Paper revision features and functions

Added cosmetic improvements, documentation improvements, CircleCI testing, and a ZENODO release as required for paper revisions

0.2.0

Version 0.2.0: Reproin

In an effort to consolidate naming schema for different sequences across the University of Pennsylvania MRI researchers, fw-heudiconv now supports our own internal Reproin naming convention. The tool fw-heudiconv-reproin allows you to upload a list of scanner sequence names and check to see if they will be compliant with our internal conventions. If your sequence names are valid, then fw-heudiconv will be able to curate your data into BIDS without the need for you to write a heuristic yourself.

To do this:

On Flywheel:

1. Upload a text file (.txt) to your Flywheel project containing your proposed sequence names, one per line.
2. Select the Flywheel Heudiconv gear
3. In place of the heuristic input, select your text file.
4. In the Configuration section, select Reproin

At the command line:

1. Create a text file (.txt) of your proposed sequence names, one per line.
2. Run the command fw-heudiconv-reproin --protocol-names <PATH_TO_YOUR_FILE> --verbose

Once your proposed sequence names have passed the reproin check, you can curate and BIDS validate your data as normal.

Note: Reproin naming schema check is not the same as BIDS curation and validation; once your sequence names have passed this check, you can be sure that the automatic curation option will happen smoothly, and you will not be required to write your own heuristic. To do this, run fw-heudiconv-curate as normal but instead of supplying a heuristic file, use the flag --heuristic reproin_Upenn.

This release also features bug fixes and internal engineering improvements

0.1.0: Added:

Added:

• fw-heudiconv-meta for managing BIDS metadata (see BIDS spec)
  • Currently only handles Participants file and sessions files on Flywheel
  • Plan for all modality agnostic files to be handled by this feature
  • Currently fw-heudiconv-export has not implemented exporting these files yet
• fw-heudiconv-clear for clearing BIDS data
• fw-heudiconv-validate for validating BIDS datasets
• --unique vs --no-unique flag for fw-heudiconv-tabulate lets you download seqInfo data for all files
• All tools support input of API key at command line

Changed:

• Heuristics are flexible to sub-{subject} vs {subject} nomenclature
• Aesthetic/printing improvements/uniformity for all tools
• fw-heudiconv-export now supports creating & naming a directory to download in with --directory-name; otherwise use --destination to create a default named directory

Fixed:

• Numerous bugfixes including acquisition sorting issues and regex search NoneType errors

Deprecated:

• fw-heudiconv-export --path flag is now deprecated. Use --destination or --directory-name instead