diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake
index 2470e9a742..3966936404 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake
@@ -1,73 +1,77 @@
set(SRC_CPP_FILES
QmitkTensorModelParametersWidget.cpp
QmitkZeppelinModelParametersWidget.cpp
QmitkStickModelParametersWidget.cpp
QmitkDotModelParametersWidget.cpp
QmitkBallModelParametersWidget.cpp
QmitkAstrosticksModelParametersWidget.cpp
QmitkPrototypeSignalParametersWidget.cpp
)
set(INTERNAL_CPP_FILES
QmitkFiberfoxView.cpp
QmitkFieldmapGeneratorView.cpp
QmitkFiberGenerationView.cpp
mitkPluginActivator.cpp
Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.cpp
)
set(UI_FILES
src/internal/QmitkFiberfoxViewControls.ui
src/internal/QmitkFieldmapGeneratorViewControls.ui
src/internal/QmitkFiberGenerationViewControls.ui
src/QmitkTensorModelParametersWidgetControls.ui
src/QmitkZeppelinModelParametersWidgetControls.ui
src/QmitkStickModelParametersWidgetControls.ui
src/QmitkDotModelParametersWidgetControls.ui
src/QmitkBallModelParametersWidgetControls.ui
src/QmitkAstrosticksModelParametersWidgetControls.ui
src/QmitkPrototypeSignalParametersWidgetControls.ui
)
set(MOC_H_FILES
src/internal/mitkPluginActivator.h
src/internal/QmitkFiberfoxView.h
src/internal/QmitkFieldmapGeneratorView.h
src/internal/QmitkFiberGenerationView.h
src/QmitkTensorModelParametersWidget.h
src/QmitkZeppelinModelParametersWidget.h
src/QmitkStickModelParametersWidget.h
src/QmitkDotModelParametersWidget.h
src/QmitkBallModelParametersWidget.h
src/QmitkAstrosticksModelParametersWidget.h
src/QmitkPrototypeSignalParametersWidget.h
src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h
)
set(CACHED_RESOURCE_FILES
plugin.xml
resources/phantom.png
resources/syntheticdata.png
resources/fieldmap.png
resources/models.png
+ resources/download.png
+ resources/right.png
+ resources/stop.png
+ resources/upload.png
)
set(QRC_FILES
resources/QmitkFiberfox.qrc
)
set(CPP_FILES )
foreach(file ${SRC_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/${file})
endforeach(file ${SRC_CPP_FILES})
foreach(file ${INTERNAL_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/internal/${file})
endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc
index e369c9cd94..6ecec32167 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc
@@ -1,10 +1,10 @@
- download.ico
- right.ico
- stop.ico
- upload.ico
circle.png
refresh.xpm
+ download.png
+ right.png
+ stop.png
+ upload.png
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.ico b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.ico
deleted file mode 100644
index a991a963c8..0000000000
Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.ico and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.png
new file mode 100644
index 0000000000..5949729192
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.ico b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.ico
deleted file mode 100644
index 6a06a666a4..0000000000
Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.ico and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.png
new file mode 100644
index 0000000000..3201e76d25
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.ico b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.ico
deleted file mode 100644
index 292166968c..0000000000
Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.ico and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.png
new file mode 100644
index 0000000000..108c60b1a1
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.ico b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.ico
deleted file mode 100644
index 9b85d6ed4b..0000000000
Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.ico and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui
index cb7474b639..fe7ddca672 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui
@@ -1,2891 +1,2891 @@
QmitkFiberfoxViewControls
0
0
490
2775
Form
-
QGroupBox {
background-color: transparent;
}
Intra-axonal Compartment
6
6
6
6
-
-
-
-
Select signal model for intra-axonal compartment.
-
Stick Model
-
Zeppelin Model
-
Tensor Model
-
Prototype Signal
-
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Volume Fraction:
-
Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers.
-
QGroupBox {
background-color: transparent;
}
Inter-axonal Compartment
6
6
6
6
-
Select signal model for intra-axonal compartment.
-
--
-
Stick Model
-
Zeppelin Model
-
Tensor Model
-
-
-
-
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Volume Fraction:
-
Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers.
-
QGroupBox {
background-color: transparent;
}
Image Settings
6
6
6
6
-
color: rgb(255, 0, 0);
Using geometry of selected image!
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
6
-
Inversion time (in ms) for inversion recovery sequences. If 0, no inversion pulse is simulated.
0
999999999
1
0
-
<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
-
Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds).
1
10000
1
50
-
<html><head/><body><p>Repetition Time <span style=" font-style:italic;">TR</span>: </p></body></html>
false
-
TE in milliseconds
1
999999999
1
100
-
Partial Fourier:
false
-
Partial fourier factor (0.5-1)
3
0.500000000000000
1.000000000000000
0.100000000000000
1.000000000000000
-
Output one image per compartment containing the corresponding volume fractions per voxel.
Reverse Phase Encoding Direction
false
-
Dwell time (time to read one line in k-space) in ms.
4
100.000000000000000
0.100000000000000
1.000000000000000
-
Number of coil elements used for the acquisiton.
1
128
1
1
-
Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation.
9999.000000000000000
-
Dwell Time:
false
-
Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present.
Disable Partial Volume Effects
false
-
Acquisition Type:
-
Fiber Radius:
-
Signal Scale:
-
<html><head/><body><p>Number of Channels:</p></body></html>
false
-
TR in milliseconds
1
999999999
1
4000
-
-
Single Shot EPI
-
Conventional Spin Echo
-
Fast Spin Echo
-
1
100000
1
100
-
-
Constant
-
Linear
-
Exponential
-
<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
-
<html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html>
false
-
<html><head/><body><p>Coil Sensitivity:</p></body></html>
false
-
<html><head/><body><p>Inversion Time <span style=" font-style:italic;">TI</span>: </p></body></html>
false
-
Output phase image and volume fraction maps.
Output Additional Images
false
-
<html><head/><body><p>Echo Train Length: </p></body></html>
false
-
Only relevant for Fast Spin Echo sequence (number of k-space lines acquired with one RF pulse)
1
999999999
1
8
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
6
-
<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 s/mm²
0
10000
100
1000
-
Gradient Directions:
-
Number of gradient directions distributed over the half sphere.
0
10000
1
30
-
Advanced Options
-
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
20
-
Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.
1
1000
1
20
-
Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.
1
1000
1
3
-
Use bvals/bvecs files
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
...
-
...
-
-
false
-
Bvecs:
false
-
Bvals:
false
-
-
false
-
QGroupBox {
background-color: transparent;
}
Extra-axonal Compartments
6
6
6
6
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Volume Fraction:
-
-
Select signal model for extra-axonal compartment.
-
Ball Model
-
Astrosticks Model
-
Dot Model
-
Prototype Signal
-
-
-
-
-
Qt::Horizontal
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Volume Fraction:
-
Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers.
-
-
-
-
Select signal model for extra-axonal compartment.
-
--
-
Ball Model
-
Astrosticks Model
-
Dot Model
-
Prototype Signal
-
-
QGroupBox {
background-color: transparent;
}
Noise and other Artifacts
6
6
6
6
-
Qt::Horizontal
-
true
QFrame::NoFrame
QFrame::Raised
0
6
0
0
6
-
Toggle between random movement and linear movement.
Randomize motion
true
-
QGroupBox {
background-color: transparent;
}
Rotation
6
9
6
6
-
Degree:
false
-
x
false
-
Axis:
false
-
Maximum rotation around x-axis.
1
-360.000000000000000
360.000000000000000
1.000000000000000
0.000000000000000
-
Maximum rotation around z-axis.
1
-360.000000000000000
360.000000000000000
1.000000000000000
15.000000000000000
-
y
false
-
z
false
-
Maximum rotation around y-axis.
1
-360.000000000000000
360.000000000000000
1.000000000000000
0.000000000000000
-
QGroupBox {
background-color: transparent;
}
Translation
6
6
6
-
Distance:
false
-
x
false
-
y
false
-
Axis:
false
-
z
false
-
Maximum translation along x-axis.
1
-1000.000000000000000
1000.000000000000000
1.000000000000000
0.000000000000000
-
Maximum translation along y-axis.
1
-1000.000000000000000
1000.000000000000000
1.000000000000000
0.000000000000000
-
Maximum translation along z-axis.
1
-1000.000000000000000
1000.000000000000000
1.000000000000000
0.000000000000000
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Motion volumes:
-
Type in the volume indices that should be affected by motion (e.g. "0 3 7" whithout quotation marks). Leave blank for motion in all volumes. Type in "random" to randomly select volumes for motion. A list of negative numbers (e.g. -1 -2 -3) excludes volumes (e.g. 1 2 3) selects all remaining volumes.
random
-
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:
-
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
40.000000000000000
-
Qt::Horizontal
-
true
QFrame::NoFrame
QFrame::Raised
6
0
0
0
0
-
Signal Reduction (%):
false
-
Global signal in last simulated volume is specified percentage lower than in the first volume.
1
100.000000000000000
1.000000000000000
6.000000000000000
-
true
QFrame::NoFrame
QFrame::Raised
6
0
0
0
0
-
Frequency Map:
false
-
Select image specifying the frequency inhomogeneities (in Hz).
-
true
QFrame::NoFrame
QFrame::Raised
QFormLayout::AllNonFixedFieldsGrow
6
0
0
0
0
-
Gradient:
false
-
Eddy current induced magnetic field gradient (in mT/m).
5
1000.000000000000000
0.001000000000000
0.002000000000000
-
Qt::Horizontal
-
Add Eddy Current Effects
false
-
Add Distortions
false
-
Add Spikes
false
-
Add Signal Drift
false
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Variance:
-
Variance of selected noise distribution.
10
0.000000000000000
999999999.000000000000000
0.001000000000000
50.000000000000000
-
Distribution:
-
Noise distribution
-
Complex Gaussian
-
Rician
-
Qt::Horizontal
-
Qt::Horizontal
-
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
-
Add Motion Artifacts
false
-
Add N/2 Ghosts
false
-
Qt::Horizontal
-
Add ringing artifacts occuring at strong edges in the image.
Add Gibbs Ringing
false
-
Qt::Horizontal
-
Add Noise
false
-
Qt::Horizontal
-
Add Aliasing
false
-
If > 0, ringing is simulated by by setting the defined percentage of higher frequencies to 0 in k-space. Otherwise, the input to the k-space simulation is generated with twice the resolution and cropped during k-space simulation (much slower).
100
10
-
Qt::Vertical
20
40
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
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>
Save Parameters
- :/QmitkFiberfox/download.ico:/QmitkFiberfox/download.ico
+ :/QmitkFiberfox/download.png:/QmitkFiberfox/download.png
-
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>
Load Parameters
- :/QmitkFiberfox/upload.ico:/QmitkFiberfox/upload.ico
+ :/QmitkFiberfox/upload.png:/QmitkFiberfox/upload.png
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
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
- :/QmitkFiberfox/right.ico:/QmitkFiberfox/right.ico
+ :/QmitkFiberfox/right.png:/QmitkFiberfox/right.png
-
QGroupBox {
background-color: transparent;
}
Input Data
6
6
6
6
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
0
-
-
-
...
-
<html><head/><body><p>Select a binary image to define the area of signal generation. Outside of the mask image only noise will be actively generated.</p></body></html>
QComboBox::AdjustToMinimumContentsLength
-
Fiber Bundle:
false
-
Save path:
false
-
Tissue Mask:
false
-
<html><head/><body><p>Select a fiber bundle to generate the white matter signal from. You can either use the fiber definition tab to manually define an input fiber bundle or you can also use any existing bundle, e.g. yielded by a tractography algorithm.</p></body></html>
QComboBox::AdjustToMinimumContentsLength
-
Template Image:
false
-
<html><head/><body><p>The parameters for the simulation (e.g. spacing, size, diffuison-weighted gradients, b-value) are adopted from this image.</p></body></html>
QComboBox::AdjustToMinimumContentsLength
-
true
Stop current simulation.
Abort Simulation
- :/QmitkFiberfox/stop.ico:/QmitkFiberfox/stop.ico
+ :/QmitkFiberfox/stop.png:/QmitkFiberfox/stop.png
-
Courier
7
true
QmitkDataStorageComboBox
QComboBox
QmitkDataStorageComboBox.h
QmitkDataStorageComboBoxWithSelectNone
QComboBox
QmitkDataStorageComboBoxWithSelectNone.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
QmitkPrototypeSignalParametersWidget
QWidget
QmitkPrototypeSignalParametersWidget.h
1
m_FiberBundleComboBox
m_MaskComboBox
m_TemplateComboBox
m_SavePathEdit
m_OutputPathButton
m_GenerateImageButton
m_AbortSimulationButton
m_SimulationStatusText
m_LoadParametersButton
m_SaveParametersButton
m_SizeX
m_SizeY
m_SizeZ
m_SpacingX
m_SpacingY
m_SpacingZ
m_UseBvalsBvecsBox
m_LoadBvalsEdit
m_LoadBvalsButton
m_LoadBvecsEdit
m_LoadBvecsButton
m_NumGradientsBox
m_BvalueBox
m_AdvancedOptionsBox_2
m_AcquisitionTypeBox
m_SignalScaleBox
m_NumCoilsBox
m_CoilSensBox
m_TEbox
m_TRbox
m_TIbox
m_LineReadoutTimeBox
m_PartialFourier
m_T2starBox
m_FiberRadius
m_ReversePhaseBox
m_RelaxationBox
m_EnforcePureFiberVoxelsBox
m_VolumeFractionsBox
m_Compartment1Box
m_Comp1VolumeFraction
m_Compartment2Box
m_Comp2VolumeFraction
m_Compartment3Box
m_Comp3VolumeFraction
m_Compartment4Box
m_Comp4VolumeFraction
m_AddNoise
m_NoiseDistributionBox
m_NoiseLevel
m_AddSpikes
m_SpikeNumBox
m_SpikeScaleBox
m_AddGhosts
m_kOffsetBox
m_AddAliasing
m_WrapBox
m_AddDistortions
m_FrequencyMapBox
m_AddDrift
m_DriftFactor
m_AddMotion
m_RandomMotion
m_MotionVolumesBox
m_MaxRotationBoxX
m_MaxRotationBoxY
m_MaxRotationBoxZ
m_MaxTranslationBoxX
m_MaxTranslationBoxY
m_MaxTranslationBoxZ
m_AddEddy
m_EddyGradientStrength
m_AddGibbsRinging
m_ZeroRinging
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/files.cmake
index 2830598670..b29fbe3471 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/files.cmake
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/files.cmake
@@ -1,51 +1,51 @@
set(INTERNAL_CPP_FILES
QmitkGibbsTrackingView.cpp
QmitkStreamlineTrackingView.cpp
Perspectives/QmitkGibbsTractographyPerspective.cpp
Perspectives/QmitkStreamlineTractographyPerspective.cpp
mitkPluginActivator.cpp
)
set(UI_FILES
src/internal/QmitkGibbsTrackingViewControls.ui
src/internal/QmitkStreamlineTrackingViewControls.ui
)
set(MOC_H_FILES
src/internal/mitkPluginActivator.h
src/internal/QmitkGibbsTrackingView.h
src/internal/QmitkStreamlineTrackingView.h
src/internal/Perspectives/QmitkGibbsTractographyPerspective.h
src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h
)
set(CACHED_RESOURCE_FILES
plugin.xml
resources/tract.png
resources/tractogram.png
resources/ml_tractography.png
- resources/upload.ico
- resources/download.ico
- resources/right.ico
- resources/stop.ico
+ resources/download.png
+ resources/right.png
+ resources/stop.png
+ resources/upload.png
)
set(QRC_FILES
resources/QmitkTractography.qrc
)
set(CPP_FILES )
foreach(file ${SRC_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/${file})
endforeach(file ${SRC_CPP_FILES})
foreach(file ${INTERNAL_CPP_FILES})
set(CPP_FILES ${CPP_FILES} src/internal/${file})
endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/QmitkTractography.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/QmitkTractography.qrc
index 4293d887c0..4bfc5c2a11 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/QmitkTractography.qrc
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/QmitkTractography.qrc
@@ -1,8 +1,8 @@
- download.ico
- right.ico
- stop.ico
- upload.ico
+ upload.png
+ download.png
+ right.png
+ stop.png
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.ico b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.ico
deleted file mode 100644
index a991a963c8..0000000000
Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.ico and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.png
new file mode 100644
index 0000000000..5949729192
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.ico b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.ico
deleted file mode 100644
index 6a06a666a4..0000000000
Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.ico and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.png
new file mode 100644
index 0000000000..3201e76d25
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.ico b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.ico
deleted file mode 100644
index 292166968c..0000000000
Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.ico and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.png
new file mode 100644
index 0000000000..108c60b1a1
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.ico b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.ico
deleted file mode 100644
index 9b85d6ed4b..0000000000
Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.ico and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.png
new file mode 100644
index 0000000000..6abef3f7d7
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.png differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui
index 82313381e7..4c040ada44 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui
@@ -1,1698 +1,1698 @@
QmitkStreamlineTrackingViewControls
0
0
453
859
0
0
QmitkTemplate
QCommandLinkButton:disabled {
border: none;
}
QGroupBox {
background-color: transparent;
}
3
3
0
40
-
QFrame::NoFrame
QFrame::Raised
0
15
0
0
6
15
-
true
0
0
true
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
0
-
true
Save parameters to json file
Save Parameters
- :/QmitkTractography/download.ico:/QmitkTractography/download.ico
+ :/QmitkTractography/download.png:/QmitkTractography/download.png
-
true
Load parameters from json file
Load Parameters
- :/QmitkTractography/upload.ico:/QmitkTractography/upload.ico
+ :/QmitkTractography/upload.png:/QmitkTractography/upload.png
-
false
Start Tractography
- :/QmitkTractography/right.ico:/QmitkTractography/right.ico
+ :/QmitkTractography/right.png:/QmitkTractography/right.png
-
true
Stop tractography and return all fibers reconstructed until now.
Stop Tractography
- :/QmitkTractography/stop.ico:/QmitkTractography/stop.ico
+ :/QmitkTractography/stop.png:/QmitkTractography/stop.png
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Input Image. ODF, tensor and peak images are currently supported.
Input Image:
-
Input Image. ODF, tensor, peak, and, in case of ML tractography, raw diffusion-weighted images are currently supported.
<html><head/><body><p><span style=" color:#ff0000;">select image in data-manager</span></p></body></html>
true
-
Tractography Forest:
-
-
0
0
0
0
75
true
0
0
0
421
254
Seeding
Specify how, where and how many tractography seed points are placed.
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Number of seed points equally distributed around selected position.
1
9999999
50
-
Radius:
-
Seedpoints are equally distributed within a sphere centered at the selected position with the specified radius (in mm).
2
50.000000000000000
0.100000000000000
2.000000000000000
-
Num. Seeds:
-
true
When checked, parameter changes cause instant retracking while in interactive mode.
Update on Parameter Change
true
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Try each seed N times until a valid streamline is obtained (only for probabilistic tractography).
Minimum fiber length (in mm)
1
999
10
-
Trials Per Seed:
-
Max. Num. Fibers:
-
Tractography is stopped after the desired number of fibers is reached, even before all seed points are processed (-1 means no limit).
-1
999999999
-1
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Seeds per Voxel:
-
Seed Image:
-
Number of seed points placed in each voxel.
1
9999999
-
-
true
Dynamically pick a seed location by click into image.
Enable Interactive Tractography
-
Qt::Vertical
20
40
0
0
435
- 169
+ 184
ROI Constraints
Specify various ROI and mask images to constrain the tractography process.
-
Mask Image:
-
Select which fibers should be accepted or rejected based on the location of their endpoints.
QComboBox::AdjustToMinimumContentsLength
-
No Constraints on EP locations
-
Both EPs in Target Image
-
Both EPs in Target Image But Different Label
-
One EP in Seed Image and One EP in Target Image
-
At Least One EP in Target Image
-
Exactly One EP in Target Image
-
No EP in Target Image
-
Endpoint Constraints:
-
Stop ROI Image:
-
Exclusion ROI Image:
-
Target ROI Image:
-
Qt::Vertical
20
40
-
-
-
-
0
- -228
+ 0
421
428
Tractography Parameters
Specify the behavior of the tractography at each streamline integration step (step size, deterministic/probabilistic, ...).
-
Minimum tract length in mm. Shorter fibers are discarded.
Minimum fiber length (in mm)
1
999.000000000000000
1.000000000000000
20.000000000000000
-
f parameter of tensor tractography. f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!).
f:
-
f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!).
2
1.000000000000000
0.100000000000000
0.000000000000000
-
Sharpen ODFs:
-
Fix Random Seed:
-
Maximum allowed angular SDTEV over 4 voxel lengths. Default: no loop check.
-1
180
-1
-
Angular Threshold:
-
Max. Tract Length:
-
Cutoff:
-
If you are using dODF images as input, it is advisable to sharpen the ODFs (min-max normalize and raise to the power of 4). This is not necessary for CSD fODFs, since they are naturally much sharper.
-
Angular threshold between two steps (in degree). Default: 90° * step_size
-1
90
1
-1
-
Qt::Vertical
20
40
-
f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!).
2
1.000000000000000
0.100000000000000
1.000000000000000
-
Toggle between deterministic and probabilistic tractography. Some modes might not be available for all types of tractography.
-
Deterministic
-
Probabilistic
-
Mode:
-
Additional threshold on the ODF magnitude. This is useful in case of CSD fODF tractography. For fODFs a good default value is 0.1, for normalized dODFs, e.g. Q-ball ODFs, this threshold should be very low (0.00025) or 0.
5
1.000000000000000
0.100000000000000
0.000250000000000
-
Min. Tract Length:
-
FA/GFA Image:
-
Loop Check:
-
Minimum tract length in mm. Shorter fibers are discarded.
Maximum fiber length (in mm)
1
999.000000000000000
1.000000000000000
400.000000000000000
-
Always produce the same random numbers.
-
Step Size:
-
ODF Cutoff:
-
Step size (in voxels)
2
0.010000000000000
10.000000000000000
0.100000000000000
0.500000000000000
-
g:
-
-
Threshold on peak magnitude, FA, GFA, ...
5
1.000000000000000
0.100000000000000
0.100000000000000
-
Peak Jitter:
-
Important for probabilistic peak tractography and peak prior. Actual jitter is drawn from a normal distribution with peak_jitter*fabs(direction_value) as standard deviation.
3
1.000000000000000
0.100000000000000
0.010000000000000
0
0
435
- 169
+ 184
Tractography Prior
-
Weight:
-
Weighting factor between prior and data.
1.000000000000000
0.100000000000000
0.500000000000000
-
Peak Image:
-
Qt::Vertical
20
40
-
If unchecked, the prior cannot create directions where there are none in the data.
true
-
New Directions from Prior:
-
Restrict to Prior:
-
-
Restrict tractography to regions where the prior is valid.
true
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
0
-
y
-
x
-
z
-
Flip Directions:
0
0
435
- 169
+ 184
Neighborhood Sampling
Specify if and how information about the current streamline neighborhood should be used.
-
Only neighborhood samples in front of the current streamline position are considered.
Use Only Frontal Samples
false
-
If checked, the majority of sampling points has to place a stop-vote for the streamline to terminate. If not checked, all sampling positions have to vote for a streamline termination.
Use Stop-Votes
false
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Num. Samples:
-
Number of neighborhood samples that are used to determine the next fiber progression direction.
50
-
Sampling Distance:
-
Sampling distance (in voxels)
2
10.000000000000000
0.100000000000000
0.250000000000000
-
Qt::Vertical
20
40
0
0
435
- 169
+ 184
Data Handling
Specify interpolation and direction flips.
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Trilinearly interpolate the input image used for tractography.
Interpolate Tractography Data
true
-
Trilinearly interpolate the ROI images used to constrain the tractography.
Interpolate ROI Images
true
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Internally flips progression directions. This might be necessary depending on the input data.
x
-
Internally flips progression directions. This might be necessary depending on the input data.
y
-
Internally flips progression directions. This might be necessary depending on the input data.
z
-
Flip directions:
-
Qt::Vertical
20
40
0
0
435
- 169
+ 184
Output and Postprocessing
Specify the tractography output (streamlines or probability maps) and postprocessing steps.
-
QFrame::NoFrame
QFrame::Raised
0
0
0
0
-
Compress fibers using the specified error constraint.
Compress Fibers
true
-
Qt::StrongFocus
Lossy fiber compression. Recommended for large tractograms. Maximum error in mm.
3
10.000000000000000
0.010000000000000
0.100000000000000
-
Output map with voxel-wise visitation counts instead of streamlines.
Output Probability Map
false
-
Qt::Vertical
20
40
QmitkSingleNodeSelectionWidget
QWidget
QmitkSingleNodeSelectionWidget.h
1