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References for commonly used techniques

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Yohan Yee edited this page May 13, 2022 · 2 revisions

Pre-processing

  • MINC suite of software tools (http://bic-mni.github.io)
  • Denoising: Coupé, P., Yger, P., Prima, S., Hellier, P., Kervrann, C., & Barillot, C. (2008). An optimized blockwise nonlocal means denoising filter for 3-D magnetic resonance images. IEEE transactions on medical imaging, 27(4), 425-441.
  • N4ITK: Tustison, N. J., Avants, B. B., Cook, P. A., Zheng, Y., Egan, A., Yushkevich, P. A., & Gee, J. C. (2010). N4ITK: improved N3 bias correction. IEEE transactions on medical imaging, 29(6), 1310-1320.

mouse

the Dorr–Steadman–Ullman atlas:

  • Dorr, A. E., Lerch, J. P., Spring, S., Kabani, N., & Henkelman, R. M. (2008). High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice. Neuroimage, 42(1), 60-69.
  • Steadman, P. E., Ellegood, J., Szulc, K. U., Turnbull, D. H., Joyner, A. L., Henkelman, R. M., & Lerch, J. P. (2014). Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas. Autism research, 7(1), 124-137.
  • Ullmann, J. F., Watson, C., Janke, A. L., Kurniawan, N. D., & Reutens, D. C. (2013). A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex. Neuroimage, 78, 196-203.
  • Richards 2011
  • Qiu 2016
  • Egan 2015

Allen Institute's CCFv3 template and reference atlas of the adult mouse brain

  • Wang, Q., Ding, S. L., Li, Y., Royall, J., Feng, D., Lesnar, P., ... & Ng, L. (2020). The Allen mouse brain common coordinate framework: a 3D reference atlas. Cell, 181(4), 936-953.

human

QC

mouse

raw data

https://github.com/CoBrALab/documentation/wiki/Mouse-QC-Manual-(Structural)

human

raw data

https://github.com/CoBrALab/documentation/wiki/Motion-Quality-Control-(QC)-Manual

maget

https://github.com/CoBrALab/documentation/wiki/MAGeT-Brain-Quality-Control-(QC)-Guide

civet

https://github.com/CoBrALab/documentation/wiki/CIVET-Quality-Control-Guidelines

Deformation-based morphometry

mouse

  • Pydpiper toolkit: Friedel, M., van Eede, M. C., Pipitone, J., Chakravarty, M. M., & Lerch, J. P. (2014). Pydpiper: a flexible toolkit for constructing novel registration pipelines. Frontiers in neuroinformatics, 8, 67.
  • ANTS registration algorithm: Avants, B. B., Tustison, N. J., Song, G., Cook, P. A., Klein, A., & Gee, J. C. (2011). A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage, 54(3), 2033-2044.

human

MAGeT

  • Chakravarty, M. M., Steadman, P., Van Eede, M. C., Calcott, R. D., Gu, V., Shaw, P., ... & Lerch, J. P. (2013). Performing label‐fusion‐based segmentation using multiple automatically generated templates. Human brain mapping, 34(10), 2635-2654.
  • Automatic Normalization Tools (ANTS) compatible with the minc-toolkit (https://github.com/vfonov/mincANTS)
  • Majority-vote label fusion: Collins, D. L., & Pruessner, J. C. (2010). Towards accurate, automatic segmentation of the hippocampus and amygdala from MRI by augmenting ANIMAL with a template library and label fusion. Neuroimage, 52(4), 1355-1366.

mouse

DSURQE

Allen Brain atlas

  • original: Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., ... & Jones, A. R. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445(7124), 168-176.
  • merged:

human

  • Hippocampus:
    • subfields: Winterburn, J. L., Pruessner, J. C., Chavez, S., Schira, M., Lobaugh, N. J., Voineskos, A. N., & Chakravarty, M. A novel in vivo atlas of human hippocampal subfields using high-resolution 3T magnetic resonance imaging. NeuroImage (2013). 10.1016/j.neuroimage.2013.02.003
    • white matter: Amaral, R. S. C., Park, M. T. M., Devenyi, G. A., Lynn, V., Pipitone, J., Winterburn, J., Chavez, S., Schira, M., Lobaugh, N., Voineskos, A. N., Pruessner, J. C., Chakravarty, M.M., & the Alzheimer’s Disease Neuroimaging Initiative. Manual segmentation of the fornix, fimbria, and alveus on high-resolution 3T MRI: Application via fully-automated mapping of the human memory circuit white and grey matter in healthy and pathological aging. NeuroImage (2016). 10.1016/j.neuroimage.2016.10.027
  • Striatum, globus pallidus, thalamus: Tullo, S., Devenyi, G. A., Patel, R., Park, M. T. M., Collins, D. L., & Chakravarty, M. M. (2018). Warping an atlas derived from serial histology to 5 high-resolution MRIs. Scientific data, 5, 180107.
  • Cerebellum: Park, M. T. M., Pipitone, J., Baer, L. H., Winterburn, J. L., Shah, Y., Chavez, S., ... & Chakravarty, M. M. (2014). Derivation of high-resolution MRI atlases of the human cerebellum at 3 T and segmentation using multiple automatically generated templates. Neuroimage, 95, 217-231.
  • Amygdala:

CIVET

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