brain_atlases: Coordinates for data from brain atlases

In cwatson/brainGraph: Graph Theory Analysis of Brain MRI Data

Coordinates for data from brain atlases

Description

Datasets containing spatial coordinates for: the original AAL atlases, the newer AAL2 atlases, Freesurfer atlases, Brainsuite, Craddock200, Dosenbach160, Harvard-Oxford, and LONI probabilistic brain atlas. In addition to coordinates, there are indices for the major lobes and hemispheres of the brain, the class variable (for Destrieux atlases), functional networks (for Dosenbach, Power, and Gordon atlases; plus the Yeo network labels for the Brainnetome atlas).

Usage

aal116

aal90

aal2.120

aal2.94

destrieux

destrieux.scgm

dk

dk.scgm

dkt

dkt.scgm

brainsuite

craddock200

dosenbach160

hoa112

lpba40

hcp_mmp1.0

power264

brainnetome

gordon333

Format

A data frame with 90 or 116 (for the original AAL atlases), 94 or 120 (for the newer AAL2 atlases), 148 or 162 (for Destrieux), 68 or 82 (for DK), 62 or 76 (for DKT), 74 (Brainsuite), 200 (Craddock), 160 (Dosenbach), 112 (Harvard-Oxford), 40 (LONI), 246 (Brainnetome), 360 (HCP), 264 (Power), or 333 (Gordon) observations on (some of) the following 19 variables:

name

a character vector of region names

x.mni

a numeric vector of x-coordinates (in MNI space)

y.mni

a numeric vector of y-coordinates (in MNI space)

z.mni

a numeric vector of z-coordinates (in MNI space)

lobe

a factor with some of levels Frontal Parietal Temporal Occipital Insula Limbic Cingulate SCGM Cerebellum (for aal116 and aal2.120) and Brainstem (for craddock200)

hemi

a factor with levels L R and B (for dosenbach160)

index

a numeric vector

name.full

a character vector of full region names, for the DK and DKT atlases

class

a factor with levels G G_and_S S, for the Destrieux atlases

network

(dosenbach160) a factor with levels default fronto-parietal cingulo-opercular sensorimotor cerebellum occipital

gyrus

(brainnetome) Abbreviated names of gyri/regions (including subcortical), with 24 unique values

gyrus.full

(brainnetome) Full names of gyrus

subregion

(brainnetome) Abbreviated names of subregions (including subdivisions of subcortical gray matter)

subregion.full

(brainnetome) Full names of subregion

Yeo_7network

(brainnetome) Factor with 8 levels consisting of SCGM plus the 7 networks from Yeo et al.

Yeo_17network

(brainnetome) Factor with 18 levels consisting of SCGM plus the 17 networks from Yeo et al.

area

(HCP) a factor with 23 cortical areas

Anatomy

(power264) Full region/gyrus names for the Power atlas; contains 53 unique regions

Brodmann

(power264) Integer values for Brodmann areas

Note

Use of the HCP parcellation is subject to the terms at https://balsa.wustl.edu/WN56. In particular: "I will acknowledge the use of WU-Minn HCP data and data derived from WU-Minn HCP data when publicly presenting any results or algorithms that benefitted from their use."

Region names in the gordon333 atlas were chosen to match those of the hcp_mmp1.0 atlas. Many were determined from the coordinates (using FSL's atlasquery), while the rest were entered manually by me. The lobe values were matched to the HCP atlas, as well.

Source

https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/atlases.html

References

Tzourio-Mazoyer, N. and Landeau, B. and Papathanassiou, D. and Crivello, F. and Etard, O. and Delcroix, N. and Mazoyer, B. and Joliot, M. (2002) Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. NeuroImage, 15(1), 273–289. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1006/nimg.2001.0978")}

Rolls, E.T. and Joliot, M. and Tzourio-Mazoyer, N. (2015) Implementation of a new parcellation of the orbitofrontal cortex in the automated anatomical labelling atlas. NeuroImage, 122, 1–5. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.neuroimage.2015.07.075")}

Destrieux, C. and Fischl, B. and Dale, A. and Halgren E. (2010) Automatic parcellation of human cortical gyri and sulci using standard anatomic nomenclature. NeuroImage, 53(1), 1–15. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.neuroimage.2010.06.010")}

Desikan, R.S. and Segonne, F. and Fischl, B. et al. (2006) An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. NeuroImage, 31, 968–980. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.neuroimage.2006.01.021")}

Klein, A. and Tourville, J. (2012) 101 labeled brain images and a consistent human cortical labeling protocol. Front Neurosci, 6. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3389/fnins.2012.00171")}

Shattuck, D.W. and Leahy, R.M. (2002) BrainSuite: an automated cortical surface identification tool. Medical Image Analysis, 8(2), 129–142.

Pantazis, D. and Joshi, A.A. and Jintao, J. and Shattuck, D.W. and Bernstein, L.E. and Damasio, H. and Leahy, R.M. (2009) Comparison of landmark-based and automatic methods for cortical surface registration. NeuroImage, 49(3), 2479–2493.

Craddock, R.C. and James, G.A. and Holtzheimer, P.E. and Hu, X.P. and Mayberg, H.S. (2012) A whole brain fMRI atlas generated via spatially constrained spectral clustering. Human Brain Mapping, 33, 1914–1928. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/hbm.21333")}

Dosenbach, N.U. and Nardos, B. and Cohen, A.L. and Fair, D.A. and Power, J.D. and Church, J.A. and Nelson, S.M. and Wig, G.S. and Vogel, A.C. and Lessov-Schlaggar, C.N. and Barnes, K.A. (2010) Prediction of individual brain maturity using fMRI. Science, 329(5997), 1358–1361.

Makris, N. and Goldstein, J.M. and Kennedy, D. et al. (2006) Decreased volume of left and total anterior insular lobule in schizophrenia. Schizophr Res, 83(2-3), 155–171.

Shattuck, D.W. and Mirza, M. and Adisetiyo, V. and Hojatkashani, C. and Salamon, G. and Narr, K.L. and Poldrack, R.A. and Bilder, R.M. and Toga, A.W. (2008) Construction of a 3D probabilistic atlas of human cortical structures. NeuroImage, 39(3), 1064–1080. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.neuroimage.2007.09.031")}

Glasser, M.F. and Coalson, T.S. and Robinson, E.C. and Hacker, C.D. and Harwell, J. and Yacoub, E. and Ugurbil, K. and Andersson, J. and Beckmann, C.F. and Jenkinson, M. and Smith, S.M. and van Essen, D.C. (2016) A multi-modal parcellation of human cerebral cortex. Nature, 536, 171–178. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nature18933")}. PMID: 27437579.

Power, J.D. and Cohen, A.L. and Nelson, S.M. and Wig, G.S. and Barnes, K.A. and Church, J.A. and Vogel, A.C. and Laumann, T.O. and Miezin, F.M. and Schlaggar, B.L. and Petersen, S.E. (2011) Functional network organization of the human brain. Neuron, 72(4), 665–678. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.neuron.2011.09.006")}

Fan, L. and Li, H. and Zhuo, J. and Zhang, Y. and Wang, J. and Chen, L. and Yang, Z. and Chu, C. and Xie, S. and Laird, A.R. and Fox, P.T. and Eickhoff, S.B. and Yu, C. and Jiang, T (2016) The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture. Cerebral Cortex, 26(8), 3508–3526. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/cercor/bhw157")}

Gordon, E.M. and Laumann, T.O. and Adeyemo, B. and Huckins, J.F. and Kelley, W.M. and Petersen, S.E. (2014) Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cerebral Cortex, 26(1), 288–303. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/cercor/bhu239")}

cwatson/brainGraph documentation built on Feb. 21, 2024, 6:33 p.m.