Quick start guide¶
fw-heudiconv at the Command Line¶
- Make sure you have the Flywheel CLI and SDK installed. Note that this is
- Download the package from pip with
pip install fw-heudiconv.
- Tabulate your DICOM header info with
fw-heudiconv-tabulate --project <MY_PROJECT> --path <OUTPUT_PATH>.
- Design your heuristic file in Python.
- Curate your dataset on Flywheel into BIDS:
fw-heudiconv-curate --project <MY_PROJECT> --heuristic <MY_HEURISTIC_FILE>. Use the flag
--dry_runto test your heuristic.
To export the dataset to your machine:
fw-heudiconv-export --project <MY_PROJECT> --path <OUTPUT_DIR>.
--subject <SUBJECT> and/or
--session <SESSION> flags to use the tool on specific subject/session labels.
fw-heudiconv as a Flywheel Gear¶
- Have the Flywheel Heudiconv gear installed on your Flywheel instance.
- Design your heuristic file in Python and upload it to your project.
- Run the Flywheel Heudiconv gear (accessible through Run Gear -> Analysis Gear), using your heuristic file as the input.
To list the sequence information for your dataset: In the “Gear Configuration” window, type “Tabulate” in the “Action” field, which will leave a sequence info table (.tsv) in the gear’s outputs.
To curate the dataset into BIDS: In the “Gear Configuration” window, type “Curate” in the “Action” field, which will curate the dataset for BIDS. Click the “dry run” button to test your heuristic first (the gear log will print out all the changes without applying them).
To export the dataset into BIDS for downloading to your machine: In the “Gear Configuration” window, type “Export” in the “Action” field, which will leave an exported BIDS dataset in the gear’s outputs. Click the “dry run” button to test your output first (the gear log will print out the expected directory structure of an export).
flaudit as a Flywheel Gear¶
- Have the flaudit gear installed on your Flywheel instance.
- Select a template subject – an ideal subject who you know has been curated correctly and has had all the required preprocessing gears run on them. Input this subject ID in the
Templatefield in the config.
- Hit Run!