diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox index 75f7d7324a..eb46de4d67 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox @@ -1,109 +1,123 @@ /** \bundlemainpage{org_diffusion} MITK Diffusion Imaging (MITK-DI) This module provides means to diffusion weighted image reconstruction, visualization and quantification. Diffusion tensors as well as different q-ball reconstruction schemes are supported. Q-ball imaging aims at recovering more detailed information about the orientations of fibers from diffusion MRI measurements and, in particular, to resolve the orientations of crossing fibers. Available sections: - \ref QmitkDiffusionImagingUserManualIssues - \ref QmitkDiffusionImagingUserManualPreprocessing - \ref QmitkDiffusionImagingUserManualTensorReconstruction - \ref QmitkDiffusionImagingUserManualQBallReconstruction - \ref QmitkDiffusionImagingUserManualDicomImport - \ref QmitkDiffusionImagingUserManualQuantification - \ref QmitkDiffusionImagingUserManualVisualizationSettings - \ref QmitkDiffusionImagingUserManualReferences - \ref QmitkDiffusionImagingUserManualTechnicalDetail + - \ref QmitkDiffusionImagingUserManualSubManuals \image html overview.png The MITK Diffusion Imaging Module \section QmitkDiffusionImagingUserManualIssues Known Issues \li Dicom Import: The dicom import has so far only been implemented for Siemens dicom images. MITK-DI is capable of reading the nrrd format, which is documented elsewhere [1, 2]. These files can be created by combining the raw image data with a corresponding textual header file. The file extension should be changed from *.nrrd to *.dwi or from *.nhdr to *.hdwi respectively in order to let MITK-DI recognize the diffusion related header information provided in the files. \section QmitkDiffusionImagingUserManualPreprocessing Preprocessing The preprocessing view gives an overview over the important features of a diffusion weighted image like the number of gradient directions, b-value and the measurement frame. Additionally it allows the extraction of the B0 image and the generation of a binary brain mask. The image volume can be modified by applying a new mesurement frame, which is useful if the measurement frame is not set correctly in the image header, or by averaging redundant gradient directions. \image html prepro1.png Preprocessing \section QmitkDiffusionImagingUserManualTensorReconstruction Tensor Reconstruction The tensor reconstruction view allows ITK based tensor reconstruction [3]. The advanced settings for ITK reconstruction let you configure a manual threshold on the non-diffusion weighted image. All voxels below this threshold will not be reconstructed and left blank. It is also possible to check for negative eigenvalues. The according voxels are also left blank. \image html tensor1.png ITK tensor reconstruction A few seconds (depending on the image size) after the reconstruction button is hit, a colored image should appear in the main window. \image html tensor4.png Tensor image after reconstruction The view also allows the generation of artificial diffusion weighted or Q-Ball images from the selected tensor image. The ODFs of the Q-Ball image are directly initialized from the tensor values and afterwards normalized. The diffusion weighted image is estimated using the l2-norm image of the tensor image as B0. The gradient images are afterwards generated using the standard tensor equation. \section QmitkDiffusionImagingUserManualQBallReconstruction Q-Ball Reconstruction The q-ball reonstruction bundle implements a variety of reconstruction methods. The different reconstruction methods are described in the following: \li Numerical: The original, numerical q-ball reconstruction presented by Tuch et al. [5] \li Standard (SH): Descoteaux's reconstruction based on spherical harmonic basis functions [6] \li Solid Angle (SH): Aganj's reconstruction with solid angle consideration [7] \li ADC-profile only: The ADC-profile reconstructed with spherical harmonic basis functions \li Raw signal only: The raw signal reconstructed with spherical harmonic basis functions \image html qballs1.png The q-ball resonstruction view B0 threshold works the same as in tensor reconstruction. The maximum l-level configures the size of the spherical harmonics basis. Larger l-values (e.g. l=8) allow higher levels of detail, lower levels are more stable against noise (e.g. l=4). Lambda is a regularisation parameter. Set it to 0 for no regularisation. lambda = 0.006 has proven to be a stable choice under various settings. \image html qballs2.png Advanced q-ball reconstruction settings This is how a q-ball image should initially look after reconstruction. Standard q-balls feature a relatively low GFA and thus appear rather dark. Adjust the level-window to solve this. \image html qballs3.png q-ball image after reconstruction \section QmitkDiffusionImagingUserManualDicomImport Dicom Import The dicom import does not cover all hardware manufacturers but only Siemens dicom images. MITK-DI is also capable of reading the nrrd format, which is documented elsewhere [1, 2]. These files can be created by combining the raw image data with a corresponding textual header file. The file extension should be changed from *.nrrd to *.dwi or from *.nhdr to *.hdwi respectively in order to let MITK-DI recognize the diffusion related header information provided in the files. In case your dicom images are readable by MITK-DI, select one or more input dicom folders and click import. Each input folder must only contain DICOM-images that can be combined into one vector-valued 3D output volume. Different patients must be loaded from different input-folders. The folders must not contain other acquisitions (e.g. T1,T2,localizer). In case many imports are performed at once, it is recommended to set the the optional output folder argument. This prevents the images from being kept in memory. \image html dicom1.png Dicom import The option "Average duplicate gradients" accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "blur radius" > 0 is configured. \section QmitkDiffusionImagingUserManualQuantification Quantification The quantification view allows the derivation of different scalar anisotropy measures for the reconstructed tensors (Fractional Anisotropy, Relative Anisotropy, Axial Diffusivity, Radial Diffusivity) or q-balls (Generalized Fractional Anisotropy). \image html quantification.png Anisotropy quantification \section QmitkDiffusionImagingUserManualVisualizationSettings ODF Visualization Setting In this small view, the visualization of ODFs and diffusion images can be configured. Depending on the selected image in the data storage, different options are shown here. For tensor or q-ball images, the visibility of glyphs in the different render windows (T)ransversal, (S)agittal, and (C)oronal can be configured here. The maximal number of glyphs to display can also be configured here for. This is usefull to keep the system response time during rendering feasible. The other options configure normalization and scaling of the glyphs. In diffusion images, a slider lets you choose the desired image channel from the vector of images (each gradient direction one image) for rendering. Furthermore reinit can be performed and texture interpolation toggled. This is how a visualization with activated glyphs should look like: \image html visualization3.png Q-ball image with ODF glyph visibility toggled ON \section QmitkDiffusionImagingUserManualReferences References 1. http://teem.sourceforge.net/nrrd/format.html 2. http://www.cmake.org/Wiki/Getting_Started_with_the_NRRD_Format 3. C.F.Westin, S.E.Maier, H.Mamata, A.Nabavi, F.A.Jolesz, R.Kikinis, "Processing and visualization for Diffusion tensor MRI", Medical image Analysis, 2002, pp 93-108 5. Tuch, D.S., 2004. Q-ball imaging. Magn Reson Med 52, 1358-1372. 6. Descoteaux, M., Angelino, E., Fitzgibbons, S., Deriche, R., 2007. Regularized, fast, and robust analytical Q-ball imaging. Magn Reson Med 58, 497-510. 7. Aganj, I., Lenglet, C., Sapiro, G., 2009. ODF reconstruction in q-ball imaging with solid angle consideration. Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging Boston, MA. 8. Goh, A., Lenglet, C., Thompson, P.M., Vidal, R., 2009. Estimating Orientation Distribution Functions with Probability Density Constraints and Spatial Regularity. Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv LNCS 5761, 877 ff. \section QmitkDiffusionImagingUserManualTechnicalDetail Technical Information for Developers The diffusion imaging module uses additional properties beside the ones in use in other modules, for further information see \subpage DiffusionImagingPropertiesPage . + +\section QmitkDiffusionImagingUserManualSubManuals Manuals of componentes + +The MITK Diffusion tools consist of further components, which have their own documentation, see: + +\subpage org_fiberprocessing +\subpage org_gibbstracking +\subpage org_odfdetails +\subpage org_pvanalysis +\subpage screenshot_maker +\subpage org_stochastictracking +\subpage org_ivim + */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox index 70612c9370..a93e08af92 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox @@ -1,25 +1,25 @@ /** -\bundlemainpage{org_fiberprocessing} Fiber Processing View +\page org_fiberprocessing Fiber Processing View This view provides everything needed to process fiber bundles. Available sections: - \ref QmitkFiberProcessingUserManualFiberManpulation - \ref QmitkFiberProcessingUserManualFiberProcessing \image html fiberprocessing.png The Fiber Processing View \section QmitkFiberProcessingUserManualFiberManpulation Fiber Bundle Manipulation Fiber extraction: Place ROIs in the 2D render widgets (cricles or polygons) and extract fibers from the bundle that pass through these ROIs by selecting the according ROI and fiber bundle in the datamanger and starting the extraction. The ROIs can be combined via logical operations. All fibers that pass through the thus generated composite ROI are extracted. \section QmitkFiberProcessingUserManualFiberProcessing Generation of additional information from fiber bundles \li Tract density image: generate a 2D heatmap from a fiber bundle \li Binary envelope: generate a binary image from a fiber bundle \li Fiber bundle image: generate a 2D rgba image representation of the fiber bundle \li Fiber endings image: generate a 2D binary image showing the locations of fiber endpoints \li Fiber endings pointset: generate a poinset containing the locations of fiber endpoints */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox index 32861f1fb2..e4d56d33b5 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox @@ -1,40 +1,40 @@ /** -\bundlemainpage{org_gibbstracking} Gibbs Tracking View +\page org_gibbstracking Gibbs Tracking View This view provides the user interface for the Gibbs Tracking algorithm, a global fiber tracking algorithm, originally proposed by Reisert et.al. [1]. Available sections: - \ref QmitkGibbsTrackingUserManualInputData - \ref QmitkGibbsTrackingUserManualParameters - \ref QmitkGibbsTrackingUserManualTrackingSurveillance - \ref QmitkGibbsTrackingUserManualReferences \image html gibbstrackingview.png The Gibbs Tracking View \section QmitkGibbsTrackingUserManualInputData Input Data Mandatory Input: \li One Q-Ball image selected in the datamanager Optional Input: \li Mask Image: Float image used as probability mask for the generation of fiber segments. Usually used as binary brain mask to reduce the searchspace of the algorithm and to avoid fibers resulting from noise outside of the brain. \li GFA Image: Float image used to automatically determine the "particle weight" parameter. \section QmitkGibbsTrackingUserManualParameters Q-Ball Reconstruction \li Number of iterations: More iterations causes the algorithm to be more stable but also to take longer to finish the tracking. Rcommended: 10⁷-10⁹ iterations. \li Particle length/width/weight controlling the contribution of each particle to the model M \li Start and end temperature controlling how fast the process reaches a stable state. (usually no change needed) \li Weighting between the internal (affinity of the model to long and straigt fibers) and external energy (affinity of the model towards the data). (usually no change needed). \li Minimum fiber length constraint. Fibers containing less segments are discarded after the tracking. (usually no change needed) \section QmitkGibbsTrackingUserManualTrackingSurveillance Surveilance of the tracking process Once started, the tracking can be monitored via the textual output that informs about the tracking progress and several stats of the current state of the algorithm. If enabled, the intermediate tracking results are displayed in the renderwindows each second. This live visualization should usually be disabled for performance reasons. It can be turned on and off during the tracking process via the according checkbox. \section QmitkGibbsTrackingUserManualReferences References [1] Reisert, M., Mader, I., Anastasopoulos, C., Weigel, M., Schnell, S., Kiselev, V.: Global fiber reconstruction becomes practical. Neuroimage 54 (2011) 955-962 */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox index 024eb4e3f3..e7098f064f 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox @@ -1,11 +1,11 @@ /** -\bundlemainpage{org_odfdetails} ODF Details View +\page org_odfdetails ODF Details View This view provides detailed information about the orentation distribution function at the current crosshair position (if a Q-Ball image is selected). A visualization of the ODF as well as the ODF values and according statistical information are displayed. \image html odfdetails.png The Gibbs Tracking View \section QmitkOdfDetailsUserManualInputData Issues At the moment this view can opnly process Q-Ball images but not tensor images. Also the normalization properties etc. of the image as well as the correct rotation of the ODF are currently not incorporated into the views visualization. */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox index 56a9baf5bf..a515ad40fc 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox @@ -1,23 +1,23 @@ /** -\bundlemainpage{org_pvanalysis} Partial Volume Analysis +\page org_pvanalysis Partial Volume Analysis The "Partial Volume Analysis" view can be found in the "Quantification" perspective. It allows for robust quantification of diffusion or other scalar measures in the presents of two classes (e.g. fiber vs. non-fiber) and partial volume between them. The algorithm estimates a probabilistic segmentation of the three classes and returns a weighted average of the measure of interest within the each class. \image html pvanalysisview.png The Partial Volume Analysis View \section QmitkPVAAnalysisUserManualExport Export All measures are automatically written to the clipboard once the estimation is updated. The histogram export is provided by the button underneath the histogram. The values can be pasted to excel or any text editor. \section QmitkPVAAnalysisUserManualAdvancedSettings Advanced Settings Are not recommended for use yet. \section QmitkPVAAnalysisUserManualSuggestedReadings Suggested Readings Diffusion tensor imaging in primary brain tumors: reproducible quantitative analysis of corpus callosum infiltration and contralateral involvement using a probabilistic mixture model. Stieltjes B, Schlüter M, Didinger B, Weber MA, Hahn HK, Parzer P, Rexilius J, Konrad-Verse O, Peitgen HO, Essig M. Neuroimage. 2006 Jun;31(2):531-42. Epub 2006 Feb 14. PMID: 16478665 */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkScreenshotMakerManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkScreenshotMakerManual.dox index 5aa9a25861..9f2e96a063 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkScreenshotMakerManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkScreenshotMakerManual.dox @@ -1,19 +1,19 @@ /** -\bundlemainpage{screenshot_maker} The Screenshot Maker +\page screenshot_maker The Screenshot Maker This module provides the functionality to create and save screenshots of the data. Available sections: - \ref QmitkScreenshotMakerUserManualUse \image html screenshot_maker_interface.png The Screenshot Maker User Interface \section QmitkScreenshotMakerUserManualUse Usage The first section offers the option of creating a screenshot of the last activated render window (thus the one, which was last clicked into). Upon clicking the button, the Screenshot Maker asks for a filename in which the screenshot is to be stored. The multiplanar Screenshot button asks for a folder, where screenshots of the three 2D views will be stored with default names. The high resolution screenshot section works the same as the simple screenshot section, aside from the fact, that the user can choose a magnification factor. In the option section one can rotate the camera in the 3D view by using the buttons. Furthermore one can choose the background colour for the screenshots, default is black. */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox index de28249594..7f899fc34a 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox @@ -1,36 +1,36 @@ /** -\bundlemainpage{org_stochastictracking} Stochastic Tracking View +\page org_stochastictracking Stochastic Tracking View This view provides the user interface for the Stochastic Fibertracking algorithm, proposed by Ngo [1]. Available sections: - \ref QmitkStochasticTrackingUserManualInputData - \ref QmitkStochasticTrackingUserManualParameters - \ref QmitkStochasticTrackingUserManualReferences \image html stochastictrackingview.png Stochastic Tracking View \image html segmentationview.png Segmentation View to define ROIs \section QmitkStochasticTrackingUserManualInputData Input Data Mandatory Input: \li For a successful execution of the stochastic tractography filter, a DWI input and a binary image defining the desired ROI are required. The ROI serves as the origin from where on the fibers are beeing tracked. Both, DWI and ROI data can be imported via drag n drop or via the opening dialog box provided by MITK. Alternatively, the segmentation view offers tools for generating ROI data. \li One DWI Image image selected in the datamanager \li One or more ROIs selected in the datamanager \section QmitkStochasticTrackingUserManualParameters Input Parameters \li Parameters such as max. tract length (Tract_len), number of total tracts per voxel (TotalTracts) and likelihood cache size in MB (Lkhd chache) are individually set by the user. \li After successfully setting necessary Input and Parameter, pressing the command button executes the algorithm. \section QmitkStochasticTrackingUserManualReferences References [1] Tri M. Ngo, Polina Golland, and Tri M. Ngo. A stochastic tractography system and applications, 2007 */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkUserIVIMViewManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkUserIVIMViewManual.dox index 6c8b113953..1ed8f2af10 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkUserIVIMViewManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkUserIVIMViewManual.dox @@ -1,41 +1,41 @@ /** -\bundlemainpage{org_ivim} Intra-voxel incoherent motion estimation (IVIM) +\page org_ivim Intra-voxel incoherent motion estimation (IVIM) The required input for the "Intra-voxel incoherent motion estimation" (IVIM) is a diffusion weighted image (.dwi or .hdwi) that was acquired with several different b-values. \image html ivimview.png The IVIM View Once an input image is selected in the datamanager, the IVIM view allows for interactive exploration of the dataset (click around in the image and watch the estimated parameters in the figure of the view) as well as generation of f-, D-, and D*-maps (activate the checkmarks and press "Generate Output Images"). The "neglect b<" threshold allows you to ignore b-values smaller then a threshold for the initial fit of f and D. D* is then estimated using all measurements. The exact values of the current fit are always given in the legend underneath the figure. \section QmitkDiffusionImagingUserManualInputData Region of interest analysis Create region of interest: To create a new segmentatin, open the "quantification" perspective, select the tab "Segmentation", and create a segmentation of the structure of interest. Alternatively, of course, you may also load a binary image from file or generate your segmentation in any other possible way. IVIM in region of interset: Go back to the "IVIM" perspective and select both, the diffusion image and the segmentation (holding the CTRL key). A red message should appear "Averaging N voxels". \section QmitkDiffusionImagingUserManualInputData Export All model parameters and corresponding curves can be exported to clipboard using the buttons underneath the figure. \section QmitkDiffusionImagingUserManualInputData Advanced Settings Advanced users, that know what they are doing, can change the method for the model-fit under "Advanced Settings" on the very bottom of the view. 3-param fit, linear fit of f/D, and fix D* are among the options. \section QmitkDiffusionImagingUserManualInputData Suggested Readings Toward an optimal distribution of b values for intravoxel incoherent motion imaging. Lemke A, Stieltjes B, Schad LR, Laun FB. Magn Reson Imaging. 2011 Jul;29(6):766-76. Epub 2011 May 5. PMID: 21549538 Differentiation of pancreas carcinoma from healthy pancreatic tissue using multiple b-values: comparison of apparent diffusion coefficient and intravoxel incoherent motion derived parameters. Lemke A, Laun FB, Klauss M, Re TJ, Simon D, Delorme S, Schad LR, Stieltjes B. Invest Radiol. 2009 Dec;44(12):769-75. PMID: 19838121 */