Behavior and Neuroimaging Core User Manual
  • About
  • Infrastructure Overview
  • XNAT
    • Getting Started
    • Accessing XNAT
    • BIDS Ready Protocols
    • New XNAT projects
    • Uploading Data
    • Downloading Data
  • Demo Dataset
    • Introduction
    • How to access it
    • Protocol Information
    • Basic analysis example: checks task
  • XNAT to BIDS
    • Getting Started
    • XNAT2BIDS Software
    • Exporting to BIDS using Oscar
      • Oscar Utility Script
        • Running xnat2bids using default configuration
        • Running xnat2bids with a custom configuration
        • Syncing your XNAT project & Oscar data directory
        • Extra tools & features
      • Step-wise via Interact Session
    • BIDS Validation
      • Oscar
      • Docker
    • Converting non-MR data
      • Physiological data
      • EEG data
  • XNAT TO BIDS (Legacy)
    • Oscar SBATCH Scripts
  • BIDS and BIDS Containers
    • Introduction to BIDS
    • mriqc
    • fmriprep
    • BIDS to NIMH Data Archive (NDA)
  • Analysis Pipelines
    • Freesurfer
    • 🚧CONN Toolbox
    • FSL topup and eddy
    • Tractography: DSI Studio
    • Brown University MRS Data Collection and Preprocessing Protocol
    • LC Model
      • Installation
      • Example Run
      • Running LCModel on your own data
    • Quantitative Susceptibility Mapping (QSM)
  • Standalone Tools
    • Multi-session spectroscopy with voxalign
    • dicomsort: a tool to organize DICOM files
    • ironmap
    • convert enhanced multi-frame DICOMs to legacy single-frame
    • DICOM anonymization
  • MRF GUIDES
    • MRI simulator room
      • Motion Trainer: Balloon Task
      • Simulating scanner triggers
    • Stimulus display & response collection
    • Eyetracking at the scanner
    • Exporting data via scannershare
    • EEG in the scanner
    • Exporting spectroscopy RDA files
  • Community
    • MRF/BNC user community meetings
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  • Using DSI Studio on Your Local Machine:
  • Using DSI Studio on Oscar:
  • Perform Whole Brain Tractography:

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  1. Analysis Pipelines

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.

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Last updated 1 year ago

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Using DSI Studio on Your Local Machine:

Download to your local machine and open the program.

Using DSI Studio on Oscar:

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

module load dsi-studio

Then enter this text to open the DSI GUI as a singularity container, bound to /oscar/data:

singularity exec -B /oscar/data /oscar/runtime/opt/dsi/chen-march2023/dsistudio_chen-2023-03-07.sif dsi_studio

singularity exec executes dsi-studio as a singularity.-B /oscar/data binds the singularity to oscar. /oscar/runtime/opt/dsi/chen-march2023/dsistudio_chen-2023-03-07.sif dsi_studio is where the DSI singularity 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).

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.

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.

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.

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
DSI Studio
Select Step T1 to open a diffusion image of your choice.
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 to use the SRC to begin reconstruction of the white matter tracts.
DSI Studio's Tracking Window, opened after selecting Step T3 and entering the FIB file.
The whole brain tractography can be viewed in the center of the Tracking Window after selecting the "Fiber Tracking" button.