Tractography: DSI Studio

DSI studio is a tractography software tool that maps white matter tracts using diffusion weighted images. This tutorial will guide you in using DSI Studio to perform whole brain tractography analysis.

Using DSI Studio on Your Local Machine:

Download DSI Studio to your local machine and open the program.

Using DSI Studio on Oscar:

Copy this text into a terminal on Oscar OpenOnDemand to load DSI Studio:

module load dsi-studio

Then enter this text to open the DSI Studio GUI from within a singularity container, while giving it access to /oscar/data/<your-data-dir> , which will be accessible at /data within the container.

singularity exec -B /oscar/data/<your-data-dir>:/data /oscar/runtime/opt/dsi/chen-march2023/dsistudio_chen-2023-03-07.sif dsi_studio

singularity exec ... dsi_studio launches dsi-studio installed in a singularity image.-B /oscar/data/<your-data-dir>:/data binds your data directory, so that programs run inside the container can access files stored there. /oscar/runtime/opt/dsi/chen-march2023/dsistudio_chen-2023-03-07.sif is where the DSI Studio singularity image is located on oscar.

Perform Whole Brain Tractography:

Select “Step T1: Open Source Images” to load diffusion MR images and create a SRC file. It is recommended to use diffusion images that have already been corrected for motion and susceptibility distortion (for example, via FSL TOPUP and Eddy).

Select Step T1 to open a diffusion image of your choice.

If there are existing .bvec and .bval files in the same directory you entered the diffusion images from, a b-table will be generated automatically. Otherwise, you may manually create a b-table by loading the files into the pop up window via the file tab in the top left corner. Once that is saved, the SRC file will be created and stored in the main window.

To manually create a b-table, enter the file tab, manually select the bval and bvec files, and hit OK. This will save the b-table as part of the SRC file.

Select "Step T2: Reconstruction" and choose the SRC file. This step converts the SRC file into an FIB file, which will be used for fiber reconstruction.

Select Step T2 to use the SRC to begin reconstruction of the white matter tracts.

A new window will appear. Confirm the appearance of the mask and select your preferred reconstruction method. Typically, QSDR is chosen for images in MNI space. Otherwise, GQI is recommended. DTI metrics will be generated even if the DTI button is not selected.

You may then press "Run Reconstruction". This may take a few minutes, and when it is complete the reconstructed image will appear in the lower section of the main window with a filename ending in ".fib.gz".

Select "Step T3: Fiber Tracking" and open the FIB file to begin generating a tractography map.

The following screen will appear. This is the "Tracking Window". By selecting the "Fiber Tracking" button, a whole brain reconstruction of fiber tracts will be created.

DSI Studio's Tracking Window, opened after selecting Step T3 and entering the FIB file.

After fiber tracking is complete, the tracking window will show the whole brain tractography map. For more information on quality assessment and troubleshooting, refer to DSI Studio's documentation.

The whole brain tractography can be viewed in the center of the Tracking Window after selecting the "Fiber Tracking" button.