PluginList

Plugin List

This page lists all available plugins in the latest release version of vIST/e. Brief tutorials have been written for a small number of plugins. Click on the plugin names to access these tutorials.

Plugin Name	Description
AxesVisualization	Places a 3D axis widget in the corner of the 3D view.
Clustering	Allows the user to merge clusters of an oversegmented fiber data set.
ConnectivityMeasures	Quantifies the connectivity strength of fibers, allowing the user to select only the strongest fibers
Crop3D	Crops the 3D data. The cropped image can be selected using the combo box in Planes Visualisation.
DTIMeasures	Computes scalar measures from DTI data sets (e.g., Fractional Anisotropy, Mean Diffusivity). If scalar measures will be used for DTI visualisation, the measure or the weighting scalar volume for color coding is selected in Planes plugin.
DTIReader	Reads DTI data stored in the ".dti" file format which is actually a text header file. The 6 binary files should be in the same directory.
FiberCutting	Allows the user to manually resize tracked fibers.
FiberFilter	Filter fibers through one or more Regions of Interest.
FiberOutput	Exports fiber data (like local scalar measure values and average length) to Excel files or text files.
FiberTracking	Track fibers using DTI data. Various methods are supported, including Streamline Tracking, Whole Volume Seeding, and Geodesic Ray-Tracing.
FiberTrackingCUDA	Same features as the Fiber Tracking plugin, but with CUDA-based accelleration for Geodesic Ray-Tracing.
FiberVisualization	Visualizes fibers. Includes various options for changing the fiber color and shape. Different Region of interests created by ROI Edit plugin can be used for seeding.
GeometryGlyphs	Creates 3D glyphs from HARDI data. Supports both Discrete Sphere Function-data and Spherical Harmonics data.
GPUGlyphs	Draws glyphs for DTI and Spherical Harmonics (4-th order) using a GPU shader.
HARDI Fiber Tracking	HARDI Fiber Tracking Plugin uses a deterministic tracking algorithm, inputs can be spherical harmonics coefficients or discrete sphere.
HARDIConverter	Convert HARDI data from one format to another (e.g., from Spherical Harmonics to Discrete Sphere Functions).
HARDIConvolutions	Enhance HARDI data using 3D kernel-based convolution.
HARDIMeasures	Compute scalar measures for HARDI data (stored in Discrete Sphere Function-format).
HARDIReader	Read the raw ".hardi" and ".sharm" files. These files are headers of raw files. The headers ".hardi"and ".sharm" which store HARDI data as Discrete Sphere and Spherical Harmonics model parameters respectively. NiftiReaderPlugin also can read HARDI data given as a Nifti file. Spherical Harmonics data can be converted to Discrete Sphere by HARDIConverter plugin.
IllustrativeClusters	Visualizes fiber data sets using simplified shapes, allowing for clear distinction between different clusters.
NiftiReader	Read data from NIfTI files. Includes support for scalar volumes, DTI data, and HARDI data (DSF and SH). Following the format described in the paper Loni MIND: Metadata for DWI If the input consists Spherical Harmonic coefficients then it can be converted to Discrete Sphere parameters and used during the runtime of vIST/e.
NiftiWriter	Saves the DTI and Scalar images in Nifti Format. Saves HARDI representations (i.e. Discrete Sphere or Spherical Harmonics) in Nifti Mind format.
PlanesVisualization	Draws three movable orthogonal slices, which are used to visualize DTI data or scalar volumes. Transfer functions created in Transfer Function plugin can be selected optionally from the combo box of the plugin GUI.
PolyDataReader	Used for reading fibers (".fbs") and Regions of Interest (".pol" and ".sr").
RayCast	Uses powerful GPU shaders to render 3D volumes.
ROIEdit	Allows the user to draw 2D Regions of Interest, which can be used for filtering and seeding. ROI drawing sequence: New button - Start Drawing button - draw the roi in 2D windows - Stop Drawing button. This ROI can be used in other pllugins (e.g. Fiber Tracking plugin)
Seeding	Generates seed points within 2D ROIs. Also supports volume seeding and fiber seeding.
StructuredPointsReader	Read data stored in the Structured Points format of VTK.
TransferFunction	Allows the user to create and modify Transfer Functions, which are used for coloring visualization components. New Transfer Function sequence: New button- Add Opacity Function - Add points by Right Mouse click and the second right click changes the color. Transfer function can be selected from the combobox in Planes plugin or Ray Casting plugin.
TransferFunctionReader	Reads Transfer Functions created with the Transfer Function plugin.
Transformation	Transforms data sets. For example, allows the user to mirror an image.
VolumeReader	Reads the ".vol" file format, which is used to store scalar volumes. ".vol" is the header file, binary data file should be at the same directory.
VTIReader	Reads the VTK Image Data file format (".vti"), DTI tensor volume saved as .vti can also be read.