How To’s – Spinal Cord Fibertracking

Spinal Cord fibertracking might be difficult to realize, depending on your MR Coils, Field, and sequences, because of EPI deformations.

This “How To” will use MR data not provided in the fMRICRoTools Samples Files. It’s up to you to use your own data.

This method should also work on Peripheral Nerves, Muscles, …

First you need to have the Dicom files registered into your Local DataBase.

The DTI files not acquired in the axial plane will be automatically reformated prior to any further processing, and being registered.

Display your Serie in the Rendering Panel by double-clicking on it in the Local DataBase Explorer:

Once done, you need to set the threshold for your serie.

Go to the Image Display Area, right click on it, go through the menus to “Adjust” and “Threshold” then Left click on the Image Display Area and move your Mouse to adjust threshold:

Threshold set will change the display in the Image Display Area:

Then go to the “Series Processing” Bottom Tab, in the “Diffusion” Tab, and click on “Compute DTI“. New parameters maps files will be registered in the Local DataBase Explorer:

Click on your Serie, then go to the “Image Tools” Top Tab, and click on “Fibertrack“:

Once done, click again on your serie in the Local DataBase Explorer, then go to the “Series Processing” Tab, in the “Tractography” Tab, “Bundles” sub-Tab. You should be able to see the Fibers Bundles “fibertrack_fibers.cbl” file in the Fibers Bundles Selection List. Click on it to select it, the Fibers Bundles will be displayed in the Rendering Panel:

Then go to the “Display” Tab of the “Tractography” Tab, and select the Fibers Bundles Rendering Directional Color Mode:

You just performed Spinal Cord Fibertracking!

Now you can load DTI parameters maps as Overlays, and do further processings (selecting Fibers Bundles using the Fibers Bundles Selection Cube, aso…)