Attention

The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.

ANTs

The ANTs framework provides open-source functionality for deformable image registration with small or large deformations. ANTs includes N4 bias correction, additional evaluation of multiple modalities and organ systems, univariate or multivariate image segmentation, tighter integration with the Insight ToolKit, a well evaluated cortical thickness pipeline and visualization tools and integration with R. ANTs serves as both a core library for further algorithm development and also as a command-line application-oriented toolkit. ANTs also has a permissive software license that allows it to be employed freely by industry. ANTs enables diffeomorphic normalization with a variety of transformation models, optimal template construction, multiple types of diffeomorphisms, multivariate similarity metrics, diffusion tensor processing and warping, image segmentation with and with-out priors and measurement of cortical thickness from probabilistic segmentations. The normalization tools, alone, provide a near limitless range of functionality and allow the user to develop customized objective functions.

Usage

ANTs can be activated using the module file:

module load apps/ANTs/2.1.0-a/gcc-4.9.4

Note: this ANTs version is 783 commits ahead of Release 2.1.0 (Commit 646459b build), which we have named Version 2.1.0-a

Test

  1. Download and unpack the following brain image data using:

    cd some_directory
wget https://github.com/stnava/BasicBrainMapping/tarball/master/stnava-BasicBrainMapping-e157693.tar.gz
tar zxvf stnava-BasicBrainMapping-e157693.tar.gz
cd stnava-BasicBrainMapping-e157693

  2. Create a batch job submission script called test.sge containing:

    #!/bin/bash
#$ -pe smp 2
#$ -l rmem=8G
#$ -o Ants.out
#$ -e Ants.err
#$ -m eba -M a.person@sheffield.ac.uk
export OMP_NUM_THREADS=$NSLOTS
module load apps/ANTs
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2  # controls multi-threading

dim=3 # image dimensionality
nm=BBM_Lesion

MultiplyImages 3 ./data/IXI594-Guys-1089-T1.nii.gz data/neg_lesion.nii.gz  data/T1_lesioned.nii.gz

antsRegistrationSyNQuick.sh -n 2 -d 3 -f data/IXI/T_template2.nii.gz -m data/T1_lesioned.nii.gz -t s -o ${nm}_diff -x data/neg_lesion.nii.gz

rm grid.nii.gz jacobian.nii.gz

CreateJacobianDeterminantImage 3 ${nm}_diff1Warp.nii.gz jacobian.nii.gz 1

CreateWarpedGridImage 3 ${nm}_diff1Warp.nii.gz grid.nii.gz 1x0x1 10x10x10 3x3x3

  3. Submit the job using qsub test.sge

The registered image/s can be viewed using ITK-SNAP.

Installation notes

ANTs was compiled using the install_ANTs.sh script, the module file is gcc-4.9.4.