Harvard-Oxford Atlas

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Harvard-Oxford Atlas
Abbreviations: HOCPA HOSPA
Category: Harvard-Oxford Atlas

Human brain atlas

Papers: DOAJ Google Scholar PubMed
Ontologies: MeSH NeuroLex Wikidata Wikipedia
Other: Google Twitter WolframAlpha

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Harvard-Oxford Atlas is a human brain atlas developed by David Kennedy, Christian Haselgrove and others. The atlas is distributed with FSL.


PyROI is a Python package that uses the atlas. It is available from:


The parcellation have been compared with other human brain atlases.[1]

Brain regions in the Brede Wiki linked to the Harvard-Oxford Atlas are listed in the category Brain regions in Harvard-Oxford Atlas.


[edit] Files

In FSL there are two XML files with labels:

  • fsl/data/atlases/HarvardOxford-Cortical.xml
  • fsl/data/atlases/HarvardOxford-Subcortical.xml

[edit] Regions

[edit] Cortical

The labels overlap with those described in Automatically parcellating the human cerebral cortex and Human cerebral cortex: localization, parcellation and morphometry with magnetic resonance imaging.

ID Brain region
0 Frontal Pole
1 Insular Cortex
2 Superior Frontal Gyrus
3 Middle Frontal Gyrus
4 Inferior Frontal Gyrus, pars triangularis
5 Inferior Frontal Gyrus, pars opercularis
6 Precentral Gyrus
7 Temporal Pole
8 Superior Temporal Gyrus, anterior division
9 Superior Temporal Gyrus, posterior division
10 Middle Temporal Gyrus, anterior division
11 Middle Temporal Gyrus, posterior division
12 Middle Temporal Gyrus, temporooccipital part
13 Inferior Temporal Gyrus, anterior division
14 Inferior Temporal Gyrus, posterior division
15 Inferior Temporal Gyrus, temporooccipital part
16 Postcentral Gyrus
17 Superior Parietal Lobule
18 Supramarginal Gyrus, anterior division
19 Supramarginal Gyrus, posterior division
20 Angular Gyrus
21 Lateral Occipital Cortex, superoir division
22 Lateral Occipital Cortex, inferior division
23 Intracalcarine Cortex
24 Frontal Medial Cortex
25 Juxtapositional Lobule Cortex (formerly Supplementary Motor Cortex)
26 Subcallosal Cortex
27 Paracingulate Gyrus
28 Cingulate Gyrus, anterior division
29 Cingulate Gyrus, posterior division
30 Precuneous Cortex
31 Cuneal Cortex
32 Frontal Orbital Cortex
33 Parahippocampal Gyrus, anterior division
34 Parahippocampal Gyrus, posterior division
35 Lingual Gyrus
36 Temporal Fusiform Cortex, anterior division
37 Temporal Fusiform Cortex, posterior division
38 Temporal Occipital Fusiform Cortex
39 Occipital Fusiform Gyrus
40 Frontal Operculum Cortex
41 Central Opercular Cortex
42 Parietal Operculum Cortex
43 Planum Polare
44 Heschl's Gyrus (includes H1 and H2)
45 Planum Temporale
46 Supracalcarine Cortex
47 Occipital Pole

Note: Lateral Occipital Cortex, superoir division is misspelled.

[edit] Subcortical

ID Brain region
0 Left Cerebral White Matter
1 Left Cerebral Cortex
2 Left Lateral Ventrical
3 Left Thalamus
4 Left Caudate
5 Left Putamen
6 Left Pallidum
7 Brain-Stem
8 Left Hippocampus
9 Left Amygdala
10 Left Accumbens
11 Right Cerebral White Matter
12 Right Cerebral Cortex
13 Right Lateral Ventricle
14 Right Thalamus
15 Right Caudate
16 Right Putamen
17 Right Pallidum
18 Right Hippocampus
19 Right Amygdala
20 Right Accumbens

[edit] Python

The Nilearn Python package will easily download the atlas and Nibabel can read that file. The neuroimaging visualization functions in Nilearn can plot that volume:

from nilearn.datasets import fetch_harvard_oxford
from nilearn.plotting import plot_glass_brain
from nibabel import load
import matplotlib.pyplot as plt
filename, labels = fetch_harvard_oxford('cort-maxprob-thr25-2mm')
volume = load(filename)

[edit] Papers

  1. Nikos Makris, Jill M. Goldstein, David Kennedy, Steven M. Hodge, Verne S. Caviness, Stephen V. Faraone, Ming T. Tsuang, Larry J. Seidman (2006). "Decreased volume of left and total anterior insular lobule in schizophrenia". Schizophrenia research 83(2-3): 155-151. doi: 10.1016/j.schres.2005.11.020. PMID: 16448806.
  2. 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, Steven M. Hodge (2005). "Structural brain magnetic resonance imaging of limbic and thalamic volumes in pediatric bipolar disorder". The American journal of psychiatry 162(7): 1256-1255. doi: 10.1176/appi.ajp.162.7.1256. PMID: 15994707.
  3. R. S. Desikan, F. Ségonne, B. Fischl, B. T. Quinn, B. C. Dickerson, D. Blacker, R. L. Buckner, A. M. Dale, R. P. Maguire, B. T. Hyman, M. S. Albert (2006). "An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest". Neuroimage 31(3): 968-980.
  4. Jill M. Goldstein, Larry J. Seidman, Nikos Makris, Todd Ahern, Liam M. O'Brien, Verne S. Jr Caviness, David N. Kennedy, Stephen V. Faraone, Ming T. Tsuang (2007). "Hypothalamic abnormalities in schizophrenia: sex effects and genetic vulnerability". Biological psychiatry 61(8): 935-935. doi: 10.1016/j.biopsych.2006.06.027. PMID: 17046727.

[edit] Critique

  1. The "Subcallosal Cortex" is encompassing rather extensive areas.
  2. The "Frontal Medial Cortex" seems to encompass rather less than what other research groups refers to as "medialfrontal".

[edit] External links

  1. http://www.cma.mgh.harvard.edu/fsl_atlas.html

[edit] References

  1. Jason W. Bohland, Hemant Bokil, Cara B. Allen, Partha P. Mitra (2009). "The brain atlas concordance problem: quantitative comparison of anatomical parcellations". PLoS ONE 4(9): e7200. doi: 10.1371/journal.pone.0007200.
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