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See DTMRI engineering pages for some of the background.

Overview of the DWI workflow

Overview of the DTI workflow

Specific Modules

Volumes Module

  • Volume module is capable of loading and saving DWI and DTI images in the NRRD file format.
  • Volume Module is capable of displaying DWI image components and DTI images as derived scalar measures.
Colore DTI
DTI volume slices colored by orientaion.

  • Volume Display GUI provides different display controls based on the type of the volume.

Tractography Module

  • Tractography Display-Load-Save module is capable of loading and saving fiber tracts in the vtkPolyData file formats.
  • Tractography Display-Load-Save module is capable of displaying fiber tracts as lines, tubes, and glyphs, all colored by different scalar properties
fiber bundles
Fiber bundles displayed as lines and glyph ellipsoids.

  • Slicer Models module also can be used to load, save, display tracts as lines, but it does not provide tensor data display

Tensor Estimation from DWI Module

  • Creates tensor volume from DWI volume.

Diffusion Tensor Scalar Measurements Module

  • Creates a specified scalar measurement of a tensor volume.

Rician LMMSE Filter Module

  • Filters a set of diffusion weighted images in the mean squared error sense using a Rician noise model. The noise parameter is automatically estimated.
  • Contributed by Santiago Aja Fernandez and Marc Niethammer

Tractography ROI Seeding Module

  • Creates fibers passing through a specified ROI
Roi seeding
Seeding from ROI example.

Tractography Fiducial Seeding Module

  • Creates fibers passing through the specified fiducial points interactively
fiducial seeding
Seeding from fiducials example.

Tractography ROI Select Module

  • Select tracts passing or not passing through ROIs

Stochastic Tractography Filter

  • Generates a map of connectivity probabilities from a DWI volume.).
  • Contributed by Tri Ngo (

ROI Tract Filter

  • Creates a new tract container containing only tracts which pass through the selected ROI's.
  • Contributed by Tri Ngo (

Generate Connectivity Map

  • Generates a volume where the value of each voxel is the number of fibers which pass through that voxel divided by the total number of sampled fibers. This value can been interpreted as the probability that a particular voxel is connected to the seed ROI by a fiber tract.
  • Contributed by Tri Ngo (