.. _references:

How to cite TractoFlow
======================

.. tip::
    If you want to analyse datasets with white-matter lesions, we highly recommends
    to use our devrived version of TractoFlow: TractoFlow Atlas based Segmentation (ABS) https://github.com/scilus/TractoFlow-ABS

If TractoFlow is used in a publication, please cite the following references:

.. [Theaud20] Theaud, G., Houde, J.-C., Boré, A., Rheault, F., Morency, F., Descoteaux, M.,TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity, NeuroImage,  https://doi.org/10.1016/j.neuroimage.2020.116889.
.. [Kurtzer17] Kurtzer GM, Sochat V, Bauer MW Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5) (2017): e0177459. https://doi.org/10.1371/journal.pone.0177459
.. [DiTomaso17] P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nature Biotechnology 35, 316–319 (2017) doi:10.1038/nbt.3820
.. [Garyfallidis14] Garyfallidis, E., Brett, M., Amirbekian, B., Rokem, A., Van Der Walt, S., Descoteaux, M., Nimmo-Smith, I., 2014. Dipy, a library for the analysis of diffusion mri data. Frontiers in neuroinformatics 8, 8.
.. [Tournier19] Tournier, J. D., Smith, R. E., Raffelt, D. A., Tabbara, R., Dhollander, T., Pietsch, M., ... & Connelly, A. (2019). MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. bioRxiv, 551739.
.. [Avants09] Avants, B.B., Tustison, N., Song, G., 2009. Advanced normalization tools (ants). Insight j 2, 1–35.
.. [Jenkinson12] Jenkinson, M., Beckmann, C.F., Behrens, T.E., Woolrich, M.W., Smith, S.M., 2012. Fsl. Neuroimage 62, 782–790.

If TractoFlow-ABS is used in a publication, please cite the following references:

.. [Theaud20] Theaud, G., Houde, J.-C., Boré, A., Rheault, F., Morency, F., Descoteaux, M.,TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity, NeuroImage,  https://doi.org/10.1016/j.neuroimage.2020.116889.
.. [Theaud19] G Theaud, JC Houde, A Bore, F Rheault, F Morency, M Descoteaux TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity https://www.biorxiv.org/content/10.1101/631952v1

Download:

:download:`References Bibtex<../data/tractoflow_references.bib>`