Wiki Guides

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 four 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 and FreeSurfer recon-all. 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

MNI-Space Atlases

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

Atlas Regions Native space
CIT168 Subcortical 16 MNI152NLin2009cAsym
Morel Thalamus 74 MNI152, FSL-aligned 182x218x182 1mm grid
Glasser HCP-MMP1.0 360 FreeSurfer-conformed 256x256x256 1mm grid
MASSP Subcortical 31 ICBM152 2009b nonlinear asymmetric, hi-res 0.5mm

Pick an atlas from the dropdown to load it over the MNI152 template. 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.

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

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.

All 16 labels are bilateral: each label merges the left and right instance of a structure into one region (e.g. “Putamen” covers both hemispheres). There are no separate left/right label pairs, so this atlas has 16 structures total, not 8 per hemisphere.

One consequence for the viewer: because a bilateral label spans both hemispheres, its centroid falls near the midline. Clicking a CIT168 row centres the crosshair between the two instances of the structure rather than on either one — scroll laterally in the axial view to reach them. The other atlases label left and right separately, so their centroids are properly lateralised.

16 regions
IDNameColourVolumeCentroid (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


Morel Thalamus Atlas

License: CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike). © University of Zurich and ETH Zurich; Andras Jakab, Remi Blanc, Gabor Szekely. This is the only one of the four shipped atlases with a non-permissive license — republishing or reusing it commercially is not permitted without separate arrangement with the copyright holders.

Source: Morel Atlas of the Human Thalamus, MNI152 space, voxelized version. Zenodo doi:10.5281/zenodo.13918589.

Cite: Jakab et al. AJNR 33(11):2110-2116 (2012); Krauth et al. NeuroImage 49(3):2053-2062 (2010).

The source LUT declares 76 labels (38 nuclei/structures per hemisphere), but 2 of them — ids 27 and 127, both “sPf” (subparafascicular nucleus) — have zero voxels in the shipped volume after the source atlas’s overlap-resolution rule. The table lists the 74 labels that are actually present.

This is the only one of the four atlases natively on the same 182x218x182 1mm grid as the shipped MNI152 template, so it required no resampling.

74 regions
IDNameColourVolumeCentroid (MNI, mm)
1 Morel_Left_AD_Anterodorsal_nucleus 9 mm³ -1.2, -9.6, 11.7
2 Morel_Left_AM_Anteromedial_nucleus 50 mm³ -2.5, -2.9, 5
3 Morel_Left_AV_Anteroventral_nucleus 279 mm³ -4.1, -6.1, 11.4
4 Morel_Left_CeM_Central_medial_nucleus 150 mm³ -3.2, -9.5, 0.3
5 Morel_Left_CL_Central_lateral_nucleus 847 mm³ -6.7, -18.9, 8.7
6 Morel_Left_CM_Centromedian_nucleus 285 mm³ -9, -20.6, 0.8
7 Morel_Left_Hb_Habenula 48 mm³ -2.7, -23.7, 1.5
8 Morel_Left_LD_Lateral_dorsal_nucleus 139 mm³ -7.3, -19.2, 15.7
9 Morel_Left_LGNmc_Lateral_geniculate_magnocellular 77 mm³ -24.9, -24.5, -8.1
10 Morel_Left_LGNpc_Lateral_geniculate_parvocellular 153 mm³ -24.5, -24.7, -5.7
11 Morel_Left_Li_Limitans_nucleus 71 mm³ -7.9, -26.6, -0.4
12 Morel_Left_LP_Lateral_posterior_nucleus 430 mm³ -15.8, -24, 12.6
13 Morel_Left_MDmc_Mediodorsal_magnocellular 207 mm³ -1.4, -14.1, 4.1
14 Morel_Left_MDpc_Mediodorsal_parvocellular 820 mm³ -4.8, -15.7, 6.4
15 Morel_Left_MGN_Medial_geniculate_nucleus 213 mm³ -16.9, -26.9, -4.6
16 Morel_Left_mtt_Mammillothalamic_tract 55 mm³ -5, -9.2, -3.8
17 Morel_Left_MV_Medioventral_nucleus 12 mm³ -1.7, -8.5, -2
18 Morel_Left_Pf_Parafascicular_nucleus 139 mm³ -5.3, -19.4, -2.1
19 Morel_Left_Po_Posterior_nucleus 58 mm³ -13.8, -25.8, -1.1
20 Morel_Left_PuA_Pulvinar_anterior 143 mm³ -13.5, -23.3, 4.4
21 Morel_Left_PuI_Pulvinar_inferior 56 mm³ -23, -29.6, -4.1
22 Morel_Left_PuL_Pulvinar_lateral 374 mm³ -22.7, -29.3, 3.5
23 Morel_Left_PuM_Pulvinar_medial 1687 mm³ -13.5, -29.9, 4.6
24 Morel_Left_Pv_Paraventricular_nucleus 4 mm³ -0.8, -8.5, 3
25 Morel_Left_RN_Red_nucleus 382 mm³ -6, -19.7, -10.2
26 Morel_Left_SG_Suprageniculate_nucleus 34 mm³ -12.7, -27.6, -3.2
28 Morel_Left_STh_Subthalamic_nucleus 239 mm³ -11.8, -12.9, -7.2
29 Morel_Left_VAmc_Ventral_anterior_magnocellular 65 mm³ -6.2, -6, 1.8
30 Morel_Left_VApc_Ventral_anterior_parvocellular 527 mm³ -9.2, -5.2, 5.9
31 Morel_Left_VLa_Ventral_lateral_anterior 300 mm³ -13.2, -11, 5
32 Morel_Left_VLpd_Ventral_lateral_posterior_dorsal 700 mm³ -11.7, -12.6, 13.8
33 Morel_Left_VLpv_Ventral_lateral_posterior_ventral 613 mm³ -12.8, -14.3, 4.9
34 Morel_Left_VM_Ventral_medial_nucleus 114 mm³ -9.1, -12.8, -1.5
35 Morel_Left_VPI_Ventral_posterior_inferior 62 mm³ -16.2, -22.9, -1.6
36 Morel_Left_VPLa_Ventral_posterior_lateral_anterior 97 mm³ -17.1, -19.5, 5.6
37 Morel_Left_VPLp_Ventral_posterior_lateral_posterior 402 mm³ -16.2, -21, 7.7
38 Morel_Left_VPM_Ventral_posterior_medial 123 mm³ -12.3, -19.8, -0.8
101 Morel_Right_AD_Anterodorsal_nucleus 7 mm³ 3.1, -9.9, 12.4
102 Morel_Right_AM_Anteromedial_nucleus 47 mm³ 3.9, -2.9, 4.9
103 Morel_Right_AV_Anteroventral_nucleus 280 mm³ 5.5, -6.1, 11.2
104 Morel_Right_CeM_Central_medial_nucleus 166 mm³ 4.5, -9.5, 0.4
105 Morel_Right_CL_Central_lateral_nucleus 823 mm³ 8.2, -18.9, 8.7
106 Morel_Right_CM_Centromedian_nucleus 288 mm³ 10.5, -20.6, 0.9
107 Morel_Right_Hb_Habenula 52 mm³ 4.3, -23.9, 1.4
108 Morel_Right_LD_Lateral_dorsal_nucleus 141 mm³ 8.8, -19.2, 15.7
109 Morel_Right_LGNmc_Lateral_geniculate_magnocellular 80 mm³ 26.2, -24.7, -8
110 Morel_Right_LGNpc_Lateral_geniculate_parvocellular 148 mm³ 26.1, -24.7, -5.6
111 Morel_Right_Li_Limitans_nucleus 72 mm³ 9.6, -26.6, -0.5
112 Morel_Right_LP_Lateral_posterior_nucleus 596 mm³ 17, -24.3, 12.9
113 Morel_Right_MDmc_Mediodorsal_magnocellular 209 mm³ 2.9, -14, 4.1
114 Morel_Right_MDpc_Mediodorsal_parvocellular 831 mm³ 6.3, -15.8, 6.4
115 Morel_Right_MGN_Medial_geniculate_nucleus 212 mm³ 18.5, -26.9, -4.6
116 Morel_Right_mtt_Mammillothalamic_tract 69 mm³ 6.5, -8.9, -2.8
117 Morel_Right_MV_Medioventral_nucleus 6 mm³ 3, -7.8, -1.7
118 Morel_Right_Pf_Parafascicular_nucleus 144 mm³ 6.7, -19.4, -2
119 Morel_Right_Po_Posterior_nucleus 63 mm³ 15.3, -25.8, -1.2
120 Morel_Right_PuA_Pulvinar_anterior 142 mm³ 15, -23.4, 4.3
121 Morel_Right_PuI_Pulvinar_inferior 56 mm³ 24.3, -29.5, -4.2
122 Morel_Right_PuL_Pulvinar_lateral 374 mm³ 24.2, -29.4, 3.4
123 Morel_Right_PuM_Pulvinar_medial 1625 mm³ 15, -30, 4.4
124 Morel_Right_Pv_Paraventricular_nucleus 3 mm³ 2, -8, 4
125 Morel_Right_RN_Red_nucleus 384 mm³ 7.5, -19.7, -10.1
126 Morel_Right_SG_Suprageniculate_nucleus 36 mm³ 14.1, -27.5, -3.4
128 Morel_Right_STh_Subthalamic_nucleus 236 mm³ 13.3, -13.1, -7.1
129 Morel_Right_VAmc_Ventral_anterior_magnocellular 65 mm³ 7.7, -5.8, 2.3
130 Morel_Right_VApc_Ventral_anterior_parvocellular 526 mm³ 10.8, -5.2, 5.9
131 Morel_Right_VLa_Ventral_lateral_anterior 303 mm³ 14.8, -11, 5.1
132 Morel_Right_VLpd_Ventral_lateral_posterior_dorsal 695 mm³ 13.1, -12.5, 13.8
133 Morel_Right_VLpv_Ventral_lateral_posterior_ventral 598 mm³ 14.4, -14.4, 4.9
134 Morel_Right_VM_Ventral_medial_nucleus 113 mm³ 10.6, -12.9, -1.5
135 Morel_Right_VPI_Ventral_posterior_inferior 63 mm³ 17.7, -22.9, -1.6
136 Morel_Right_VPLa_Ventral_posterior_lateral_anterior 94 mm³ 18.7, -19.5, 5.4
137 Morel_Right_VPLp_Ventral_posterior_lateral_posterior 400 mm³ 17.6, -20.9, 7.6
138 Morel_Right_VPM_Ventral_posterior_medial 124 mm³ 13.8, -19.8, -0.8


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
IDNameColourVolumeCentroid (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 four shipped atlases. It was resampled onto the 1mm template grid for the viewer.

31 regions
IDNameColourVolumeCentroid (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


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.
  • FreeSurfer recon-all writes the volumetric parcellations aparc.DKTatlas+aseg.mgz, aparc.a2009s+aseg.mgz, aparc+aseg.mgz and aseg.mgz, along with the finer ThalamicNuclei.v13.T1.mgz and lh/rh.hippoAmygLabels-T1.v22.mgz segmentations.

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.

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/.


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
IDNameColourVolumeCentroid (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
IDNameColourVolumeCentroid (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
IDNameColourVolumeCentroid (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
IDNameColourVolumeCentroid (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


See Also

  • Atlas Resampling — how the toolbox aligns an atlas to a subject’s field data
  • Analyzer — the primary consumer of ROI/atlas selection
  • Pre-Processing — how the subject-space atlases get generated
  • Return to Wiki