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.

https://www.nitrc.org/projects/csaodf-hough

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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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Version	Published	Release Notes
2.1	24 May 2024	Bug fixes.	Download
2.0	26 Jun 2021	New functions have been added for connectivity computation (connMatrix, FreeSurferLUT) and augmentation (augConnMatrix), and DTI analysis (reconDT, DT2ODF). Further updates and bug fixes.	Download
1.13	18 Dec 2018	Minor update.	Download
1.12	9 Nov 2018	Minor update.	Download
1.11	5 Nov 2018	Minor update.	Download
1.1	29 Oct 2018	The gradient-table verification function checkGradTable.m has been added (Aganj et al, Sci Rep 2018).	Download
1.0.6.0	14 Mar 2018	Minor update.	Download
1.0.5.0	14 Mar 2018	ODFs can now be visualized by choosing either magnitude or orientation color-coding.	Download
1.0.4.0	21 Nov 2017	Minor update in visualization.	Download
1.0.3.0	18 Apr 2017	Minor update.	Download
1.0.2.0	12 Apr 2017	Minor update.	Download
1.0.1.0	12 Apr 2017	Minor update.	Download
1.0.0.0	11 Apr 2017		Download

MLA	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.
APA	Aganj, I., Lenglet, C., Sapiro, G., Yacoub, E., Ugurbil, K., & Harel, N. (2010). Reconstruction of the orientation distribution function in single- and multiple-shell q-ball imaging within constant solid angle. Magnetic Resonance in Medicine, 64(2), 554–566. Wiley. Retrieved from https://doi.org/10.1002%2Fmrm.22365
BibTeX	@article{Aganj_2010, doi = {10.1002/mrm.22365}, url = {https://doi.org/10.1002%2Fmrm.22365}, year = 2010, month = {jun}, publisher = {Wiley}, volume = {64}, number = {2}, pages = {554--566}, author = {Iman Aganj and Christophe Lenglet and Guillermo Sapiro and Essa Yacoub and Kamil Ugurbil and Noam Harel}, title = {Reconstruction of the orientation distribution function in single- and multiple-shell q-ball imaging within constant solid angle}, journal = {Magnetic Resonance in Medicine} }

MLA	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.
APA	Aganj, I., Lenglet, C., Jahanshad, N., Yacoub, E., Harel, N., Thompson, P. M., & Sapiro, G. (2011). A Hough transform global probabilistic approach to multiple-subject diffusion MRI tractography. Medical Image Analysis, 15(4), 414–425. Elsevier BV. Retrieved from https://doi.org/10.1016%2Fj.media.2011.01.003
BibTeX	@article{Aganj_2011, doi = {10.1016/j.media.2011.01.003}, url = {https://doi.org/10.1016%2Fj.media.2011.01.003}, year = 2011, month = {aug}, publisher = {Elsevier {BV}}, volume = {15}, number = {4}, pages = {414--425}, author = {Iman Aganj and Christophe Lenglet and Neda Jahanshad and Essa Yacoub and Noam Harel and Paul M. Thompson and Guillermo Sapiro}, title = {A Hough transform global probabilistic approach to multiple-subject diffusion {MRI} tractography}, journal = {Medical Image Analysis} }

MLA	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.
APA	Aganj, I. (2018). Automatic Verification of the Gradient Table in Diffusion-Weighted MRI Based on Fiber Continuity. Scientific Reports, 8(1). Springer Science and Business Media LLC. Retrieved from https://doi.org/10.1038%2Fs41598-018-34940-4
BibTeX	@article{Aganj_2018, doi = {10.1038/s41598-018-34940-4}, url = {https://doi.org/10.1038%2Fs41598-018-34940-4}, year = 2018, month = {nov}, publisher = {Springer Science and Business Media {LLC}}, volume = {8}, number = {1}, author = {Iman Aganj}, title = {Automatic Verification of the Gradient Table in Diffusion-Weighted {MRI} Based on Fiber Continuity}, journal = {Scientific Reports} }

MLA	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.
APA	Aganj, I., Mora, J., Frau‐Pascual, A., & Fischl, B. (2023). Exploratory correlation of the human structural connectome with non‐MRI variables in Alzheimer’s disease. Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring, 15(4). Wiley. Retrieved from http://dx.doi.org/10.1002/dad2.12511
BibTeX	@article{Aganj_2023, title={Exploratory correlation of the human structural connectome with non‐MRI variables in Alzheimer’s disease}, volume={15}, ISSN={2352-8729}, url={http://dx.doi.org/10.1002/dad2.12511}, DOI={10.1002/dad2.12511}, number={4}, journal={Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring}, publisher={Wiley}, author={Aganj, Iman and Mora, Jocelyn and Frau‐Pascual, Aina and Fischl, Bruce}, year={2023}, month=oct }

CSA-QBI and Hough Tractography for Diffusion MRI

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