Usage

fw-heudiconv can be run either from the command line, or on Flywheel as a gear. See below for command line instructions.

Tabulate

Tabulate DICOM header info from a project on Flywheel

usage: fw-heudiconv-tabulate [-h] --project PROJECT [--path PATH]
                             [--subject SUBJECT [SUBJECT ...]]
                             [--session SESSION [SESSION ...]] [--verbose]
                             [--dry-run] [--unique | --no-unique]
                             [--api-key API_KEY]

Named Arguments

--project	The project in flywheel
--path	Path to download .tsv file Default: “.”
--subject	The subject label(s)
--session	The session label(s)
--verbose	Print ongoing messages of progress Default: False
--dry-run	Don’t apply changes Default: False
--unique	Default: False
--no-unique	Default: True
--api-key	API Key

Curate

Use a heudiconv heuristic to curate data into BIDS on flywheel

usage: fw-heudiconv-curate [-h] --project PROJECT --heuristic HEURISTIC
                           [--subject SUBJECT [SUBJECT ...]]
                           [--session SESSION [SESSION ...]] [--verbose]
                           [--dry-run] [--api-key API_KEY]

Named Arguments

--project	The project in flywheel
--heuristic	Path to a heudiconv-style heuristic file
--subject	The subject label(s)
--session	The session label(s)
--verbose	Print ongoing messages of progress Default: False
--dry-run	Don’t apply changes Default: False
--api-key	API Key

Export

Export BIDS-curated data from Flywheel

usage: fw-heudiconv-export [-h] --project PROJECT [--path PATH]
                           [--subject SUBJECT [SUBJECT ...]]
                           [--session SESSION [SESSION ...]]
                           [--folders FOLDERS [FOLDERS ...]]
                           [--attachments ATTACHMENTS [ATTACHMENTS ...]]
                           [--dry-run] [--destination DESTINATION]
                           [--directory-name DIRECTORY_NAME]
                           [--api-key API_KEY] [--verbose]

Named Arguments

--project	The project in flywheel
--path	The target directory to download [DEPRECATED. PLEASE USE <DESTINATION> INSTEAD]
--subject	The subject(s) to export
--session	The session(s) to export
--folders	The BIDS folders to export Default: [‘anat’, ‘dwi’, ‘fmap’, ‘func’, ‘perf’]
--attachments	Only download attachment files matching these names
--dry-run	Don’t apply changes (only print the directory tree to the console) Default: False
--destination	Path to destination directory Default: “.”
--directory-name
	Name of destination directory Default: “bids_directory”
--api-key	API Key
--verbose	Print ongoing messages of progress Default: False

Validate

Validate BIDS-curated data on Flywheel. A simple wrapper around the original BIDS Validator https://github.com/bids-standard/bids-validator

usage: fw-heudiconv-validate [-h] [--directory DIRECTORY]
                             [--project PROJECT [PROJECT ...]]
                             [--subject SUBJECT [SUBJECT ...]]
                             [--session SESSION [SESSION ...]] [--verbose]
                             [--tabulate TABULATE] [--api-key API_KEY]

Named Arguments

--directory	Temp space used for validation Default: “.”
--project	The project on Flywheel
--subject	The subject(s) on Flywheel to validate
--session	The session(s) on Flywheel to validate
--verbose	Pass on <VERBOSE> flag to bids-validator Default: False
--tabulate	Directory to save tabulation of errors Default: “.”
--api-key	API Key

Clear

Go nuclear: clear BIDS data from Flywheel

usage: fw-heudiconv-clear [-h] --project PROJECT [PROJECT ...]
                          [--subject SUBJECT [SUBJECT ...]]
                          [--session SESSION [SESSION ...]] [--verbose]
                          [--dry-run] [--api-key API_KEY]

Named Arguments

--project	The project in flywheel
--subject	The subject label(s)
--session	The session label(s)
--verbose	Print ongoing messages of progress Default: False
--dry-run	Don’t apply changes Default: False
--api-key	API Key

flaudit

flaudit runs as a gear on Flywheel. See the Quick Start guide for usage.