README.md

In wulms/bidsconvertr: Converts DICOM data to NIfTI and structure the NIfTI data in BIDS specification

This is the legacy repository of BIDSconvertR. Please visit the new repository for LTS: BIDSconvertR

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Documentation

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

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

Features

• 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

How to cite:

Wulms, Niklas. 2022. Wulms/Bidsconvertr. Zenodo. https://doi.org/10.5281/ZENODO.5878407.

Milestones / To-Do's

• publish the BIDSconvertR
• testing the tool on MAC systems

wulms/bidsconvertr documentation built on Sept. 17, 2023, 11:22 p.m.