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.