hbcd_motion (CBRAIN Tool Config ID: 7604)

Container: docker://inclab/hbcd_motion_postproc:1.0.0
Documentation: https://hbcd-motion-postproc.readthedocs.io/en/latest/index.html
Boutiques Descriptor: https://portal.cbrain.mcgill.ca/tool_configs/7604/boutiques_descriptor.json
name: hbcd_motion
description: A tool to run analyses on BIDS formatted inertial measurement unit data.

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
subject_dir	n/a	BidsSubject	Subject folder for BIDS (folders name should be sub-XXXXX).

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
postproc_output_dir	n/a	qwerty	The name of the output folder. 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.
stop_on_error	–stop_on_error	True	Try to return a non-zero exit status when an error occurs.
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
output_dir	[POSTRPOC_OUTPUT_DIR]/[SUBJECT_DIR]	[DERIVATIVES_PREFIX]hbcd_motion	This is the output containing the subject directory.

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]; axivity_postproc [SUBJECT_DIR] [POSTRPOC_OUTPUT_DIR] participant [SESSION_ID] [INTERVAL] [PA_MEASURE] [PA_SIDE] [ENTROPY_TYPE] [ENTROPY_MEASURE] [STOP_ON_ERROR]

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: hbcd_motion

File Group	How Many To Keep	Term	Included (True)/Excluded (False)
LeftCalibration	All	acq-calibration	True
		motion.tsv	True
		task-LeftLegMovement	True
RightCalibration	All	acq-calibration	True
		motion.tsv	True
		task-RightLegMovement	True
LeftPrimary	All	acq-primary	True
		motion.tsv	True
		task-LeftLegMovement	True
RightPrimary	All	acq-primary	True
		motion.tsv	True
		task-RightLegMovement	True
scans.tsv	All	scans.tsv	True
sessions.tsv	All	sessions.tsv	True