desikanKillianyTourvilleLabeling: Cortical and deep gray matter labeling using...

In ANTsX/ANTsRNet: Neural Networks for Medical Image Processing

Cortical and deep gray matter labeling using Desikan-Killiany-Tourville

Description

Perform DKT labeling using deep learning

Usage

desikanKillianyTourvilleLabeling(
  t1,
  doPreprocessing = TRUE,
  returnProbabilityImages = FALSE,
  doLobarParcellation = FALSE,
  antsxnetCacheDirectory = NULL,
  verbose = FALSE
)

Arguments

t1	raw or preprocessed 3-D T1-weighted brain image.
doPreprocessing	perform preprocessing. See description above.
returnProbabilityImages	whether to return the two sets of probability images for the inner and outer labels.
doLobarParcellation	perform lobar parcellation (also divided by hemisphere).
antsxnetCacheDirectory	destination directory for storing the downloaded template and model weights. Since these can be resused, if is.null(antsxnetCacheDirectory), these data will be downloaded to the subdirectory ~/.keras/ANTsXNet/.
verbose	print progress.

Details

The labeling is as follows:

• Label 0:background

  Inner labels:

• Label 4:left lateral ventricle

• Label 5:left inferior lateral ventricle

• Label 6:left cerebellem exterior

• Label 7:left cerebellum white matter

• Label 10:left thalamus proper

• Label 11:left caudate

• Label 12:left putamen

• Label 13:left pallidium

• Label 14:3rd ventricle

• Label 15:4th ventricle

• Label 16:brain stem

• Label 17:left hippocampus

• Label 18:left amygdala

• Label 24:CSF

• Label 25:left lesion

• Label 26:left accumbens area

• Label 28:left ventral DC

• Label 30:left vessel

• Label 43:right lateral ventricle

• Label 44:right inferior lateral ventricle

• Label 45:right cerebellum exterior

• Label 46:right cerebellum white matter

• Label 49:right thalamus proper

• Label 50:right caudate

• Label 51:right putamen

• Label 52:right palladium

• Label 53:right hippocampus

• Label 54:right amygdala

• Label 57:right lesion

• Label 58:right accumbens area

• Label 60:right ventral DC

• Label 62:right vessel

• Label 72:5th ventricle

• Label 85:optic chasm

• Label 91:left basal forebrain

• Label 92:right basal forebrain

• Label 630:cerebellar vermal lobules I-V

• Label 631:cerebellar vermal lobules VI-VII

• Label 632:cerebellar vermal lobules VIII-X

  Outer labels:

• Label 1002:left caudal anterior cingulate

• Label 1003:left caudal middle frontal

• Label 1005:left cuneus

• Label 1006:left entorhinal

• Label 1007:left fusiform

• Label 1008:left inferior parietal

• Label 1009:left inferior temporal

• Label 1010:left isthmus cingulate

• Label 1011:left lateral occipital

• Label 1012:left lateral orbitofrontal

• Label 1013:left lingual

• Label 1014:left medial orbitofrontal

• Label 1015:left middle temporal

• Label 1016:left parahippocampal

• Label 1017:left paracentral

• Label 1018:left pars opercularis

• Label 1019:left pars orbitalis

• Label 1020:left pars triangularis

• Label 1021:left pericalcarine

• Label 1022:left postcentral

• Label 1023:left posterior cingulate

• Label 1024:left precentral

• Label 1025:left precuneus

• Label 1026:left rostral anterior cingulate

• Label 1027:left rostral middle frontal

• Label 1028:left superior frontal

• Label 1029:left superior parietal

• Label 1030:left superior temporal

• Label 1031:left supramarginal

• Label 1034:left transverse temporal

• Label 1035:left insula

• Label 2002:right caudal anterior cingulate

• Label 2003:right caudal middle frontal

• Label 2005:right cuneus

• Label 2006:right entorhinal

• Label 2007:right fusiform

• Label 2008:right inferior parietal

• Label 2009:right inferior temporal

• Label 2010:right isthmus cingulate

• Label 2011:right lateral occipital

• Label 2012:right lateral orbitofrontal

• Label 2013:right lingual

• Label 2014:right medial orbitofrontal

• Label 2015:right middle temporal

• Label 2016:right parahippocampal

• Label 2017:right paracentral

• Label 2018:right pars opercularis

• Label 2019:right pars orbitalis

• Label 2020:right pars triangularis

• Label 2021:right pericalcarine

• Label 2022:right postcentral

• Label 2023:right posterior cingulate

• Label 2024:right precentral

• Label 2025:right precuneus

• Label 2026:right rostral anterior cingulate

• Label 2027:right rostral middle frontal

• Label 2028:right superior frontal

• Label 2029:right superior parietal

• Label 2030:right superior temporal

• Label 2031:right supramarginal

• Label 2034:right transverse temporal

• Label 2035:right insula

Performing the lobar parcellation is based on the FreeSurfer division described here:

https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

Frontal lobe:

• Label 1002:left caudal anterior cingulate

• Label 1003:left caudal middle frontal

• Label 1012:left lateral orbitofrontal

• Label 1014:left medial orbitofrontal

• Label 1017:left paracentral

• Label 1018:left pars opercularis

• Label 1019:left pars orbitalis

• Label 1020:left pars triangularis

• Label 1024:left precentral

• Label 1026:left rostral anterior cingulate

• Label 1027:left rostral middle frontal

• Label 1028:left superior frontal

• Label 2002:right caudal anterior cingulate

• Label 2003:right caudal middle frontal

• Label 2012:right lateral orbitofrontal

• Label 2014:right medial orbitofrontal

• Label 2017:right paracentral

• Label 2018:right pars opercularis

• Label 2019:right pars orbitalis

• Label 2020:right pars triangularis

• Label 2024:right precentral

• Label 2026:right rostral anterior cingulate

• Label 2027:right rostral middle frontal

• Label 2028:right superior frontal

  Parietal:

• Label 1008:left inferior parietal

• Label 1010:left isthmus cingulate

• Label 1022:left postcentral

• Label 1023:left posterior cingulate

• Label 1025:left precuneus

• Label 1029:left superior parietal

• Label 1031:left supramarginal

• Label 2008:right inferior parietal

• Label 2010:right isthmus cingulate

• Label 2022:right postcentral

• Label 2023:right posterior cingulate

• Label 2025:right precuneus

• Label 2029:right superior parietal

• Label 2031:right supramarginal

  Temporal:

• Label 1006:left entorhinal

• Label 1007:left fusiform

• Label 1009:left inferior temporal

• Label 1015:left middle temporal

• Label 1016:left parahippocampal

• Label 1030:left superior temporal

• Label 1034:left transverse temporal

• Label 2006:right entorhinal

• Label 2007:right fusiform

• Label 2009:right inferior temporal

• Label 2015:right middle temporal

• Label 2016:right parahippocampal

• Label 2030:right superior temporal

• Label 2034:right transverse temporal

  Occipital:

• Label 1005:left cuneus

• Label 1011:left lateral occipital

• Label 1013:left lingual

• Label 1021:left pericalcarine

• Label 2005:right cuneus

• Label 2011:right lateral occipital

• Label 2013:right lingual

• Label 2021:right pericalcarine

  Other outer labels:

• Label 1035:left insula

• Label 2035:right insula

Preprocessing on the training data consisted of:

• n4 bias correction,

• denoising,

• brain extraction, and

• affine registration to MNI. The input T1 should undergo the same steps. If the input T1 is the raw T1, these steps can be performed by the internal preprocessing, i.e. set doPreprocessing = TRUE

Value

list consisting of the segmentation image and probability images for each label.

Author(s)

Tustison NJ

Examples

## Not run: 
library( ANTsRNet )
library( keras )

image <- antsImageRead( "t1.nii.gz" )
results <- desikanKillianyTourvilleLabeling( image )

## End(Not run)

ANTsX/ANTsRNet documentation built on April 28, 2024, 12:16 p.m.