CSA-QBI and Hough Tractography for Diffusion MRI

Version 2.1 (67.3 KB) by Iman Aganj
Matlab codes for Diffusion MRI CSA-ODF computation, Hough tractography, and connectomic analysis.
Updated 24 May 2024

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This diffusion-weighted MRI processing toolbox can be used to:
• Compute the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) (Aganj et al, MRM 2010).
• Perform Hough-transform tractography (Aganj et al, MedIA 2011).
• Visualize ODFs and tracts, and export them for further analysis.
• Verify the correctness of the diffusion gradient table (Aganj, Sci Rep 2018).
• Compute and interactively visualize the connectivity matrix.
• Augment the connectivity matrix with indirect connections (Aganj et al, ISMRM 2014, Aganj et al, A&D DADM 2023).
For short tutorials, see EXAMPLE.m and EXAMPLE_CLI.m.
If available, GPUs can be used to speed up the computation.

Cite As

I. Aganj, "Orientation Distribution Function in Constant Solid Angle (CSA-ODF) and Hough-Transform Tractography Toolbox", 2021. www.nitrc.org/projects/csaodf-hough

Aganj, Iman, et al. “Reconstruction of the Orientation Distribution Function in Single- and Multiple-Shell q-Ball Imaging within Constant Solid Angle.” Magnetic Resonance in Medicine, vol. 64, no. 2, Wiley, June 2010, pp. 554–66, doi:10.1002/mrm.22365.

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Aganj, Iman, et al. “A Hough Transform Global Probabilistic Approach to Multiple-Subject Diffusion MRI Tractography.” Medical Image Analysis, vol. 15, no. 4, Elsevier BV, Aug. 2011, pp. 414–25, doi:10.1016/j.media.2011.01.003.

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Aganj, Iman. “Automatic Verification of the Gradient Table in Diffusion-Weighted MRI Based on Fiber Continuity.” Scientific Reports, vol. 8, no. 1, Springer Science and Business Media LLC, Nov. 2018, doi:10.1038/s41598-018-34940-4.

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I. Aganj, G. Prasad, P. Srinivasan, A. Yendiki, P. M. Thompson, and B. Fischl, “Structural brain network augmentation via Kirchhoff's laws,” in Proceedings of the Joint Annual Meeting of ISMRM-ESMRMB, Milan, Italy, 2014. https://cds.ismrm.org/protected/14MProceedings/PDFfiles/2665.pdf

Aganj, Iman, et al. “Exploratory Correlation of the Human Structural Connectome with Non‐MRI Variables in Alzheimer’s Disease.” Alzheimer’s Dementia: Diagnosis, Assessment Disease Monitoring, vol. 15, no. 4, Wiley, Oct. 2023, doi:10.1002/dad2.12511.

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MATLAB Release Compatibility
Created with R2024a
Compatible with any release
Platform Compatibility
Windows macOS Linux

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Version Published Release Notes

Bug fixes.


New functions have been added for connectivity computation (connMatrix, FreeSurferLUT) and augmentation (augConnMatrix), and DTI analysis (reconDT, DT2ODF). Further updates and bug fixes.


Minor update.


Minor update.


Minor update.


The gradient-table verification function checkGradTable.m has been added (Aganj et al, Sci Rep 2018).

Minor update.

ODFs can now be visualized by choosing either magnitude or orientation color-coding.

Minor update in visualization.

Minor update.

Minor update.

Minor update.