Awesome
<!-- README.md is generated from README.Rmd. Please edit that file -->This is the legacy repository of BIDSconvertR. Please visit the new repository for LTS: BIDSconvertR
<a href='https://wulms.bidsconvertr.io'><img src="inst/figure/BIDSconvertR.png" align="right" height="150"/></a> The hexagonal sticker was made using the iconspackage and based on the MRI svg graphics provided by Flaticon and mavadee FlaticonLink. |
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