cookpa/antsxbratsreg22singularity

Containerized implementation of

ANTsXBratsReg22Singularity

Containerized implementation of the ANTsX BrATS-Reg22 entry.

See

https://github.com/satrajitgithub/BraTS_Reg_submission_instructions/blob/master/BraTS_Reg_instructions_singularity.md

for details of the run script.

The container defaults to using 8 threads in the registration; this may be changed to N threads with --env ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=N.

ANTs methodology

The registrations are performed using the algorithm here

https://github.com/ntustison/BraTS-Reg22#apply-antsregistrationsyns2-with-t1-contrast-enhanced-to-validation-data

using the t1ce images as input.

Reproducible results

There is run-to-run variability as a result of random sampling, and precision errors in the ITK Mattes Mutual Information filter.

Random sampling can be disabled with a fixed random seed X by setting the evironment variable ANTS_RANDOM_SEED=X. To make the registration fully deterministic, set the random seed and also ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1.

Container image

The container image is available at

https://cloud.sylabs.io/library/cookpa/brats_reg/brats_reg_antsx