ANTs

Eigenanatomy

Functional MRI

Background

Brainomics

lungomics, cardiomics ...

Registration

Cortical Thickness

Atropos + N4

N4

Atropos

antsAtroposN4.sh iterates between N4 <-> Atropos to improve segmentation results.

Usage:

antsAtroposN4.sh -d imageDimension

-a inputImage

-x maskImage

-m n4AtroposIterations

-n atroposIterations

-c numberOfClasses

-l posteriorLabelForN4Mask

-o outputPrefix

<OPTARGS>

Example:

bash /Users/ntustison/Pkg/ANTs/bin/bin/antsAtroposN4.sh -d 3 -i t1.nii.gz -x mask.nii.gz -l segmentationTemplate.nii.gz -p segmentationPriors%d.nii.gz -o output

Required arguments:

-d: image dimension 2 or 3 (for 2- or 3-dimensional image)

-a: input image Anatomical image, typically T1. If more than one anatomical image

is specified, subsequently specified images are used during the

segmentation process.

-x: mask image Mask defining the region of interest.

-m: max. N4 <-> Atropos iterations Maximum number of (outer loop) iterations between N4 <-> Atropos.

-n: max. Atropos iterations Maximum number of (inner loop) iterations in Atropos.

-c: number of segmentation classes Number of classes defining the segmentation

-l: posterior label for N4 weight mask Which posterior probability image should be used to define the

N4 weight mask. Can also specify multiple posteriors in which

case the chosen posteriors are added.

-o: output prefix The following images are created:

* /Users/ntustison/Desktop//tmp2517//tmpN4Corrected.nii.gz

* /Users/ntustison/Desktop//tmp2517//tmpSegmentation.nii.gz

* /Users/ntustison/Desktop//tmp2517//tmpSegmentationPosteriors.nii.gz

Optional arguments:

-p: segmentation priors Prior probability images initializing the segmentation.

Specified using c-style formatting, e.g. -p labelsPriors%02d.nii.gz.

-r: mrf Specifies MRF prior (of the form '[weight,neighborhood]', e.g.

'[0.1,1x1x1]' which is default).

-s: image file suffix Any of the standard ITK IO formats e.g. nrrd, nii.gz (default), mhd

-k: keep temporary files Keep temporary files on disk (default = false).

-w: Atropos prior segmentation weight Atropos spatial prior probability weight for the segmentation (default = 0)

http://www.ncbi.nlm.nih.gov/pubmed/20378467

Segmentation

Pure tissue

weight mask

We minimize the contribution of

partial voluming in estimating the

bias field.

Bias Correction

Advanced Normalization Tools