The BIDSconvertR

The BIDSconvertR R-package converts MRI DICOM data into BIDS-specification.

Note

We welcome feedback on usability or new features for the BIDSconvertR, which is still in development.

Aim

The goal of BIDSconvertR is to provide a workflow that can:

  • open the BIDS conversion to both beginner and advanced R-users

  • convert DICOM to NIfTI data using dcm2niix (REF)

  • structure this data according to the BIDS specification (REF)

  • validate the manually entered sequence-ID’s by color-coding

  • enable easy access to the BIDS-Validator (Website/Docker) (REF)

  • provide the papayaWidget viewer (REF) for inspecting images

  • enable continuous application during data acquisition in ongoing studies

Features

  • Renaming of unclean subject-ID’s or session-ID’s.
    • This requires a fundamental understanding of strings and regular expressions in R

  • Color coding is used to validate manually entered sequence-ID’s.

When new files or sequences are added, the’sequence mapper’ determines whether they are new. Then it reopens until everything is declared in accordance with BIDS. Files that have already been processed are bypassed.

Technical requirements

  • Supported and tested on Microsoft 10 and Ubuntu 22.04.

  • Not tested on MacOS, but it should work. You could try it out and let me know if there are any problems.

What the user needs to know to apply the BIDSconvertR

Important

What it isn’t:

A fully automated workflow that takes care of everything. You must have a basic understanding of files, folders, and DICOMS, as described below.

  • What exactly is a folder or file? What happened to my data?

  • What is a DICOM-containing folder?

  • What is the difference between a subject- and sequence-ID?

  • What exactly is BIDS?

  • Is my sequence name a valid BIDS sequence name?

So, if you can manually rename and restructure the folders according to BIDS, you can run the tool to scale things up.

Introduction:

Tutorial: