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Citation

HemiSpec separates citations for the original scientific method, the preprocessing software, and the HemiSpec software/downstream work.

Original cross-hemispheric DGN and ANS/RNS framework

Cite this paper whenever you use or describe the cross-hemispheric DGN reconstruction method, ANS, or RNS:

Wang, G., Jiang, N., Ma, Y., Suo, D., Liu, T., Funahashi, S., & Yan, T. (2024). Using a deep generation network reveals neuroanatomical specificity in hemispheres. Patterns, 5(4), 100930. https://doi.org/10.1016/j.patter.2024.100930

HemiSpec uses the following public terminology consistently:

  • ANS: absolute neuroanatomical specificity.
  • RNS: relative neuroanatomical specificity.

HemiSpec documentation preserves those names and abbreviations.

FSL preprocessing

The study process_single_subject.sh workflow and the packaged reorientation-enhanced variant use FSL, BET, FAST, and FLIRT. Cite the tools that materially support your preprocessing methods:

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

Smith, S. M. (2002). Fast robust automated brain extraction. Human Brain Mapping, 17(3), 143–155. https://doi.org/10.1002/hbm.10062

Zhang, Y., Brady, M., & Smith, S. (2001). Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm. IEEE Transactions on Medical Imaging, 20(1), 45–57. https://doi.org/10.1109/42.906424

Jenkinson, M., & Smith, S. (2001). A global optimisation method for robust affine registration of brain images. Medical Image Analysis, 5(2), 143–156. https://doi.org/10.1016/S1361-8415(01)00036-6

HemiSpec software citation

For software use, cite the public HemiSpec release/archive record when available and retain the software version in the Methods section. Until an archival DOI is registered, use the repository CITATION.cff metadata together with the release tag and access date.

Do not replace the Wang et al. citation with a software citation: the original scientific method and the software implementation are separate contributions and should be credited separately.

HemiSpec downstream manuscripts

A manuscript marked “in preparation” is not a stable public citation. Cite a HemiSpec downstream manuscript only after a public preprint, journal article, or archival record exists. Until then, describe the analysis as performed with HemiSpec and report the exact software version/commit.

Suggested Methods wording

T1-weighted images were converted to MNI152 1.5 mm gray-matter probability maps using an FSL-based workflow (BET, FAST, and FLIRT), thresholded at a GM probability of 0.15, and supplied to HemiSpec. Cross-hemispheric reconstruction and ANS/RNS computation followed the framework introduced by Wang et al. (2024). Software version, model bundle, thresholds, and optional validation settings were recorded for reproducibility.