How To’s – DTI, Tractography & Structural Connectom

This How To uses the “DUCREUX DENIS” Case.

The goal is to automatically extract the white matter fibers bundles, and to compute the structural connectom of a DTI/DSI MR sequence using Tractography.

To be able to do so, you need to select a DTI serie first.

This is done by clicking on the “Ducreux Denis” name, then the serie date “20150128” then by double-clicking on the serie name “DTI Hardi 60 2 mm”.

The serie will be loaded and displayed:

In order to extract fibers bundles, the software needs to perform a batch of tasks among which Brain Extraction, Coregistration to Template, Motion Correction, then processing the DTI parameters, performing the Fibertracking, extracting Fibers Bundles, computing the structural connectom, and creating reports, which can be displayed as described here, of Extracted Fibers Bundles and of Structural Connectom with stats values (see the Fibers-Bundles-Analysis and the Structural-Connectom pdf files at the end of this page).

This is a long process (about 1 hour on a 12 cores CPU).

First of all, go to the Series Processing Tab then click on “Stct. Connectom”, and wait.

You will see from times to times the windows changing, meaning the software is processing the data:

  • Fibertracking the whole brain:


  • Extracting all Fibers Bundles one by one:
  • Computing the Structural Connectom:

  • Finally Registering all the extracted White Matter Bundles

When done, in the “Tractography” Tab, go to the “Bundles” Tab, you’ll see all the extracted bundles:

You can select/deselect each of them by clicking on it, and rotating moving the brain on the 3D Renderer Window.

In the Diffusion Tab, there are Icons for changing the Rendering Mode, the colors, aso…