diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp
index f4f2f98986..00e2761710 100644
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp
@@ -1,697 +1,697 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "itkTractsToDWIImageFilter.h"
#include <boost/progress.hpp>
#include <vtkSmartPointer.h>
#include <vtkPolyData.h>
#include <vtkCellArray.h>
#include <vtkPoints.h>
#include <vtkPolyLine.h>
#include <itkImageRegionIteratorWithIndex.h>
#include <mitkGibbsRingingArtifact.h>
#include <itkResampleImageFilter.h>
#include <itkNearestNeighborInterpolateImageFunction.h>
#include <itkBSplineInterpolateImageFunction.h>
#include <itkCastImageFilter.h>
#include <itkImageFileWriter.h>
#include <itkRescaleIntensityImageFilter.h>
#include <itkWindowedSincInterpolateImageFunction.h>
#include <itkResampleDwiImageFilter.h>
#include <itkKspaceImageFilter.h>
#include <itkDftImageFilter.h>
namespace itk
{
TractsToDWIImageFilter::TractsToDWIImageFilter()
: m_CircleDummy(false)
, m_VolumeAccuracy(10)
, m_Upsampling(1)
, m_NumberOfRepetitions(1)
, m_EnforcePureFiberVoxels(false)
, m_InterpolationShrink(10)
, m_FiberRadius(20)
, m_SignalScale(300)
, m_kOffset(0)
, m_tLine(1)
, m_UseInterpolation(false)
{
m_Spacing.Fill(2.5); m_Origin.Fill(0.0);
m_DirectionMatrix.SetIdentity();
m_ImageRegion.SetSize(0, 10);
m_ImageRegion.SetSize(1, 10);
m_ImageRegion.SetSize(2, 10);
}
TractsToDWIImageFilter::~TractsToDWIImageFilter()
{
}
std::vector< TractsToDWIImageFilter::DoubleDwiType::Pointer > TractsToDWIImageFilter::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images )
{
// create slice object
SliceType::Pointer slice = SliceType::New();
ImageRegion<2> region;
region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]);
region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]);
slice->SetLargestPossibleRegion( region );
slice->SetBufferedRegion( region );
slice->SetRequestedRegion( region );
slice->Allocate();
// frequency map slice
SliceType::Pointer fMap = NULL;
if (m_FrequencyMap.IsNotNull())
{
fMap = SliceType::New();
ImageRegion<2> region;
region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]);
region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]);
fMap->SetLargestPossibleRegion( region );
fMap->SetBufferedRegion( region );
fMap->SetRequestedRegion( region );
fMap->Allocate();
}
boost::progress_display disp(images.size()*images[0]->GetVectorLength()*images[0]->GetLargestPossibleRegion().GetSize(2));
std::vector< DoubleDwiType::Pointer > outImages;
for (int i=0; i<images.size(); i++)
{
DoubleDwiType::Pointer image = images.at(i);
DoubleDwiType::Pointer newImage = DoubleDwiType::New();
newImage->SetSpacing( m_Spacing );
newImage->SetOrigin( m_Origin );
newImage->SetDirection( m_DirectionMatrix );
newImage->SetLargestPossibleRegion( m_ImageRegion );
newImage->SetBufferedRegion( m_ImageRegion );
newImage->SetRequestedRegion( m_ImageRegion );
newImage->SetVectorLength( image->GetVectorLength() );
newImage->Allocate();
DiffusionSignalModel<double>* signalModel;
if (i<m_FiberModels.size())
signalModel = m_FiberModels.at(i);
else
signalModel = m_NonFiberModels.at(i-m_FiberModels.size());
for (int g=0; g<image->GetVectorLength(); g++)
for (int z=0; z<image->GetLargestPossibleRegion().GetSize(2); z++)
{
++disp;
// extract slice from channel g
for (int y=0; y<image->GetLargestPossibleRegion().GetSize(1); y++)
for (int x=0; x<image->GetLargestPossibleRegion().GetSize(0); x++)
{
SliceType::IndexType index2D;
index2D[0]=x; index2D[1]=y;
DoubleDwiType::IndexType index3D;
index3D[0]=x; index3D[1]=y; index3D[2]=z;
SliceType::PixelType pix2D = image->GetPixel(index3D)[g];
slice->SetPixel(index2D, pix2D);
if (fMap.IsNotNull())
fMap->SetPixel(index2D, m_FrequencyMap->GetPixel(index3D));
}
// inverse fourier transform slice
ComplexSliceType::Pointer fSlice;
itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New();
idft->SetInput(slice);
idft->SetkOffset(m_kOffset);
idft->SettLine(m_tLine);
idft->SetFrequencyMap(fMap);
idft->Update();
fSlice = idft->GetOutput();
fSlice = RearrangeSlice(fSlice);
// add artifacts
for (int a=0; a<m_KspaceArtifacts.size(); a++)
{
m_KspaceArtifacts.at(a)->SetT2(signalModel->GetT2());
fSlice = m_KspaceArtifacts.at(a)->AddArtifact(fSlice);
}
// save k-space slice of s0 image
if (g==m_FiberModels.at(0)->GetFirstBaselineIndex())
for (int y=0; y<fSlice->GetLargestPossibleRegion().GetSize(1); y++)
for (int x=0; x<fSlice->GetLargestPossibleRegion().GetSize(0); x++)
{
DoubleDwiType::IndexType index3D;
index3D[0]=x; index3D[1]=y; index3D[2]=z;
SliceType::IndexType index2D;
index2D[0]=x; index2D[1]=y;
double kpix = sqrt(fSlice->GetPixel(index2D).real()*fSlice->GetPixel(index2D).real()+fSlice->GetPixel(index2D).imag()*fSlice->GetPixel(index2D).imag());
m_KspaceImage->SetPixel(index3D, m_KspaceImage->GetPixel(index3D)+kpix);
}
// fourier transform slice
SliceType::Pointer newSlice;
itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New();
dft->SetInput(fSlice);
dft->Update();
newSlice = dft->GetOutput();
// put slice back into channel g
for (int y=0; y<fSlice->GetLargestPossibleRegion().GetSize(1); y++)
for (int x=0; x<fSlice->GetLargestPossibleRegion().GetSize(0); x++)
{
DoubleDwiType::IndexType index3D;
index3D[0]=x; index3D[1]=y; index3D[2]=z;
DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D);
SliceType::IndexType index2D;
index2D[0]=x; index2D[1]=y;
pix3D[g] = newSlice->GetPixel(index2D);
newImage->SetPixel(index3D, pix3D);
}
}
outImages.push_back(newImage);
}
return outImages;
}
TractsToDWIImageFilter::ComplexSliceType::Pointer TractsToDWIImageFilter::RearrangeSlice(ComplexSliceType::Pointer slice)
{
ImageRegion<2> region = slice->GetLargestPossibleRegion();
ComplexSliceType::Pointer rearrangedSlice = ComplexSliceType::New();
rearrangedSlice->SetLargestPossibleRegion( region );
rearrangedSlice->SetBufferedRegion( region );
rearrangedSlice->SetRequestedRegion( region );
rearrangedSlice->Allocate();
int xHalf = region.GetSize(0)/2;
int yHalf = region.GetSize(1)/2;
for (int y=0; y<region.GetSize(1); y++)
for (int x=0; x<region.GetSize(0); x++)
{
SliceType::IndexType idx;
idx[0]=x; idx[1]=y;
vcl_complex< double > pix = slice->GetPixel(idx);
if( idx[0] < xHalf )
idx[0] = idx[0] + xHalf;
else
idx[0] = idx[0] - xHalf;
if( idx[1] < yHalf )
idx[1] = idx[1] + yHalf;
else
idx[1] = idx[1] - yHalf;
rearrangedSlice->SetPixel(idx, pix);
}
return rearrangedSlice;
}
void TractsToDWIImageFilter::GenerateData()
{
// check input data
if (m_FiberBundle.IsNull())
itkExceptionMacro("Input fiber bundle is NULL!");
int numFibers = m_FiberBundle->GetNumFibers();
if (numFibers<=0)
itkExceptionMacro("Input fiber bundle contains no fibers!");
if (m_FiberModels.empty())
itkExceptionMacro("No diffusion model for fiber compartments defined!");
if (m_NonFiberModels.empty())
itkExceptionMacro("No diffusion model for non-fiber compartments defined!");
int baselineIndex = m_FiberModels[0]->GetFirstBaselineIndex();
if (baselineIndex<0)
itkExceptionMacro("No baseline index found!");
// determine k-space undersampling
for (int i=0; i<m_KspaceArtifacts.size(); i++)
if ( dynamic_cast<mitk::GibbsRingingArtifact<double>*>(m_KspaceArtifacts.at(i)) )
m_Upsampling = dynamic_cast<mitk::GibbsRingingArtifact<double>*>(m_KspaceArtifacts.at(i))->GetKspaceCropping();
if (m_Upsampling<1)
m_Upsampling = 1;
if (m_TissueMask.IsNotNull())
{
// use input tissue mask
m_Spacing = m_TissueMask->GetSpacing();
m_Origin = m_TissueMask->GetOrigin();
m_DirectionMatrix = m_TissueMask->GetDirection();
m_ImageRegion = m_TissueMask->GetLargestPossibleRegion();
if (m_Upsampling>1)
{
ImageRegion<3> region = m_ImageRegion;
region.SetSize(0, m_ImageRegion.GetSize(0)*m_Upsampling);
region.SetSize(1, m_ImageRegion.GetSize(1)*m_Upsampling);
itk::Vector<double> spacing = m_Spacing;
spacing[0] /= m_Upsampling;
spacing[1] /= m_Upsampling;
itk::RescaleIntensityImageFilter<ItkUcharImgType,ItkUcharImgType>::Pointer rescaler = itk::RescaleIntensityImageFilter<ItkUcharImgType,ItkUcharImgType>::New();
rescaler->SetInput(0,m_TissueMask);
rescaler->SetOutputMaximum(100);
rescaler->SetOutputMinimum(0);
rescaler->Update();
itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::Pointer resampler = itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::New();
resampler->SetInput(rescaler->GetOutput());
resampler->SetOutputParametersFromImage(m_TissueMask);
resampler->SetSize(region.GetSize());
resampler->SetOutputSpacing(spacing);
resampler->Update();
m_TissueMask = resampler->GetOutput();
}
MITK_INFO << "Using tissue mask";
}
// initialize output dwi image
OutputImageType::Pointer outImage = OutputImageType::New();
outImage->SetSpacing( m_Spacing );
outImage->SetOrigin( m_Origin );
outImage->SetDirection( m_DirectionMatrix );
outImage->SetLargestPossibleRegion( m_ImageRegion );
outImage->SetBufferedRegion( m_ImageRegion );
outImage->SetRequestedRegion( m_ImageRegion );
outImage->SetVectorLength( m_FiberModels[0]->GetNumGradients() );
outImage->Allocate();
OutputImageType::PixelType temp;
temp.SetSize(m_FiberModels[0]->GetNumGradients());
temp.Fill(0.0);
outImage->FillBuffer(temp);
// is input slize size a power of two?
int x=m_ImageRegion.GetSize(0); int y=m_ImageRegion.GetSize(1);
if ( x%2 == 1 )
x += 1;
if ( y%2 == 1 )
y += 1;
// if not, adjust size and dimension (needed for FFT); zero-padding
if (x!=m_ImageRegion.GetSize(0))
{
MITK_INFO << "Adjusting image width: " << m_ImageRegion.GetSize(0) << " --> " << x << " --> " << x*m_Upsampling;
m_ImageRegion.SetSize(0, x);
}
if (y!=m_ImageRegion.GetSize(1))
{
MITK_INFO << "Adjusting image height: " << m_ImageRegion.GetSize(1) << " --> " << y << " --> " << y*m_Upsampling;
m_ImageRegion.SetSize(1, y);
}
// initialize k-space image
m_KspaceImage = ItkDoubleImgType::New();
m_KspaceImage->SetSpacing( m_Spacing );
m_KspaceImage->SetOrigin( m_Origin );
m_KspaceImage->SetDirection( m_DirectionMatrix );
m_KspaceImage->SetLargestPossibleRegion( m_ImageRegion );
m_KspaceImage->SetBufferedRegion( m_ImageRegion );
m_KspaceImage->SetRequestedRegion( m_ImageRegion );
m_KspaceImage->Allocate();
m_KspaceImage->FillBuffer(0);
// apply undersampling to image parameters
m_UpsampledSpacing = m_Spacing;
m_UpsampledImageRegion = m_ImageRegion;
m_UpsampledSpacing[0] /= m_Upsampling;
m_UpsampledSpacing[1] /= m_Upsampling;
m_UpsampledImageRegion.SetSize(0, m_ImageRegion.GetSize()[0]*m_Upsampling);
m_UpsampledImageRegion.SetSize(1, m_ImageRegion.GetSize()[1]*m_Upsampling);
// everything from here on is using the upsampled image parameters!!!
if (m_TissueMask.IsNull())
{
m_TissueMask = ItkUcharImgType::New();
m_TissueMask->SetSpacing( m_UpsampledSpacing );
m_TissueMask->SetOrigin( m_Origin );
m_TissueMask->SetDirection( m_DirectionMatrix );
m_TissueMask->SetLargestPossibleRegion( m_UpsampledImageRegion );
m_TissueMask->SetBufferedRegion( m_UpsampledImageRegion );
m_TissueMask->SetRequestedRegion( m_UpsampledImageRegion );
m_TissueMask->Allocate();
m_TissueMask->FillBuffer(1);
}
// resample frequency map
if (m_FrequencyMap.IsNotNull())
{
itk::ResampleImageFilter<ItkDoubleImgType, ItkDoubleImgType>::Pointer resampler = itk::ResampleImageFilter<ItkDoubleImgType, ItkDoubleImgType>::New();
resampler->SetInput(m_FrequencyMap);
resampler->SetOutputParametersFromImage(m_FrequencyMap);
resampler->SetSize(m_UpsampledImageRegion.GetSize());
resampler->SetOutputSpacing(m_UpsampledSpacing);
resampler->Update();
m_FrequencyMap = resampler->GetOutput();
}
// initialize volume fraction images
m_VolumeFractions.clear();
for (int i=0; i<m_FiberModels.size()+m_NonFiberModels.size(); i++)
{
ItkDoubleImgType::Pointer tempimg = ItkDoubleImgType::New();
tempimg->SetSpacing( m_UpsampledSpacing );
tempimg->SetOrigin( m_Origin );
tempimg->SetDirection( m_DirectionMatrix );
tempimg->SetLargestPossibleRegion( m_UpsampledImageRegion );
tempimg->SetBufferedRegion( m_UpsampledImageRegion );
tempimg->SetRequestedRegion( m_UpsampledImageRegion );
tempimg->Allocate();
tempimg->FillBuffer(0);
m_VolumeFractions.push_back(tempimg);
}
// resample fiber bundle for sufficient voxel coverage
double segmentVolume = 0.0001;
float minSpacing = 1;
if(m_UpsampledSpacing[0]<m_UpsampledSpacing[1] && m_UpsampledSpacing[0]<m_UpsampledSpacing[2])
minSpacing = m_UpsampledSpacing[0];
else if (m_UpsampledSpacing[1] < m_UpsampledSpacing[2])
minSpacing = m_UpsampledSpacing[1];
else
minSpacing = m_UpsampledSpacing[2];
FiberBundleType fiberBundle = m_FiberBundle->GetDeepCopy();
fiberBundle->ResampleFibers(minSpacing/m_VolumeAccuracy);
double mmRadius = m_FiberRadius/1000;
if (mmRadius>0)
segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/m_VolumeAccuracy;
// generate double images to work with because we don't want to lose precision
// we use a separate image for each compartment model
std::vector< DoubleDwiType::Pointer > compartments;
for (int i=0; i<m_FiberModels.size()+m_NonFiberModels.size(); i++)
{
DoubleDwiType::Pointer doubleDwi = DoubleDwiType::New();
doubleDwi->SetSpacing( m_UpsampledSpacing );
doubleDwi->SetOrigin( m_Origin );
doubleDwi->SetDirection( m_DirectionMatrix );
doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion );
doubleDwi->SetBufferedRegion( m_UpsampledImageRegion );
doubleDwi->SetRequestedRegion( m_UpsampledImageRegion );
doubleDwi->SetVectorLength( m_FiberModels[0]->GetNumGradients() );
doubleDwi->Allocate();
DoubleDwiType::PixelType pix;
pix.SetSize(m_FiberModels[0]->GetNumGradients());
pix.Fill(0.0);
doubleDwi->FillBuffer(pix);
compartments.push_back(doubleDwi);
}
double interpFact = 2*atan(-0.5*m_InterpolationShrink);
double maxVolume = 0;
vtkSmartPointer<vtkPolyData> fiberPolyData = fiberBundle->GetFiberPolyData();
vtkSmartPointer<vtkCellArray> vLines = fiberPolyData->GetLines();
vLines->InitTraversal();
MITK_INFO << "Generating signal of " << m_FiberModels.size() << " fiber compartments";
boost::progress_display disp(numFibers);
for( int i=0; i<numFibers; i++ )
{
++disp;
vtkIdType numPoints(0);
vtkIdType* points(NULL);
vLines->GetNextCell ( numPoints, points );
if (numPoints<2)
continue;
for( int j=0; j<numPoints; j++)
{
double* temp = fiberPolyData->GetPoint(points[j]);
itk::Point<float, 3> vertex = GetItkPoint(temp);
itk::Vector<double> v = GetItkVector(temp);
itk::Vector<double, 3> dir(3);
if (j<numPoints-1)
dir = GetItkVector(fiberPolyData->GetPoint(points[j+1]))-v;
else
dir = v-GetItkVector(fiberPolyData->GetPoint(points[j-1]));
itk::Index<3> idx;
itk::ContinuousIndex<float, 3> contIndex;
m_TissueMask->TransformPhysicalPointToIndex(vertex, idx);
m_TissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex);
if (!m_UseInterpolation) // use nearest neighbour interpolation
{
if (!m_TissueMask->GetLargestPossibleRegion().IsInside(idx) || m_TissueMask->GetPixel(idx)<=0)
continue;
// generate signal for each fiber compartment
for (int k=0; k<m_FiberModels.size(); k++)
{
DoubleDwiType::Pointer doubleDwi = compartments.at(k);
m_FiberModels[k]->SetFiberDirection(dir);
DoubleDwiType::PixelType pix = doubleDwi->GetPixel(idx);
pix += segmentVolume*m_FiberModels[k]->SimulateMeasurement();
doubleDwi->SetPixel(idx, pix );
if (pix[baselineIndex]>maxVolume)
maxVolume = pix[baselineIndex];
}
continue;
}
double frac_x = contIndex[0] - idx[0];
double frac_y = contIndex[1] - idx[1];
double frac_z = contIndex[2] - idx[2];
if (frac_x<0)
{
idx[0] -= 1;
frac_x += 1;
}
if (frac_y<0)
{
idx[1] -= 1;
frac_y += 1;
}
if (frac_z<0)
{
idx[2] -= 1;
frac_z += 1;
}
frac_x = atan((0.5-frac_x)*m_InterpolationShrink)/interpFact + 0.5;
frac_y = atan((0.5-frac_y)*m_InterpolationShrink)/interpFact + 0.5;
frac_z = atan((0.5-frac_z)*m_InterpolationShrink)/interpFact + 0.5;
// use trilinear interpolation
itk::Index<3> newIdx;
for (int x=0; x<2; x++)
{
frac_x = 1-frac_x;
for (int y=0; y<2; y++)
{
frac_y = 1-frac_y;
for (int z=0; z<2; z++)
{
frac_z = 1-frac_z;
newIdx[0] = idx[0]+x;
newIdx[1] = idx[1]+y;
newIdx[2] = idx[2]+z;
double frac = frac_x*frac_y*frac_z;
// is position valid?
if (!m_TissueMask->GetLargestPossibleRegion().IsInside(newIdx) || m_TissueMask->GetPixel(newIdx)<=0)
continue;
// generate signal for each fiber compartment
for (int k=0; k<m_FiberModels.size(); k++)
{
DoubleDwiType::Pointer doubleDwi = compartments.at(k);
m_FiberModels[k]->SetFiberDirection(dir);
DoubleDwiType::PixelType pix = doubleDwi->GetPixel(newIdx);
pix += segmentVolume*frac*m_FiberModels[k]->SimulateMeasurement();
doubleDwi->SetPixel(newIdx, pix );
if (pix[baselineIndex]>maxVolume)
maxVolume = pix[baselineIndex];
}
}
}
}
}
}
MITK_INFO << "Generating signal of " << m_NonFiberModels.size() << " non-fiber compartments";
ImageRegionIterator<ItkUcharImgType> it3(m_TissueMask, m_TissueMask->GetLargestPossibleRegion());
boost::progress_display disp3(m_TissueMask->GetLargestPossibleRegion().GetNumberOfPixels());
double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2];
double fact = 1;
if (m_FiberRadius<0.0001)
fact = voxelVolume/maxVolume;
while(!it3.IsAtEnd())
{
++disp3;
DoubleDwiType::IndexType index = it3.GetIndex();
if (it3.Get()>0)
{
// get fiber volume fraction
DoubleDwiType::Pointer fiberDwi = compartments.at(0);
DoubleDwiType::PixelType fiberPix = fiberDwi->GetPixel(index); // intra axonal compartment
if (fact>1) // auto scale intra-axonal if no fiber radius is specified
{
fiberPix *= fact;
fiberDwi->SetPixel(index, fiberPix);
}
double f = fiberPix[baselineIndex];
if (f>voxelVolume || f>0 && m_EnforcePureFiberVoxels) // more fiber than space in voxel?
{
fiberDwi->SetPixel(index, fiberPix*voxelVolume/f);
for (int i=1; i<m_FiberModels.size(); i++)
{
DoubleDwiType::PixelType pix; pix.Fill(0.0);
compartments.at(i)->SetPixel(index, pix);
- m_VolumeFractions.at(i)->SetPixel(index, voxelVolume);
+ m_VolumeFractions.at(i)->SetPixel(index, 1);
}
}
else
{
m_VolumeFractions.at(0)->SetPixel(index, f);
double nonf = voxelVolume-f; // non-fiber volume
double inter = 0;
if (m_FiberModels.size()>1)
inter = nonf * f/voxelVolume; // intra-axonal fraction of non fiber compartment scales linearly with f
double other = nonf - inter; // rest of compartment
double singleinter = inter/(m_FiberModels.size()-1);
// adjust non-fiber and intra-axonal signal
for (int i=1; i<m_FiberModels.size(); i++)
{
DoubleDwiType::Pointer doubleDwi = compartments.at(i);
DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index);
if (pix[baselineIndex]>0)
pix /= pix[baselineIndex];
pix *= singleinter;
doubleDwi->SetPixel(index, pix);
- m_VolumeFractions.at(i)->SetPixel(index, singleinter);
+ m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume);
}
for (int i=0; i<m_NonFiberModels.size(); i++)
{
DoubleDwiType::Pointer doubleDwi = compartments.at(i+m_FiberModels.size());
DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index) + m_NonFiberModels[i]->SimulateMeasurement()*other*m_NonFiberModels[i]->GetWeight();
doubleDwi->SetPixel(index, pix);
- m_VolumeFractions.at(i+m_FiberModels.size())->SetPixel(index, other*m_NonFiberModels[i]->GetWeight());
+ m_VolumeFractions.at(i+m_FiberModels.size())->SetPixel(index, other/voxelVolume*m_NonFiberModels[i]->GetWeight());
}
}
}
++it3;
}
// do k-space stuff
- if (!m_KspaceArtifacts.empty())
+ if (!m_KspaceArtifacts.empty() || m_kOffset>0)
{
MITK_INFO << "Adjusting complex signal";
compartments = DoKspaceStuff(compartments);
}
MITK_INFO << "Summing compartments and adding noise";
unsigned int window = 0;
unsigned int min = itk::NumericTraits<unsigned int>::max();
ImageRegionIterator<DWIImageType> it4 (outImage, outImage->GetLargestPossibleRegion());
DoubleDwiType::PixelType signal; signal.SetSize(m_FiberModels[0]->GetNumGradients());
boost::progress_display disp4(outImage->GetLargestPossibleRegion().GetNumberOfPixels());
while(!it4.IsAtEnd())
{
++disp4;
DWIImageType::IndexType index = it4.GetIndex();
signal.Fill(0.0);
// adjust fiber signal
for (int i=0; i<m_FiberModels.size(); i++)
signal += compartments.at(i)->GetPixel(index)*m_SignalScale;
// adjust non-fiber signal
for (int i=0; i<m_NonFiberModels.size(); i++)
signal += compartments.at(m_FiberModels.size()+i)->GetPixel(index)*m_SignalScale;
DoubleDwiType::PixelType accu = signal; accu.Fill(0.0);
for (int i=0; i<m_NumberOfRepetitions; i++)
{
DoubleDwiType::PixelType temp = signal;
m_NoiseModel->AddNoise(temp);
accu += temp;
}
signal = accu/m_NumberOfRepetitions;
for (int i=0; i<signal.Size(); i++)
{
if (signal[i]>0)
signal[i] = floor(signal[i]+0.5);
else
signal[i] = ceil(signal[i]-0.5);
if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]>window)
window = signal[i];
if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]<min)
min = signal[i];
}
it4.Set(signal);
++it4;
}
window -= min;
unsigned int level = window/2 + min;
m_LevelWindow.SetLevelWindow(level, window);
this->SetNthOutput(0, outImage);
}
itk::Point<float, 3> TractsToDWIImageFilter::GetItkPoint(double point[3])
{
itk::Point<float, 3> itkPoint;
itkPoint[0] = point[0];
itkPoint[1] = point[1];
itkPoint[2] = point[2];
return itkPoint;
}
itk::Vector<double, 3> TractsToDWIImageFilter::GetItkVector(double point[3])
{
itk::Vector<double, 3> itkVector;
itkVector[0] = point[0];
itkVector[1] = point[1];
itkVector[2] = point[2];
return itkVector;
}
vnl_vector_fixed<double, 3> TractsToDWIImageFilter::GetVnlVector(double point[3])
{
vnl_vector_fixed<double, 3> vnlVector;
vnlVector[0] = point[0];
vnlVector[1] = point[1];
vnlVector[2] = point[2];
return vnlVector;
}
vnl_vector_fixed<double, 3> TractsToDWIImageFilter::GetVnlVector(Vector<float,3>& vector)
{
vnl_vector_fixed<double, 3> vnlVector;
vnlVector[0] = vector[0];
vnlVector[1] = vector[1];
vnlVector[2] = vector[2];
return vnlVector;
}
}
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui
index ca102b4d97..1e9af9ab77 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui
@@ -1,2166 +1,2166 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>QmitkFiberfoxViewControls</class>
<widget class="QWidget" name="QmitkFiberfoxViewControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>493</width>
<height>1532</height>
</rect>
</property>
<property name="windowTitle">
<string>Form</string>
</property>
<layout class="QGridLayout" name="gridLayout_2">
<item row="0" column="0">
<widget class="QTabWidget" name="tabWidget">
<property name="currentIndex">
<number>0</number>
</property>
<widget class="QWidget" name="tab">
<attribute name="title">
<string>Fiber Definition</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_8">
<item row="7" column="0">
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
<item row="0" column="0">
<widget class="QLabel" name="m_FiberGenMessage">
<property name="styleSheet">
<string notr="true">color: rgb(255, 0, 0);</string>
</property>
<property name="text">
<string>Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the "Signal Generation" tab.</string>
</property>
<property name="textFormat">
<enum>Qt::AutoText</enum>
</property>
<property name="alignment">
<set>Qt::AlignJustify|Qt::AlignVCenter</set>
</property>
<property name="wordWrap">
<bool>true</bool>
</property>
</widget>
</item>
<item row="5" column="0">
<widget class="QGroupBox" name="groupBox_7">
<property name="title">
<string>Fiducial Options</string>
</property>
<layout class="QGridLayout" name="gridLayout_16">
<item row="0" column="0">
<widget class="QCheckBox" name="m_ConstantRadiusBox">
<property name="toolTip">
<string>All fiducials are treated as circles with the same radius as the first fiducial. </string>
</property>
<property name="text">
<string>Use Constant Fiducial Radius</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QCommandLinkButton" name="m_AlignOnGrid">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center.</string>
</property>
<property name="text">
<string>Align With Grid</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="6" column="0" colspan="2">
<widget class="QGroupBox" name="groupBox_4">
<property name="title">
<string>Operations</string>
</property>
<layout class="QGridLayout" name="gridLayout_11">
<item row="4" column="0">
<widget class="QCommandLinkButton" name="m_CopyBundlesButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Copy Bundles</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QCommandLinkButton" name="m_TransformBundlesButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Transform Selection</string>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QFrame" name="frame_4">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_12">
<property name="margin">
<number>0</number>
</property>
<item row="1" column="2">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_18">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Y</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QDoubleSpinBox" name="m_XrotBox">
<property name="toolTip">
<string>Rotation angle (in degree) around x-axis.</string>
</property>
<property name="minimum">
<double>-360.000000000000000</double>
</property>
<property name="maximum">
<double>360.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_22">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Axis:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="2">
<widget class="QDoubleSpinBox" name="m_YrotBox">
<property name="toolTip">
<string>Rotation angle (in degree) around y-axis.</string>
</property>
<property name="minimum">
<double>-360.000000000000000</double>
</property>
<property name="maximum">
<double>360.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_21">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Translation:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="3" column="3">
<widget class="QDoubleSpinBox" name="m_ZtransBox">
<property name="toolTip">
<string>Translation (in mm) in direction of the z-axis.</string>
</property>
<property name="minimum">
<double>-1000.000000000000000</double>
</property>
<property name="maximum">
<double>1000.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="3" column="2">
<widget class="QDoubleSpinBox" name="m_YtransBox">
<property name="toolTip">
<string>Translation (in mm) in direction of the y-axis.</string>
</property>
<property name="minimum">
<double>-1000.000000000000000</double>
</property>
<property name="maximum">
<double>1000.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_17">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>X</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_20">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Rotation:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="1" column="3">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_19">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Z</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="3">
<widget class="QDoubleSpinBox" name="m_ZrotBox">
<property name="toolTip">
<string>Rotation angle (in degree) around z-axis.</string>
</property>
<property name="minimum">
<double>-360.000000000000000</double>
</property>
<property name="maximum">
<double>360.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QDoubleSpinBox" name="m_XtransBox">
<property name="toolTip">
<string>Translation (in mm) in direction of the x-axis.</string>
</property>
<property name="minimum">
<double>-1000.000000000000000</double>
</property>
<property name="maximum">
<double>1000.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="4" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_24">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Scaling:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="4" column="1">
<widget class="QDoubleSpinBox" name="m_XscaleBox">
<property name="toolTip">
<string>Scaling factor for selected fiber bundle along the x-axis.</string>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="singleStep">
<double>0.010000000000000</double>
</property>
<property name="value">
<double>1.000000000000000</double>
</property>
</widget>
</item>
<item row="4" column="2">
<widget class="QDoubleSpinBox" name="m_YscaleBox">
<property name="toolTip">
<string>Scaling factor for selected fiber bundle along the y-axis.</string>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="singleStep">
<double>0.010000000000000</double>
</property>
<property name="value">
<double>1.000000000000000</double>
</property>
</widget>
</item>
<item row="4" column="3">
<widget class="QDoubleSpinBox" name="m_ZscaleBox">
<property name="toolTip">
<string>Scaling factor for selected fiber bundle along the z-axis.</string>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="singleStep">
<double>0.010000000000000</double>
</property>
<property name="value">
<double>1.000000000000000</double>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="5" column="0">
<widget class="QCommandLinkButton" name="m_JoinBundlesButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Join Bundles</string>
</property>
</widget>
</item>
<item row="6" column="0">
<widget class="QCheckBox" name="m_IncludeFiducials">
<property name="toolTip">
<string>If checked, the fiducials belonging to the modified bundle are also modified.</string>
</property>
<property name="text">
<string>Include Fiducials</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="4" column="0">
<widget class="QGroupBox" name="groupBox_8">
<property name="title">
<string>Fiber Options</string>
</property>
<layout class="QGridLayout" name="gridLayout_15">
<item row="2" column="0">
<widget class="QFrame" name="frame_5">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_9">
<property name="margin">
<number>0</number>
</property>
<item row="2" column="0">
<widget class="QFrame" name="m_AdvancedFiberOptionsFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_21">
<property name="margin">
<number>0</number>
</property>
<item row="1" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_5">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Tension:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_8">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Fiber Sampling:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QDoubleSpinBox" name="m_TensionBox">
<property name="toolTip">
<string/>
</property>
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>-1.000000000000000</double>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>0.000000000000000</double>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QSpinBox" name="m_FiberSamplingBox">
<property name="toolTip">
<string>Fiber sampling points (per cm)</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>100</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
<number>10</number>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QDoubleSpinBox" name="m_BiasBox">
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>-1.000000000000000</double>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>0.000000000000000</double>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_7">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Bias:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_6">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Continuity:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QDoubleSpinBox" name="m_ContinuityBox">
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>-1.000000000000000</double>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>0.000000000000000</double>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="1" column="0">
<widget class="QFrame" name="frame_2">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_25">
<property name="margin">
<number>0</number>
</property>
<property name="verticalSpacing">
<number>6</number>
</property>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_4">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>#Fibers:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QSpinBox" name="m_FiberDensityBox">
<property name="toolTip">
<string>Specify number of fibers to generate for the selected bundle.</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>1000000</number>
</property>
<property name="singleStep">
<number>100</number>
</property>
<property name="value">
<number>100</number>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
</item>
<item row="3" column="0">
<widget class="QCommandLinkButton" name="m_GenerateFibersButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Generate Fibers</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QFrame" name="frame_3">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_5">
<property name="margin">
<number>0</number>
</property>
<item row="0" column="1">
<widget class="QComboBox" name="m_DistributionBox">
<property name="toolTip">
<string>Select fiber distribution inside of the fiducials.</string>
</property>
<item>
<property name="text">
<string>Uniform</string>
</property>
</item>
<item>
<property name="text">
<string>Gaussian</string>
</property>
</item>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_9">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Fiber Distribution:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="2">
<widget class="QDoubleSpinBox" name="m_VarianceBox">
<property name="toolTip">
<string>Variance of the gaussian</string>
</property>
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>0.001000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="singleStep">
<double>0.010000000000000</double>
</property>
<property name="value">
<double>0.100000000000000</double>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="0" column="0">
<widget class="QFrame" name="frame_8">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_22">
<property name="margin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QCheckBox" name="m_RealTimeFibers">
<property name="toolTip">
<string>Disable to only generate fibers if "Generate Fibers" button is pressed.</string>
</property>
<property name="text">
<string>Real Time Fibers</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QCheckBox" name="m_AdvancedOptionsBox">
<property name="toolTip">
<string>Disable to only generate fibers if "Generate Fibers" button is pressed.</string>
</property>
<property name="text">
<string>Advanced Options</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
</item>
<item row="3" column="0">
<widget class="QFrame" name="frame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_3">
<property name="margin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QPushButton" name="m_CircleButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="maximumSize">
<size>
<width>30</width>
<height>30</height>
</size>
</property>
<property name="toolTip">
<string>Draw elliptical fiducial.</string>
</property>
<property name="text">
<string/>
</property>
<property name="icon">
<iconset resource="../../resources/QmitkDiffusionImaging.qrc">
<normaloff>:/QmitkDiffusionImaging/circle.png</normaloff>:/QmitkDiffusionImaging/circle.png</iconset>
</property>
<property name="iconSize">
<size>
<width>32</width>
<height>32</height>
</size>
</property>
<property name="checkable">
<bool>false</bool>
</property>
<property name="flat">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QPushButton" name="m_FlipButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="maximumSize">
<size>
<width>30</width>
<height>30</height>
</size>
</property>
<property name="toolTip">
<string>Flip fiber waypoints of selcted fiducial around one axis.</string>
</property>
<property name="text">
<string/>
</property>
<property name="icon">
<iconset resource="../../resources/QmitkDiffusionImaging.qrc">
<normaloff>:/QmitkDiffusionImaging/refresh.xpm</normaloff>:/QmitkDiffusionImaging/refresh.xpm</iconset>
</property>
<property name="iconSize">
<size>
<width>32</width>
<height>32</height>
</size>
</property>
<property name="checkable">
<bool>false</bool>
</property>
<property name="flat">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="2">
<spacer name="horizontalSpacer">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="tab_2">
<attribute name="title">
<string>Signal Generation</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_4">
<item row="5" column="0">
<widget class="QGroupBox" name="m_IntraAxonalGroupBox">
<property name="title">
<string>Intra-axonal Compartment</string>
</property>
<layout class="QGridLayout" name="gridLayout_13">
<item row="0" column="0">
<widget class="QComboBox" name="m_Compartment1Box">
<property name="toolTip">
<string>Select signal model for intra-axonal compartment.</string>
</property>
<item>
<property name="text">
<string>Stick Model</string>
</property>
</item>
<item>
<property name="text">
<string>Zeppelin Model</string>
</property>
</item>
<item>
<property name="text">
<string>Tensor Model</string>
</property>
</item>
</widget>
</item>
<item row="1" column="0">
<widget class="QmitkStickModelParametersWidget" name="m_StickWidget1" native="true"/>
</item>
<item row="2" column="0">
<widget class="QmitkZeppelinModelParametersWidget" name="m_ZeppelinWidget1" native="true"/>
</item>
<item row="3" column="0">
<widget class="QmitkTensorModelParametersWidget" name="m_TensorWidget1" native="true"/>
</item>
</layout>
</widget>
</item>
<item row="0" column="0">
<widget class="QGroupBox" name="groupBox_2">
<property name="title">
<string>Data</string>
</property>
<layout class="QGridLayout" name="gridLayout_10">
<item row="0" column="0" rowspan="2" colspan="2">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_16">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Fiber Bundle:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="2" rowspan="2">
<widget class="QLabel" name="m_FiberBundleLabel">
<property name="text">
<string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string>
</property>
<property name="wordWrap">
<bool>true</bool>
</property>
</widget>
</item>
<item row="3" column="0" colspan="2">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_3">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Tissue Mask:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="3" column="2">
<widget class="QLabel" name="m_TissueMaskLabel">
<property name="text">
<string><html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html></string>
</property>
<property name="wordWrap">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="7" column="0">
<widget class="QGroupBox" name="groupBox_6">
<property name="title">
<string>Extra-axonal Compartments</string>
</property>
<layout class="QGridLayout" name="gridLayout_14">
<item row="6" column="0">
<widget class="QComboBox" name="m_Compartment3Box">
<property name="toolTip">
<string>Select signal model for extra-axonal compartment.</string>
</property>
<item>
<property name="text">
<string>Ball Model</string>
</property>
</item>
<item>
<property name="text">
<string>Astrosticks Model</string>
</property>
</item>
<item>
<property name="text">
<string>Dot Model</string>
</property>
</item>
</widget>
</item>
<item row="8" column="0">
<widget class="QmitkAstrosticksModelParametersWidget" name="m_AstrosticksWidget1" native="true"/>
</item>
<item row="14" column="0">
<widget class="QmitkAstrosticksModelParametersWidget" name="m_AstrosticksWidget2" native="true"/>
</item>
<item row="13" column="0">
<widget class="QmitkBallModelParametersWidget" name="m_BallWidget2" native="true"/>
</item>
<item row="7" column="0">
<widget class="QmitkBallModelParametersWidget" name="m_BallWidget1" native="true"/>
</item>
<item row="12" column="0">
<widget class="QComboBox" name="m_Compartment4Box">
<property name="toolTip">
<string>Select signal model for extra-axonal compartment.</string>
</property>
<item>
<property name="text">
<string>--</string>
</property>
</item>
<item>
<property name="text">
<string>Ball Model</string>
</property>
</item>
<item>
<property name="text">
<string>Astrosticks Model</string>
</property>
</item>
<item>
<property name="text">
<string>Dot Model</string>
</property>
</item>
</widget>
</item>
<item row="11" column="0">
<widget class="Line" name="line_2">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
<item row="15" column="0">
<widget class="QmitkDotModelParametersWidget" name="m_DotWidget2" native="true"/>
</item>
<item row="16" column="0">
<widget class="QFrame" name="m_Comp4FractionFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_18">
<property name="margin">
<number>0</number>
</property>
<item row="0" column="1">
<widget class="QDoubleSpinBox" name="m_Comp4FractionBox">
<property name="toolTip">
<string>Weighting factor between the two extra-axonal compartments.</string>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>0.300000000000000</double>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="m_NoiseLabel_3">
<property name="text">
<string>Compartment Fraction:</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="9" column="0">
<widget class="QmitkDotModelParametersWidget" name="m_DotWidget1" native="true"/>
</item>
</layout>
</widget>
</item>
<item row="2" column="0">
<widget class="QCommandLinkButton" name="m_GenerateImageButton">
<property name="enabled">
<bool>true</bool>
</property>
<property name="toolTip">
<string>Start DWI generation from selected fiebr bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated.</string>
</property>
<property name="text">
<string>Generate Image</string>
</property>
</widget>
</item>
<item row="4" column="0">
<widget class="QGroupBox" name="groupBox">
<property name="title">
<string>Image Settings</string>
</property>
<layout class="QGridLayout" name="gridLayout">
<item row="7" column="0">
<widget class="QFrame" name="m_AdvancedSignalOptionsFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_23">
<property name="margin">
<number>0</number>
</property>
<property name="horizontalSpacing">
<number>6</number>
</property>
<item row="1" column="0">
<widget class="QLabel" name="m_TensorsToDWINumDirsLabel_5">
<property name="text">
<string>Signal Scale:</string>
</property>
</widget>
</item>
<item row="6" column="0">
<widget class="QLabel" name="m_TensorsToDWINumDirsLabel_3">
<property name="text">
<string>Interpolation Shrink:</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_15">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Line Readout Time: </string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="5" column="1">
<widget class="QSpinBox" name="m_FiberRadius">
<property name="toolTip">
<string>Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation.</string>
</property>
<property name="minimum">
<number>0</number>
</property>
<property name="maximum">
<number>1000</number>
</property>
<property name="value">
<number>0</number>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QDoubleSpinBox" name="m_LineReadoutTimeBox">
<property name="toolTip">
<string>T2* relaxation time (in milliseconds).</string>
</property>
<property name="maximum">
<double>100.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>1.000000000000000</double>
</property>
</widget>
</item>
<item row="5" column="0">
<widget class="QLabel" name="m_TensorsToDWINumDirsLabel_4">
<property name="text">
<string>Fiber Radius:</string>
</property>
</widget>
</item>
<item row="4" column="1">
<widget class="QSpinBox" name="m_T2starBox">
<property name="toolTip">
<string>Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds).</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>10000</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
<number>50</number>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QSpinBox" name="m_TEbox">
<property name="toolTip">
<string>TE in milliseconds</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>10000</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
<number>100</number>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QSpinBox" name="m_RepetitionsBox">
<property name="toolTip">
<string>Number of signal averages. Increase to reduce noise.</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>100</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
<number>1</number>
</property>
</widget>
</item>
<item row="6" column="1">
<widget class="QSpinBox" name="m_InterpolationShrink">
<property name="toolTip">
<string><html><head/><body><p>Large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation). 1000 equals nearest neighbour interpolation.</p></body></html></string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>1000</number>
</property>
<property name="value">
<number>1000</number>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QSpinBox" name="m_SignalScaleBox">
<property name="toolTip">
<string>TE in milliseconds</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>10000</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
<number>100</number>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWINumDirsLabel_2">
<property name="text">
<string>Repetitions:</string>
</property>
</widget>
</item>
<item row="9" column="0">
<widget class="QCheckBox" name="m_KspaceImageBox">
<property name="text">
<string>Output k-Space Image</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_13">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string><html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html></string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="8" column="0">
<widget class="QCheckBox" name="m_EnforcePureFiberVoxelsBox">
<property name="toolTip">
<string>Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present.</string>
</property>
<property name="text">
<string>Disable Partial Volume Effects</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
<item row="4" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_12">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string><html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html></string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="7" column="0">
<widget class="QCheckBox" name="m_RelaxationBox">
<property name="toolTip">
<string><html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html></string>
</property>
<property name="text">
<string>Simulate Signal Relaxation</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="10" column="0">
<widget class="QCheckBox" name="m_VolumeFractionsBox">
<property name="toolTip">
- <string>Output one image per compartment containing the corresponding volume fractions (in mm³) per voxel.</string>
+ <string>Output one image per compartment containing the corresponding volume fractions per voxel.</string>
</property>
<property name="text">
<string>Output Volume Fractions</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="m_GeometryMessage">
<property name="styleSheet">
<string notr="true">color: rgb(255, 0, 0);</string>
</property>
<property name="text">
<string>Using geometry of selected image!</string>
</property>
</widget>
</item>
<item row="4" column="0">
<widget class="QLabel" name="m_DiffusionPropsMessage">
<property name="styleSheet">
<string notr="true">color: rgb(255, 0, 0);</string>
</property>
<property name="text">
<string>Using gradients of selected DWI!</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QFrame" name="m_GeometryFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_7">
<property name="margin">
<number>0</number>
</property>
<item row="2" column="2">
<widget class="QDoubleSpinBox" name="m_SpacingY">
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>0.100000000000000</double>
</property>
<property name="maximum">
<double>50.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>2.000000000000000</double>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="label_2">
<property name="text">
<string>Image Spacing:</string>
</property>
</widget>
</item>
<item row="2" column="3">
<widget class="QDoubleSpinBox" name="m_SpacingZ">
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>0.100000000000000</double>
</property>
<property name="maximum">
<double>50.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>2.000000000000000</double>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QDoubleSpinBox" name="m_SpacingX">
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>0.100000000000000</double>
</property>
<property name="maximum">
<double>50.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>2.000000000000000</double>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="label">
<property name="text">
<string>Image Dimensions:</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QSpinBox" name="m_SizeX">
<property name="toolTip">
<string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>1000</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
<number>11</number>
</property>
</widget>
</item>
<item row="0" column="2">
<widget class="QSpinBox" name="m_SizeY">
<property name="toolTip">
<string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>1000</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
<number>11</number>
</property>
</widget>
</item>
<item row="0" column="3">
<widget class="QSpinBox" name="m_SizeZ">
<property name="toolTip">
<string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>1000</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
<number>3</number>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="5" column="0">
<widget class="QFrame" name="m_TensorsToDWIFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_24">
<property name="margin">
<number>0</number>
</property>
<property name="spacing">
<number>6</number>
</property>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWINumDirsLabel">
<property name="text">
<string>Gradient Directions:</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QSpinBox" name="m_NumGradientsBox">
<property name="toolTip">
<string>Number of gradient directions distributed over the half sphere.</string>
</property>
<property name="minimum">
<number>0</number>
</property>
<property name="maximum">
<number>10000</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
<number>30</number>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>b-Value:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QSpinBox" name="m_BvalueBox">
<property name="toolTip">
<string>b-value in mm/s²</string>
</property>
<property name="minimum">
<number>0</number>
</property>
<property name="maximum">
<number>10000</number>
</property>
<property name="singleStep">
<number>100</number>
</property>
<property name="value">
<number>1000</number>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="6" column="0">
<widget class="QCheckBox" name="m_AdvancedOptionsBox_2">
<property name="text">
<string>Advanced Options</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="10" column="0">
<spacer name="verticalSpacer_2">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
<item row="9" column="0">
<widget class="QGroupBox" name="groupBox_3">
<property name="title">
<string>Noise and other Artifacts</string>
</property>
<layout class="QGridLayout" name="gridLayout_6">
<item row="8" column="0">
<widget class="QFrame" name="m_GibbsRingingFrame">
<property name="enabled">
<bool>true</bool>
</property>
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QFormLayout" name="formLayout_4">
<property name="horizontalSpacing">
<number>6</number>
</property>
<property name="margin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_14">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>k-Space Undersampling:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QComboBox" name="m_KspaceUndersamplingBox">
<property name="toolTip">
<string>Image is upsampled using this factor, afterwards fourier transformed, cropped to the original size and then inverse fourier transformed.</string>
</property>
<property name="currentIndex">
<number>0</number>
</property>
<item>
<property name="text">
<string>2</string>
</property>
</item>
<item>
<property name="text">
<string>4</string>
</property>
</item>
<item>
<property name="text">
<string>8</string>
</property>
</item>
<item>
<property name="text">
<string>16</string>
</property>
</item>
<item>
<property name="text">
<string>32</string>
</property>
</item>
<item>
<property name="text">
<string>64</string>
</property>
</item>
<item>
<property name="text">
<string>128</string>
</property>
</item>
<item>
<property name="text">
<string>256</string>
</property>
</item>
</widget>
</item>
</layout>
</widget>
</item>
<item row="5" column="0">
<widget class="QCheckBox" name="m_AddDistortions">
<property name="text">
<string>Add Distortions</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
<item row="7" column="0">
<widget class="QCheckBox" name="m_AddGibbsRinging">
<property name="text">
<string>Add Gibbs Ringing</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QCheckBox" name="m_AddNoise">
<property name="text">
<string>Add Rician Noise</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QFrame" name="m_NoiseFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QFormLayout" name="formLayout_5">
<property name="margin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QLabel" name="m_NoiseLabel">
<property name="text">
<string>Variance:</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QDoubleSpinBox" name="m_NoiseLevel">
<property name="toolTip">
<string>Variance of Rician noise model.</string>
</property>
<property name="decimals">
<number>4</number>
</property>
<property name="minimum">
<double>0.000000000000000</double>
</property>
<property name="maximum">
<double>100000.000000000000000</double>
</property>
<property name="singleStep">
<double>0.001000000000000</double>
</property>
<property name="value">
<double>25.000000000000000</double>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="3" column="0">
<widget class="QCheckBox" name="m_AddGhosts">
<property name="text">
<string>Add N/2 Ghosts</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
<item row="4" column="0">
<widget class="QFrame" name="m_GhostFrame">
<property name="enabled">
<bool>true</bool>
</property>
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QFormLayout" name="formLayout_6">
<property name="horizontalSpacing">
<number>6</number>
</property>
<property name="margin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_23">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>K-Space Line Offset:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QDoubleSpinBox" name="m_kOffsetBox">
<property name="toolTip">
<string>A larger offset increases the inensity of the ghost image.</string>
</property>
<property name="decimals">
<number>3</number>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
<double>0.010000000000000</double>
</property>
<property name="value">
<double>0.100000000000000</double>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="6" column="0">
<widget class="QFrame" name="m_DistortionsFrame">
<property name="enabled">
<bool>true</bool>
</property>
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QFormLayout" name="formLayout_7">
<property name="horizontalSpacing">
<number>6</number>
</property>
<property name="margin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_25">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Frequency Map:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QmitkDataStorageComboBox" name="m_FrequencyMapBox">
<property name="toolTip">
<string>Select image specifying the frequency inhomogeneities (in Hz).</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
</item>
<item row="6" column="0">
<widget class="QGroupBox" name="groupBox_5">
<property name="title">
<string>Inter-axonal Compartment</string>
</property>
<layout class="QGridLayout" name="gridLayout_17">
<item row="3" column="0">
<widget class="QmitkTensorModelParametersWidget" name="m_TensorWidget2" native="true"/>
</item>
<item row="1" column="0">
<widget class="QmitkZeppelinModelParametersWidget" name="m_ZeppelinWidget2" native="true"/>
</item>
<item row="0" column="0">
<widget class="QComboBox" name="m_Compartment2Box">
<property name="toolTip">
<string>Select signal model for intra-axonal compartment.</string>
</property>
<item>
<property name="text">
<string>--</string>
</property>
</item>
<item>
<property name="text">
<string>Stick Model</string>
</property>
</item>
<item>
<property name="text">
<string>Zeppelin Model</string>
</property>
</item>
<item>
<property name="text">
<string>Tensor Model</string>
</property>
</item>
</widget>
</item>
<item row="2" column="0">
<widget class="QmitkStickModelParametersWidget" name="m_StickWidget2" native="true"/>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
</widget>
</item>
</layout>
</widget>
<customwidgets>
<customwidget>
<class>QmitkTensorModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkTensorModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkStickModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkStickModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkZeppelinModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkZeppelinModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkBallModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkBallModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkAstrosticksModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkAstrosticksModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkDotModelParametersWidget</class>
<extends>QWidget</extends>
<header>QmitkDotModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkDataStorageComboBox</class>
<extends>QComboBox</extends>
<header location="global">QmitkDataStorageComboBox.h</header>
</customwidget>
</customwidgets>
<tabstops>
<tabstop>m_CircleButton</tabstop>
<tabstop>m_FlipButton</tabstop>
<tabstop>m_RealTimeFibers</tabstop>
<tabstop>m_AdvancedOptionsBox</tabstop>
<tabstop>m_DistributionBox</tabstop>
<tabstop>m_VarianceBox</tabstop>
<tabstop>m_FiberDensityBox</tabstop>
<tabstop>m_FiberSamplingBox</tabstop>
<tabstop>m_TensionBox</tabstop>
<tabstop>m_ContinuityBox</tabstop>
<tabstop>m_BiasBox</tabstop>
<tabstop>m_GenerateFibersButton</tabstop>
<tabstop>m_ConstantRadiusBox</tabstop>
<tabstop>m_AlignOnGrid</tabstop>
<tabstop>m_XrotBox</tabstop>
<tabstop>m_YrotBox</tabstop>
<tabstop>m_ZrotBox</tabstop>
<tabstop>m_XtransBox</tabstop>
<tabstop>m_YtransBox</tabstop>
<tabstop>m_ZtransBox</tabstop>
<tabstop>m_XscaleBox</tabstop>
<tabstop>m_YscaleBox</tabstop>
<tabstop>m_ZscaleBox</tabstop>
<tabstop>m_TransformBundlesButton</tabstop>
<tabstop>m_CopyBundlesButton</tabstop>
<tabstop>m_JoinBundlesButton</tabstop>
<tabstop>m_IncludeFiducials</tabstop>
<tabstop>m_GenerateImageButton</tabstop>
<tabstop>m_SizeX</tabstop>
<tabstop>m_SizeY</tabstop>
<tabstop>m_SizeZ</tabstop>
<tabstop>m_SpacingX</tabstop>
<tabstop>m_SpacingY</tabstop>
<tabstop>m_SpacingZ</tabstop>
<tabstop>m_NumGradientsBox</tabstop>
<tabstop>m_BvalueBox</tabstop>
<tabstop>m_AdvancedOptionsBox_2</tabstop>
<tabstop>m_RepetitionsBox</tabstop>
<tabstop>m_SignalScaleBox</tabstop>
<tabstop>m_TEbox</tabstop>
<tabstop>m_LineReadoutTimeBox</tabstop>
<tabstop>m_T2starBox</tabstop>
<tabstop>m_FiberRadius</tabstop>
<tabstop>m_InterpolationShrink</tabstop>
<tabstop>m_EnforcePureFiberVoxelsBox</tabstop>
<tabstop>m_KspaceImageBox</tabstop>
<tabstop>m_Compartment1Box</tabstop>
<tabstop>m_Compartment2Box</tabstop>
<tabstop>m_Compartment3Box</tabstop>
<tabstop>m_Compartment4Box</tabstop>
<tabstop>m_Comp4FractionBox</tabstop>
<tabstop>m_AddNoise</tabstop>
<tabstop>m_NoiseLevel</tabstop>
<tabstop>m_AddGhosts</tabstop>
<tabstop>m_kOffsetBox</tabstop>
<tabstop>m_AddDistortions</tabstop>
<tabstop>m_FrequencyMapBox</tabstop>
<tabstop>m_AddGibbsRinging</tabstop>
<tabstop>m_KspaceUndersamplingBox</tabstop>
<tabstop>tabWidget</tabstop>
</tabstops>
<resources>
<include location="../../resources/QmitkDiffusionImaging.qrc"/>
</resources>
<connections/>
</ui>