Deprecated: Please use pl-N4BiasFieldCorrection

https://github.com/FNNDSC/pl-N4BiasFieldCorrection

N4 Bias Field Correction

ChRIS ds plugin wrapper around ANTsPy N4BiasFieldCorrection.

N4 is a variant of the popular N3 (nonparameteric nonuniform normalization) retrospective bias correction algorithm.

Usage

Easiest way to run is using singularity.

mkdir in out
cp 1.nii 2.nii 3.nii in/
singularity exec docker://fnndsc/pl-ants_n4biasfieldcorrection:0.2.7.1 bfc in/ out/

Multithreading is used to parallelize on inputs. CPU usage can be limited using a container engine like docker or podman.

docker run --rm -u $(id -u):$(id -g) --userns=host     \
    --cpuset-cpus 0-4                                  \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw   \
    fnndsc/pl-ants_n4biasfieldcorrection:0.2.7.1 bfc   \
    /incoming /outgoing