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 (https://github.com/rordenlab/dcm2niix)

• structure this data according to the BIDS specification (https://bids-specification.readthedocs.io/en/stable/)

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

• enable easy access to the BIDS-Validator (Website/Docker) (https://bids-standard.github.io/bids-validator/)

• provide the papayaWidget viewer (https://github.com/muschellij2/papayaWidget) for inspecting images

• enable continuous application during data acquisition in ongoing studies

Features

• Creation of a ‘user_settings’ file that

  • stores all settings and

  • can be used to relaunch the conversion in case of new acquired data in ongoing studies

• Optional renaming of subject-ID’s or session-ID’s

  • Extraction of the subject-ID’s

  • Removal of redundant strings

• Conversion with DCM2NIIX (Chris Rorden)

  • Anonymization of metadata for the BIDS Folder

  • Extraction of metadata with potentially identifying information that is stored in a separate folder

• Shiny-App for BIDS sequence editing

  • Color-coded BIDS validation for manually entered sequence-ID’s

  • Selection of ‘relevant’ sequences for the BIDS folder

• Automatic start of BIDS-Validator

  • in Docker if it is installed or

  • on the BIDS-Validator homepage

• Shiny-App for navigating through the BIDS folder

  • image viewing and visual quality control

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?

• How to create valid BIDS sequence names?

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

Overview:

• BIDSconvertR
• Workflow visualization
• Citation

Installation:

• Install R, dependencies and RStudio
• Install the BIDSconvertR
• Requirements

Tutorial:

• The installation procedure
• The BIDSconvertR workflow

Workflow (Detailed):

• Starting the workflow
• Creation of ‘user settings’ file.

Workflow (optional file cleaning):

• Advanced features

Workflow (rest):

• dcm2niix conversion
• GUI: The sequence mapper
• BIDS validation
• GUI: BIDS viewer

Additional information:

• What is in my ‘user_settings.R’ file?
• dcm2niix customisation
• Table of functions
• Table of diagnostic files