diff --git a/Modules/DiffusionImaging/MiniApps/Documentation/DiffusionMiniApps.dox b/Modules/DiffusionImaging/MiniApps/Documentation/DiffusionMiniApps.dox index 17e565d72f..b47a2d0313 100644 --- a/Modules/DiffusionImaging/MiniApps/Documentation/DiffusionMiniApps.dox +++ b/Modules/DiffusionImaging/MiniApps/Documentation/DiffusionMiniApps.dox @@ -1,184 +1,199 @@ /** \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 $./MitkDiffusionMiniApps BatchedFolderRegistration -i /home/inputFolder/ -o /home/outputFolder/ -f Patien01_2010-1_T2.nrrd -m .dwi -r 1,1,2 \endcode \note Registration methods assume that both images occupy roughly the same space. It may happend that this is not the case, and therefore registration fails. In this case you can try the -c option which uses the same origin for both images. \subsection CopyGeometry Copy Geometry Copies the geometry (origin) of the source image to the target image. -\subsection DicomLoad Dicom Loader -Dicom Tools allow to parse dicom folders and export NRRD or DWI files, using standard naming. +\subsection ImageResampler Resampling of Images + +This tool can be used to resample images in different ways. One way is by specifying the spacing. +Transforming an image test.nrrd to have a spacing of 1x1x3 mm can be done using this command: + +\code +$./MitkDiffusionMiniApps ImageResampler -i test.nrrd -s 1,1,3 -o resampledImage.nrrd +\endcode + +Alternatively this program can be used to resample by reference. This will resample the input image to the grid provided by the reference image +and also ensure they occupy the same physical space (that is the input image will have the same origin and voxel dimensions) + +\code +$./MitkDiffusionMiniApps ImageResampler -i test.nrrd -r referenceImage.nrrd -o resampledImage.nrrd +\endcode + +\note Resampling by reference image can also be applied to MR Diffusion data (.dwi files). + -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 Extracts ODF peaks from the given spherical harmonics coefficient image. Input image type is an image that contains a vector with the spherical harmonics coefficients as pixel type: Image< Vector< float, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder >, 3 > \subsection PeakAngularErr Peak Angular Error Calculates the angular error between two sets of input directions. The directions are stored as images. Each image voxel contains one direction vector. Such images are for example the output of the fiber direction extraction miniapp. \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 Extracts the voxel-wise main fiber directions from a tractogram. \subsection Streamline Streamline Tracking See \ref org_mitk_views_streamlinetracking for the GUI equivalent of this tool. Performs streamline tractography on a tensor image. \subsection GibbsTracking Gibbs Fiber Tracking See \ref org_mitk_views_gibbstracking for the GUI equivalent of this tool. Performs global Gibbs tractography on a tensor/Q-ball/SH-coefficient image. \subsection FibProcessing Fiber Processing Post-process a fiber bundle. Provides the possibility to \li remove short/long fiber tracks \li apply curvature threshold \li resample a fiber bundle (linear and spline based) \li compress a fiber bundle (lossy) \li transform fiber bundle (scale, translate, rotate) \li mirror fiber bundle \subsection FibFoxProcessing Fiberfox 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. */