BIDSconvertR

DOI BIDS Github License: GPL v3

BIDSconvertR logo

The hexagonal sticker was made using the iconspackage and based on the MRI svg graphics provided by Flaticon and mavadee FlaticonLink.

Aim

BIDSconvertR aims to provide a workflow that can:

  • do the task inside of the R environment

  • convert DICOM data to NIfTI (with the awesome dcm2niix

  • structure this data according to the BIDS specification

Features

  • continuous application

    • lazy processing of already existing files

    • easy application during data collection in ongoing studies

  • user-friendliness (minimial terminal interaction required)

    • user dialog with message boxes guiding the users through the workflow

    • Shiny App (GUI) for sequence editing and data inspection

  • file cleaning

    • Renaming of subject-IDs or session-IDs with regular expressions.

    • Renaming of session-IDs

  • BIDS validation

    • verification (color-coded) of sequence-IDs (comparing the entered sequence-IDs to regular expressions according to BIDS)

    • implemented validation with BIDS-Validator (Website/Docker)

  • quality control

    • user-friendly (papayaWidget image viewer) for BIDS datasets

  • pseudonymized BIDS output (only metadata)

    • all potentially identifiable metadata was removed from images and JSONs

Note

Only the metadata contained within the BIDS folder is free of potentially identifiable information. Follow the legal terms when sharing your dataset and consider additional defacing, pseudonymization, or both.

Milestones / To-Do’s

  • publish the BIDSconvertR

  • testing the tool on MAC systems

  • create Docker container

  • move image viewer into separate package

  • adapt code to CRAN requirements