BLeG
The Bezgin-Lewis-extended-Gordon parcellation.
This is an extension of Evan Gordon's surface-based cortical parcellation based on patterns of functional connectivity; the extension constructs and utilizes the surfaces for the deep subcortical structures (thalamus, caudate, pallidus, and putamen) in addition to the cortical surfaces, in order to support analyses that span all of these structures. This data is meant to accompany Lewis et al. 2021, Human Brain Mapping.
(Lewis, J. D., Bezgin, G., Fonov, V. S., Collins, D. L., & Evans, A. C. (2021). A sub+cortical fMRI-based surface parcellation. Human Brain Mapping, 1– 17. https://doi.org/10.1002/hbm.25675)
The BLeG parcellation was constructed on the surfaces derived from the mni_icbm152_t1_tal_nlin_sym_09a template, using CIVET-2.1.0. Here, we provide the CIVET surfaces and corresponding label files (These are for CIVET-2.1.0; they should not be used with earlier versions of CIVET). The mni_icbm152_t1_tal_nlin_sym_09a template is provided here in MINC, NIFTI and MGZ formats, for use with MNI, HCP, and FreeSurfer viewers, respectively. The surfaces and label files are also available in those three formats, for both the cortex and the subcortical structures. We also provide masks to exclude regions adjacent to the ventricles for use with measures like white/gray contrast (for the caudate and thalamus). Masking BLeG may leave parts of parcels; it may be desirable to identify parcels that extend out of the mask, and discard the complete parcel. These masks are also provided in the same three formats.
The FreeSurfer directory contains a derivative variant of the parcelletion, constructed on the fsaverageT1 using the aseg file for that volume to define the subcortical volumes. That volume is available here in the native MGZ format as well as in NIFTI. The FreeSurfer surfaces and labels are available for the cortex and the subcortical structures in both FreeSurfer native format and the GIFTI format. We again provide masks to exclude regions adjacent to the ventricles for use with measures like white/gray contrast (for the caudate and thalamus). Masking BLeG may leave parts of parcels; it may be desirable to identify parcels that extend out of the mask, and discard the complete parcel. These masks are also provided in FreeSurfer 'annot' as well as GIFTI formats.
The BigBrain surfaces and labels sit on the full8_400um_optbal template, which is available in both NIFTI format (.nii) and in FreeSurfer format (.mgz). The surface and label files are available only for the cortex, as the BigBrain template is not an actual t1w-volume and our subcortical tools are not reliable with it. Those files are also available in formats for use with the HCP viewer (.gii) and with the FreeSurfer viewer (.white,.annot).
We welcome suggestions for other representations that would be useful.
Note that the large (template) files are annexed, so, only the placeholder files, not the content, will be downloaded by default. If the content is needed locally, it can be downloaded using gin get-content.
Note that the GIFTI versions of the CIVET surfaces and labels were created by Andrew Reid; and the BigBrain and FreeSurfer mappings were performed by Lindsay Lewis. Please see:
Lewis, L.B. et al. (2020) ‘A multimodal surface matching (MSM) surface registration pipeline to bridge atlases across the MNI and the Freesurfer/Human Connectome Project Worlds’, in: Annual Meeting of the Organization for Human Brain Mapping.
