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 nf-pediatric, here is a list of citations to include (adapt it depending on which profile you ran):
Citations
Section titled “Citations”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”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
Henschel, L., Conjeti, S., Estrada, S., Diers, K., Fischl, B., & Reuter, M. (2020). FastSurfer—A fast and accurate deep learning based neuroimaging pipeline. NeuroImage, 219, 117012. https://doi.org/10.1016/j.neuroimage.2020.117012
Fischl, B. (2012). FreeSurfer. NeuroImage, 62(2), 774–781. https://doi.org/10.1016/j.neuroimage.2012.01.021
K Gopinath, DN Greeve, S Das, S Arnold, C Magdamo, JE Iglesias: Cortical analysis of heterogeneous clinical brain MRI scans for large-scale neuroimaging studies, https://arxiv.org/abs/2305.01827
B Billot, DN Greve, O Puonti, A Thielscher, K Van Leemput, B Fischl, AV Dalca, JE Iglesias: SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining, Medical Image Analysis, 83, 102789 (2023)
B Billot, C Magdamo, SE Arnold, S Das, JE Iglesias: Robust machine learning segmentation for large-scale analysis of heterogeneous clinical brain MRI datasets, PNAS, 120(9), e2216399120 (2023)
SynthSR: a public AI tool to turn heterogeneous clinical brain scans into high-resolution T1-weighted images for 3D morphometry JE Iglesias, B Billot, Y Balbastre, C Magdamo, S Arnold, S Das, B Edlow, D Alexander, P Golland, B Fischl, Science Advances, 9(5), eadd3607 (2023)
Adamson, C.L., Alexander, B., Ball, G. et al. Parcellation of the neonatal cortex using Surface-based Melbourne Children’s Regional Infant Brain atlases (M-CRIB-S). Sci Rep 10, 4359 (2020). https://doi.org/10.1038/s41598-020-61326-2
Ciric, R., Thompson, W.H., Lorenz, R. et al. TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models. Nat Methods 19, 1568–1571 (2022). https://doi.org/10.1038/s41592-022-01681-2
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.
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.