How to cite
Until a paper is available (we are working on it!), please cite the github link in your research papers and all softwares used within sf-tractomics, here is a list of citations to include (adapt it depending on which profile you ran):
Framework
Section titled “Framework”Valcourt Caron A, Boré A, Edde M, Gagnon A, Thoumyre S, Royer A, Rheault, F, Descoteaux M. nf-neuro : developing maintainable pipelines for seamless processing of diffusion MRI. Proc. of the ISMRM Workhop on 40th Years of Diffusion. 2025 Fev.
Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
Pipeline tools
Section titled “Pipeline tools”Theaud G, Houde JC, Boré A, Rheault F, Morency F, Descoteaux M. TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity. Neuroimage. 2020 Sep;218:116889. doi: 10.1016/j.neuroimage.2020.116889. Epub 2020 May 21. PMID: 32447016.
Renauld, E., Boré, A., Poirier, C., Valcourt Caron, A., Karan, P., Théberge, A., Théaud, G., Edde, M., Poulin, P., Girard, G., Houde, J-C., Gagnon, A., St-Onge, E., Little, G., Legarreta, J. H., Thoumyre, S., Grenier, G., Ocampo-Pineda, M., Battochio, M., Beaudoin, V., Joanisse, A., Petit, L., Rheault, F., Descoteaux, M. In revision, Tractography analysis with the scilpy toolbox.
St-Onge, E., Schilling, K. G., & Rheault, F. (2023). BundleSeg: A versatile, reliable and reproducible approach to white matter bundle segmentation (No. arXiv:2308.10958). arXiv. https://doi.org/10.48550/arXiv.2308.10958
Tournier, J.-D., Smith, R., Raffelt, D., Tabbara, R., Dhollander, T., Pietsch, M., Christiaens, D., Jeurissen, B., Yeh, C.-H., & Connelly, A. (2019). MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 202, 116137. https://doi.org/10.1016/j.neuroimage.2019.116137
Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., & Smith, S. M. (2012). FSL. NeuroImage, 62(2), 782–790. https://doi.org/10.1016/j.neuroimage.2011.09.015
Tustison, N. J., Cook, P. A., Holbrook, A. J., Johnson, H. J., Muschelli, J., Devenyi, G. A., Duda, J. T., Das, S. R., Cullen, N. C., Gillen, D. L., Yassa, M. A., Stone, J. R., Gee, J. C., & Avants, B. B. (2021). The ANTsX ecosystem for quantitative biological and medical imaging. Scientific Reports, 11(1), 9068. https://doi.org/10.1038/s41598-021-87564-6
Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
When using experimental AI registration and segmentation features
Section titled “When using experimental AI registration and segmentation features”Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV. SynthMorph: Learning Contrast-Invariant Registration Without Acquired Images. IEEE Trans Med Imaging. 2022 Mar;41(3):543-558. doi: 10.1109/TMI.2021.3116879. Epub 2022 Mar 2. PMID: 34587005; PMCID: PMC8891043.
Billot B, Greve DN, Puonti O, Thielscher A, Van Leemput K, Fischl B, Dalca AV, Iglesias JE; ADNI. SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining. Med Image Anal. 2023 May;86:102789. doi: 10.1016/j.media.2023.102789. Epub 2023 Feb 25. PMID: 36857946; PMCID: PMC10154424.
Hoopes A, Mora JS, Dalca AV, Fischl B, Hoffmann M. SynthStrip: skull-stripping for any brain image. Neuroimage. 2022 Oct 15;260:119474. doi: 10.1016/j.neuroimage.2022.119474. Epub 2022 Jul 13. PMID: 35842095; PMCID: PMC9465771.
Iglesias JE. A ready-to-use machine learning tool for symmetric multi-modality registration of brain MRI. Sci Rep. 2023 Apr 24;13(1):6657. doi: 10.1038/s41598-023-33781-0. PMID: 37095168; PMCID: PMC10126156.
Atlases and common space templates
Section titled “Atlases and common space templates”Fonov V, Evans AC, Botteron K, Almli CR, McKinstry RC, Collins DL; Brain Development Cooperative Group. Unbiased average age-appropriate atlases for pediatric studies. Neuroimage. 2011 Jan 1;54(1):313-27. doi: 10.1016/j.neuroimage.2010.07.033. Epub 2010 Jul 23. PMID: 20656036; PMCID: PMC2962759.
Fonov VS, Evans AC, McKinstry RC, Almli CR, Collins DL, Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. NeuroImage. 2009 Jul; 47(1);S102. doi: 10.1016/S1053-8119(09)70884-5.
Zhang S, Arfanakis K. Evaluation of standardized and study-specific diffusion tensor imaging templates of the adult human brain: Template characteristics, spatial normalization accuracy, and detection of small inter-group FA differences. Neuroimage. 2018 May 15;172:40-50. doi: 10.1016/j.neuroimage.2018.01.046. Epub 2018 Jan 28. PMID: 29414497; PMCID: PMC5910210.
Software packaging/containerisation tools
Section titled “Software packaging/containerisation tools”Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.