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FSL Add FSL compatable colin atlas and full histology and table Mar 29, 2018
labels
stl
surfaces
README.md
colin_striatum_subdivisions_RMINC.csv
colin_tgps_RMINC.csv
colin_thalamus_subdivisions_RMINC.csv
full_histology.csv
label-names-striatum-subdivisions.csv
label-names-thalamus-globus_pallidus-striatum.csv
label-names-thalamus-subdivisions.csv

README.md

Colin-27 Subcortical Atlases

The atlases in this folder are based on the Colin-27 Average Brain:

http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27

When using these atlases, please cite:

Chakravarty MM, Bertrand G, Hodge CP, Sadikot AF, Collins DL. The creation
of a brain atlas for image guided neurosurgery using serial histological
data. Neuroimage. 2006;30(2):359-76.

Whole thalamus, Globus Pallidus and Striatum

label file: labels/thalamus-globus_pallidus-striatum.mnc

Label: 1 - left striatum Label: 2 - left globus pallidus Label: 3 - left thalamus Label: 4 - right striatum Label: 5 - right globus pallidus Label: 6 - right thalamus

surfaces:

  • thalamus:
    • surfaces/thalamus-left.obj
    • surfaces/thalamus-right.obj
  • globus pallidus:
    • surfaces/globus_pallidus-left.obj
    • surfaces/globus_pallidus-right.obj
  • striatum:
    • surfaces/striatum-left.obj
    • surfaces/striatum-right.obj

Subdivisions of the striatum

label file: labels/striatum-subdivisions.mnc

Label: 100 - left nucleus accumbens / ventral striatum
Label: 101 - left precommissural putamen
Label: 102 - left precommissural caudate
Label: 104 - left postcommissural caudate
Label: 105 - left postcommissural putamen
Label: 110 - right nucleus accumbens / ventral striatum
Label: 111 - right precommissural putamen
Label: 112 - right precommissural caudate
Label: 114 - right postcommissural caudate
Label: 115 - right postcommissural putamen

Surface labels:

  • surfaces/striatum-subdivisions-left-labels.txt
  • surfaces/striatum-subdivisions-right-labels.txt

Subdivisions of the thalamus

label file: labels/thalamus-subdivisions.mnc

Label: 1   - left lateral geniculate nucleus (LGN)
Label: 2   - left medial geniculate nucleus (MGN)
Label: 3   - left anterior nuclei
Label: 4   - left central nuclei
Label: 5   - left lateral dorsal
Label: 6   - left lateral posterior
Label: 7   - left medial dorsal
Label: 8   - left pulvinar
Label: 9   - left ventral anterior nucleus
Label: 10  - left ventral lateral nucleus
Label: 11  - left ventral posterior nucleus
Label: 21  - right lateral geniculate nucleus (LGN)
Label: 22  - right medial geniculate nucleus (MGN)
Label: 23  - right anterior nuclei
Label: 24  - right central nuclei
Label: 25  - right lateral dorsal
Label: 26  - right lateral posterior
Label: 27  - right medial dorsal
Label: 28  - right pulvinar
Label: 29  - right ventral anterior nucleus
Label: 30  - right ventral lateral nucleus
Label: 31  - right ventral posterior nucleus

Surface labels:

  • surfaces/thalamus-subdivisions-left-labels.txt
  • surfaces/thalamus-subdivisions-right-labels.txt