doDeMeanIntensities.value()){
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(1));
				Matrix intensity=m->getScalars();
				cout<<intensity.Nrows()<<" "<<intensity.Ncols()<<" "<<static_cast<unsigned int>(intensity.Nrows())<<endl;
				float avg=0;
				for (unsigned int i=0; i<static_cast<unsigned int>(intensity.Nrows());i++)
					avg+=intensity.element(i,0);//sum values
				
				avg/=intensity.Nrows();//normalize

				for (unsigned int i=0; i<static_cast<unsigned int>(intensity.Nrows());i++)
					intensity.element(i,0)-=avg;//demean
				
				m->setScalars(intensity);	
				m->save(outname.value());
				
				delete m;
			}else if (doDeformSurface.value())
			{
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				volume<float> image;
				read_volume(image, inname.value());
				m->deformSurface<float,unsigned int>(image, dof.value(), w_im.value(), w_tan.value(), w_tri.value(), w_norm.value(),thresh.value(),100,toggle.value(),inmeshname.value());
				m->save(outname.value());
				delete m;	
					
			}else if (doMeshReg_LeastSq.value()){
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				meshUtils* mtarg = new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(0));
				Matrix Points_src=m->getPointsAsMatrix();
				
				Matrix fmat=mtarg->reg_leastsq(Points_src, dof.value());
				delete mtarg;

				m->meshReg(fmat);
				m->save((outname.value()+".vtk").c_str());
				ofstream fmatout;
				fmatout.open((outname.value()+".mat").c_str());
				for (int i=0;i<4;i++)
				{
					for (int j=0;j<4;j++)
						fmatout<<fmat.element(i,j)<<" ";
					fmatout<<endl;
				}
				fmatout.close();
				delete m;
			}else if (doGetMeshFromModel.value())
			{
					meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
					meshUtils* mout = new meshUtils();
					mout->setPoints(m->getPointsAsMatrix());
					mout->setPolygons(m->getPolygons());
					mout->save(outname.value());
					delete m;
					delete mout;
			}else if (doVertexLDA_LOO.value())
			{
				
				//load target
				ifstream ftarg;
				ftarg.open(inname.value().c_str());
				int temp;
				unsigned int count=0;
				while (ftarg>>temp)
					count++;
				ftarg.close();	
				
				ColumnVector target(count);
				ftarg.open(inname.value().c_str());
				count=0;
				while (ftarg>>temp)
				{
					target.element(count)=temp;
					cout<<"target "<<temp<<endl;
					count++;
				}
				ftarg.close();	
				
				//base is usually average mesh
				meshUtils* mbase = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				
	//creates mean target mesh from data
//				Matrix alignedPoints=mbase->alignSurfaces(inmeshname2.value(),dof.value(),"nosave");
//				for (int i=0;i<5;i++)
//				{
//					
//					if (i>0)
//						alignedPoints=mbase->alignSurfaces(inmeshname2.value(),dof.value(),"nosave");
//					
//					
//					Matrix meanPts(mbase->getPointsAsMatrix().Nrows(),3);
//					for (unsigned int i=1;i<static_cast<unsigned int>(alignedPoints.Nrows());i+=3)
//					{
//						MVdisc* vertDisc = new MVdisc();
//						Matrix m=(vertDisc->getGroupMeans(alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols()),target)).Column(1);					
//						//cout<<"i "<<i<<" "<<m.Nrows()<<" "<<m.Ncols()<<endl;
//						meanPts.Row((i-1)/3+1)=(vertDisc->getGroupMeans(alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols()),target)).Column(1).t();
//						delete vertDisc;
//					}
//					mbase->setPoints(meanPts);
//					
//				}
				
				
				Matrix alignedPoints=mbase->alignSurfaces(inmeshname2.value(),dof.value(),outname.value()+"_aligned.vtk");
				
				//do for each vertex 
				vector<float> v_accuracy;
				unsigned int Npoints = static_cast<unsigned int>(alignedPoints.Nrows())/3;
				unsigned int Nc=alignedPoints.Ncols()+5;
				unsigned int Nc0=alignedPoints.Ncols();
		                Matrix v_results(Npoints,Nc);
				ColumnVector LDAres;
				for (unsigned int i=1;i<Npoints*3;i+=3)
				{
					MVdisc* vertDisc = new MVdisc();					
					//Matrix test=alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols());
					//	vertDisc->estimateLDAParams(alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols()),target);
					Matrix discData=alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols());
					if (toggle.value()) //use neighbouring vertices as well
					{
						vector< vector<unsigned int> > neigh = first_mesh::findNeighbours<unsigned int>(mbase->getPolygonsAsVectorOfVectors<unsigned int>(),alignedPoints.Nrows()/3);
						for (unsigned int j=0; j<neigh.at(i).size();j++)
							discData=discData & alignedPoints.SubMatrix(neigh.at(i).at(j)*3,neigh.at(i).at(j)*3+2,1,alignedPoints.Ncols());
					}
					cout<<"discData "<<discData.Nrows()<<" "<<discData.Ncols()<<endl;

					LDAres = vertDisc->run_LOO_LDA(discData,target);
					float accuracy = LDAres(discData.Ncols()+1);
					cout<<"accuracy "<<accuracy<<endl;
					v_accuracy.push_back(accuracy);
					v_results.SubMatrix((i+2)/3,(i+2)/3,1,Nc)=LDAres.t();
					delete vertDisc;
				}
				       if (fullLDAoutput.value()) {
				        string outputname=outname.value(), basename=outname.value();
					unsigned int tpidx=Nc0+2, tnidx=Nc0+3, fpidx=Nc0+4, fnidx=Nc0+5;
				        for (unsigned int nn=1; nn<=Nc; nn++) {
					  mbase->setScalars(v_results.SubMatrix(1,Npoints,nn,nn));
					  if (nn==Nc0+1) { outputname = basename + "_accuracy.vtk" ; } 
					  else if (nn==tpidx) { outputname = basename + "_TP.vtk"; }
					  else if (nn==tnidx) { outputname = basename + "_TN.vtk"; }
					  else if (nn==fpidx) { outputname = basename + "_FP.vtk"; }
					  else if (nn==fnidx) { outputname = basename + "_FN.vtk"; }
					  else { outputname = basename + "_trueclass_" + num2str(nn) + ".vtk"; }
					  mbase->save(outputname);
				        }
					// Calculate sensitivity and specificity: sens=TP/(TP+FN), spec=TN/(TN+FP)
					Matrix sens(Npoints,1), spec(Npoints,1);
					for (unsigned int mm=1; mm<=Npoints; mm++) {
					  // sens = TP/(TP+FN)
					  sens(mm,1)=v_results(mm,tpidx)/(v_results(mm,tpidx)+v_results(mm,fnidx));  
					  // spec = TN/(TN+FP)
					  spec(mm,1)=v_results(mm,tnidx)/(v_results(mm,tnidx)+v_results(mm,fpidx));  
					}
					  mbase->setScalars(sens);
					  mbase->save(basename + "_sens.vtk");
					  mbase->setScalars(spec);
					  mbase->save(basename + "_spec.vtk");
				       } else {
					 mbase->setScalars<float>(v_accuracy);
					 mbase->save(outname.value());
				       }
			} else if (doVertexLDA_save.value())
			{
						
				//load target
				ifstream ftarg;
				ftarg.open(inname.value().c_str());
				int temp;
				unsigned int count=0;
				while (ftarg>>temp)
					count++;
				ftarg.close();	
				
				ColumnVector target(count);
				ftarg.open(inname.value().c_str());
				count=0;
				while (ftarg>>temp)
				{
					target.element(count)=temp;
					cout<<"target "<<temp<<endl;
					count++;
				}
				ftarg.close();	
			
				//base is usually average mesh
				meshUtils* mbase = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
//				Matrix alignedPoints=mbase->alignSurfaces(inmeshname2.value(),dof.value(),"nosave");
//				for (int i=0;i<5;i++)
//				{
//					
//					if (i>0)
//						alignedPoints=mbase->alignSurfaces(inmeshname2.value(),dof.value(),"nosave");
//					
//					
//					Matrix meanPts(mbase->getPointsAsMatrix().Nrows(),3);
//					for (unsigned int i=1;i<static_cast<unsigned int>(alignedPoints.Nrows());i+=3)
//					{
//						MVdisc* vertDisc = new MVdisc();
//						Matrix m=(vertDisc->getGroupMeans(alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols()),target)).Column(1);					
//						//cout<<"i "<<i<<" "<<m.Nrows()<<" "<<m.Ncols()<<endl;
//						meanPts.Row((i-1)/3+1)=(vertDisc->getGroupMeans(alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols()),target)).Column(1).t();
//						delete vertDisc;
//					}
//					mbase->setPoints(meanPts);
//					
//				}
				
//				cout<<"done looping align"<<endl;
				Matrix alignedPoints=mbase->alignSurfaces(inmeshname2.value(),dof.value(),outname.value()+"_aligned.vtk");

				//do for each vertex 
//				vector<float> v_accuracy;
				MVdisc* vertDisc = new MVdisc();					

				for (unsigned int i=1;i<static_cast<unsigned int>(alignedPoints.Nrows());i+=3)
				{
					//Matrix test=alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols());
				//	vertDisc->estimateLDAParams(alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols()),target);
					Matrix discData=alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols());
					if (toggle.value()) //use neighbouring vertices as well
					{
						vector< vector<unsigned int> > neigh = first_mesh::findNeighbours<unsigned int>(mbase->getPolygonsAsVectorOfVectors<unsigned int>(),alignedPoints.Nrows()/3);
						for (unsigned int j=0; j<neigh.at(i).size();j++)
							discData=discData & alignedPoints.SubMatrix(neigh.at(i).at(j)*3,neigh.at(i).at(j)*3+2,1,alignedPoints.Ncols());
					}
				cout<<"discData "<<discData.Nrows()<<" "<<discData.Ncols()<<endl;
				if (i==1)
					vertDisc->estimateLDAParams(discData,target);
				else
					vertDisc->estimateAndAppendLDAParams(discData,target);
				//	cout<<"accuracy "<<accuracy<<endl;
				//	 v_accuracy.push_back(accuracy);	
				//	 delete vertDisc;
				}
			//	mbase->setScalars<float>(v_accuracy);
				vertDisc->saveLDAParams(outname.value(),mbase->getPolygons());
				
				delete vertDisc;
				delete mbase;
				
			}else if (doVertexLDA_loadAndApply.value())
			{
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				Matrix Mean1_all=m->getPointsAsMatrix();
				Matrix Mean2_all=m->getField("mean2");
				Matrix Cov_vecs_all=m->getField("Covariance_EigVecs");
				Matrix Cov_vals_all=m->getField("Covariance_EigVals");
				vector<unsigned int> nsub_all=first_newmat_vector::vectorToVector<unsigned int>(m->getField("number_of_subjects"));
				
				Matrix alignedPoints=m->alignSurfaces(inmeshname2.value(),dof.value(),outname.value()+"_aligned.vtk");

				//unsigned int subject=1;
				vector<int> v_class;
				fslvtkIO* fout = new fslvtkIO();
				
				for (unsigned int subject=1; subject<=(unsigned)alignedPoints.Ncols() ;subject++)
				{
					//do for each vertex
					int p_count=1; 
					for (unsigned int i=1;i<static_cast<unsigned int>(alignedPoints.Nrows());i+=3,p_count++)
					{
						MVdisc* vertDisc = new MVdisc();					
						//Matrix test=alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols());
						//	vertDisc->estimateLDAParams(alignedPoints.SubMatrix(i,i+2,1,alignedPoints.Ncols()),target);
						//cout<<"i apply "<<i<<" "<<p_count<<" "<<Mean2_all.Nrows()<<" "<<Mean2_all.Ncols()<<" "<<Cov_vecs_all.Nrows()<<" "<<Cov_vecs_all.Nrows()<<" "<<endl;
						
						vertDisc->set_LDA_Params( ( Mean1_all.SubMatrix(p_count,p_count,1,3).t() | Mean2_all.SubMatrix(p_count,p_count,1,3).t() ) ,\
												  Cov_vecs_all.SubMatrix(i,i+2,1,3), \
												  first_newmat_vector::vectorToVector<float>( Cov_vals_all.SubMatrix(i,i+2,1,1) ), \
												  nsub_all );
						ColumnVector discData=alignedPoints.SubMatrix(i,i+2,subject,subject);
						v_class.push_back( static_cast<int>(vertDisc->applyLDA(discData, 0.0 )) );						
						
						delete vertDisc;
					}
					
					if (subject==1)
					{
						fout->setPoints(alignedPoints.Column(subject));
						fout->setPolygons(m->getPolygons());
					}else
					{
						fout->appendPointsAndPolygons( first_newmat_vector::wrapMatrix(alignedPoints.Column(subject)), m->getPolygons());
					}
				}
				fout->setScalars(v_class);

				fout->save(outname.value());
				delete fout;
				delete m;
			//	mbase->setScalars<float>(v_accuracy);
				//vertDisc->saveLDAParams(outname.value());
			}else if (doGetMaxScalar.value())
			{
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				cout<<m->maxScalar()<<endl;
				delete m;
			}else if (doGetMeanScalar.value())
			{
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				cout<<m->meanScalar()<<endl;
				delete m;
				
			}else if (doSampleProfiles.value()){
				volume<float> image;
				read_volume(image,inname.value());
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				m->sampleMeshProfilesFromImage(image,0.5,dof.value());	
				vector<int> ipp;
				ipp.push_back(dof.value());
				m->addFieldData(ipp,"ipp","int");
				vector<float> samp_inter;
				samp_inter.push_back(0.5);
				m->addFieldData(samp_inter,"samplingInterval","float");
				
				m->save(outname.value());
		
				
			}else if (doDisplayNumericField.value())
			{
				
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				m->displayNumericField(inname.value());
				delete m;
				
			}else if (doDisplayNumericFieldNames.value())
			{
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				m->displayNumericFieldDataNames();
				delete m;
			}else if (doAverageSurfaces.value())
			{
				ifstream fin(inmeshname.value().c_str());
				string filename;
				Matrix Points_all;
				int count=0;
				while (fin>>filename)
				{
					meshUtils* m = new meshUtils(filename,static_cast<meshUtils::DataType>(0));
					if (count==0)
						Points_all=m->getPointsAsMatrix();					
						else
							Points_all+=m->getPointsAsMatrix();					
					delete m;
					count++;
				}
				Points_all/=count;
				meshUtils* m = new meshUtils(filename,static_cast<meshUtils::DataType>(0));
				m->setPoints(Points_all);
				m->save(outname.value());
				delete m;
			}else if(doAddScalars.value())
		  {
		  cout<<"sample grid"<<endl;
		
		meshUtils* m1 = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
		meshUtils* m2 = new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(0));
	
		m1->setScalars(m1->getScalars()+m2->getScalars());
		m1->save(outname.value());
		
		delete m1;
		delete m2;
		}else if(doDivideScalarsByScalar.value())
		  {
		   cout<<"sample grid"<<endl;
		  
		meshUtils* m1 = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));

		m1->setScalars(m1->getScalars()/thresh.value());
	
		m1->save(outname.value());
		  
		delete m1;
		  }else if(doReplaceScalarsByScalars.value())
		  {
		  cout<<"sample grid"<<endl;
		
		cout<<"sample grid"<<endl;
		
		meshUtils* m1 = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
		meshUtils* m2 = new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(0));
		m1->setScalars(m2->getScalars());
		m1->save(outname.value());
		
		delete m1;
		delete m2;
		}else if(doAddVertices.value())
		   { 
		  cout<<"sample grid"<<endl;
		
		meshUtils* m1 = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
		meshUtils* m2 = new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(0));
		m1->setPoints(m1->getPointsAsMatrix()+m2->getPointsAsMatrix());
		m1->save(outname.value());
		
		delete m1;
		delete m2;
		}else if(doDivideVerticesByScalar.value())
		  {
		  
		meshUtils* m1 = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
		m1->setPoints(m1->getPointsAsMatrix()/thresh.value());
		m1->save(outname.value());

		delete m1;
		  }else if (doSubtractConstantFromScalars.value()){
		  		    
		  meshUtils* m1 = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));

		  m1->setScalars(m1->getScalars()-thresh.value());
		  
		  m1->save(outname.value());
		    
		  delete m1;
		  
			}else if (doAddMeshes.value())
		  {
		    meshUtils* m1 = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
		    meshUtils* m2 = new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(0));
		    m1->setPoints(m1->getPointsAsMatrix() + m2->getPointsAsMatrix());
		    m1->save(outname.value());
		    delete m1;
		    delete m2;

			}else if (doSubtractMeshes.value())
		  {
		    meshUtils* m1 = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
		    meshUtils* m2 = new meshUtils(inmeshname2.value(),static_cast<meshUtils::DataType>(0));
		    m1->setPoints(m1->getPointsAsMatrix() - m2->getPointsAsMatrix());
		    m1->save(outname.value());
		    delete m1;
		    delete m2;

		  }else if (doMeshToBvars.value()){
			  
		  shapeModel* model ;
		  model=shapeModel::loadAndCreateShapeModel(inname.value(),verbose.value());

			  meshUtils* m1 = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));

			  Matrix fmatM(4,4); 
			  

			  ifstream ifmat;
			  ifmat.open(flirtmatname.value().c_str());
			  for (int i=0; i<4 ; i++)
			    {
			      for (int j=0; j<4 ; j++)
				{
				  float ftemp;
				  ifmat>>ftemp;
				  if (verbose.value()) cout<<ftemp<<" ";
				  fmatM.element(i,j)=ftemp;
				}
			      if (verbose.value()) cout<<endl;
			    }

			  // //invert matrix and assigned previous for purpose of looping
			  // xfm_NEWMAT_To_Vector(fmatM,fmatv_org);
			  fmatM=fmatM.i();
			  //concert to vector form
			  vector< vector<float> > fmatv2;
			  fmatv2=first_newmat_vector::matrixToVector<float>(fmatM.t());

			  			  model->registerModel(fmatv2);

			  vector<float> mean_mesh=model->smean;
			  vector<float> mesh=m1->getPointsAsVector<float>();			
			  vector<float> sqrtseigs= model->sqrtseigs;
			  vector< vector<float> > modes=model->smodes;

			  //subtract off mean 
			  vector<float>::iterator i_mean=mean_mesh.begin();
			  for (vector<float>::iterator i_m1=mesh.begin();i_m1!=mesh.end();i_m1++,i_mean++)
			    {
					cout<<*i_m1<<" "<<*i_mean<<endl;
			      *i_m1-=*i_mean;
					cout<<*i_m1<<endl;
			    }
			  
			  vector<float> bvars;			  
			  vector<float>::iterator i_eig=sqrtseigs.begin();
			  for (vector< vector<float> >::iterator n_mode=modes.begin();n_mode!=modes.end();i_eig++,n_mode++)
			  {
				  cout<<"eigs "<<*i_eig<<endl;
			      vector<float>::iterator i_m1=mesh.begin();
			      double dot=0;
			      for (vector<float>::iterator i=n_mode->begin();i!=n_mode->end();i++,i_m1++)
				  {
					//  cout<<"dot "<<dot<<" "<<*i<<" "<<*i_m1<<endl;

					  dot+=(*i)*(*i_m1);
				  }		
				  cout<<"dot "<<dot<<" "<<(*i_eig)<<endl;
				  

/*
				  i_m1=mesh.begin();
				  for (vector<float>::iterator i=n_mode->begin();i!=n_mode->end();i++,i_m1++)
				  {
					  //cout<<"dot "<<dot<<" "<<*i<<" "<<*i_m1<<endl;
					  *i_m1-=dot*(*i);
					 // cout<<"dot2 "<<dot<<" "<<*i<<" "<<*i_m1<<endl;

				  }
*/				  
				  
				  cout<<"dot end "<<dot/(*i_eig)<<endl;
			      bvars.push_back(dot/(*i_eig));
			 
			  }
			  
			  bvars=model->getOrigSpaceBvars(bvars);
			  
			  ofstream fout;
			//  string name=outname+".bvars";
			  fout.open(outname.value().c_str());
			  fout.precision(10);
			  fout<<"this is a bvars file"<<endl;
			  
			  fout<<inname.value()<<endl;
			  fout<<"NumberOfSubjects "<<1<<endl;
			  fout<<inmeshname.value()<<" ";
			  fout<<bvars.size()<<" ";
			  
#ifdef PPC64
			  int n=0;
#endif
			  
			  for (vector<float>::iterator i=bvars.begin();i!=bvars.end();i++){
				  fout.write(reinterpret_cast<const char *>(&(*i)),sizeof(*i));
#ifdef PPC64
				  if ((n++ % 50) == 0) fout.flush();
#endif
			  }
			  
			  //-----------------read flirt matrix-------------------////////
			  vector< vector<float> > fmatv;
			  ifstream flirt_in(flirtmatname.value().c_str());
			  for (int i=0;i<4;i++)
			  {
				  vector<float> row;
				  for (int j=0;j<4;j++)
				  {
					  float temp;
					  flirt_in>>temp;
					  row.push_back(temp);
					  
					  }
				  fmatv.push_back(row);
			  }
			  
			  for (vector< vector<float> >::const_iterator i=fmatv.begin();i!=fmatv.end();i++)
				  for (vector<float>::const_iterator i2=i->begin();i2!=i->end();i2++)
					  fout.write(reinterpret_cast<const char *>(&(*i2)),sizeof(*i2));
			
			  fout<<endl;
			  fout.close();
		
			
			
			  // cout<<"Square Residual "<<mesh.SumSquare()<<endl;
			 
		  }else if (doDrawMeshScalars.value())
		  {
			  
			  meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
			 
			  volume<float> image;
			  volume<int> count;

			  read_volume(image,inname.value());
			  image=0;
			  copyconvert(image,count);

			  
			  
			  for (int i=0;i<m->getNumberOfPolygons();i++)
			  {
				  m->drawTriangleScalars(image,count,i);
			  }
			  
			  for (int i=0;i<image.xsize();i++)
				  for (int j=0;j<image.xsize();j++)
					  for (int k=0;k<image.xsize();k++)
							if (image.value(i,j,k)>0)
								image.value(i,j,k)/=count.value(i,j,k);
			  save_volume(image,outname.value());
			  save_volume(count,"count");

			  
			  delete m;
			  
			  
		  }else{
			
				//load target
				ifstream ftarg;
				ftarg.open(inname.value().c_str());
				int temp;
				unsigned int count=0;
				while (ftarg>>temp)
					count++;
				ftarg.close();	
				
				ColumnVector target(count);
				ftarg.open(inname.value().c_str());
				count=0;
				while (ftarg>>temp)
				{
					target.element(count)=temp;
					cout<<"target "<<temp<<endl;
					count++;
				}
				ftarg.close();	
				
				
				meshUtils* m = new meshUtils(inmeshname.value(),static_cast<meshUtils::DataType>(0));
				Matrix Sc=m->getScalars();
		
				unsigned int npts=642;
						Matrix Sc_rate=Sc.SubMatrix(1,npts,1,1);
				Sc_rate=0;
				for (unsigned int j=0;j<(Sc.Nrows()/npts) ; j++)
				{
					float frac=0;
					for (unsigned int i=0; i<npts;i++)
					{
						frac+=Sc.element(i+j*npts,0);
						if (Sc.element(i+j*npts,0) ==target.element(j))
							Sc_rate.element(i,0)++;
					}
					cout<<"j frac "<<j<<" "<<frac/npts<<endl;
				}
				
				Matrix tempM;
				tempM=m->getPointsAsMatrix().SubMatrix(1,npts,1,3);
				m->setPoints(tempM);
				m->setScalars(Sc_rate/(Sc.Nrows()/npts));
				m->save(outname.value());
				delete m;
			
			}
		      }catch(exception& e){
				
				cout<<e.what()<<endl;
				return 1;
			}
			
		}catch(X_OptionError& e) {
	options.usage();
		cerr << endl << e.what() << endl;
			exit(EXIT_FAILURE);
		} catch(std::exception &e) {
			cerr << e.what() << endl;
		} 
		
  return 0;// do_work(argc,argv);
}