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BIDS converter

brkraw bids The usage of the command-line tool ‘brkraw’ for BIDS data organization.

  • Upgraded feature to reduce the burden on renaming and organizing according to BIDS guideline.
  • The fully organized data can be generated by creating and fill out a BIDS datasheet (MS Excel format) from the large set of raw Bruker data. Simply put all raw Bruker data (or zipped) into a folder and run ‘brkraw bids_helper’ command with <input dir> and your preferred <output filename>.
  • The JSON syntax template allows building a JSON metadata to meet the BIDS requirement for each converted image. The module provides this JSON syntax template according to BIDS v1.2.2 in case of adding the option ‘-j’ on the command.
  • The bids_convert command also will generate empty template of dataset_description.json and README to better fit with BIDS guideline, please make sure test your data with official BIDS validator

  • Below command shows how to generate BIDS datasheet with JSON syntax template
$ brkraw bids_helper <input dir> <output filename> -j
  • After updating the datasheet and syntax, the below command will generate a fully organized BIDS dataset to <output dir> with JSON header files for each converted image by parsing the parameters specified on <JSON syntax template.json>.
$ brkraw bids_convert <input dir> <BIDS datasheet.xlsx> -j <JSON syntax template.json> -o <output dir>
  • To learn more detail about building your own JSON syntax template, please check our example in Jupyter Notebooks