Subfield atlases in MNI-ICBM 152 space (2009c symmetric)
Author: Juan Eugenio Iglesias E-mail: jiglesiasgonzalez [at] mgh.harvard.edu' Rather than directly contacting the author, please post your questions on this module to the FreeSurfer mailing list at freesurfer [at] nmr.mgh.harvard.edu If you use these tools in your analysis, please cite: Hippocampus: A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI. Iglesias, J.E., Augustinack, J.C., Nguyen, K., Player, C.M., Player, A., Wright, M., Roy, N., Frosch, M.P., Mc Kee, A.C., Wald, L.L., Fischl, B., and Van Leemput, K. Neuroimage, 115, July 2015, 117-137. Amygdala: High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas. Saygin ZM & Kliemann D (joint 1st authors), Iglesias JE, van der Kouwe AJW, Boyd E, Reuter M, Stevens A, Van Leemput K, Mc Kee A, Frosch MP, Fischl B, Augustinack JC. Neuroimage, 155, July 2017, 370-382. Brainstem: Bayesian segmentation of brainstem structures in MRI. Iglesias, J.E., Van Leemput, K., Bhatt, P., Casillas, C., Dutt, S., Schuff, N., Truran-Sacrey, D., Boxer, A., and Fischl, B. NeuroImage, 113, June 2015, 184-195. Thalamus: A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. Iglesias, J.E., Insausti, R., Lerma-Usabiaga, G., Bocchetta, M., Van Leemput, K., Greve, D., van der Kouwe, A., Caballero-Gaudes, C., Paz-Alonso, P. Neuroimage (accepted). See also: HippocampalSubfieldsAndNucleiOfAmygdala, BrainstemSubstructures, ThalamicNuclei, SubregionSegmentation
Our substructure segmentation tools rely on probabilistic atlases of neuroanatomy that: (i) do not have image intensities, only label probabilities; and (ii) do not live in any standard space, but rather their own. Several users have requested a version of these atlases in a standard space. Here, we provide a version of the labels probabilities that lives approximately in ICBM 152 2009c (symmetric) space: The atlas itself can be downloaded from the website of the McConnell Brain Imaging Centre at McGill University, or directly from here.. Please note that the atlas probabilities live in the same world coordinates as the atlas, but not in the same voxel grid. You can always resmple the label probabilities if needed, e.g., with mri_convert (-rl flag).
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