diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.cpp index 988523a146..f3bf77e2e7 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.cpp +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.cpp @@ -1,48 +1,48 @@ /*=================================================================== 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 #include #include using namespace mitk; template< class ScalarType > ChiSquareNoiseModel< ScalarType >::ChiSquareNoiseModel() { m_RandGen.seed(); } template< class ScalarType > ChiSquareNoiseModel< ScalarType >::~ChiSquareNoiseModel() { } template< class ScalarType > void ChiSquareNoiseModel< ScalarType >::SetSeed(int seed) { if (seed>=0) m_RandGen.seed(seed); else m_RandGen.seed(); } template< class ScalarType > void ChiSquareNoiseModel< ScalarType >::AddNoise(PixelType& pixel) { for( unsigned int i=0; i QmitkAstrosticksModelParametersWidgetControls 0 0 410 106 0 0 Form - + + 0 + + + 0 + + + 0 + + 0 Use random number and orientation of sticks. Randomize Sticks true QFrame::NoFrame QFrame::Raised - + + 0 + + + 0 + + + 0 + + 0 <html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html> T2 relaxation time of this compartment (in milliseconds). 10000 80 - <html><head/><body><p><span style=" font-style:italic;">d</span>:</p></body></html> + <html><head/><body><p><span style=" font-style:italic;">d [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s</span><span style=" font-style:italic;">]</span>:</p></body></html> Diffusivity along sticks. 5 1.000000000000000 0.000100000000000 0.001000000000000 m_T2box m_D1box m_RandomCheck diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkBallModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkBallModelParametersWidgetControls.ui index f32a8da795..16e5f0a9d4 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkBallModelParametersWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkBallModelParametersWidgetControls.ui @@ -1,80 +1,89 @@ QmitkBallModelParametersWidgetControls 0 0 410 78 0 0 Form - + + 0 + + + 0 + + + 0 + + 0 - <html><head/><body><p><span style=" font-style:italic;">d</span>:</p></body></html> + <html><head/><body><p><span style=" font-style:italic;">d [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html> <html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html> T2 relaxation time of this compartment (in milliseconds). 10000 80 Diffusivity along stick. 5 1.000000000000000 0.000100000000000 0.001000000000000 m_T2box m_D1box diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkStickModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkStickModelParametersWidgetControls.ui index f85e3255ac..8b6911712d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkStickModelParametersWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkStickModelParametersWidgetControls.ui @@ -1,80 +1,89 @@ QmitkStickModelParametersWidgetControls 0 0 410 78 0 0 Form - + + 0 + + + 0 + + + 0 + + 0 - <html><head/><body><p><span style=" font-style:italic;">d</span>:</p></body></html> + <html><head/><body><p><span style=" font-style:italic;">d [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html> <html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html> T2 relaxation time of this compartment (in milliseconds). 10000 110 Diffusivity along stick. 5 1.000000000000000 0.000100000000000 0.001000000000000 m_T2box m_D1box diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkTensorModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkTensorModelParametersWidgetControls.ui index a11ce9c8d4..bceeeec920 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkTensorModelParametersWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkTensorModelParametersWidgetControls.ui @@ -1,151 +1,160 @@ QmitkTensorModelParametersWidgetControls 0 0 410 167 0 0 Form - + + 0 + + + 0 + + + 0 + + 0 <html><head/><body><p><span style=" font-style:italic;">FA</span>:</p></body></html> - <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">⟂1</span>:</p></body></html> + <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">⟂1</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html> Diffusivity along second eigenvector. 5 1.000000000000000 0.000100000000000 0.000250000000000 - <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">||</span>:</p></body></html> + <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">||</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html> Diffusivity along largest eigenvector. 5 1.000000000000000 0.000100000000000 0.001000000000000 Diffusivity along third eigenvector. 5 1.000000000000000 0.000100000000000 0.000250000000000 - <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">⟂2</span>:</p></body></html> + <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">⟂2</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html> Fractional anisotropy of resulting tensor. <html><head/><body><p>-</p></body></html> <html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html> T2 relaxation time of this compartment (in milliseconds). 10000 110 m_T2box m_D1box m_D2box m_D3box diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkZeppelinModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkZeppelinModelParametersWidgetControls.ui index 210e2fcb3c..8fc23021d0 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkZeppelinModelParametersWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkZeppelinModelParametersWidgetControls.ui @@ -1,124 +1,133 @@ QmitkZeppelinModelParametersWidgetControls 0 0 410 116 0 0 Form - + + 0 + + + 0 + + + 0 + + 0 Fractional anisotropy of resulting tensor. <html><head/><body><p>-</p></body></html> Diffusivity along second and third eigenvector. 5 1.000000000000000 0.000100000000000 0.000250000000000 T2 relaxation time of this compartment (in milliseconds). 10000 110 Diffusivity along largest eigenvector. 5 1.000000000000000 0.000100000000000 0.001000000000000 - <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">⟂</span>:</p></body></html> + <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">⟂</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html> - <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">||</span>:</p></body></html> + <html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">||</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html> <html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html> <html><head/><body><p><span style=" font-style:italic;">FA</span>:</p></body></html> m_T2box m_D1box m_D2box 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 e6c6d981f0..427a246e7b 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,3031 +1,3031 @@ QmitkFiberfoxViewControls 0 0 435 2274 Form Load Parameters :/QmitkDiffusionImaging/general_icons/upload.ico:/QmitkDiffusionImaging/general_icons/upload.ico 0 Fiber Definition Qt::Vertical 20 40 color: rgb(255, 0, 0); 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. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true Fiducial Options All fiducials are treated as circles with the same radius as the first fiducial. Use Constant Fiducial Radius false false Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center. Align With Grid :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Operations false Join Bundles :/QmitkDiffusionImaging/general_icons/plus.ico:/QmitkDiffusionImaging/general_icons/plus.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Y false Rotation angle (in degree) around x-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false Copy Bundles :/QmitkDiffusionImaging/general_icons/copy2.ico:/QmitkDiffusionImaging/general_icons/copy2.ico false Transform Selection :/QmitkDiffusionImaging/general_icons/refresh.ico:/QmitkDiffusionImaging/general_icons/refresh.ico If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Distance of fiber sampling points (in mm) 1 0.100000000000000 0.100000000000000 1.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false Generate Fibers :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QFrame::NoFrame QFrame::Raised 0 0 0 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/refresh.xpm:/QmitkDiffusionImaging/refresh.xpm 32 32 false true Qt::Horizontal 40 20 Signal Generation Data Tissue Mask: false <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true Fiber Bundle: false <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Save path: false QFrame::NoFrame QFrame::Raised 0 0 0 0 0 - ... Noise and other Artifacts Qt::Horizontal Add Noise false Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Shrink FOV (%): false Shrink FOV by this percentage. 1 0.000000000000000 90.000000000000000 0.100000000000000 25.000000000000000 Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Num. Spikes: The number of randomly occurring signal spikes. 1 Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. 0.100000000000000 0.100000000000000 Scale: !!!EXPERIMENTAL!!! Add Eddy Current Effects false Add Spikes false QFrame::NoFrame QFrame::Raised 0 0 0 0 Variance: Variance of selected noise distribution. 4 0.000000000000000 999999999.000000000000000 0.001000000000000 50.000000000000000 Distribution: Noise distribution Rician Chi-squared Add N/2 Ghosts false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). Qt::Horizontal Qt::Horizontal Qt::Horizontal true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 6 0 0 Toggle between random movement and linear movement. Randomize motion true Rotation 0 9 0 0 Degree: false x false Axis: false Maximum rotation around x-axis. 1 360.000000000000000 1.000000000000000 0.000000000000000 Maximum rotation around z-axis. 1 360.000000000000000 1.000000000000000 15.000000000000000 y false z false Maximum rotation around y-axis. 1 360.000000000000000 1.000000000000000 0.000000000000000 Translation 0 0 0 Distance: false x false y false Axis: false z false Maximum translation along x-axis. 1 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along y-axis. 1 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along z-axis. 1 1000.000000000000000 1.000000000000000 0.000000000000000 Add Motion Artifacts false Add Distortions false Add Aliasing false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 0.250000000000000 true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 0 0 0 Magnitude: false Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). 5 1000.000000000000000 0.001000000000000 0.005000000000000 color: rgb(255, 0, 0); Experimental! Qt::Horizontal Qt::Horizontal Image Settings QFrame::NoFrame QFrame::Raised 0 0 0 0 6 TE in milliseconds 1 10000 1 100 <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> Simulate Signal Relaxation true Signal Scale: Fiber Radius: Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 0 1000 0 Line Readout Time: false <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> false Number of signal averages. Increase to reduce noise. 1 100 1 1 Repetitions: T2* relaxation time (in milliseconds). 100.000000000000000 0.100000000000000 1.000000000000000 Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false Output one image per compartment containing the corresponding volume fractions per voxel. Output Volume Fractions false <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> false Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). 1 10000 1 50 TE in milliseconds 1 10000 1 100 color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 0 0 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 3 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 - b-Value: + <html><head/><body><p>b-Value<span style=" font-style:italic;"> [s/mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">]</span>:</p></body></html> false - b-value in mm/s² + b-value in s/mm² 0 10000 100 1000 Advanced Options true <html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html> Start Simulation :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Intra-axonal Compartment Select signal model for intra-axonal compartment. Stick Model Zeppelin Model Tensor Model true Stop current simulation. Abort Simulation :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico Extra-axonal Compartments Select signal model for extra-axonal compartment. Ball Model Astrosticks Model Dot Model Select signal model for extra-axonal compartment. -- Ball Model Astrosticks Model Dot Model Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Qt::Vertical 20 40 Inter-axonal Compartment Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model 8 true Save Parameters :/QmitkDiffusionImaging/general_icons/download.ico:/QmitkDiffusionImaging/general_icons/download.ico QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 m_CircleButton m_FlipButton m_RealTimeFibers m_AdvancedOptionsBox m_DistributionBox m_VarianceBox m_FiberDensityBox m_FiberSamplingBox m_TensionBox m_ContinuityBox m_BiasBox m_GenerateFibersButton m_ConstantRadiusBox m_AlignOnGrid m_XrotBox m_YrotBox m_ZrotBox m_XtransBox m_YtransBox m_ZtransBox m_XscaleBox m_YscaleBox m_ZscaleBox m_TransformBundlesButton m_CopyBundlesButton m_JoinBundlesButton m_IncludeFiducials m_GenerateImageButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_RepetitionsBox m_SignalScaleBox m_TEbox m_LineReadoutTimeBox m_T2starBox m_FiberRadius m_RelaxationBox m_EnforcePureFiberVoxelsBox m_VolumeFractionsBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_AddNoise m_NoiseLevel m_AddSpikes m_SpikeNumBox m_SpikeScaleBox m_AddGhosts m_kOffsetBox m_AddAliasing m_WrapBox m_AddDistortions m_FrequencyMapBox m_AddMotion m_RandomMotion m_MaxRotationBoxX m_MaxRotationBoxY m_MaxRotationBoxZ m_MaxTranslationBoxX m_MaxTranslationBoxY m_MaxTranslationBoxZ m_AddEddy m_EddyGradientStrength m_AddGibbsRinging m_SaveParametersButton m_LoadParametersButton tabWidget