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Use heudiconv heuristics for BIDS curation on flywheel

Project description

Heudiconv-Style BIDS curation for Flywheel

Quick Start Guide

As a command line tool:

  1. Make sure you have the Flywheel CLI and SDK installed. Note that this is flywheel-sdk and NOT flywheel.

  2. Download the package from pip with pip install fw-heudiconv, OR Clone or download this repository to your machine. Use the flag --dry_run=True to test your heuristic.

To curate a dataset on Flywheel into BIDS: fw-heudiconv-curate --project <MY_PROJECT> --heuristic <MY_HEURISTIC_FILE>

To export the dataset to your machine: fw-heudiconv-export --project <MY_PROJECT> --path <OUTPUT_DIR>

To list the sequence information for your dataset: fw-heudiconv-tabulate --project <MY_PROJECT> --path <OUTPUT_PATH>

On Flywheel:

  1. Have the Flywheel Heudiconv gear installed on your Flywheel instance.

  2. Design your heuristic file and upload it to your project.

  3. Run the Flywheel Heudiconv gear (accessible through Run Gear -> Analysis Gear), using your heuristic file as the input...

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).

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.


See the wiki for more detailed instructions!

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