Terms, data sources and acknowledgements
The brain atlas on this site is assembled from openly licensed research data. This page records what was used, under what terms, who produced it, and the conditions under which this site may be used.
Not a medical device. Everything on this site is provided for education and research. It is not intended for diagnosis, treatment planning, or any other clinical purpose, and must not be used as a substitute for assessment by a qualified clinician. Individual brain anatomy varies considerably from a template average.
1. Atlas data sources
Harvard-Oxford cortical and subcortical structural atlases
113 structures, 1 mm, maximum probability at a 25 percent threshold. Released under CC BY-SA 4.0. Distributed with FSL but not the property of the University of Oxford — the FSL licence explicitly places these atlases under Creative Commons terms, which permit redistribution and commercial use with share-alike.
Makris N, Goldstein JM, Kennedy D, et al. Decreased volume of left and total anterior
insular lobule in schizophrenia. Schizophrenia Research 2006;83(2–3):155–171.
Frazier JA, Chiu S, Breeze JL, et al. Structural brain magnetic resonance imaging of limbic
and thalamic volumes in pediatric bipolar disorder. American Journal of Psychiatry
2005;162(7):1256–1265.
Desikan RS, Ségonne F, Fischl B, et al. An automated labeling system for subdividing the
human cerebral cortex on MRI scans into gyral based regions of interest.
NeuroImage 2006;31(3):968–980.
Goldstein JM, Seidman LJ, Makris N, et al. Hypothalamic abnormalities in schizophrenia: sex
effects and genetic vulnerability. Biological Psychiatry 2007;61(8):935–945.
AAL2 Automated Anatomical Labelling
120 structures including 26 cerebellar regions, 2 mm. Released under the GNU General Public License. Provides the cerebellar coverage that Harvard-Oxford lacks.
Rolls ET, Joliot M, Tzourio-Mazoyer N. Implementation of a new parcellation of the
orbitofrontal cortex in the automated anatomical labeling atlas.
NeuroImage 2015;122:1–5.
Tzourio-Mazoyer N, Landeau B, Papathanassiou D, et al. Automated anatomical labeling of
activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject
brain. NeuroImage 2002;15(1):273–289.
Jülich histological atlas
121 structures at 1 mm, from cyto- and myelo-architectonic mapping of ten post-mortem brains. It is included because it supplies what a grey-matter parcellation cannot: the fibre tracts — superior longitudinal fascicle, callosal body, optic and acoustic radiations, fornix, uncinate — together with named visual and auditory areas such as V4, V5 and the primary auditory subdivisions TE1.0 to TE1.2. Without it, disorders whose substrate is a tract could only be described in words. The published atlas is a set of probability maps; the version shown here is a maximum-probability labelling at a 25 per cent threshold, matching the convention used for Harvard-Oxford.
Distributed with FSL and used under the FSL licence, which permits academic and non-commercial use. This is more restrictive than the licences covering the other atlases on this page.
Eickhoff SB, Stephan KE, Mohlberg H, Grefkes C, Fink GR, Amunts K, Zilles K. A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data. NeuroImage 2005;25(4):1325–1335.
FreeSurfer fsaverage cortical surface
The folded cortical surface shown in the 3D view is the fsaverage pial surface. A volumetric template such as MNI152 is an average of many brains, which blurs the cortical folds away; a surface-based average preserves the real gyral and sulcal geometry. The surface was transformed from MNI305 into MNI152 space using FreeSurfer's published affine, then subdivided and smoothed for display.
Used under the terms of the FreeSurfer Software License Agreement (Massachusetts General Hospital), which permits redistribution.
Fischl B. FreeSurfer. NeuroImage 2012;62(2):774–781.
Fischl B, Sereno MI, Tootell RBH, Dale AM. High-resolution intersubject averaging and a
coordinate system for the cortical surface. Human Brain Mapping 1999;8(4):272–284.
MNI152 template
The anatomical underlay for the slice views is the MNI152 non-linear 6th generation T1 template — the reference space in which Harvard-Oxford is defined.
Copyright © 1993–2004 Louis Collins, McConnell Brain Imaging Centre, Montreal
Neurological Institute, McGill University. Permission to use, copy, modify and distribute
this software and its documentation for any purpose and without fee is hereby granted,
provided that the above copyright notice appear in all copies. The authors and McGill
University make no representations about the suitability of this software for any purpose.
It is provided “as is” without express or implied warranty.
Fonov V, Evans AC, Botteron K, et al. Unbiased average age-appropriate atlases for
pediatric studies. NeuroImage 2011;54(1):313–327.
What was derived for this site
The published Harvard-Oxford atlas is a four-dimensional probabilistic volume. It was reduced to a single maximum-probability label volume at a 25 percent threshold, and per-structure surface meshes were generated by marching cubes with Gaussian pre-smoothing and volume-preserving Taubin smoothing. AAL2 meshes were generated the same way, upsampled before meshing because the source grid is 2 mm. These derived files inherit the licence of the atlas they came from.
The structure descriptions, groupings and reference points shown in the detail panel were written and computed for this site, and are offered under CC BY 4.0.
2. Software
NiiVue
All 3D and slice rendering is done by NiiVue, under the BSD 2-Clause licence. github.com/niivue/niivue
Barlow and Barlow Condensed
Typefaces by Jeremy Tribby, under the SIL Open Font License 1.1.
Tooling
Mesh generation used nibabel, scikit-image, SciPy and trimesh. Atlas volumes were obtained via the atlasreader and nilearn distributions, which redistribute the upstream data under the licences recorded above.
3. Terms of use
What you may do
You may use this site freely for study, teaching and research, and you may reuse the atlas data under the licences of its original sources noting that Harvard-Oxford carries a share-alike obligation and AAL2 is copyleft. Screenshots exported from the atlas may be reproduced provided the sources on this page are credited.
What this site is not
It is not a clinical tool, not a diagnostic aid, and carries no warranty of accuracy, completeness or fitness for any purpose. Atlas boundaries are probabilistic and approximate. SignalsLab accepts no liability for any decision taken on the basis of material published here.
External links
Links to third-party sites are provided for convenience. SignalsLab is not responsible for their content or their handling of your data.
Privacy
This site is static. It sets no cookies, runs no analytics and collects no personal data. Atlas data is loaded directly from this domain; nothing you do in the viewer is transmitted anywhere. If you email us, that correspondence is kept only for the purpose of replying.
Contact
Corrections to the anatomical descriptions, or to any attribution on this page, are welcome at himanshu@signalslab.in.
4. Acknowledgements
This atlas exists because of researchers who chose to release their work openly: the teams at the Centre for Morphometric Analysis and the Martinos Center behind Harvard-Oxford, the GIN group behind AAL, the FreeSurfer developers at Massachusetts General Hospital, the McConnell Brain Imaging Centre at the Montreal Neurological Institute, and the NiiVue maintainers. None of them are affiliated with SignalsLab, and none have endorsed this site.
If you use this atlas in published work, please cite the original atlas papers listed in section 1. Additonally, following is a addtional tool development at signals lab you may contact for more above cognitive atals tools.