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.