Diffusion MRI pre-processing (DESIGNER) and parameter estimation (TMI)

Welcome to the NYU diffusion biophysics group documentation page. The group is led by Els Fieremans and Dmitry Novikov, and has developed a number of tools for preprocessing and extracting parameters from diffusion MRI data. Features include denoising using MPPCA (Veraart 2016), gibbs artifact correction using RPG (Lee 2021), the DESIGNER preprocessing pipeline (Ades-Aron 2018), the standard model imaging toolbox (Coelho 2022), and more!

This website documents DESIGNER version 2.0 and onwards. Prior versions of the DESIGNER package are officially deprecated and are no longer being maintained. GitHub code for designer-v2 is available here.

Both Designer-v2 and TMI are built as mrtrix3 external packages. Please see our installation, usage, and examples pages for information on how to run designer.

This webpage is still under development! Please excuse us for any missing information and don’t hesitate to reach out if you have immediate issues with package installation.

References

All toolboxes are subject to specific referencing. Each project is accompanied by at least one article for citation.

Ades-Aron, B., Veraart, J., Kochunov, P., McGuire, S., Sherman, P., Kellner, E., Novikov, D.S. & Fieremans, E. (2018). Evaluation of the accuracy and precision of the diffusion parameter EStImation with Gibbs and NoisE removal pipeline. Neuroimage, 183, 532-543.

Veraart, J., Novikov, D. S., Christiaens, D., Ades-Aron, B., Sijbers, J., & Fieremans, E. (2016). Denoising of diffusion MRI using random matrix theory. Neuroimage, 142, 394-406.

Lee, H. H., Novikov, D. S., & Fieremans, E. (2021). Removal of partial Fourier‐induced Gibbs (RPG) ringing artifacts in MRI. Magnetic resonance in medicine, 86(5), 2733-2750.

Coelho, S., Baete, S. H., Lemberskiy, G., Ades-Aron, B., Barrol, G., Veraart, J., Novikov, D.S. & Fieremans, E. (2022). Reproducibility of the Standard Model of diffusion in white matter on clinical MRI systems. Neuroimage. 2022 Aug 15, 257:119290

Chen, J., Ades-Aron, B., Lee, H.H., Mehrin, S., Pang, M., Novikov, D. S., Veraart, J., & Fieremans, E. (2024). Optimization and validation of the DESIGNER preprocessing pipeline for clinical diffusion MRI in white matter aging. Imaging Neuroscience, 2 1–17

Getting Help

The easiest source for references on these tools is right here. In addition, concerns raised in the issues section will reach the developers.

Contributors

  • https://github.com/badesar1
  • https://med.nyu.edu/faculty/els-d-fieremans
  • https://github.com/jchen33344
  • https://github.com/jelleveraart
  • https://github.com/leehhtw
  • https://github.com/rcleija
  • https://santiagocoelho.github.io

NYU License

Copyright (c) 2023 New York University

Permission is hereby granted, free of charge, to any non-commercial entity (‘Recipient’) obtaining a copy of this software and associated documentation files (the ‘Software’), to the Software solely for non-commercial research, including the rights to use, copy and modify the Software, subject to the following conditions:

  1. The above copyright notice and this permission notice shall be included by Recipient in all copies or substantial portions of the Software.

  2. THE SOFTWARE IS PROVIDED ‘AS IS’, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BELIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF ORIN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

  3. In no event shall NYU be liable for direct, indirect, special, incidental or consequential damages in connection with the Software. Recipient will defend, indemnify and hold NYU harmless from any claims or liability resulting from the use of the Software by recipient.

  4. Neither anything contained herein nor the delivery of the Software to recipient shall be deemed to grant the Recipient any right or licenses under any patents or patent application owned by NYU.

  5. The Software may only be used for non-commercial research and may not be used for clinical care.

  6. Any publication by Recipient of research involving the Software shall cite the references listed below.