diff --git a/Documentation/Doxygen/UserManual/MiniApps.dox b/Documentation/Doxygen/UserManual/MiniApps.dox index 104522399f..08878e82d2 100644 --- a/Documentation/Doxygen/UserManual/MiniApps.dox +++ b/Documentation/Doxygen/UserManual/MiniApps.dox @@ -1,70 +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 +The MiniApps are built in a self-describing way. When calling a MiniApp without any arguments 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 */