BIDSconvertR
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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
Features
continuous application
lazy processing of already existing files
easy application during data collection in ongoing studies
user-friendliness (minimial 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
Note
Only the metadata contained within the BIDS folder is free of potentially identifiable information. Follow the legal terms when sharing your dataset and consider additional defacing, pseudonymization, or both.
Milestones / To-Do’s
publish the BIDSconvertR
testing the tool on MAC systems
create Docker container
move image viewer into separate package
adapt code to CRAN requirements