diff --git a/Documentation/Doxygen/UserManual/MiniApps.dox b/Documentation/Doxygen/UserManual/MiniApps.dox new file mode 100644 index 0000000000..104522399f --- /dev/null +++ b/Documentation/Doxygen/UserManual/MiniApps.dox @@ -0,0 +1,70 @@ +/** +\page MiniAppExplainPage MITK MiniApps + +\section MiniAppDescription What are MiniApps + +MiniApps are small compilations of command line tools. Each of these tools is designed to fulfill one simple task, +e.g. resample an image or extract image statistics of a given region of interest (ROI). Several tools that relate to +a similiar topic or research area are grouped into one MiniApp. + +They are intended to provide command line access to a variety of features of MITK, thus facilitating batched processing of data. + +\section MiniAppUsage Usage + +The MiniApps are built in a self-describing way. When calling a MiniApp without any arguements it will list +all available sub-tools. When calling e.g. the DiffusionMiniApp it will look similarly to this: + +\code +$./MitkDiffusionMiniApps + +Please choose the mini app to execute: +(0) BatchedFolderRegistration +(1) CopyGeometry +(2) DicomFolderDump +(3) DiffusionIndices +(4) DwiDenoising +(5) ExportShImage +(6) ExtractImageStatistics +(7) FiberDirectionExtraction +(8) FiberProcessing +(9) FileFormatConverter +(10) GibbsTracking +(11) LocalDirectionalFiberPlausibility +(12) MultishellMethods +(13) NetworkCreation +(14) NetworkStatistics +(15) PeakExtraction +(16) PeaksAngularError +(17) QballReconstruction +(18) StreamlineTracking +(19) TensorDerivedMapsExtraction +(20) TensorReconstruction +Please select: +\endcode + +In order to select one of those tools simply append the displayed name to call, e.g. GibbsTracking +this will provide a listing of the parameters of that tool: +\code +$./MitkDiffusionMiniApps GibbsTracking + +[1.081] Start GibbsTracking .. + -i, --input, input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image) + -p, --parameters, parameter file (.gtp) + -m, --mask, binary mask image (optional) + -s, --shConvention, sh coefficient convention (FSL, MRtrix) (optional), (default: FSL) + -o, --outFile, output fiber bundle (.fib) + -f, --noFlip, do not flip input image to match MITK coordinate convention (optional) +\endcode + +To execute the tool with parameters an exemplary call would look like this: + +\code +$./MitkDiffusionMiniApps GibbsTracking -i test.dti -p param.gtp -o /tmp/fiber.fib +\endcode + + +\section MiniAppAvailableList Available MiniApps + +\li \ref DiffusionMiniApps + +*/ diff --git a/Documentation/Doxygen/UserManual/UserManualPortal.dox b/Documentation/Doxygen/UserManual/UserManualPortal.dox index 995dddb941..94b5bf8e9d 100644 --- a/Documentation/Doxygen/UserManual/UserManualPortal.dox +++ b/Documentation/Doxygen/UserManual/UserManualPortal.dox @@ -1,20 +1,21 @@ /** \usersguidemainpage{UserManualPortal} MITK: User Manual To get an introduction to the usage of any MITK based application please read \ref MITKUserManualPage. It will give you an overview of most of the common questions, such as how to load or save data or navigate within it. This is a good starting point for first questions. Depending on what kind of work you intend do perform with MITK, certain applications are better suited to your needs than others. MITK offers a number of these Applications, each of which features a set of Plugins, which can solve certain tasks. To Learn more about MITK applications, please visit the \ref ApplicationsPage. For more specific information on how a plugin operates you can find the plugin documentation in \ref PluginListPage. The Plugin documentation usually explains the functionality in depth and should solve most problems you might encounter with the plugin. Depending on the application you are using you might have only some or all of the listed plugins available. Lastly, if your question is not answered here, please use our Mailinglist to let us know about your problem. Alternatively, you can contact us directly.

UserManualPortalTopics List of topics

-*/ \ No newline at end of file +*/ diff --git a/Modules/DiffusionImaging/MiniApps/Documentation/DiffusionMiniApps.dox b/Modules/DiffusionImaging/MiniApps/Documentation/DiffusionMiniApps.dox new file mode 100644 index 0000000000..36ba822295 --- /dev/null +++ b/Modules/DiffusionImaging/MiniApps/Documentation/DiffusionMiniApps.dox @@ -0,0 +1,180 @@ +/** +\page DiffusionMiniApps MITK Diffusion MiniApps + +\tableofcontents + +The respective MiniApp is called MitkDiffusionMiniApp and is shipped with the current MITK Diffusion installer. +This page intends to provide an overview of all tools that are included in the DiffusionMiniApp. Also it relates them +to the respective Plugin in the MITK Diffusion application (if one exists). +For a detailed list of parameters call the according tool without any arguments (see \ref MiniAppExplainPage for details on this) or refer its Plugin equivalent. + +\section Preprocessing Preprocessing Tools + + +\subsection BatchedFolderRegistratuion Batched Folder Registration + +Allows to register a series of images (of different modalities, including diffusion weighted) to one reference image. It allows to register derived resources (e.g. a segmentation on +a T2 image) using the transformation of the original (T2) image. + +For the following examples assume a folder containing a longitudinal study with T1,T2, DWI images and segmentations (ROI) : + +\code +Patien01_2010-1.dwi +Patien01_2010-1_T1.nrrd +Patien01_2010-1_T2.nrrd +Patien01_2010-1_ROI.nrrd +Patien01_2010-2.dwi +Patien01_2010-2_T1.nrrd +Patien01_2010-2_T2.nrrd +Patien01_2010-2_ROI.nrrd +Patien01_2010-3.dwi +Patien01_2010-3_T1.nrrd +Patien01_2010-3_T2.nrrd +Patien01_2010-3_ROI.nrrd +Patien01_2010-4.dwi +Patien01_2010-4_T1.nrrd +Patien01_2010-4_T2.nrrd +Patien01_2010-4_ROI.nrrd +\endcode + +All T2 and DWI images are to be co-registered to the first T2 image, this can be achieved by the following two calls: + +\code + $./MitkDiffusionMiniApps BatchedFolderRegistration -i /home/inputFolder/ -o /home/outputFolder/ -f Patien01_2010-1_T2.nrrd -m T2.nrrd + $./MitkDiffusionMiniApps BatchedFolderRegistration -i /home/inputFolder/ -o /home/outputFolder/ -f Patien01_2010-1_T2.nrrd -m .dwi +\endcode + +The segmentations where performed on the T1 image and are therefore related to the image space of the respective T1 image, +so they can be bound to these images by marking them as derived resources. To register them both you would call + +\code +$./bin/MitkDiffusionMiniApps BatchedFolderRegistration -i /home/inputFolder/ -o /home/outputFolder/ -f Patien01_2010-1_T2.nrrd -m _T1.nrrd -d _ROI.nrrd -b +\endcode + +\note the suffixes of '_T1.nrrd' and '_ROI.nrrd' must have the same length! + +The parameter -b designates the derived resource as binary such that a nearest neighbor interpolation is used. + +All images (execpt for DWI files) are resample to the reference image, to resample to a specific spacing append the desired +spacing like this (e.g. 1 x 1 x 2 mm) + +\code +$./MitkDiffusionMiniApps BatchedFolderRegistration -i /home/inputFolder/ -o /home/outputFolder/ -f Patien01_2010-1_T2.nrrd -m .dwi -r 1,1,2 +\endcode + +\note Registration methods assume that both images occupy roughly the same space. It may happend that this is not the case, +and therefore registration fails. In this case you can try the -c option which uses the same origin for both images. + + +\subsection CopyGeometry Copy Geometry + +Copies the geometry (origin) of the source image to the target image. + +\subsection DicomLoad Dicom Loader + +Dicom Tools allow to parse dicom folders and export NRRD or DWI files, using standard naming. + +TODO enhance Docu, when MiniApp is ready .. + +\subsection TensorRecon Tensor Reconstruction +See \ref QmitkDiffusionImagingUserManualTensorReconstruction for the GUI equivalent of this tool. + +Takes a .dwi, .fsl/.fslgz file as input and saves the computed reconstructed tensor to the specified file. +It also allows for a threshold to be set, to exclude low b values from the reconstruction process. + +\code +./MitkDiffusionMiniApps TensorReconstruction -i /home/user/sample.dwi -o /home/user/tensors.dti -t 50 +\endcode + +\subsection QballRecon Qball Reconstruction + +See \ref QmitkDiffusionImagingUserManualQBallReconstruction for the GUI equivalent of this tool. + +\code +./MitkDiffusionMiniApps QballReconstruction -i /home/user/sample.dwi -o /home/user/tensors.qbi -t 50 -r .006 -shc /home/user/coeffs.csv +\endcode + +\subsection PeakExtraction Peak Extraction + + +\subsection PeakAngularErr Peak Angular Error + +\section DiffusionMeasures Diffusion Related Measures + +\subsection DiffusionIndices Diffusion Indices + +See \ref QmitkDiffusionImagingUserManualQuantification for the GUI equivalent of this tool. + +Computes a selected tensor derived indices (fa, gfa, ra, ad, rd, ca, l2, l3, md) given a +Tensor, Q-ball or FSL/MRTrix SH-coefficient image. E.g. to compute the fraction anisotropy call + +\code +./MitkDiffusionMiniApps DiffusionIndices -i /home/user/input.dti -idx fa -o /home/user/fa_image.nrrd +\endcode + +\subsection AllDiffusionIndices Tensor Derived Maps Extraction + +Similar to \ref DiffusionIndices . But computes all of the following indices FA, RA, MD, CA, RD, AD at once. +Also the input is a regular .dwi file, the tensor reconstruction is done implicitly (using a b0 threshold of 50). + + +\section FibTracking Fiber Tracking and Processing Methods + +\subsection FibDirection Fiber Direction Extraction + +TODO Peter ? + +\subsection Streamline Streamline Tracking + +See \ref org_mitk_views_streamlinetracking for the GUI equivalent of this tool. + +Performs a streamline tracking on a tensor image. + +\subsection GibbsTracking Gibbs Fiber Tracking + +See \ref org_mitk_views_gibbstracking for the GUI equivalent of this tool. + +Performs a Gibbs tracking on a tensor image. + +\subsection FibProcessing Fiber Processing + +Post-process a fiber bundle. Provides the possibility to + +\li remove short/long fiber tracks +\li combine fiber bundles +\li resample a fiber bundle +\li scale bundle in each direction independently + + +\subsection FibFoxProcessing Fiber Fox Processing + +See \ref QmitkFiberfoxViewUserManualSignalGeneration for the GUI equivalent of this tool. + +Generates a signal from a fiber bundle provided a reference DWI and a parameter file. The parameter file can be generated +using the Fiberfox plugin (sub-tab) Signal Generation. + +\subsection FormatConv File Format Converter + +Determines the data type and converts the input file (if possible) to .NRRD (regular image), +.DWI (diffusion image) or .FIB (fiber bundle). + +\subsection MultiShell Multishell Methods + +Computes several fits on an images (Kurtosis,Bi-Exponential, ADC). + +These fits are part of the Preprocessing Plugin \ref QmitkDiffusionImagingUserManualPreprocessing . + +\section NetworkTools Connectomics + +\subsection NetworkCreation Network Creation + +See \ref org_mitk_views_connectomicsdata for the GUI equivalent of this tool. + +Creates a network based on a brain parcellation and a fiber image. + +\subsection NetworkStatistics Network Statistics + +See \ref org_mitk_views_connectomicsstatistics for the GUI equivalent of this tool. + +Calculates several network statistics for a given connectome. +*/