replace NIH HPC module load commands

nimh-dsst / dsst-defacing-pipeline

Defacing algorithm to improve and evaluate accuracy for large datasets.

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replace NIH HPC module load commands #15

Closed Arshitha closed 1 year ago

Arshitha commented 2 years ago

The deface.py and register.py scripts use module load commands to run afni and FSL commands. As a way of generalizing these scripts, these can be replaced by function that looks for AFNI and FSL environment variables within the user's current environment.

Arshitha commented 1 year ago

Containerizing the pipeline would ensure that afni and fsl availability. However, this package has been primarily developed and tested on NIH HPC, and advertised as such.