maedoc/autotvb/region-atlas

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TVB default connectivity region names and indices for the 76-region Hagmann parcellation. Use when setting region-specific parameters (stimulus weights, x0, model.I), selecting regions by name, or mapping neuroscience labels to TVB indices. Triggers on region, index, label, V1, V2, M1, hippocampus, atlas, parcellation.

Install

npx vskill@latest install maedoc/autotvb/region-atlas

SKILL.md

TVB Default 76-Region Atlas

The default Connectivity.from_file() loads the Hagmann parcellation (76 regions). Region names and indices are:

 0: medial orbitofrontal (l)     1: medial orbitofrontal (r)
 2: frontal pole (l)            3: frontal pole (r)
 4: insula (l)                  5: insula (r)
 6: temporal pole (l)           7: temporal pole (r)
 8: superior temporal (l)       9: superior temporal (r)
10: parahippocampal (l)        11: parahippocampal (r)
12: amygdala (l)              13: amygdala (r)
14: precentral (l)             15: precentral (r)       ← M1
16: postcentral (l)            17: postcentral (r)      ← S1
18: superior parietal (l)      19: superior parietal (r)
20: supramarginal (l)          21: supramarginal (r)
22: lingual (l)                23: lingual (r)
24: pericalcarine (l)          25: pericalcarine (r)    ← V1
26: cuneus (l)                 27: cuneus (r)
28: lateral occipital (l)      29: lateral occipital (r) ← V2 area
30: precuneus (l)              31: precuneus (r)
32: rostral anterior cingulate (l) 33: rostral anterior cingulate (r)
34: caudal anterior cingulate (l)  35: caudal anterior cingulate (r)
36: posterior cingulate (l)    37: posterior cingulate (r)
38: isthmus cingulate (l)      39: isthmus cingulate (r)
40: hippocampus (l)            41: hippocampus (r)
42: fusiform (l)               43: fusiform (r)
44: parietal operculum (l)     45: parietal operculum (r)
46: bankssts (l)               47: bankssts (r)
48: entorhinal (l)             49: entorhinal (r)
50: rostral middle frontal (l) 51: rostral middle frontal (r)
52: caudal middle frontal (l) 53: caudal middle frontal (r)  ← DLPFC
54: pars opercularis (l)      55: pars opercularis (r)
56: pars triangularis (l)     57: pars triangularis (r)
58: pars orbitalis (l)        59: pars orbitalis (r)
60: lateral orbitofrontal (l) 61: lateral orbitofrontal (r)
62: transverse temporal (l)   63: transverse temporal (r)  ← A1
64: superior frontal (l)      65: superior frontal (r)
66: frontal pole (l)          67: frontal pole (r)  [duplicate label]
68: thalamus proper (l)       69: thalamus proper (r)
70: caudate (l)               71: caudate (r)
72: putamen (l)               73: putamen (r)
74: pallidum (l)              75: pallidum (r)

Common neuroscience labels → TVB indices

LabelTVB region nameIndex
V1pericalcarine (l)/(r)24, 25
V2lateral occipital (l)/(r)28, 29
A1transverse temporal (l)/(r)62, 63
M1precentral (l)/(r)14, 15
S1postcentral (l)/(r)16, 17
DLPFCcaudal middle frontal (l)/(r)52, 53
hippocampushippocampus (l)/(r)40, 41
amygdalaamygdala (l)/(r)12, 13
ACCcaudal anterior cingulate (l)/(r)34, 35
PCCposterior cingulate (l)/(r)36, 37
thalamusthalamus proper (l)/(r)68, 69

Safe lookup pattern

python
conn = connectivity.Connectivity.from_file()
conn.speed = 4.0
conn.configure()
labels = conn.region_labels  # list of 76 strings
# Find index by partial name match
v1_idx = [i for i, l in enumerate(labels) if "pericalcarine" in l]
# Use to set stimulus weights
stim_weights = numpy.zeros((76, 1))
stim_weights[v1_idx, 0] = 1.0

Critical warnings

  • Never use invented labels like "rHC" or "rCCP" — they do not exist in the atlas.
  • Always verify with conn.region_labels before assigning region-specific parameters.
  • Left = even-ish indices (0,2,4...), Right = odd-ish — but NOT guaranteed. Always look up by name.

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