Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging. ANTs extracts information from complex datasets that include imaging (Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute.

ANTs development is led by Brian Avants and supported by other researchers and developers at PICSL and other institutions.

• ANTs website

• Module Name: ANTs (see the modules page for more information)
• Some of the ANTs scripts and executables are multi-threaded. Several of them use the variable ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS to se the number of threads.
• Example files in $ANTS_TESTDATA (this variable is set when you load the module)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=5g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ cd /data/$USER/myruns

[user@cn3144 ~]$ module load ANTs

[user@cn3144 ~]$ cp -pr $ANTS_TESTDATA .

[user@cn3144 ~]$ cd TESTDATA/stnava-asymmetry-f8ecc74 

[user@cn3144 ~]$ ./asymmetry.sh -d 2 -a 0 -f data/symm_t.nii.gz -m data/asymm_s.nii.gz -o XXXX
inputs: data/symm_t.nii.gz data/asymm_s.nii.gz XXXX 2
 CenterOfMass [133.032, 163.98]
Using double precision for computations.
Input scalar image: data/asymm_s.nii.gz
Reference image: data/asymm_s.nii.gz
[...]
 1DIAGNOSTIC,    30, 2.079582101904e-04, -4.725553011784e-04, 2.0881e+01, 5.1356e-01,
  Elapsed time (stage 0): 2.0949e+01


Total elapsed time: 2.0950e+01

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. myANTs.sh). For example:

#!/bin/bash
#
# this file is called myANTs.sh
#
module load ANTs
cd /data/$USER/mydir
cp -pr $ANTS_TESTDATA .
cd TESTDATA/stnava-asymmetry-f8ecc74
./asymmetry.sh -d 2 -a 0 -f data/symm_t.nii.gz -m data/asymm_s.nii.gz -o XXXX

Submit this job using the Slurm sbatch command.

sbatch myANTs.sh

The command above will allocate 2 CPUs and 4 GB of memory to the job, which is sufficient for this test.

Some of the ANTs scripts and executables are multi-threaded. Several of them use the variable ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS to set the number of threads. For these ANTs programs, you can add the following line in your batch script:

export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$SLURM_CPUS_PER_TASK

sbatch --cpus-per-task=8 myANTs.sh

Other ANTs programs allow for explicit setting of the number of threads. For example, the following ANTs scripts have a '-n' option to set the number of threads:

antsRegistrationSpaceTime.sh
antsRegistrationSyNQuick.sh
antsRegistrationSyN.sh

Your job may require more than 4 GB of memory, so you may need to specify the memory when submitting. e.g.

$ sbatch --mem=5g myjob.bat

Create a swarmfile (e.g. ANTs.swarm). For example:

cd /path/to/mydir; ./asymmetry.sh -d 2 -a 0 -f data/sym.nii.1.gz -m data/asym.nii.1.gz -o out1
cd /path/to/mydir; ./asymmetry.sh -d 2 -a 0 -f data/sym.nii.2.gz -m data/asym.nii.2.gz -o out2
cd /path/to/mydir; ./asymmetry.sh -d 2 -a 0 -f data/sym.nii.3.gz -m data/asym.nii.3.gz -o out3
[...]   

Submit this job using the swarm command.

swarm -f ANTs.swarm [-g #] [-t #] --module TEMPLATE