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wiheto / esfmri_connectivity

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Templateflow requirements #1

Closed wiheto closed 4 years ago

wiheto commented 5 years ago

What we need:

Atlases for King et al 2019, the amygdala ROI on Templateflow.

Relates to:

[PROC] fmriprep (V1.5) will be run for the pre-processing (Esteban et al. 2019). Pre-op structural MRIs will be used for co-registration of post-op images. fmridenoise will be run, and the best fitting denoising strategy will be chosen (best fitting strategy will be evaluated by considering the lower correlation with framewise displacement and the least degree of freedom loss). Data will be band-passed filtered between 0.008 and 0.1 Hz. The 400 parcels from Schaeffer et al. 2017 will be used to parcellate the cortex. This parcellation will be supplemented with 13 subcortical ROIs from the Oxford-Harvard subcortical atlas (amygdala excluded) and ten cerebellum ROIs from the King et al. 2019 multi-domain task-based parcellation. The amygdala ROI will be split into three regions, based on an MRI atlas of amygdala nuclei (Tyszka & Pauli 2016): central, cortico-medial, and basolateral, corresponding to subdivisions of the amygdala that have been linked to segregated functional networks in prior human fMRI studies (Bickart et al. 2012).

wiheto commented 5 years ago

Amygdala atlas is found here: https://osf.io/m485f/?show=revision - In FSL MNI space

King is found here: http://www.diedrichsenlab.org/imaging/mdtb.htm - King was derived using SPM12 (known through correspondence).

wiheto commented 4 years ago

@oesteban do you know about SPM12's MNI to MNI2009c yet?