diff --git a/Documentation/Doxygen/2-UserManual/MiniApps.dox b/Documentation/Doxygen/2-UserManual/MiniApps.dox index 40a3835f29..b75d671971 100644 --- a/Documentation/Doxygen/2-UserManual/MiniApps.dox +++ b/Documentation/Doxygen/2-UserManual/MiniApps.dox @@ -1,61 +1,64 @@ /** -\page MiniAppExplainPage MITK MiniApps +\page AdvancedTopicsPage Advanced MITK user topics -\section MiniAppExplainPageDescription What are MiniApps +\section MiniAppExplainPage MITK MiniApps + +

What are MiniApps?

MiniApps are small command line tools. Generally the purpose of 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). They are intended to provide command line access to a variety of features of MITK, thus facilitating batched processing of data. -\section MiniAppExplainPageUsage Usage +

Usage

Each MiniApp should provide information about its usage. If it is called without parameters it will output help information about expected inputs, outputs and parameters. Below you can see the help output of the MitkGibbsTracking MiniApp: \code $./MitkGibbsTracking -i, --input, input image (tensor, ODF 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 -\section MiniAppExplainPageWorkbenchIntegration Integrating a command line tool into MITK Workbench +

Integrating a command line tool into MITK Workbench

The executable file has be to be announced in MITK Workbench. This can be done in Preferences window: Click 'Window' -> 'Preferences', and select 'Command Line Modules'. You can add directories containing executable files or you can select single executable files. Click 'OK' button. The configured command line tools are now available via the drop-down box of the Command Line Modules tab. \warning The build configuration of your MiniApp should match the build configuration of your MITK application. This is especially relevant for developers. Combining a Release application and Debug MiniApp or vice versa might not work. -\section MiniAppExplainPageAvailableList Available MiniApps +

Available MiniApps in MITK

-\li \subpage DiffusionMiniApps \li \subpage mitkBasicImageProcessingMiniAppsPortalPage \li \subpage mitkClassificationMiniAppsPortalPage -\section MiniAppExplainPageTechnicalInformation Technical Information + + +

Technical Information

MiniApps follow the Slicer Execution Model in describing themselves via xml: \code $./GibbsTracking --xml Fiber Tracking and Processing Methods Gibbs Tracking MBI ... \endcode \note Full conformity is still a work in progress. */ diff --git a/Documentation/Doxygen/2-UserManual/UserManualPortal.dox b/Documentation/Doxygen/2-UserManual/UserManualPortal.dox index 168ee94ac7..36d07ca892 100644 --- a/Documentation/Doxygen/2-UserManual/UserManualPortal.dox +++ b/Documentation/Doxygen/2-UserManual/UserManualPortal.dox @@ -1,17 +1,17 @@ /** \usersguidemainpage{UserManualPortal} MITK User Manual To get an introduction to the usage of any MITK based application please read \ref MITKWorkbenchManualPage. 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. 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.

List of topics

*/