Brain Atlases

Overview

Atlases reach TI-Toolbox two different ways, and the distinction matters when you define an ROI:

• MNI-space atlases are shipped with the toolbox as ready-to-use NIfTI volumes in resources/atlas/. They are the same seven volumes for every user, and SimNIBS transforms a selected label into your subject’s space at run time.
• Subject-space atlases are generated per subject during preprocessing by SimNIBS charm/subject_atlas and FastSurfer or optional FreeSurfer. Existing FreeSurfer outputs are also read. Nothing is shipped — they only exist once you have run the pipeline on a head model. The browser below uses the ernie example subject so you can see what they look like.

Both families are queried through the same ROI picker used in flex-search, ex-search, and the analyzer.

	MNI-space	Subject-space
Shipped with the toolbox	Yes, in resources/atlas/	No — generated per subject
Same for every user	Yes	No
Produced by	Bundled with TI-Toolbox	charm and recon-all

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MNI-Space Atlases

TI-Toolbox ships seven atlases as MNI-space NIfTI volumes:

Atlas	Regions	Native space
CIT168 Subcortical (left/right)	32	MNI152NLin2009cAsym
Glasser HCP-MMP1.0	360	FreeSurfer-conformed 256x256x256 1mm grid
MASSP Subcortical	31	ICBM152 2009b nonlinear asymmetric, hi-res 0.5mm
Harvard-Oxford cortical, lateralized	96	MNI152NLin6Asym, FSL 182x218x182 1mm grid
Harvard-Oxford subcortical	21	MNI152NLin6Asym, FSL 182x218x182 1mm grid
Cerebellum-MNIfnirt (Diedrichsen 2009)	28	MNI152NLin6Asym, FSL 182x218x182 1mm grid
Schaefer 2018, 400 parcels / 7 networks	400	MNI152NLin6Asym, FSL 182x218x182 1mm grid

The four FSL-grid atlases sit on exactly the grid SimNIBS’s mni2subject warps assume (their headers were checked against the shipped MNI152_T1_1mm.nii.gz), so they need no template correction; see Which MNI template for the other three.

Every one of them is a label volume, including Glasser: that is a cortical parcellation, but it is distributed as a NIfTI, so you target it through the ROI picker’s Subcortical mode, not the Cortical mode. The picker knows which is which because each atlas declares it in resources/atlas/manifest.json, and it will not offer you an atlas the mode you are in cannot read. TI-Toolbox ships no MNI-space surface parcellation; the Cortical mode’s atlases are your own subject’s, built by preprocessing.

In MNI mode, the Optimizer’s and Analyzer’s target pane has an Explode button next to Clear selection. It fades the scalp and pushes every atlas region outward, mostly sideways, so deep or hidden structures can be seen and clicked; press it again to collapse them, and your selection is unaffected. Explode is available for MNI atlases only, and because the MNI atlases are split into left and right regions, a click selects one hemisphere.

Explode on the CIT168 atlas (32 regions) in MNI mode.

Licence, attribution and citation

Atlases are other people’s data. If you publish work that used one, cite it; if you redistribute TI-Toolbox, these are the terms you are redistributing under. Each row is also machine-readable in resources/atlas/manifest.json.

Atlas	Licence	May be redistributed	Cite
CIT168 Subcortical	CC BY 4.0	Yes	Pauli W. M., Nili A. N., Tyszka J. M. Scientific Data 5:180063 (2018). doi:10.1038/sdata.2018.63
MASSP 2021 Subcortical	CC BY 4.0	Yes	Bazin P.-L. et al. eLife 9:e59430 (2020); atlas release doi:10.21942/uva.19646328
Glasser HCP-MMP1.0	WU-Minn HCP Open Access Data Use Terms	Yes, under those same terms	Glasser M. F. et al. Nature 536:171-178 (2016). doi:10.1038/nature18933
Harvard-Oxford cortical / subcortical	CC BY-SA 4.0 (FSL licence page)	Yes, share-alike	Desikan R. S. et al. NeuroImage 31:968-980 (2006); Frazier J. A. et al. Am J Psychiatry 162:1256-1265 (2005); Makris N. et al. Schizophr Res 83:155-171 (2006)
Cerebellum-MNIfnirt	CC BY-SA 4.0 (same FSL sentence)	Yes, share-alike	Diedrichsen J. et al. NeuroImage 46:39-46 (2009). doi:10.1016/j.neuroimage.2009.01.045
Schaefer 2018 400/7	MIT (CBIG)	Yes	Schaefer A. et al. Cerebral Cortex 28:3095-3114 (2018). doi:10.1093/cercor/bhx179
MNI152 T1 1mm template	MNI/McGill permissive (any purpose, without fee, keep the notice)	Yes	Copyright (C) 1993-2009 Louis Collins, McConnell Brain Imaging Centre, MNI, McGill University

Using Glasser also carries an acknowledgement: “Data were provided [in part] by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University.”

The full notices, with copyright holders, are in the repository’s NOTICE file.

Every shipped atlas names one hemisphere per label, apart from true midline structures (cerebellar vermis, brain stem, third and fourth ventricle, fornix). Picking “Left-Putamen” targets the left putamen only; to target both, pick both.

Not shipped

Bilateral CIT168 and Harvard-Oxford cortical (CIT168_labeling_MNI152NLin2009cAsym.nii.gz, HarvardOxford-cort-maxprob-thr25-1mm.nii.gz) were shipped until 2026-09-23. Each of their labels covered a structure in both hemispheres, so choosing one region silently targeted both sides. They were replaced by CIT168_labeling_lateralized_MNI152NLin2009cAsym.nii.gz (label k became 2k-1 left and 2k right) and FSL’s own lateralized HarvardOxford-cortl-maxprob-thr25-1mm.nii.gz (same numbering). A configuration that still names an old file stops with a sentence naming its replacement; pick the side(s) you meant from the new atlas.

Morel thalamus atlas (MorelMNI152_labeling_1mm.nii.gz, 74 nuclei) was shipped until 2026-09-17 and has been removed. Its licence is CC BY-NC-SA 4.0 (Zenodo record 13918589; (C) University of Zurich and ETH Zurich, Andras Jakab, Remi Blanc and Gabor Szekely), which forbids commercial use — a promise TI-Toolbox’s own GPL-3 licence cannot make for you, so a GPL-3 project cannot redistribute it. A configuration that still names it stops with “The Morel atlas is no longer shipped (CC BY-NC-SA); see docs/wiki/atlases.md”; pick another thalamic target (Harvard-Oxford subcortical or MASSP both label the thalamus; neither subdivides it into nuclei) or, if your own use is non-commercial, fetch the atlas from Zenodo yourself and import it as a custom NIfTI mask. The plan for bringing it back as an optional, user-fetched download is recorded in resources/atlas/README.md § Not shipped. Cite, if you use it: Krauth A. et al. NeuroImage 49(3):2053-2062 (2010); Jakab A. et al. AJNR 33(11):2110-2116 (2012).

Which MNI template, and how far off

SimNIBS warps between MNI and your subject with the deformation fields charm wrote into m2m_<id>/toMNI/, and those were computed against FSL’s MNI152_T1_1mm.nii.gz, i.e. MNI152NLin6Asym. CIT168 and Glasser are defined in MNI152NLin2009cAsym and MASSP in 2009b, so their labels travel through a warp that targets a slightly different template. The templates differ by roughly 1.3 mm globally.

Measured on the ernie example subject, against charm’s own subcortical segmentation (m2m_ernie/segmentation/labeling.nii.gz) for the same structure:

Target	Distance between centroids
CIT168 putamen vs charm Left+Right-Putamen	1.05 mm
CIT168 caudate vs charm Left+Right-Caudate	2.20 mm
MASSP thalamus (left) vs charm Left-Thalamus	2.00 mm
MASSP thalamus (right) vs charm Right-Thalamus	1.19 mm

That is the same order as the disagreement between two segmentations of the same structure, and it is accepted rather than corrected. Every optimization and analysis writes a ROI plate (roi_plate.png) showing the mask that will actually be used on your subject’s own T1 — look at it before you trust a deep target.

Pick an atlas from the dropdown to load it over the MNI152 template. The browser shows CIT168, Glasser and MASSP; the Harvard-Oxford, Cerebellum and Schaefer atlases are described below and offered in the ROI picker, but are not yet in this browser. Click any row in a label table below to jump the crosshair to that region’s centroid — the viewer switches atlases automatically if needed. Only the template and the currently selected atlas are ever loaded.

Atlas: CIT168 Subcortical Glasser HCP-MMP1.0 MASSP Subcortical

Overlay opacity is fixed at 70% over the grayscale MNI152 template. Colours match each atlas's own lookup table.

Interactive viewer unavailable. Your browser does not support WebGL2, which the viewer requires. The label tables remain fully searchable — use the centroid column to locate a region in your own viewer.

CIT168 Subcortical Atlas

Pauli WM, Nili AN, Tyszka JM. A high-resolution probabilistic in vivo atlas of human subcortical brain nuclei. Scientific Data 5:180063 (2018). doi:10.1038/sdata.2018.63.

The shipped volume is a deterministic label map, derived locally from the paper’s probabilistic masks by winner-takes-highest-probability at a 0.05 minimum-probability threshold. The probability maps themselves are not shipped — only the resulting hard segmentation.

The published labeling is bilateral (16 labels, each covering a structure in both hemispheres). TI-Toolbox ships it split at the midline (x = 0 mm of its own template) since 2026-09-23: 32 labels, where the paper’s label k is 2k-1 (Left-…, x < 0) and 2k (Right-…, x ≥ 0), made by dev/build_lateralized_atlases.py. Nothing else about the map changes.

The label table below comes from the docs atlas browser, which still carries the 16 bilateral labels until its assets are regenerated with dev/build_atlas_assets.py; its centroids therefore fall near the midline.

16 regions

ID	Name	Colour	Volume	Centroid (MNI, mm)
1	CIT168_Pu_Putamen		18506 mm³	0.2, 1.4, 0.3
2	CIT168_Ca_Caudate		17614 mm³	0.4, 5.9, 9.2
3	CIT168_NAC_Nucleus_accumbens		1483 mm³	-0.3, 8.2, -10.2
4	CIT168_EXA_Extended_amygdala		797 mm³	0, 3, -0.6
5	CIT168_GPe_External_globus_pallidus		2904 mm³	-0.4, -1, -0.4
6	CIT168_GPi_Internal_globus_pallidus		1638 mm³	0.1, -4.9, -4.6
7	CIT168_SNc_Substantia_nigra_pars_compacta		454 mm³	0, -20, -14.2
8	CIT168_RN_Red_nucleus		1130 mm³	0.2, -19.5, -9.1
9	CIT168_SNr_Substantia_nigra_pars_reticulata		1259 mm³	0.4, -16.3, -13.5
10	CIT168_PBP_Parabrachial_pigmented_nucleus		447 mm³	-0.2, -19.2, -12.1
11	CIT168_VTA_Ventral_tegmental_area		208 mm³	-0.2, -22, -17.5
12	CIT168_VeP_Ventral_pallidum		409 mm³	0.7, 3.3, -8.9
13	CIT168_HN_Habenular_nuclei		226 mm³	0.4, -23.5, 3
14	CIT168_HTH_Hypothalamus		3360 mm³	-0.1, -4.3, -9.4
15	CIT168_MN_Mammillary_nuclei		309 mm³	0, -8, -14.9
16	CIT168_STH_Subthalamic_nucleus		622 mm³	-0.1, -12.1, -7.2

Glasser HCP-MMP1.0 Atlas

Glasser MF, Coalson TS, Robinson EC, et al. A multi-modal parcellation of human cerebral cortex. Nature 536(7615):171-178 (2016). doi:10.1038/nature18933.

360 labels (180 per hemisphere), using the atlas’s native sparse indexing scheme: left-hemisphere regions are numbered 1-180, right-hemisphere regions 1001-1180. The shipped volume is natively on a FreeSurfer-conformed 256x256x256 1mm grid, not the 182x218x182 MNI152 grid, so it was resampled onto the template grid for the viewer.

360 regions

ID	Name	Colour	Volume	Centroid (MNI, mm)
1	L-V1		13812 mm³	-10.1, -84.2, 1.8
2	L-MST		794 mm³	-44.7, -67.3, 11.8
3	L-V6		1402 mm³	-15.1, -79.1, 30.8
4	L-V2		9515 mm³	-12, -82.1, 4
5	L-V3		7106 mm³	-16.6, -84.8, 7.3
6	L-V4		4782 mm³	-29.6, -86, -1.5
7	L-V8		1361 mm³	-30.1, -76, -13.1
8	L-4		10776 mm³	-26.5, -20.2, 55.7
9	L-3b		5451 mm³	-38.5, -22.8, 53.6
10	L-FEF		1787 mm³	-40.7, -5.6, 52.4
11	L-PEF		1006 mm³	-47.9, -0.5, 40.1
12	L-55b		2422 mm³	-48.5, -1.1, 50.1
13	L-V3A		2191 mm³	-15.3, -90.4, 27.9
14	L-RSC		2830 mm³	-5.2, -34.2, 21.9
15	L-POS2		3261 mm³	-9.3, -72.1, 36.2
16	L-V7		1005 mm³	-24.5, -86.4, 29.8
17	L-IPS1		1751 mm³	-24.5, -74.8, 38
18	L-FFC		3848 mm³	-42.5, -61.1, -18.1
19	L-V3B		639 mm³	-27.2, -81.7, 17.6
20	L-LO1		619 mm³	-39.2, -82.2, 8.1
21	L-LO2		1179 mm³	-45.7, -86, 1.9
22	L-PIT		1392 mm³	-43.9, -84.4, -10.7
23	L-MT		620 mm³	-43.3, -70.2, 14.5
24	L-A1		1023 mm³	-43.5, -25.2, 12.2
25	L-PSL		2154 mm³	-58.3, -45.7, 25.8
26	L-SFL		3873 mm³	-8.4, 16, 63.9
27	L-PCV		2245 mm³	-6.4, -51.4, 48.1
28	L-STV		2322 mm³	-62.5, -49.2, 18
29	L-7Pm		1601 mm³	-4.3, -69.4, 50.8
30	L-7m		2128 mm³	-4, -63.5, 34.9
31	L-POS1		2531 mm³	-11.1, -58.8, 14
32	L-23d		1261 mm³	-3.3, -18.8, 39.7
33	L-v23ab		916 mm³	-3.8, -56.5, 18.9
34	L-d23ab		1607 mm³	-3.3, -41.7, 31.9
35	L-31pv		950 mm³	-10.2, -46, 32.4
36	L-5m		1483 mm³	-7.1, -40.6, 61.2
37	L-5mv		1651 mm³	-13.6, -37.4, 50
38	L-23c		2259 mm³	-11.2, -30.1, 42.9
39	L-5L		2249 mm³	-15.2, -48.7, 71.5
40	L-24dd		2665 mm³	-6.6, -13.6, 49.5
41	L-24dv		1076 mm³	-8.7, 0.7, 44
42	L-7AL		2134 mm³	-22.4, -51.2, 65.3
43	L-SCEF		3500 mm³	-6.3, 4.5, 58.5
44	L-6ma		3941 mm³	-20.6, 4.4, 67.3
45	L-7Am		2995 mm³	-7.8, -60.1, 61.4
46	L-7PL		1695 mm³	-15, -72.7, 56.8
47	L-7PC		3151 mm³	-38.3, -47.2, 60.2
48	L-LIPv		1681 mm³	-30.8, -57.2, 54.4
49	L-VIP		1890 mm³	-23.8, -63.1, 64
50	L-MIP		1872 mm³	-25.9, -67.2, 48.9
51	L-1		6590 mm³	-47.8, -25.9, 54.5
52	L-2		4278 mm³	-37.9, -33.2, 51.1
53	L-3a		2247 mm³	-33.5, -22.1, 44.6
54	L-6d		2916 mm³	-35.3, -13.6, 66
55	L-6mp		3701 mm³	-13.7, -13.9, 70
56	L-6v		2075 mm³	-59.4, 3.9, 32
57	L-p24pr		1422 mm³	-4.2, 0.2, 39.5
58	L-33pr		1354 mm³	-3.7, 15.1, 25.4
59	L-a24pr		1095 mm³	-6.2, 19.6, 30
60	L-p32pr		1569 mm³	-8.5, 15.7, 38.3
61	L-a24		2085 mm³	-5.7, 40.6, -4.5
62	L-d32		2228 mm³	-8.4, 42.1, 25
63	L-8BM		3122 mm³	-5.3, 32.2, 44.6
64	L-p32		1180 mm³	-11.1, 50.2, -2.9
65	L-10r		1589 mm³	-6.8, 51.4, -10.6
66	L-47m		799 mm³	-35.9, 32.9, -14.3
67	L-8Av		4807 mm³	-39, 17.2, 50.7
68	L-8Ad		3386 mm³	-24.2, 28.9, 42.4
69	L-9m		6338 mm³	-6.8, 55.4, 23.1
70	L-8BL		3377 mm³	-12.9, 35.8, 53.6
71	L-9p		3426 mm³	-21, 47.1, 37.3
72	L-10d		3644 mm³	-12.7, 66.1, 6.2
73	L-8C		4085 mm³	-43.9, 13.2, 36.5
74	L-44		2435 mm³	-54.2, 15.6, 13.2
75	L-45		3762 mm³	-51.5, 26.6, 2.2
76	L-47l		2527 mm³	-46.7, 29.7, -10.9
77	L-a47r		4167 mm³	-41.6, 48.7, -11.4
78	L-6r		3029 mm³	-52.5, 6.9, 17.1
79	L-IFJa		1513 mm³	-43.1, 12.6, 26.3
80	L-IFJp		960 mm³	-39.9, 3.3, 29.1
81	L-IFSp		1589 mm³	-49.2, 23.2, 21.2
82	L-IFSa		2057 mm³	-46.8, 33.6, 10.3
83	L-p9-46v		2871 mm³	-47.9, 29, 25.7
84	L-46		4863 mm³	-39.6, 38, 31.3
85	L-a9-46v		3314 mm³	-40.8, 51.2, 9.6
86	L-9-46d		4534 mm³	-30.2, 45.9, 24
87	L-9a		3706 mm³	-22.1, 57.7, 23.2
88	L-10v		3906 mm³	-4.7, 52.5, -18.2
89	L-a10p		1964 mm³	-28.4, 58.9, -5.1
90	L-10pp		1997 mm³	-15, 63.1, -14.8
91	L-11l		3531 mm³	-26.7, 49.4, -15.2
92	L-13l		2429 mm³	-23.3, 30.4, -19.3
93	L-OFC		4560 mm³	-10.7, 34, -24.7
94	L-47s		2795 mm³	-33.1, 21.3, -20.6
95	L-LIPd		1008 mm³	-30.3, -54, 43.3
96	L-6a		4233 mm³	-25.7, -2.4, 54.2
97	L-i6-8		1764 mm³	-30.9, 8.1, 57.2
98	L-s6-8		1336 mm³	-22.5, 23.4, 56.3
99	L-43		1889 mm³	-57.1, -1.6, 9.9
100	L-OP4		2332 mm³	-58, -15.1, 16
101	L-OP1		1275 mm³	-45.4, -24.1, 20
102	L-OP2-3		943 mm³	-39.9, -17.1, 19.2
103	L-52		725 mm³	-39.2, -21.4, 0.9
104	L-RI		1149 mm³	-39.4, -34.6, 19.7
105	L-PFcm		1486 mm³	-50.7, -31.8, 20.5
106	L-PoI2		2752 mm³	-40.7, -3.3, -0.2
107	L-TA2		1518 mm³	-51.9, 1.6, -5.3
108	L-FOP4		2522 mm³	-41.3, 12.9, 5.2
109	L-MI		2102 mm³	-37.2, 11.1, 2.4
110	L-Pir		2517 mm³	-28.9, 2.8, -17.7
111	L-AVI		1446 mm³	-31.4, 25.1, -3.3
112	L-AAIC		1859 mm³	-35.5, 13.9, -11.6
113	L-FOP1		879 mm³	-50.8, 0.8, 4.5
114	L-FOP3		754 mm³	-36.4, 2.4, 13
115	L-FOP2		750 mm³	-42.8, -5.2, 14.6
116	L-PFt		1983 mm³	-56.6, -25.8, 36.5
117	L-AIP		1999 mm³	-40.5, -39.1, 42.6
118	L-EC		2232 mm³	-23.8, -12.2, -30.8
119	L-PreS		1817 mm³	-16.8, -34.7, -12.2
120	L-H		4527 mm³	-26.4, -23.9, -15
121	L-ProS		1222 mm³	-20.9, -55.1, 4.1
122	L-PeEc		4938 mm³	-31, -8.9, -33.3
123	L-STGa		2509 mm³	-51.3, 13, -17.7
124	L-PBelt		1719 mm³	-52.7, -25.7, 8.8
125	L-A5		3346 mm³	-63.4, -15.2, -2
126	L-PHA1		1281 mm³	-24.4, -37.4, -14.4
127	L-PHA3		2023 mm³	-31.8, -37.4, -18.1
128	L-STSda		1944 mm³	-54, -5.5, -12.5
129	L-STSdp		1994 mm³	-52.8, -32.8, 1
130	L-STSvp		2898 mm³	-56.3, -35.1, -3.4
131	L-TGd		10192 mm³	-39.1, 11.9, -34.9
132	L-TE1a		5227 mm³	-61, -5.9, -22.6
133	L-TE1p		7116 mm³	-61.7, -49.9, -9.5
134	L-TE2a		5691 mm³	-58.1, -24.7, -27.6
135	L-TF		3986 mm³	-43.4, -20.2, -30.8
136	L-TE2p		4115 mm³	-48.7, -42.7, -21.1
137	L-PHT		4182 mm³	-57.6, -62.2, 3.2
138	L-PH		3453 mm³	-45.6, -66, -6.1
139	L-TPOJ1		2102 mm³	-55.7, -45.4, 9.9
140	L-TPOJ2		1930 mm³	-52.4, -62.1, 15.9
141	L-TPOJ3		1290 mm³	-47, -73, 21.3
142	L-DVT		1806 mm³	-17.8, -73.1, 34.9
143	L-PGp		2501 mm³	-37.7, -85.2, 24.8
144	L-IP2		2102 mm³	-42.9, -46.2, 44.3
145	L-IP1		1692 mm³	-30.7, -68.3, 39.4
146	L-IP0		1203 mm³	-31, -77.3, 25.6
147	L-PFop		1797 mm³	-63.3, -24.6, 23.3
148	L-PF		5457 mm³	-61.3, -36.2, 35.8
149	L-PFm		8220 mm³	-50.9, -55.8, 44.4
150	L-PGi		4791 mm³	-47.3, -63.6, 27.9
151	L-PGs		4552 mm³	-40, -75.9, 40.9
152	L-V6A		904 mm³	-21.3, -85.9, 42
153	L-VMV1		939 mm³	-21.5, -53.4, -6
154	L-VMV3		941 mm³	-28, -60.8, -11.4
155	L-PHA2		783 mm³	-33.3, -36.4, -11.3
156	L-V4t		1037 mm³	-50.7, -78.2, 8.7
157	L-FST		1324 mm³	-45.3, -69.4, 5
158	L-V3CD		876 mm³	-38, -88, 12.2
159	L-LO3		438 mm³	-39.9, -76.9, 14.8
160	L-VMV2		639 mm³	-28.7, -53.3, -6.2
161	L-31pd		1428 mm³	-9, -52.6, 35
162	L-31a		1260 mm³	-4.3, -36.6, 43.3
163	L-VVC		2487 mm³	-31.6, -50.6, -18.4
164	L-25		1912 mm³	-4.6, 21.2, -11.9
165	L-s32		604 mm³	-8.6, 35.1, -14
166	L-pOFC		2565 mm³	-13, 12.4, -19.1
167	L-PoI1		1811 mm³	-39.4, -12.1, -2.8
168	L-Ig		841 mm³	-36.2, -15.5, 14.8
169	L-FOP5		1297 mm³	-36.5, 27.4, 3.9
170	L-p10p		2116 mm³	-25.8, 61.5, 3.6
171	L-p47r		2133 mm³	-44.8, 43.8, 1
172	L-TGv		3694 mm³	-37.8, -1, -45.1
173	L-MBelt		1242 mm³	-44.8, -17.2, 4.6
174	L-LBelt		820 mm³	-44.9, -27.8, 9
175	L-A4		3514 mm³	-63.3, -21.7, 8.5
176	L-STSva		1694 mm³	-52.4, -9.4, -16.9
177	L-TE1m		3339 mm³	-64.7, -26.9, -14.7
178	L-PI		1033 mm³	-44.9, -4.3, -13.1
179	L-a32pr		1759 mm³	-7.9, 30.6, 28
180	L-p24		2394 mm³	-5, 38.5, 11
1001	R-V1		13406 mm³	12.2, -80.6, 4.1
1002	R-MST		1036 mm³	49.1, -64.4, 7.9
1003	R-V6		1559 mm³	18, -76.7, 30.7
1004	R-V2		9420 mm³	12.4, -78.1, 5.7
1005	R-V3		7481 mm³	17.8, -85.1, 9.9
1006	R-V4		4537 mm³	30.3, -83.9, -0.5
1007	R-V8		1175 mm³	30.8, -76, -12.3
1008	R-4		10254 mm³	27.1, -17.3, 57
1009	R-3b		4350 mm³	37.6, -20.1, 52.3
1010	R-FEF		1889 mm³	44.2, -2.2, 51.5
1011	R-PEF		1258 mm³	47.5, 2.9, 36.9
1012	R-55b		1537 mm³	49.5, 2.5, 46.8
1013	R-V3A		2212 mm³	18.7, -88.4, 30.3
1014	R-RSC		3067 mm³	5.6, -35.6, 20.5
1015	R-POS2		3093 mm³	10.9, -69.7, 37.8
1016	R-V7		1041 mm³	28.7, -82.2, 34.2
1017	R-IPS1		1750 mm³	26, -72, 41.5
1018	R-FFC		4402 mm³	41.2, -54.9, -19.5
1019	R-V3B		731 mm³	30, -75.7, 21.6
1020	R-LO1		909 mm³	39.9, -79.9, 5.4
1021	R-LO2		1062 mm³	45.7, -82.2, -1.6
1022	R-PIT		1386 mm³	43, -82.8, -11.7
1023	R-MT		1005 mm³	50.4, -69.8, 11.5
1024	R-A1		796 mm³	43, -22.2, 11.3
1025	R-PSL		2759 mm³	64.2, -37, 27.2
1026	R-SFL		3055 mm³	7.8, 19.4, 64
1027	R-PCV		2416 mm³	6, -50.2, 49.5
1028	R-STV		2294 mm³	58.5, -45.1, 21
1029	R-7Pm		1308 mm³	5.4, -66, 50.5
1030	R-7m		2067 mm³	4.5, -62.1, 33.9
1031	R-POS1		2727 mm³	13.6, -56.4, 16.2
1032	R-23d		1513 mm³	2.9, -21, 38.8
1033	R-v23ab		1089 mm³	4.1, -55.2, 18.1
1034	R-d23ab		1106 mm³	3.1, -40.9, 32.6
1035	R-31pv		1022 mm³	9.2, -44, 33.4
1036	R-5m		2079 mm³	6.4, -38.3, 62.9
1037	R-5mv		1996 mm³	12.6, -37.5, 51.9
1038	R-23c		2498 mm³	10.3, -29.4, 43.4
1039	R-5L		2327 mm³	13.4, -47.8, 72.6
1040	R-24dd		2820 mm³	6.6, -12.9, 51.3
1041	R-24dv		1349 mm³	8.5, 0.5, 45.7
1042	R-7AL		2030 mm³	22.5, -50.7, 68.7
1043	R-SCEF		3371 mm³	5.6, 6.1, 58.1
1044	R-6ma		4251 mm³	20, 7, 66.1
1045	R-7Am		2379 mm³	8.2, -59.3, 61
1046	R-7PL		1363 mm³	12.2, -71.5, 59
1047	R-7PC		3415 mm³	36, -46.1, 61.6
1048	R-LIPv		1783 mm³	28.2, -57.2, 54.9
1049	R-VIP		1577 mm³	22.4, -61.6, 64.4
1050	R-MIP		2403 mm³	25.8, -68, 52.4
1051	R-1		5925 mm³	47.4, -21.6, 54.7
1052	R-2		4727 mm³	38.4, -29.9, 51.7
1053	R-3a		2286 mm³	31.5, -20.4, 47.1
1054	R-6d		2909 mm³	36.2, -11.4, 64.7
1055	R-6mp		3105 mm³	17.6, -11, 68.3
1056	R-6v		2516 mm³	59.4, 7, 29.8
1057	R-p24pr		1724 mm³	3.2, -2.1, 39.9
1058	R-33pr		1316 mm³	4.3, 14.5, 25.7
1059	R-a24pr		1474 mm³	4, 19.5, 32.2
1060	R-p32pr		1305 mm³	9.5, 15.2, 38.1
1061	R-a24		2152 mm³	5.8, 38.8, -2.4
1062	R-d32		2374 mm³	7.4, 39.9, 25.6
1063	R-8BM		3436 mm³	4.9, 32.3, 45.4
1064	R-p32		1765 mm³	6.7, 49.9, -4.8
1065	R-10r		1053 mm³	7.2, 52.6, -10.7
1066	R-47m		781 mm³	33.2, 34.5, -13.5
1067	R-8Av		5902 mm³	39.8, 19.4, 47.9
1068	R-8Ad		3492 mm³	24, 32.4, 41.5
1069	R-9m		5881 mm³	6.6, 55.4, 19.3
1070	R-8BL		4078 mm³	12.5, 44.1, 47.5
1071	R-9p		2488 mm³	21, 51.5, 33.5
1072	R-10d		3096 mm³	9.3, 68, 4.5
1073	R-8C		3134 mm³	39.9, 18.2, 36
1074	R-44		2589 mm³	53.7, 19.3, 12.8
1075	R-45		2962 mm³	52.3, 27.4, 3
1076	R-47l		2592 mm³	45.8, 35.5, -14.3
1077	R-a47r		3763 mm³	38.8, 53.2, -8.8
1078	R-6r		3981 mm³	52.8, 10.4, 12.3
1079	R-IFJa		1405 mm³	44, 16.5, 25.1
1080	R-IFJp		740 mm³	39.4, 7.2, 27.2
1081	R-IFSp		1730 mm³	45.5, 28.4, 19.2
1082	R-IFSa		2641 mm³	47.4, 38.7, 5
1083	R-p9-46v		4635 mm³	46.9, 33.4, 25.2
1084	R-46		4394 mm³	36, 41.3, 30.1
1085	R-a9-46v		2628 mm³	40.1, 53.4, 8.8
1086	R-9-46d		4666 mm³	28.6, 50.5, 21.2
1087	R-9a		3048 mm³	19.7, 63.2, 19
1088	R-10v		2667 mm³	3.3, 54, -16.8
1089	R-a10p		1748 mm³	24.7, 62.2, -8.9
1090	R-10pp		2487 mm³	12.4, 63.6, -16.9
1091	R-11l		3793 mm³	26, 49.1, -16.3
1092	R-13l		1757 mm³	20.6, 30.6, -19.4
1093	R-OFC		5232 mm³	8.2, 35.2, -24.9
1094	R-47s		3080 mm³	32.4, 24.1, -19.6
1095	R-LIPd		869 mm³	30.4, -54.7, 46
1096	R-6a		3752 mm³	25.9, -0.5, 53
1097	R-i6-8		2418 mm³	33, 8.9, 57.4
1098	R-s6-8		2132 mm³	20.4, 24.8, 57.7
1099	R-43		1678 mm³	54.5, 0.1, 9
1100	R-OP4		2409 mm³	57.3, -10.5, 13.3
1101	R-OP1		1072 mm³	42.8, -19, 18.1
1102	R-OP2-3		792 mm³	38.9, -12.7, 18
1103	R-52		580 mm³	38.9, -19.4, 1.4
1104	R-RI		1334 mm³	43.1, -30.9, 19.9
1105	R-PFcm		1485 mm³	48.4, -27.9, 22.8
1106	R-PoI2		2676 mm³	40.8, -0.9, -1.7
1107	R-TA2		1726 mm³	51.8, 3, -5.8
1108	R-FOP4		1678 mm³	38.7, 16.1, 6.4
1109	R-MI		1960 mm³	38.2, 13, 0.2
1110	R-Pir		2044 mm³	29.8, 4.5, -18.8
1111	R-AVI		1792 mm³	32.9, 26.1, -4.3
1112	R-AAIC		1691 mm³	33.9, 15.4, -13.4
1113	R-FOP1		932 mm³	46.2, 5, 4.5
1114	R-FOP3		614 mm³	34.8, 7.8, 11
1115	R-FOP2		720 mm³	40.6, -0.8, 14.5
1116	R-PFt		2039 mm³	56.2, -20.2, 37
1117	R-AIP		2542 mm³	38.3, -38, 44.2
1118	R-EC		2254 mm³	21.8, -11.2, -30
1119	R-PreS		1558 mm³	17.1, -33.1, -11.9
1120	R-H		4110 mm³	26.6, -19, -17.4
1121	R-ProS		1055 mm³	22.2, -50.7, 3.5
1122	R-PeEc		4807 mm³	29.2, -6.5, -34.5
1123	R-STGa		2187 mm³	50.8, 14.3, -18.1
1124	R-PBelt		1439 mm³	57, -19.4, 9.1
1125	R-A5		3881 mm³	62.1, -16.1, -2.1
1126	R-PHA1		1168 mm³	23.5, -35.2, -15.5
1127	R-PHA3		1122 mm³	32.6, -37.1, -15.5
1128	R-STSda		2389 mm³	51.9, -3.4, -14.7
1129	R-STSdp		2605 mm³	49.2, -29.4, -0.8
1130	R-STSvp		2515 mm³	59.5, -31.5, -2.9
1131	R-TGd		10269 mm³	38.3, 14.4, -35.1
1132	R-TE1a		4180 mm³	61, -3.5, -23.5
1133	R-TE1p		6010 mm³	61.7, -44.7, -12.2
1134	R-TE2a		5753 mm³	56.1, -19.9, -28.9
1135	R-TF		4752 mm³	41.6, -19.6, -30.5
1136	R-TE2p		3040 mm³	47.8, -39.6, -20.7
1137	R-PHT		3410 mm³	60, -54.4, -3.8
1138	R-PH		3205 mm³	47.9, -63.3, -9.6
1139	R-TPOJ1		3938 mm³	54.6, -45.2, 13.1
1140	R-TPOJ2		2068 mm³	52.6, -56.4, 9.3
1141	R-TPOJ3		1277 mm³	45.2, -61.4, 18.1
1142	R-DVT		2176 mm³	19, -70.2, 35.6
1143	R-PGp		3740 mm³	45, -77.2, 25.4
1144	R-IP2		1861 mm³	42.4, -42.1, 45.8
1145	R-IP1		1632 mm³	33.5, -67.3, 41
1146	R-IP0		1239 mm³	33.9, -74.1, 27.6
1147	R-PFop		1783 mm³	62.2, -19.7, 23.1
1148	R-PF		5251 mm³	60.4, -30.3, 38.7
1149	R-PFm		8141 mm³	51.3, -49.7, 45.9
1150	R-PGi		4970 mm³	51.3, -59.9, 29.5
1151	R-PGs		3366 mm³	43, -69.9, 42.9
1152	R-V6A		734 mm³	22.1, -83.2, 44.3
1153	R-VMV1		1219 mm³	19.4, -52.8, -7.2
1154	R-VMV3		1242 mm³	26.8, -60.8, -10.5
1155	R-PHA2		771 mm³	31.6, -34.2, -12.4
1156	R-V4t		1249 mm³	50.8, -73.7, 0.1
1157	R-FST		1683 mm³	50.8, -63.8, 1.7
1158	R-V3CD		1222 mm³	38.1, -83.3, 13.2
1159	R-LO3		915 mm³	42.8, -73.7, 14.1
1160	R-VMV2		923 mm³	26.5, -54, -7
1161	R-31pd		864 mm³	10.6, -51.9, 35.1
1162	R-31a		1116 mm³	5.2, -39.9, 41.4
1163	R-VVC		2753 mm³	29.2, -49.4, -18.1
1164	R-25		2235 mm³	3.1, 18.6, -11.8
1165	R-s32		1015 mm³	3.3, 35.8, -15.7
1166	R-pOFC		2951 mm³	14.4, 12.2, -18.7
1167	R-PoI1		1835 mm³	38.9, -8, -6.5
1168	R-Ig		1077 mm³	37.1, -11.8, 12.8
1169	R-FOP5		1365 mm³	38.3, 27.5, 4.1
1170	R-p10p		2365 mm³	24.2, 61.3, 2.2
1171	R-p47r		1761 mm³	45.2, 46.4, -3
1172	R-TGv		4515 mm³	35.6, 0.1, -45.6
1173	R-MBelt		1236 mm³	45.6, -15.5, 5.3
1174	R-LBelt		901 mm³	47.9, -25.7, 11.4
1175	R-A4		3610 mm³	65.1, -16.6, 6.6
1176	R-STSva		1900 mm³	54.8, -10.8, -15.7
1177	R-TE1m		3429 mm³	64.9, -24.6, -15.5
1178	R-PI		1058 mm³	44.4, -2.4, -13.5
1179	R-a32pr		1118 mm³	9.6, 28.6, 30.2
1180	R-p24		2442 mm³	4.9, 37, 15.2

MASSP Subcortical Parcellation

31 labels, natively at 0.5mm resolution in ICBM152 2009b nonlinear-asymmetric hi-res space — the highest native resolution of the shipped atlases. It was resampled onto the 1mm template grid for the viewer.

31 regions

ID	Name	Colour	Volume	Centroid (MNI, mm)
1	Striatum-left		13937 mm³	-21, 5.4, 2.9
2	Striatum-right		13706 mm³	20.3, 6.9, 2.8
3	Subthalamic-Nucleus-left		146 mm³	-10.5, -12.4, -8.4
4	Subthalamic-Nucleus-right		152 mm³	10.5, -11.8, -8.7
5	Substantia-Nigra-left		763 mm³	-9.3, -17.1, -14.4
6	Substantia-Nigra-right		734 mm³	9.4, -16.7, -14.4
7	Red-Nucleus-left		385 mm³	-5.2, -19.1, -9.9
8	Red-Nucleus-right		381 mm³	5.2, -18.8, -9.8
9	Globus-Pallidus-pars-interna-left		730 mm³	-18.8, -5.1, -5.2
10	Globus-Pallidus-pars-interna-right		697 mm³	18.3, -4, -5.6
11	Globus-Pallidus-pars-externa-left		1982 mm³	-21.4, -2.7, -1.7
12	Globus-Pallidus-pars-externa-right		2025 mm³	21.1, -1.6, -1.8
13	Thalamus-left		10255 mm³	-12.4, -19.5, 5.8
14	Thalamus-right		9844 mm³	12.1, -18.3, 6
15	Lateral-Ventricle-left		12606 mm³	-14.6, -15, 13.6
16	Lateral-Ventricle-right		11925 mm³	14.7, -14.7, 13.6
17	Third-Ventricle		2907 mm³	0.1, -19, 4.2
18	Fourth-Ventricle		1856 mm³	-0.3, -43.9, -32.5
19	Amygdala-left		1753 mm³	-25.2, -5.2, -21.4
20	Amygdala-right		1741 mm³	24.8, -4, -22
21	Internal-Capsule-left		5449 mm³	-19.3, -4.3, 8.8
22	Internal-Capsule-right		5499 mm³	18.9, -2.6, 8.5
23	Ventral-Tegmental-Area-left		375 mm³	-3.3, -18.4, -13.3
24	Ventral-Tegmental-Area-right		364 mm³	3.9, -17.9, -12.9
25	Fornix		1985 mm³	-1, -16.3, 10.2
26	Periaqueductal-Gray-left		305 mm³	-2.3, -31.6, -10.6
27	Periaqueductal-Gray-right		336 mm³	1.8, -31.4, -10.5
28	Pedunculopontine-Nucleus-left		205 mm³	-8, -30.7, -16.3
29	Pedunculopontine-Nucleus-right		242 mm³	7.7, -30.5, -15.8
30	Claustrum-left		1124 mm³	-35.1, -2.3, -1.1
31	Claustrum-right		979 mm³	34.8, -0.7, -2.5

Harvard-Oxford Cortical and Subcortical Atlases

The FSL structural atlases from the Harvard Center for Morphometric Analysis, shipped as the maximum-probability maps at the 25 % threshold, 1 mm (HarvardOxford-cortl-maxprob-thr25-1mm.nii.gz, FSL’s lateralized cortical map, 96 labels = 48 structures x left/right, odd = left, even = right; HarvardOxford-sub-maxprob-thr25-1mm.nii.gz, 21 subcortical labels). The files are FSL’s own, unmodified (NeuroDebian fsl-harvard-oxford-cortical-lateralized-atlas and fsl-harvard-oxford-atlases, both 5.0.7-2); the label names come from FSL’s XML, with ids = XML index + 1 as FSL’s maxprob images encode them. Until 2026-09-23 the non-lateralized 48-label cortical map was shipped instead, whose labels each covered both hemispheres.

Licence CC BY-SA 4.0 — the FSL licence page states that “The Cerebellum and Harvard-Oxford atlases, whilst not being the property of Oxford, are released under the CC BY-SA 4.0 licence”.

The subcortical map labels the thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens and brain stem per hemisphere, plus whole-hemisphere cortex / white matter and the ventricles (kept so the file is unmodified; they are not TI targets). Both maps are natively on the FSL 182x218x182 1 mm grid, the same grid as the shipped template.

Cerebellum-MNIfnirt Atlas

Diedrichsen J., Balsters J. H., Flavell J., Cussans E., Ramnani N. A probabilistic MR atlas of the human cerebellum. NeuroImage 46(1):39-46 (2009). doi:10.1016/j.neuroimage.2009.01.045.

The FNIRT-normalised maximum-probability map at the 25 % threshold, 1 mm (Cerebellum-MNIfnirt-maxprob-thr25-1mm.nii.gz, 28 labels: lobules I-IV to X, left / right / vermis). CC BY-SA 4.0 by the same FSL sentence as Harvard-Oxford. Natively on the FSL 1 mm grid.

Schaefer 2018 Atlas (400 parcels, 7 networks)

Schaefer A., Kong R., Gordon E. M., Laumann T. O., Zuo X.-N., Holmes A. J., Eickhoff S. B., Yeo B. T. T. Local-global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI. Cerebral Cortex 28(9):3095-3114 (2018). doi:10.1093/cercor/bhx179.

Schaefer2018_400Parcels_7Networks_order_FSLMNI152_1mm.nii.gz from ThomasYeoLab/CBIG (MIT), with CBIG’s own LUT. 400 cortical parcels — 1-200 left, 201-400 right — each named by its Yeo 7-network membership (7Networks_LH_Vis_1, 7Networks_RH_Default_PFCdPFCm_3, …). Its header matches the shipped FSL MNI152_T1_1mm.nii.gz exactly, so it is on the MNI152NLin6Asym grid. Like Glasser it is a cortical parcellation distributed as a label volume, so you target it through the picker’s Subcortical mode.

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Subject-Space Atlases

These are not shipped. They are produced for each subject during preprocessing, and live under that subject’s own derivatives:

• SimNIBS charm writes the tissue segmentation m2m_{subject}/segmentation/labeling.nii.gz, plus the surface parcellations lh/rh.{subject}_DK40.annot, _a2009s.annot and _HCP_MMP1.annot.
• FastSurfer --seg_only (v3) writes aparc.DKTatlas+aseg.deep.mgz. It does not produce thalamic nuclei or hippocampal/amygdala subregion atlases. See pre-processing.
• Optional FreeSurfer recon-all produces the volumetric parcellations aparc.DKTatlas+aseg.mgz, aparc.a2009s+aseg.mgz, aparc+aseg.mgz and aseg.mgz, with finer thalamic nuclei and hippocampal/amygdala subregions available as additional operations after reconstruction. Existing ThalamicNuclei.v13.T1.mgz and lh/rh.hippoAmygLabels-T1.v22.mgz outputs remain readable.

The gallery includes legacy FreeSurfer atlases for reference; their presence here does not mean a new v3 FastSurfer run produces them.

The viewer below uses the ernie example subject that ships with SimNIBS, so the anatomy is a real head model rather than a template average. The surface .annot parcellations are not shown — they are cortical surface files, not volumes, and cannot be overlaid on a NIfTI.

Read the coordinates as subject space. The centroid column here is in ernie’s own scanner/world coordinates, not MNI. The same structure will sit at different coordinates in your own subject.

Atlas: CHARM tissue labeling Desikan-Killiany-Tourville (aparc.DKTatlas+aseg) Destrieux (aparc.a2009s+aseg) MASSP subcortical (subject space)

Overlaid on ernie's own T1, not a template. Colours come from each atlas's lookup table — the FreeSurfer parcellations use the standard FreeSurferColorLUT.txt shipped in resources/atlas/.

Interactive viewer unavailable. Your browser does not support WebGL2. The label tables remain fully searchable.

CHARM Tissue Labeling

Produced by SimNIBS charm as m2m_{subject}/segmentation/labeling.nii.gz, with its own labeling_LUT.txt alongside. This is the tissue segmentation the head model is built from — grey and white matter, CSF, skull, scalp and the rest — not a cortical parcellation. It is what the analyzer reads when you pick a tissue-level ROI in voxel space.

56 regions

ID	Name	Colour	Volume	Centroid (subject, mm)
2	Left-Cerebral-White-Matter		242374 mm³	-24.5, 7.7, 28.3
3	Left-Cerebral-Cortex		301185 mm³	-28.4, 8.1, 26.1
4	Left-Lateral-Ventricle		8372 mm³	-11, 14, 23.4
5	Left-Inf-Lat-Vent		536 mm³	-30.5, 9.6, -1.1
7	Left-Cerebellum-White-Matter		15523 mm³	-17.1, -22.5, -23.4
8	Left-Cerebellum-Cortex		58029 mm³	-21.8, -30.6, -25.5
10	Left-Thalamus-Proper		8128 mm³	-8.6, 7.5, 17.8
11	Left-Caudate		3375 mm³	-9.6, 34.3, 24.6
12	Left-Putamen		6109 mm³	-21.9, 28.1, 14.5
13	Left-Pallidum		2352 mm³	-15.4, 24, 12.6
14	3rd-Ventricle		1094 mm³	2.3, 16.6, 10.3
15	4th-Ventricle		2338 mm³	1.6, -14.1, -21.6
16	Brain-Stem		23545 mm³	1.6, -0.5, -19.3
17	Left-Hippocampus		4298 mm³	-22.8, 5.3, 0.5
18	Left-Amygdala		1978 mm³	-20.4, 24, -2.4
24	CSF		1193 mm³	2.6, 6.6, 20.2
26	Left-Accumbens-area		620 mm³	-6.3, 39.1, 10
28	Left-VentralDC		4366 mm³	-8.3, 11.5, 3.1
29	Left-undetermined		16 mm³	4.7, 25.1, -13.6
30	Left-vessel		17 mm³	-23.3, 27.4, 7.5
31	Left-choroid-plexus		181 mm³	-16.7, 0.4, 17.1
41	Right-Cerebral-White-Matter		245412 mm³	27.9, 10.6, 28.9
42	Right-Cerebral-Cortex		301790 mm³	31.7, 11.3, 26.5
43	Right-Lateral-Ventricle		9013 mm³	16.2, 15, 24.4
44	Right-Inf-Lat-Vent		276 mm³	33.6, 15.5, -3.5
46	Right-Cerebellum-White-Matter		14793 mm³	20.5, -21.4, -24.5
47	Right-Cerebellum-Cortex		58270 mm³	25.1, -28.6, -26.2
49	Right-Thalamus-Proper		7346 mm³	12, 10.8, 18.1
50	Right-Caudate		3433 mm³	15.6, 36.5, 24.4
51	Right-Putamen		5727 mm³	27.2, 29.8, 13.5
52	Right-Pallidum		2509 mm³	19.6, 27, 12.3
53	Right-Hippocampus		4709 mm³	26.5, 6.9, 1
54	Right-Amygdala		1966 mm³	24.3, 24.8, -3.2
58	Right-Accumbens-area		613 mm³	10.9, 40, 9.3
60	Right-VentralDC		4147 mm³	12.4, 12.3, 3.3
62	Right-vessel		49 mm³	27.7, 25.9, 6.2
63	Right-choroid-plexus		335 mm³	19.9, 1.7, 19.5
72	5th-Ventricle		3 mm³	3.3, 49.2, 22.4
77	WM-hypointensities		562 mm³	1.2, 4.5, 25
80	non-WM-hypointensities		3 mm³	-9.7, 21.5, 10.7
85	Optic-Chiasm		90 mm³	0.4, 29.9, -0.3
501	Air-Internal		95891 mm³	0.9, 57.3, -40.1
502	Artery		13666 mm³	-1, 14, -61
506	Eyes		17903 mm³	2.5, 89.3, -12.5
507	Other-Tissues		1206194 mm³	1, 12.1, -61.3
508	Rectus-Muscles		2563 mm³	1.9, 71.1, -12.2
509	Mucosa		48699 mm³	2.8, 84.2, -42
511	Skin		392939 mm³	0.8, 10.5, -9.7
512	Spinal-Cord		7754 mm³	0.2, -12.5, -84.8
514	Vein		47952 mm³	0, -15.2, -7.2
515	Bone-Cortical		624881 mm³	1.4, 20, -9.2
516	Bone-Cancellous		117065 mm³	0, 15.5, -7.2
517	Background		6919720 mm³	-1.1, 35.9, -15
520	Cortical-CSF		219245 mm³	1.7, 15.6, 21.6
525	Fat		734282 mm³	-0.6, 16, -34.8
530	Optic-Nerve		1051 mm³	3, 48.8, -5.8

Desikan-Killiany-Tourville (aparc.DKTatlas+aseg)

FreeSurfer recon-all output combining the DKT cortical parcellation with the aseg subcortical segmentation in one volume. Klein A, Tourville J. 101 labeled brain images and a consistent human cortical labeling protocol. Frontiers in Neuroscience 6:171 (2012). doi:10.3389/fnins.2012.00171.

Cortical labels use FreeSurfer’s 1000+/2000+ convention (left/right hemisphere); subcortical structures keep their aseg ids below 100. This is one of the voxel atlases the analyzer offers.

102 regions

ID	Name	Colour	Volume	Centroid (subject, mm)
2	Left-Cerebral-White-Matter		259148 mm³	-24.7, 7.5, 27.7
4	Left-Lateral-Ventricle		6135 mm³	-10.7, 17.4, 24.1
5	Left-Inf-Lat-Vent		332 mm³	-30.8, 7.7, 0.2
7	Left-Cerebellum-White-Matter		16019 mm³	-16.1, -21.6, -21.9
8	Left-Cerebellum-Cortex		63477 mm³	-23.4, -30.3, -25.5
10	Left-Thalamus-Proper		9903 mm³	-9.6, 8, 18.5
11	Left-Caudate		3533 mm³	-9.7, 35.1, 25.1
12	Left-Putamen		5321 mm³	-21.9, 27.6, 15.2
13	Left-Pallidum		2046 mm³	-17.1, 21.6, 13.2
14	3rd-Ventricle		858 mm³	2.3, 17.7, 9.7
15	4th-Ventricle		1844 mm³	1.1, -14.4, -21.6
16	Brain-Stem		24505 mm³	1.5, -0.1, -18.2
17	Left-Hippocampus		4434 mm³	-22.2, 7.1, -0.3
18	Left-Amygdala		1975 mm³	-20.1, 24.9, -2.4
24	CSF		908 mm³	2.6, 9, 20.6
26	Left-Accumbens-area		602 mm³	-5.7, 38.9, 10.1
28	Left-VentralDC		4978 mm³	-8.1, 13.2, 3.7
31	Left-choroid-plexus		468 mm³	-18.1, 0.1, 18.2
41	Right-Cerebral-White-Matter		260940 mm³	28.1, 10.3, 28.1
43	Right-Lateral-Ventricle		7478 mm³	16.5, 15.9, 24.5
44	Right-Inf-Lat-Vent		235 mm³	32.8, 14.6, -2.3
46	Right-Cerebellum-White-Matter		14577 mm³	18.9, -20.7, -23
47	Right-Cerebellum-Cortex		62759 mm³	25.9, -28.4, -26.3
49	Right-Thalamus-Proper		8250 mm³	12.8, 10, 18.9
50	Right-Caudate		3768 mm³	15.7, 37.2, 24.4
51	Right-Putamen		5215 mm³	27.2, 29.4, 14.1
52	Right-Pallidum		2269 mm³	21.8, 24, 12.8
53	Right-Hippocampus		4577 mm³	26.1, 7.7, 0.4
54	Right-Amygdala		1929 mm³	23.6, 25.3, -3.8
58	Right-Accumbens-area		680 mm³	10, 39, 8.8
60	Right-VentralDC		5249 mm³	11.8, 13.8, 3.3
62	Right-vessel		14 mm³	28, 24.8, 6.4
63	Right-choroid-plexus		532 mm³	22, 1.4, 19.4
77	WM-hypointensities		706 mm³	-3.4, 10.7, 22.1
85	Optic-Chiasm		201 mm³	1.1, 32.2, -1.8
251	CC_Posterior		1062 mm³	2.3, -5.9, 23.7
252	CC_Mid_Posterior		636 mm³	2.6, 9.6, 31.5
253	CC_Central		937 mm³	3, 24.8, 31.5
254	CC_Mid_Anterior		664 mm³	3.3, 39.2, 33.3
255	CC_Anterior		1318 mm³	3.3, 52.1, 23.4
1002	ctx-lh-caudalanteriorcingulate		3591 mm³	-3.7, 44.4, 44.3
1003	ctx-lh-caudalmiddlefrontal		8588 mm³	-33, 31.6, 58.5
1005	ctx-lh-cuneus		4888 mm³	-7.1, -57.3, 17.2
1006	ctx-lh-entorhinal		1500 mm³	-21.5, 23.1, -14.5
1007	ctx-lh-fusiform		8119 mm³	-34.4, -19.7, -7.4
1008	ctx-lh-inferiorparietal		12796 mm³	-35.9, -47.8, 27.7
1009	ctx-lh-inferiortemporal		10693 mm³	-43, 3.6, -12.8
1010	ctx-lh-isthmuscingulate		3073 mm³	-5.6, -18.9, 22.9
1011	ctx-lh-lateraloccipital		13836 mm³	-29, -60.5, -1
1012	ctx-lh-lateralorbitofrontal		10206 mm³	-21.2, 63.2, 4.3
1013	ctx-lh-lingual		7954 mm³	-13.5, -39.7, -1.9
1014	ctx-lh-medialorbitofrontal		5197 mm³	-3, 64.6, 3.7
1015	ctx-lh-middletemporal		14839 mm³	-52.9, 1.9, -1.9
1016	ctx-lh-parahippocampal		2268 mm³	-22.1, -0.8, -5.3
1017	ctx-lh-paracentral		5750 mm³	-5.3, -4.9, 59.6
1018	ctx-lh-parsopercularis		4673 mm³	-42.7, 39.9, 24.4
1019	ctx-lh-parsorbitalis		3010 mm³	-37.9, 61.6, 9.5
1020	ctx-lh-parstriangularis		4675 mm³	-42.4, 60.9, 21.8
1021	ctx-lh-pericalcarine		1982 mm³	-10, -53.7, 4.8
1022	ctx-lh-postcentral		14247 mm³	-42.3, -3.1, 48.4
1023	ctx-lh-posteriorcingulate		4266 mm³	-4, 4.9, 44.9
1024	ctx-lh-precentral		16789 mm³	-36.6, 13.2, 49.7
1025	ctx-lh-precuneus		11896 mm³	-7, -34.2, 38
1026	ctx-lh-rostralanteriorcingulate		3636 mm³	-2.5, 65.4, 19.9
1027	ctx-lh-rostralmiddlefrontal		14132 mm³	-34.4, 66.1, 37.4
1028	ctx-lh-superiorfrontal		30452 mm³	-10.3, 60, 51.7
1029	ctx-lh-superiorparietal		14323 mm³	-22.8, -41.4, 50.1
1030	ctx-lh-superiortemporal		18288 mm³	-46.4, 14.3, 7.5
1031	ctx-lh-supramarginal		9738 mm³	-47.1, -20.5, 38.3
1034	ctx-lh-transversetemporal		1503 mm³	-41.5, 1.5, 19.1
1035	ctx-lh-insula		7040 mm³	-32, 28.4, 16.2
2002	ctx-rh-caudalanteriorcingulate		4248 mm³	7.5, 51.1, 43.3
2003	ctx-rh-caudalmiddlefrontal		8581 mm³	34.8, 37.6, 60.4
2005	ctx-rh-cuneus		4170 mm³	8.3, -53.9, 17.7
2006	ctx-rh-entorhinal		1200 mm³	24, 23.6, -14.9
2007	ctx-rh-fusiform		8527 mm³	36.1, -14.8, -8.7
2008	ctx-rh-inferiorparietal		17392 mm³	41, -38.7, 30
2009	ctx-rh-inferiortemporal		10093 mm³	47.4, 5.1, -12.4
2010	ctx-rh-isthmuscingulate		3203 mm³	8.2, -19, 24.1
2011	ctx-rh-lateraloccipital		14805 mm³	31.1, -55.5, -0.8
2012	ctx-rh-lateralorbitofrontal		10691 mm³	25.8, 64.9, 3.6
2013	ctx-rh-lingual		8776 mm³	14.7, -37, -2.1
2014	ctx-rh-medialorbitofrontal		4667 mm³	7.7, 66, 5.1
2015	ctx-rh-middletemporal		12745 mm³	56, 4.4, 0.8
2016	ctx-rh-parahippocampal		2125 mm³	25.1, 1.3, -5.3
2017	ctx-rh-paracentral		5612 mm³	8.4, -3.9, 60.8
2018	ctx-rh-parsopercularis		5501 mm³	50.5, 40, 27.1
2019	ctx-rh-parsorbitalis		3020 mm³	45.1, 60.8, 9
2020	ctx-rh-parstriangularis		5658 mm³	49.4, 62.4, 21.3
2021	ctx-rh-pericalcarine		2201 mm³	10.6, -50.1, 6.1
2022	ctx-rh-postcentral		11984 mm³	40.3, -2.8, 53.5
2023	ctx-rh-posteriorcingulate		4725 mm³	6.8, 7.8, 46
2024	ctx-rh-precentral		15809 mm³	40.2, 15.3, 52.6
2025	ctx-rh-precuneus		11572 mm³	8.8, -33.5, 40.4
2026	ctx-rh-rostralanteriorcingulate		3381 mm³	8.5, 68.2, 22.8
2027	ctx-rh-rostralmiddlefrontal		15086 mm³	41.3, 68.3, 36.2
2028	ctx-rh-superiorfrontal		30653 mm³	15.1, 63.1, 50.2
2029	ctx-rh-superiorparietal		13219 mm³	23.3, -41.2, 50.2
2030	ctx-rh-superiortemporal		18149 mm³	50.3, 22, 6.3
2031	ctx-rh-supramarginal		8371 mm³	51.3, -8.9, 39.3
2034	ctx-rh-transversetemporal		1063 mm³	44.5, 10.3, 19.1
2035	ctx-rh-insula		7067 mm³	37.1, 30.3, 15.5

Destrieux (aparc.a2009s+aseg)

FreeSurfer recon-all output combining the Destrieux cortical parcellation with aseg. Destrieux C, Fischl B, Dale A, Halgren E. Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage 53(1):1-15 (2010). doi:10.1016/j.neuroimage.2010.06.010.

The finest of the cortical parcellations here, splitting cortex into gyral (G_) and sulcal (S_) units. Cortical ids run in the 11100+/12100+ range.

188 regions

ID	Name	Colour	Volume	Centroid (subject, mm)
2	Left-Cerebral-White-Matter		259148 mm³	-24.7, 7.5, 27.7
4	Left-Lateral-Ventricle		6135 mm³	-10.7, 17.4, 24.1
5	Left-Inf-Lat-Vent		332 mm³	-30.8, 7.7, 0.2
7	Left-Cerebellum-White-Matter		16019 mm³	-16.1, -21.6, -21.9
8	Left-Cerebellum-Cortex		63477 mm³	-23.4, -30.3, -25.5
10	Left-Thalamus-Proper		9903 mm³	-9.6, 8, 18.5
11	Left-Caudate		3533 mm³	-9.7, 35.1, 25.1
12	Left-Putamen		5321 mm³	-21.9, 27.6, 15.2
13	Left-Pallidum		2046 mm³	-17.1, 21.6, 13.2
14	3rd-Ventricle		858 mm³	2.3, 17.7, 9.7
15	4th-Ventricle		1844 mm³	1.1, -14.4, -21.6
16	Brain-Stem		24505 mm³	1.5, -0.1, -18.2
17	Left-Hippocampus		4434 mm³	-22.2, 7.1, -0.3
18	Left-Amygdala		1975 mm³	-20.1, 24.9, -2.4
24	CSF		908 mm³	2.6, 9, 20.6
26	Left-Accumbens-area		602 mm³	-5.7, 38.9, 10.1
28	Left-VentralDC		4978 mm³	-8.1, 13.2, 3.7
31	Left-choroid-plexus		468 mm³	-18.1, 0.1, 18.2
41	Right-Cerebral-White-Matter		260940 mm³	28.1, 10.3, 28.1
43	Right-Lateral-Ventricle		7478 mm³	16.5, 15.9, 24.5
44	Right-Inf-Lat-Vent		235 mm³	32.8, 14.6, -2.3
46	Right-Cerebellum-White-Matter		14577 mm³	18.9, -20.7, -23
47	Right-Cerebellum-Cortex		62759 mm³	25.9, -28.4, -26.3
49	Right-Thalamus-Proper		8250 mm³	12.8, 10, 18.9
50	Right-Caudate		3768 mm³	15.7, 37.2, 24.4
51	Right-Putamen		5215 mm³	27.2, 29.4, 14.1
52	Right-Pallidum		2269 mm³	21.8, 24, 12.8
53	Right-Hippocampus		4577 mm³	26.1, 7.7, 0.4
54	Right-Amygdala		1929 mm³	23.6, 25.3, -3.8
58	Right-Accumbens-area		680 mm³	10, 39, 8.8
60	Right-VentralDC		5249 mm³	11.8, 13.8, 3.3
62	Right-vessel		14 mm³	28, 24.8, 6.4
63	Right-choroid-plexus		532 mm³	22, 1.4, 19.4
77	WM-hypointensities		706 mm³	-3.4, 10.7, 22.1
85	Optic-Chiasm		201 mm³	1.1, 32.2, -1.8
251	CC_Posterior		1062 mm³	2.3, -5.9, 23.7
252	CC_Mid_Posterior		636 mm³	2.6, 9.6, 31.5
253	CC_Central		937 mm³	3, 24.8, 31.5
254	CC_Mid_Anterior		664 mm³	3.3, 39.2, 33.3
255	CC_Anterior		1318 mm³	3.3, 52.1, 23.4
11101	ctx_lh_G_and_S_frontomargin		2461 mm³	-20.3, 87.9, 15.9
11102	ctx_lh_G_and_S_occipital_inf		4240 mm³	-36.7, -50.7, -10.3
11103	ctx_lh_G_and_S_paracentral		3379 mm³	-6.3, -13.7, 68.1
11104	ctx_lh_G_and_S_subcentral		4250 mm³	-51.8, 10.8, 26.7
11105	ctx_lh_G_and_S_transv_frontopol		2078 mm³	-15.9, 94.3, 24.9
11106	ctx_lh_G_and_S_cingul-Ant		5343 mm³	-4.1, 68, 26.1
11107	ctx_lh_G_and_S_cingul-Mid-Ant		2798 mm³	-4.4, 39.2, 47.5
11108	ctx_lh_G_and_S_cingul-Mid-Post		3224 mm³	-5, 10.8, 48
11109	ctx_lh_G_cingul-Post-dorsal		1888 mm³	-1.5, -14.6, 35.9
11110	ctx_lh_G_cingul-Post-ventral		777 mm³	-7, -20.5, 12.9
11111	ctx_lh_G_cuneus		3195 mm³	-4.3, -61.3, 14.4
11112	ctx_lh_G_front_inf-Opercular		3990 mm³	-43.9, 36.4, 21.9
11113	ctx_lh_G_front_inf-Orbital		1414 mm³	-40.9, 60.4, 11.6
11114	ctx_lh_G_front_inf-Triangul		2773 mm³	-45.9, 59.7, 20.3
11115	ctx_lh_G_front_middle		14513 mm³	-34.3, 55.2, 49.6
11116	ctx_lh_G_front_sup		22482 mm³	-6.7, 50.4, 57.2
11117	ctx_lh_G_Ins_lg_and_S_cent_ins		1675 mm³	-33.6, 19.5, 12.5
11118	ctx_lh_G_insular_short		2670 mm³	-32.8, 35.8, 13.6
11119	ctx_lh_G_occipital_middle		5274 mm³	-37.9, -58.6, 7.2
11120	ctx_lh_G_occipital_sup		2573 mm³	-12.4, -67.1, 24.1
11121	ctx_lh_G_oc-temp_lat-fusifor		4404 mm³	-32.8, -19.3, -8.9
11122	ctx_lh_G_oc-temp_med-Lingual		5582 mm³	-10.3, -43.3, -3.1
11123	ctx_lh_G_oc-temp_med-Parahip		3065 mm³	-20.9, 12.2, -10.4
11124	ctx_lh_G_orbital		7005 mm³	-27, 65.2, 4
11125	ctx_lh_G_pariet_inf-Angular		6348 mm³	-37.4, -48.8, 33.9
11126	ctx_lh_G_pariet_inf-Supramar		6352 mm³	-50.4, -18.8, 37.3
11127	ctx_lh_G_parietal_sup		8428 mm³	-21.4, -41.8, 56.9
11128	ctx_lh_G_postcentral		5363 mm³	-45, -3.1, 55.9
11129	ctx_lh_G_precentral		7905 mm³	-39.7, 13.1, 55.3
11130	ctx_lh_G_precuneus		7328 mm³	-4.3, -35.4, 41.4
11131	ctx_lh_G_rectus		2751 mm³	-1.9, 69.3, 1
11132	ctx_lh_G_subcallosal		1325 mm³	-4.9, 38.8, 5.9
11133	ctx_lh_G_temp_sup-G_T_transv		1427 mm³	-43.9, 4.6, 18.9
11134	ctx_lh_G_temp_sup-Lateral		6019 mm³	-53.2, 18.2, 8.8
11135	ctx_lh_G_temp_sup-Plan_polar		2539 mm³	-39, 34.1, 0.9
11136	ctx_lh_G_temp_sup-Plan_tempo		2380 mm³	-51.4, -14.8, 24.9
11137	ctx_lh_G_temporal_inf		6164 mm³	-46.8, -1.5, -12.6
11138	ctx_lh_G_temporal_middle		8376 mm³	-56.6, 2.9, -2.5
11139	ctx_lh_Lat_Fis-ant-Horizont		581 mm³	-36.9, 64, 14.6
11140	ctx_lh_Lat_Fis-ant-Vertical		530 mm³	-40.9, 49.4, 21.7
11141	ctx_lh_Lat_Fis-post		1520 mm³	-36.9, -11.5, 25.7
11143	ctx_lh_Pole_occipital		2926 mm³	-12.7, -71.3, -8.2
11144	ctx_lh_Pole_temporal		5349 mm³	-32.7, 36.9, -18.2
11145	ctx_lh_S_calcarine		2767 mm³	-13.8, -39.3, 7.5
11146	ctx_lh_S_central		4522 mm³	-32.8, 1.4, 52.2
11147	ctx_lh_S_cingul-Marginalis		1842 mm³	-11.9, -16.1, 49.8
11148	ctx_lh_S_circular_insula_ant		1087 mm³	-26.5, 48.9, 11.6
11149	ctx_lh_S_circular_insula_inf		2199 mm³	-36.9, 13.9, 9.1
11150	ctx_lh_S_circular_insula_sup		3161 mm³	-30.7, 31.2, 26.5
11151	ctx_lh_S_collat_transv_ant		1343 mm³	-36, 9.4, -10.2
11152	ctx_lh_S_collat_transv_post		828 mm³	-23.3, -51.4, -6.6
11153	ctx_lh_S_front_inf		3248 mm³	-38.8, 54, 35.8
11154	ctx_lh_S_front_middle		2547 mm³	-23.8, 71.6, 38.3
11155	ctx_lh_S_front_sup		5152 mm³	-21.1, 42.9, 56.8
11156	ctx_lh_S_interm_prim-Jensen		364 mm³	-48, -33.4, 38.3
11157	ctx_lh_S_intrapariet_and_P_trans		5222 mm³	-25.3, -41.2, 41.1
11158	ctx_lh_S_oc_middle_and_Lunatus		1592 mm³	-31.1, -58.4, 4.4
11159	ctx_lh_S_oc_sup_and_transversal		1960 mm³	-25.8, -56.8, 17.6
11160	ctx_lh_S_occipital_ant		809 mm³	-45.2, -38.6, -0.9
11161	ctx_lh_S_oc-temp_lat		1372 mm³	-44, -16.6, -5.7
11162	ctx_lh_S_oc-temp_med_and_Lingual		3524 mm³	-26.4, -19.3, -1.1
11163	ctx_lh_S_orbital_lateral		524 mm³	-39, 74.8, 19.3
11164	ctx_lh_S_orbital_med-olfact		1271 mm³	-10.8, 54, 2.5
11165	ctx_lh_S_orbital-H_Shaped		2813 mm³	-22.7, 67.5, 6.9
11166	ctx_lh_S_parieto_occipital		3390 mm³	-12.7, -43.1, 22.8
11167	ctx_lh_S_pericallosal		1676 mm³	-2.2, 22.8, 27.2
11168	ctx_lh_S_postcentral		5043 mm³	-38, -15.2, 51.2
11169	ctx_lh_S_precentral-inf-part		3160 mm³	-40.2, 29, 41.8
11170	ctx_lh_S_precentral-sup-part		1947 mm³	-26.2, 13.4, 59.9
11171	ctx_lh_S_suborbital		977 mm³	-4.3, 70.3, 8.7
11172	ctx_lh_S_subparietal		2147 mm³	-8.8, -26.2, 37.4
11173	ctx_lh_S_temporal_inf		2798 mm³	-49.8, -7.6, -4.2
11174	ctx_lh_S_temporal_sup		9289 mm³	-46.6, -16.2, 13.4
11175	ctx_lh_S_temporal_transverse		710 mm³	-44.7, 1.3, 14.2
12101	ctx_rh_G_and_S_frontomargin		1787 mm³	23.1, 91.3, 13.3
12102	ctx_rh_G_and_S_occipital_inf		2961 mm³	38.6, -46, -8.6
12103	ctx_rh_G_and_S_paracentral		3425 mm³	8.4, -12.6, 68.3
12104	ctx_rh_G_and_S_subcentral		3336 mm³	55.5, 15.8, 28.5
12105	ctx_rh_G_and_S_transv_frontopol		2584 mm³	20, 96.1, 25.2
12106	ctx_rh_G_and_S_cingul-Ant		7050 mm³	9.8, 71.1, 26.5
12107	ctx_rh_G_and_S_cingul-Mid-Ant		4271 mm³	8.3, 43.5, 50
12108	ctx_rh_G_and_S_cingul-Mid-Post		3903 mm³	8, 13, 50.3
12109	ctx_rh_G_cingul-Post-dorsal		2067 mm³	4.8, -14.5, 37.3
12110	ctx_rh_G_cingul-Post-ventral		970 mm³	9.2, -20.7, 13.4
12111	ctx_rh_G_cuneus		2897 mm³	6.7, -55.9, 14.8
12112	ctx_rh_G_front_inf-Opercular		4178 mm³	52.4, 37.2, 23.3
12113	ctx_rh_G_front_inf-Orbital		1537 mm³	49.8, 63.3, 11.5
12114	ctx_rh_G_front_inf-Triangul		2906 mm³	52.8, 58.5, 23.6
12115	ctx_rh_G_front_middle		11655 mm³	41, 56.3, 49.1
12116	ctx_rh_G_front_sup		18878 mm³	11.1, 54.2, 57.8
12117	ctx_rh_G_Ins_lg_and_S_cent_ins		1576 mm³	39.4, 23.8, 12.3
12118	ctx_rh_G_insular_short		2570 mm³	38, 37.8, 13.6
12119	ctx_rh_G_occipital_middle		6010 mm³	41.7, -50.5, 8.8
12120	ctx_rh_G_occipital_sup		3292 mm³	15.6, -62.4, 24.3
12121	ctx_rh_G_oc-temp_lat-fusifor		5735 mm³	34.7, -22.3, -9.7
12122	ctx_rh_G_oc-temp_med-Lingual		5792 mm³	11.8, -38.6, -2.4
12123	ctx_rh_G_oc-temp_med-Parahip		2656 mm³	23.8, 14.3, -10.6
12124	ctx_rh_G_orbital		7678 mm³	31.6, 65.1, 2.8
12125	ctx_rh_G_pariet_inf-Angular		7779 mm³	42.4, -40.1, 38
12126	ctx_rh_G_pariet_inf-Supramar		5062 mm³	56, -7.4, 38.5
12127	ctx_rh_G_parietal_sup		5966 mm³	21.5, -38.2, 60.1
12128	ctx_rh_G_postcentral		4346 mm³	42.3, -3.7, 61
12129	ctx_rh_G_precentral		7811 mm³	40.5, 14, 61.1
12130	ctx_rh_G_precuneus		6752 mm³	5.3, -36.2, 45.9
12131	ctx_rh_G_rectus		2176 mm³	6.7, 68.9, 2.4
12132	ctx_rh_G_subcallosal		942 mm³	7.3, 40.2, 5.2
12133	ctx_rh_G_temp_sup-G_T_transv		983 mm³	47.9, 14.4, 18.6
12134	ctx_rh_G_temp_sup-Lateral		6219 mm³	59.4, 21.7, 9.1
12135	ctx_rh_G_temp_sup-Plan_polar		3017 mm³	42, 37, -0.5
12136	ctx_rh_G_temp_sup-Plan_tempo		1662 mm³	53.6, -2, 27.7
12137	ctx_rh_G_temporal_inf		5740 mm³	52.7, -0.7, -11.2
12138	ctx_rh_G_temporal_middle		7446 mm³	60.1, 1.9, 2.1
12139	ctx_rh_Lat_Fis-ant-Horizont		766 mm³	44.8, 61.3, 17.7
12140	ctx_rh_Lat_Fis-ant-Vertical		539 mm³	48, 47.6, 23.6
12141	ctx_rh_Lat_Fis-post		1841 mm³	38.6, -0.5, 29.2
12143	ctx_rh_Pole_occipital		4971 mm³	14.3, -68.2, -6.4
12144	ctx_rh_Pole_temporal		5393 mm³	35.6, 37.7, -19
12145	ctx_rh_S_calcarine		2870 mm³	15.9, -34.1, 9.6
12146	ctx_rh_S_central		4127 mm³	35.4, 4, 53.8
12147	ctx_rh_S_cingul-Marginalis		2118 mm³	13.3, -13.5, 50.6
12148	ctx_rh_S_circular_insula_ant		1129 mm³	34.4, 50.2, 10.7
12149	ctx_rh_S_circular_insula_inf		1951 mm³	41.7, 20, 7.2
12150	ctx_rh_S_circular_insula_sup		2523 mm³	36.9, 34.6, 25.6
12151	ctx_rh_S_collat_transv_ant		1875 mm³	41.3, 11, -14.5
12152	ctx_rh_S_collat_transv_post		506 mm³	20.4, -51, -5.6
12153	ctx_rh_S_front_inf		4075 mm³	43.8, 49.9, 38.3
12154	ctx_rh_S_front_middle		6022 mm³	33.4, 75, 40.1
12155	ctx_rh_S_front_sup		5432 mm³	25.3, 53.3, 55.6
12156	ctx_rh_S_interm_prim-Jensen		473 mm³	47.9, -21.2, 43.7
12157	ctx_rh_S_intrapariet_and_P_trans		5881 mm³	29.8, -36.5, 46.3
12158	ctx_rh_S_oc_middle_and_Lunatus		1479 mm³	33.5, -52.1, 2.5
12159	ctx_rh_S_oc_sup_and_transversal		2232 mm³	28.3, -52.5, 19.4
12160	ctx_rh_S_occipital_ant		1035 mm³	45, -30.5, 9.5
12161	ctx_rh_S_oc-temp_lat		1652 mm³	45.3, -14.1, -3.7
12162	ctx_rh_S_oc-temp_med_and_Lingual		3626 mm³	28.6, -15.9, -2.2
12163	ctx_rh_S_orbital_lateral		1198 mm³	45.3, 75.9, 18.2
12164	ctx_rh_S_orbital_med-olfact		1188 mm³	15.1, 54.2, 2
12165	ctx_rh_S_orbital-H_Shaped		3253 mm³	29.5, 68.1, 6.4
12166	ctx_rh_S_parieto_occipital		3360 mm³	14.5, -40.7, 27.1
12167	ctx_rh_S_pericallosal		2242 mm³	7.8, 30, 29.8
12168	ctx_rh_S_postcentral		3948 mm³	39.2, -10.2, 53.1
12169	ctx_rh_S_precentral-inf-part		3025 mm³	43.5, 29.6, 43.8
12170	ctx_rh_S_precentral-sup-part		1894 mm³	29.8, 16.2, 61.6
12171	ctx_rh_S_suborbital		552 mm³	9.8, 72.4, 8.6
12172	ctx_rh_S_subparietal		2013 mm³	10.6, -25.2, 39.4
12173	ctx_rh_S_temporal_inf		1532 mm³	55.7, -1.2, -4.2
12174	ctx_rh_S_temporal_sup		11339 mm³	47.8, -10.2, 16.5
12175	ctx_rh_S_temporal_transverse		619 mm³	51, 9, 17.5

MASSP Subcortical (Subject Space)

The bundled MNI MASSP parcellation warped into the subject’s own space, written by preprocessing as m2m_{subject}/segmentation/massp2021_subject.nii.gz. Same 31 labels as the MNI-space MASSP above, and the same provenance caveat applies — no citation, license or DOI is recorded in this repository.

Comparing this table with the MNI one is a useful check on how far a subject’s subcortical anatomy departs from the template.

31 regions

ID	Name	Colour	Volume	Centroid (subject, mm)
1	Striatum-left		12101 mm³	-14.7, 30.4, 17.4
2	Striatum-right		11308 mm³	19.7, 32.9, 16.8
3	Subthalamic-Nucleus-left		1140 mm³	0.3, 17.2, 12.9
4	Subthalamic-Nucleus-right		990 mm³	2.5, 16.3, 12.9
5	Substantia-Nigra-left		1391 mm³	-1.8, 13.9, 7.8
6	Substantia-Nigra-right		1317 mm³	4.3, 14.2, 7.9
7	Red-Nucleus-left		951 mm³	-0.8, 13.7, 11.1
8	Red-Nucleus-right		992 mm³	3.6, 14.6, 12
9	Globus-Pallidus-pars-interna-left		1301 mm³	-5.3, 18.7, 12.5
10	Globus-Pallidus-pars-interna-right		1350 mm³	7.1, 19.6, 11.8
11	Globus-Pallidus-pars-externa-left		2262 mm³	-9.9, 22.6, 13.7
12	Globus-Pallidus-pars-externa-right		2300 mm³	13.9, 24.1, 13
13	Thalamus-left		8910 mm³	-9.5, 8, 17.3
14	Thalamus-right		8344 mm³	11.5, 10.7, 17.9
15	Lateral-Ventricle-left		8554 mm³	-10.1, 14.9, 23.5
16	Lateral-Ventricle-right		8689 mm³	14.8, 14, 23.9
17	Third-Ventricle		2407 mm³	1.9, 10, 15.2
18	Fourth-Ventricle		1771 mm³	0.9, -7.3, -12.9
19	Amygdala-left		1653 mm³	-17.1, 22.9, 0.7
20	Amygdala-right		1578 mm³	19.5, 23.8, 0.2
21	Internal-Capsule-left		4333 mm³	-14.2, 21.8, 21.7
22	Internal-Capsule-right		4281 mm³	19, 24.5, 21.2
23	Ventral-Tegmental-Area-left		361 mm³	-0.4, 10.7, 6.7
24	Ventral-Tegmental-Area-right		382 mm³	4.4, 9.4, 7.9
25	Fornix		1060 mm³	0.8, 13.7, 21.5
26	Periaqueductal-Gray-left		286 mm³	-0.8, 0.9, 3.3
27	Periaqueductal-Gray-right		283 mm³	2.2, -0.8, 2.7
28	Pedunculopontine-Nucleus-left		182 mm³	-6.7, 3.2, 0
29	Pedunculopontine-Nucleus-right		188 mm³	6.9, 4, 0.5
30	Claustrum-left		631 mm³	-28.2, 24.4, 14
31	Claustrum-right		487 mm³	34.8, 27, 11.7

Atlas Resampling

Voxel-space ROI analysis requires the atlas and the field NIfTI to sit on the same voxel grid. They often do not: the field is written on the simulation’s grid, while a subject-space parcellation comes off recon-all at whatever resolution that ran at. Before masking, Analyzer brings the atlas onto the field’s grid so the two are compared voxel-for-voxel.

Validation on sub-ernie with the DKT parcellation. Top: an atlas cropped to the field’s dimensions keeps its own affine, so the shapes match but the geometry does not — a shape-only check passes it straight through and the parcellation lands on the wrong anatomy, with only 13% of labelled voxels agreeing with where they belong. Comparing the affine as well forces the resample, and agreement goes to 100%. Bottom: on a 0.5 mm target grid, voxel centres fall between source centres. An interpolating order blends neighbouring region ids and produces 3,708 values (1.80% of voxels, magenta) that exist in neither the atlas nor FreeSurferColorLUT.txt; nearest-neighbour produces none. Axial slices, neurological convention.

ROI analysis on the corrected grid

_Two ROI analyses on sub-ernie, each shown as the region on the subject T1, the TI field it sits in, and the statistics the analyzer reports once the atlas is on the field grid. Left insula (L_Insula simulation): 6,528 voxels, mean 0.076 V/m. Left thalamus (Thalamus simulation): 8,045 voxels, mean 0.127 V/m. The cyan outline is the atlas region; the coloured area is that region intersected with the tissue.

A grid is a shape and an affine. A volume is left untouched only when it already matches the field on both. Shape alone does not identify a grid — two volumes can agree on dimensions while sampling entirely different anatomy, and that case is silent: the analysis returns an ROI mask, statistics and a CSV, all describing the wrong tissue.

Labels are discrete, so the interpolation order is nearest-neighbour, always. Atlases carry region ids and tissue masks carry 0/1 flags. Any interpolating order averages neighbouring values, and the average of two region ids is a third id belonging to some unrelated structure — or to nothing at all. The resample uses nibabel.processing.resample_from_to(..., order=0); voxels falling outside the source field of view become 0 (background). The same routine handles tissue-mask NIfTIs, and both .nii/.nii.gz and FreeSurfer .mgz atlases are accepted.

Caching. The result is written next to the original atlas as {atlas_stem}_resampled_{width}x{height}x{depth}_{grid}.nii.gz, where {grid} is a short hash of the target affine — part of the key for the same reason it is part of the equality check. A later analysis on the same grid reuses that file, so the cost is paid once per (atlas, grid) pair. Original atlas files are never modified, and caching is best-effort: if the atlas directory is not writable, the analysis proceeds on the in-memory result rather than failing.

Resampling is logged at INFO level, so a mismatch is visible in the analyzer’s log rather than silent:

INFO | tit.analyzer | Resampling aparc.DKTatlas+aseg.mgz: (256, 256, 256) -> (256, 256, 208) (nearest-neighbour)

See Also

• Analyzer — the primary consumer of ROI/atlas selection
• Pre-Processing — how the subject-space atlases get generated
• Return to Wiki