What are the labels Mindboggle uses?

Mindboggle uses labels from complementary labeling protocols:

Below are lists of brain label names and numbers that can be generated by this program, along with other aggregate lists and colormaps.

Authors:

Copyright 2015, Mindboggle team (http://mindboggle.info), Apache v2.0 License


DKT cortical labeling protocol (31 labels)

Four labels have been removed from the 35 cortical labels (“ctx-”) of the Desikan-Killiany (DK) protocol (see footnote #1): bankstss (1001, 2001), corpus callosum (1004, 2004), frontal pole (1032, 2032), and temporal pole (1033, 2033).

  • 1002, “left caudal anterior cingulate”
  • 1003, “left caudal middle frontal”
  • 1005, “left cuneus”
  • 1006, “left entorhinal”
  • 1007, “left fusiform”
  • 1008, “left inferior parietal”
  • 1009, “left inferior temporal”
  • 1010, “left isthmus cingulate”
  • 1011, “left lateral occipital”
  • 1012, “left lateral orbitofrontal”
  • 1013, “left lingual”
  • 1014, “left medial orbitofrontal”
  • 1015, “left middle temporal”
  • 1016, “left parahippocampal”
  • 1017, “left paracentral”
  • 1018, “left pars opercularis”
  • 1019, “left pars orbitalis”
  • 1020, “left pars triangularis”
  • 1021, “left pericalcarine”
  • 1022, “left postcentral”
  • 1023, “left posterior cingulate”
  • 1024, “left precentral”
  • 1025, “left precuneus”
  • 1026, “left rostral anterior cingulate”
  • 1027, “left rostral middle frontal”
  • 1028, “left superior frontal”
  • 1029, “left superior parietal”
  • 1030, “left superior temporal”
  • 1031, “left supramarginal”
  • 1034, “left transverse temporal”
  • 1035, “left insula”
  • 2002, “right caudal anterior cingulate”
  • 2003, “right caudal middle frontal”
  • 2005, “right cuneus”
  • 2006, “right entorhinal”
  • 2007, “right fusiform”
  • 2008, “right inferior parietal”
  • 2009, “right inferior temporal”
  • 2010, “right isthmus cingulate”
  • 2011, “right lateral occipital”
  • 2012, “right lateral orbitofrontal”
  • 2013, “right lingual”
  • 2014, “right medial orbitofrontal”
  • 2015, “right middle temporal”
  • 2016, “right parahippocampal”
  • 2017, “right paracentral”
  • 2018, “right pars opercularis”
  • 2019, “right pars orbitalis”
  • 2020, “right pars triangularis”
  • 2021, “right pericalcarine”
  • 2022, “right postcentral”
  • 2023, “right posterior cingulate”
  • 2024, “right precentral”
  • 2025, “right precuneus”
  • 2026, “right rostral anterior cingulate”
  • 2027, “right rostral middle frontal”
  • 2028, “right superior frontal”
  • 2029, “right superior parietal”
  • 2030, “right superior temporal”
  • 2031, “right supramarginal”
  • 2034, “right transverse temporal”
  • 2035, “right insula”

Noncortex label numbers and names

These labels were converted from Neuromorphometrics BrainCOLOR subcortex labels to be consistent with FreeSurfer labels in FreeSurferColorLUT.txt.

Five labels did not have counterparts in FreeSurfer:
  • 71, “cerebellar vermal lobules I-V”
  • 72, “cerebellar vermal lobules VI-VII”
  • 73, “cerebellar vermal lobules VIII-X”
  • 75, “left basal forebrain”
  • 76, “right basal forebrain”
and were reassigned to unused numbers in FreeSurferColorLUT.txt:
  • 630, “cerebellar vermal lobules I-V”
  • 631, “cerebellar vermal lobules VI-VII”
  • 632, “cerebellar vermal lobules VIII-X”
  • 91, “left basal forebrain”
  • 92, “right basal forebrain”
  • 16, “Brain stem”
  • 24, “CSF”
  • 14, “3rd ventricle”
  • 15, “4th ventricle”
  • 72, “5th ventricle”
  • 85, “optic chiasm”
  • 4, “left lateral ventricle”
  • 5, “left inferior lateral ventricle”
  • 6, “left cerebellum exterior”
  • 7, “left cerebellum white matter”
  • 10, “left thalamus proper”
  • 11, “left caudate”
  • 12, “left putamen”
  • 13, “left pallidum”
  • 17, “left hippocampus”
  • 18, “left amygdala”
  • 25, “left lesion”
  • 26, “left accumbens area”
  • 28, “left ventral DC”
  • 30, “left vessel”
  • 91, “left basal forebrain”
  • 43, “right lateral ventricle”
  • 44, “right inferior lateral ventricle”
  • 45, “right cerebellum exterior”
  • 46, “right cerebellum white matter”
  • 49, “right thalamus proper”
  • 50, “right caudate”
  • 51, “right putamen”
  • 52, “right pallidum”
  • 53, “right hippocampus”
  • 54, “right amygdala”
  • 57, “right lesion”
  • 58, “right accumbens area”
  • 60, “right ventral DC”
  • 62, “right vessel”
  • 92, “right basal forebrain”
  • 630, “cerebellar vermal lobules I-V”
  • 631, “cerebellar vermal lobules VI-VII”
  • 632, “cerebellar vermal lobules VIII-X”

Sulcus names from the DKT labeling protocol (callosal sulcus removed)

  • “frontomarginal sulcus”
  • “superior frontal sulcus”
  • “inferior frontal sulcus”
  • “precentral sulcus”
  • “central sulcus”
  • “postcentral sulcus”
  • “intraparietal sulcus”
  • “1st segment of post. sup. temporal sulcus / primary intermediate sulcus”
  • “sylvian fissure”
  • “lateral occipital sulcus”
  • “anterior occipital sulcus”
  • “superior temporal sulcus”
  • “inferior temporal sulcus”
  • “circular sulcus”
  • “1st transverse temporal sulcus and Heschl’s sulcus”
  • “cingulate sulcus”
  • “paracentral sulcus”
  • “parietooccipital fissure”
  • “calcarine fissure”
  • “superior rostral sulcus”
  • “lateral H-shaped orbital sulcus”
  • “olfactory sulcus”
  • “occipitotemporal sulcus”
  • “collateral sulcus”

Sulcus abbreviations

  • “fms”
  • “sfrs”
  • “ifrs”
  • “prcs”
  • “cs”
  • “pocs”
  • “itps”
  • “csts1/pis”
  • “ls”
  • “locs”
  • “aocs”
  • “sts”
  • “its”
  • “crs”
  • “ftts/hs”
  • “cgs”
  • “pcs”
  • “pos”
  • “ccs”
  • “sros”
  • “lhos”
  • “olfs”
  • “ots”
  • “cos”

Lists of label pairs that define DKT sulcus boundaries

1000 [left] or 2000 [right] would be added to the numbers below to match the cortical label numbers above:

  • [[12,28]],
  • [[3,28], [27,28]],
  • [[3,18],[3,19],[3,20], [18,27],[19,27],[20,27]],
  • [[24,28], [3,24],[24,27], [18,24],[19,24],[20,24]],
  • [[22,24]],
  • [[22,29], [22,31]],
  • [[29,31], [8,29]],
  • [[8,31]],
  • [[30,31]],
  • [[8,11], [11,29]],
  • [[11,15], [9,11]],
  • [[15,30]],
  • [[9,15]],
  • [[12,35], [30,35], [34,35], [2,35],[10,35],[23,35],[26,35],
    [22,35], [24,35], [31,35]],
  • [[30,34]],
  • [[2,14],[10,14],[14,23],[14,26], [2,28],[10,28],[23,28],[26,28],
    [2,17],[10,17],[17,23],[17,26], [17,25]],
  • [[17,28]],
  • [[5,25]],
  • [[13,25], [2,13],[10,13],[13,23],[13,26]],
  • [[14,28]],
  • [[3,12],[12,27], [12,18],[12,19],[12,20]],
  • [[12,14]],
  • [[7,9], [7,11]],
  • [[6,7], [7,16], [7,13]]]

Regions bounded by sulcal fundi

A ‘*’ denotes boundaries given principally by a sulcal fundus but which frequently require “jumps” across gyri. Jason Tourville handles separately definitions that explicitly rely on non-fundus boundaries like the margins of sulcal banks.

Lateral surface:

  • frontomarginal sulcus: [12,28]
  • superior frontal: [3,28],[27,28]
  • inferior frontal: [3,18],[3,19],[3,20], [18,27],[19,27],[20,27]
  • precentral: [24,28]*, [[3,24],[24,27]]*, [[18,24],[19,24],[20,24]]*
  • central sulcus: [22,24]
  • postcentral: [22,29],[22,31], not:[22,24]
  • intraparietal: [29,31], [8,29]
  • primary intermediate sulcus /
    1st segment of the posterior superior temporal sulcus: [8,31]* (footnote #2)
  • sylvian fissure: [30,31]*, not:[18,30] (footnote #3)
  • lateral occipital sulcus: [8,11]*,[11,29]*
  • anterior occipital sulcus: [11,15]*,[9,11]
  • superior temporal sulcus: [15,30]
  • inferior temporal sulcus: [9,15]*

PeriSylvian area (folds within the Sylvian fissure):

  • circular sulcus: [12,35],[30,35],[34,35], [2,35],[10,35],[23,35],[26,35],
    [22,35], [24,35], [31,35]
  • 1st transverse temporal sulcus: [30,34] (footnote #4)
  • Heschl’s sulcus: [30,34]

Medial surface:

  • cingulate sulcus: [2,14],[10,14],[14,23],[14,26] (footnote #5)
    [2,28],[10,28],[23,28],[26,28], [2,17],[10,17],[17,23],[17,26], [17,25]
  • paracentral sulcus: [17,28]*
  • parietooccipital fissure: [5,25]
  • calcarine fissure: [13,25], [2,13],[10,13],[13,23],[13,26] not:[5,13] (footnote #6)
  • superior rostral sulcus: [14,28]
  • callosal sulcus: [2,4],[4,10],[4,23],[4,26]

Ventral surface:

  • lateral H-shaped orbital sulcus: [3,12],[12,27], [12,18],[12,19],[12,20]
  • olfactory sulcus: [12,14]
  • occipitotemporal sulcus: [7,9],[7,11]
  • collateral sulcus: [6,7], [7,13], [7,16]

Boundaries that will NEVER be derived by fundi

(...but instead by curvature, etc.)

Regions bounded by sulcal margins:

  • interhemispheric fissure, dorsal margin:
    [17,28],[17,24],[17,22],[25,29],[5,29],[5,11]
  • calcarine sulcus, dorsal margin: [5,21]
  • calcarine sulcus, ventral margin: [21,13]

Regions with additional non-sulcal boundaries with subcortical regions:

  • [16,6,9,30,12,14]

Possible ways to combine or eliminate regions (from Jason Tourville’s notes)

  1. Temporal (33) and frontal (32) poles, and bankstss (1) (see footnote #1) regions eliminated, corresponding cortex absorbed by adjacent regions.
  2. Caudal (2), isthmus (10), posterior (23), and rostral anterior (26) cingulate combined to form single cingulate region (2).
  3. Caudal (3) and rostral (27) middle frontal regions combined to form single middle frontal region (3).
  4. Opercular (18), orbital (19), and triangular (20) inferior frontal regions could combine to form a single inferior frontal region (18) (footnote #7).
  5. Parahippocampal + entorhinal cortex + and lingual gyrus?

Footnotes

[1] This was eliminated because it spanned the superior temporal sulcus fundus
and because the anterior boundary was ambiguous.
[2] For “1st segment posterior superior temporal sulcus /
primary intermediate sulcus” the standard abbreviations are “csts1/pis” or, if you like, you can just drop the “pis” part and go with csts1, which forms the bulk of the boundary. The abbreviation is used in the recent Petrides atlas and some other sources and stands for “caudal superior temporal sulcus, 1st segment”.
[3] For “1st transverse temporal sulcus and Heschl sulcus” it’s important
to realize that these are two different sulci that form two different boundaries around Heschl’s gyrus (the former is the anterior boundary; the latter is the posterior boundary). So both should be included. The standard abbreviations are “ftts” and “hs”. It may appear that these sulci form a single, unbroken boundary of Heschl’s gyrus, but they actually do not intersect. So for labeling figures, having an abbreviation associated with a line in front of Heschl’s and one associated with a line behind Heschl’s is fine. And accurate.
[4] The insula lies between these regions and is separated from them by the
circular sulcus which is marked by an easily distinguished fold deep within the Sylvian fissure.
[5] This is the case in some, but not all, hemispheres. It occurs when the
superior rostral sulcus fails to intersect with the cingulate sulcus.
[6] The pericalcarine region lies between these 2 regions. As defined in
“Regions bounded by sulcal margins”, the pericalcarine cortex (21) dorsal (with 5) and ventral (with 13) boundaries are formed by the lateral margins of the dorsal and ventral banks of the calcarine sulcus rather than a sulcal fundus; because this region spans the sulcal fundus, we cannot simply incorporate portions of the region into the adjacent regions based on the fundus.
[7] This is a perfectly reasonable aggregation of these [inferior frontal]
regions and is the one reflected in the sulcus/region pairings above. An alternative breakdown would be to lump 19 with lateral orbitofrontal cortex (12) and use the anterior horizontal ramus of the sylvian fissure as the boundary between 18 and 12. Anatomically, both aggregations are defensible but one or the other may suit your needs better. [Regarding the lack of a full, consistent sulcal anterior boundary for the inferior frontal gyrus]: This will be the case for several regions, i.e., in practice, many boundaries are not formed by sulci but instead require ‘jumps’ across gyri (paths along regions of different direction curvature). This can be variable, (e.g., the precentral sulcus is consistently formed by two or more disconnected components) or implicit in the definition of the boundary (e.g., the anterior boundary between orbital inferior frontal gyrus (19) and rostral middle frontal gyrus (27) requires a ‘jump’ over the lateral orbital gyrus.