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Directories and Structure

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Tyler K. Collins edited this page Oct 30, 2019 · 3 revisions

derivatives/BIDS-Lossless-EEG

Directory Explanation
code Contains all necessary scripts and configuration files required to run the lossless pipeline. See section following the log section.
log Contains useful debugging information and necessary intermediate pipeline files. See below section for more details.
sub-* Subject folders containing the final output of the pipeline.

derivatives/BIDS-Lossless-EEG/log

Log is automatically populated with scripts when you execute the pipeline. Folders are generated for every script identified by the script that was run followed by the date and time of the scripts execution. These folders contain:

  • A specific .m file for each subject data file.
  • A specific .err file for each subject if an error occurred.
  • A specific .log file for each subject that records the remote system command window.
  • A single .sh submit script that contains the job commands that were sent to the remote servers. (Remote Jobs Only)

Note: When debugging errors, this is the most important folder as you can see what is happening by using these four files.

derivatives/BIDS-Lossless-EEG/code

This folder contains the body of the pipeline and houses all scripts and configurations.

Directory Explanation
config This folder contains all of the configuration files and remote initialization files that are needed for the EEGLAB plugins. Configuration files will have a .cfg or .txt extension. The naming of each configuration file should mirror the script that it goes with.
dependencies Contains packages that the pipeline is dependent on. All folders within should be their own git repository, with their own documentation.
misc Miscellaneous support pieces such Amica parameter files, EEG montage files, and event renaming files are stored here.
scripts Folder containing all of the script files that make up processes behind the pipeline. These have the extension .htb and are called History Template Batch as they are executed in the batch_context extensions.
tools Various script files to be used as in-house optimizers, diagnostics, or cleanup scripts for remotes.

Note: Excluded files at this level are git repository specific and have no actual effect on the pipeline.

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