made (CBRAIN Tool Config ID: 7856)
Container: docker://dcanumn/hbcd-made:1.5.2
Documentation: https://hbcd-made.readthedocs.io/en/latest/#
Boutiques Descriptor: https://portal.cbrain.mcgill.ca/tool_configs/7856/boutiques_descriptor.json
name: MADE_EEG_Pipeline
description: The Maryland Analysis of Developmental EEG (MADE) Pipeline is an EEG pipeline that (in this form) takes a BIDS-EEG directory structure with ‘*.set’ files as input.
External Requirements
These are file-based requirements, external to the pipeline, that must be satisfied for processing to occur. The “Argument IDs” field corresponds to input “id”s within the tool Boutiques Descriptor. “Value”s correspond to either specific configuration files (if there is a numeric value), or otherwise broader file types within CBRAIN (if the entry is text-based).
Argument ID |
Flag |
Value |
Description |
|---|---|---|---|
SubjectDirectory |
n/a |
BidsSubject |
The study-wide BIDS directory. In CBRAIN this is also referred to (and used) as the subject directory since a new BIDS dir will be made for the selected subject prior to processing. |
JSONSettings |
n/a |
The json file with settings to configure processing |
Other Processing Settings
These additional settings cover everything outside of files that are used as inputs during processing. The settings cover numeric values, flags, outputs directories, and other settings that are used to configure processing.
Argument ID |
Flag |
Value |
Description |
|---|---|---|---|
MADEOutputDirectoryName |
n/a |
qwerty |
The name of the output directory to store outcomes of preprocessing and reports. When processing is ran via CBRAIN only subject-specific files/folders will be saved, so the naming of the output folder will not influence the final naming/destination of files/folders. |
derivatives_prefix |
n/a |
Folders to put before the pipeline specific folder. By default this will look like DataProvider/derivatives/PipelineName, where pipeline name is specific to the current pipeline. The provided string must end in / |
Pipeline Outputs
Following processing, a number of files and folders are identified as outputs that should be saved for future reference. In the following table the ‘Path Relative to Working Directory’ column specifies the location of files that should be saved (with ‘*’ denoting wildcards). The output location for these files in the final ‘DataProvider’ is specified in the ‘Path in Output Data Provider’ column. In the case of HBCD the [DERIVATIVES_PREFIX] entry is empty.
ID |
Path Relative to Working Directory |
Path in Output DataProvider |
Description |
|---|---|---|---|
OutputDirectory |
[MADEOutputDirectoryName]/[SubjectDirectory] |
[DERIVATIVES_PREFIX]made |
This is the directory where the overall outputs are to be stored. |
Command Line Template
The following code-snippet highlights how the tool is referenced on the command-line. The code being displayed is executed within the tool’s container. Some of the directives may describe file manipulations to prepare for processing, and other directives will describe the primary processing command. At the time of processing, the text in brackets will be replaced by text that has been provided to configure processing.
true [DERIVATIVES_PREFIX]; made [SubjectDirectory] [MADEOutputDirectoryName] participant [JSONSettings] [ParticipantLabel] [SessionLabel] [FileExtension] [SkipInterim]
File Selection For Processing
The first step of selecting a candidate for processing is determining whether the right files are present. In HBCD processing, pipelines are always run on one session worth of data at a time. With that in mind, we (mostly) query the contents of a subject’s session folder to determine if processing should occur and also which files should be included in processing. For every pipeline there will be at least one requirement group that determines what files are needed for processing to occur. Within a requirement group, there may be criteria that address multiple file (or modality) types, which are known as ‘File Groups’. For processing to occur, the minumum number of files surviving all Included/Excluded terms for a given ‘File Group’ must be satisfied.
To allow for more flexible selection of files for processing, there are often multiple ‘Requirement Groups’. The contents of each ‘File Group’ across ‘Requirement Groups’ must be the same, but which ‘File Groups’ are defined can be different. If multiple ‘Requirement Groups’ are present for the current pipeline, there will be multiple tables in this section. Only one ‘Requirement Group’ needs to be satisfied for processing to occur. If one requirement group is satisfied, then files from all ‘File Groups’ will be included in processing.
Beyond the files that are chosen from this procedure, other associated files defined via the table here will also be included in processing.
Requirement Group: made
File Group |
How Many To Keep |
Term |
Included (True)/Excluded (False) |
|---|---|---|---|
eeg |
All |
acq-eeg |
True |
scans.tsv |
All |
scans.tsv |
True |