tree extract

Usage

Run using mc_script tree extract after installation or using ~ndcn0236/bin/mc_script tree extract on jalapeno.

Import in python using from mcutils.scripts.tree import extract

Documentation

Extract filenames from a FileTree

All matching, existing files and directories are returned. The -I,–ignore flag can be used to find for which runs the pipeline crashed, for example: mc_script tree extract T1w -I T1w_bet will give you all the files for which the T1w file exists, but the corresponding T1w_bet file does not.

Functions

CLI interface

add_to_parser([parser])	Creates the parser of the command line arguments
run_from_args(args)	Runs the script based on a Namespace containing the command line arguments