Harvard Oxford atlas

Access

See nilearn.datasets.fetch_atlas_harvard_oxford.

Notes

Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis.

T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label.

See also Makris et al.[1], Desikan et al.[2], Frazier et al.[3], Goldstein et al.[4].

Content

• atlas_type: str. Type of atlas. See Probabilistic atlas and Deterministic atlas.

• labels: list of str. List of the names of the regions.

• lut: pandas.DataFrame. Act as a look up table (lut) with at least columns ‘index’ and ‘name’. Formatted according to ‘dseg.tsv’ format from BIDS.

• maps: nibabel.nifti1.Nifti1Image. It is a 4D image with shape (182, 218, 182, 48) if a Probabilistic atlas is requested, and a 3D image with shape (182, 218, 182) and 48 regions (+ background) if a maximum probability atlas is requested. In the latter case, the image contains integer values which can be interpreted as the indices in the list of labels.

• template: str. The standardized space of analysis in which the data is provided.

References

[1]

Nikos Makris, Jill M. Goldstein, David Kennedy, Steven M. Hodge, Verne S. Caviness, Stephen V. Faraone, Ming T. Tsuang, and Larry J. Seidman. Decreased volume of left and total anterior insular lobule in schizophrenia. Schizophrenia Research, 83(2-3):155–171, April 2006. doi:10.1016/j.schres.2005.11.020.

[2]

Rahul S Desikan, Florent Ségonne, Bruce Fischl, Brian T Quinn, Bradford C Dickerson, Deborah Blacker, Randy L Buckner, Anders M Dale, R Paul Maguire, Bradley T Hyman, and others. An automated labeling system for subdividing the human cerebral cortex on mri scans into gyral based regions of interest. Neuroimage, 31(3):968–980, 2006.

[3]

Jean A Frazier, Sufen Chiu, Janis L Breeze, Nikos Makris, Nicholas Lange, David N Kennedy, Martha R Herbert, Eileen K Bent, Vamsi K Koneru, Megan E Dieterich, and others. Structural brain magnetic resonance imaging of limbic and thalamic volumes in pediatric bipolar disorder. American Journal of Psychiatry, 162(7):1256–1265, 2005.

[4]

Jill M Goldstein, Larry J Seidman, Nikos Makris, Todd Ahern, Liam M O’Brien, Verne S Caviness Jr, David N Kennedy, Stephen V Faraone, and Ming T Tsuang. Hypothalamic abnormalities in schizophrenia: sex effects and genetic vulnerability. Biological psychiatry, 61(8):935–945, 2007.

License

See https://fsl.fmrib.ox.ac.uk/fsl/docs/license.html