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The code is documented at https://bidsconvertr.github.io. Please visit the documentation for a detailed description of the BIDSconvertR

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
• validate the compatibility with BIDS with the BIDS validator
• visualize the images with papayaViewer and papayaWidget

• continuous application
  • lazy processing of already existing files
  • easy application during data collection in ongoing studies
• user-friendliness (minimal 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

Wulms N, Eppe S, Dehghan‑Nayyeri M, Streeter A, Bonberg N, Berger K, Sundermann B, Minnerup H. (2023). The R package for DICOM to brain imaging data structure conversion Nature Scientific Data. 2023 Oct 04. doi: 10.1038/s41597‑023‑ 02583‑4 https://doi.org/10.1038/s41597-023-02583-4

Wulms, Niklas. 2023. BIDSconvertR. Zenodo. https://doi.org/10.5281/ZENODO.5878407.