A script, relying on libBIDS.sh which converts NIFTI images in a BIDS dataset to MINC, and inserts JSON metadata into the header of each MINC file according to the inheritance principles in BIDS.
MINC files are generated as a BIDS derivatives dataset, with the same directory structure and filenames as the orignal NIFTI files.
bids2mnc uses libBIDS.sh for loading and manipulating the BIDS dataset structure, and jq for manipulating JSON metadata inside BIDS.
Conversion is achieved with nii2mnc, available in minc-tools, available as
packages in many major Linux distributions, or otherwise available in the mega package
minc-toolkit and
minc-toolkit-v2
$ git clone --recursive https://github.com/CoBrALab/bids2mnc.git # Recursive needed to pull in libBIDS.sh dependency
$ cd bids2mnc
$ ./bids2mnc.sh /path/to/bids/dataset$ bids2mnc.sh
A tool to generate metadata-rich MINC files from a BIDS dataset
Usage: ./bids2minc.sh [-h|--help] [-r|--row-filter <arg>] [--(no-)clobber] [--(no-)debug] [--(no-)dry-run] <bids_path>
<bids_path>: Path to BIDS dataset
-h, --help: Prints help
-r, --row-filter: Filter BIDS files for conversion using regex on row content format <column_name>:<regex_pattern> (empty by default)
--clobber, --no-clobber: Overwrite existing files (off by default)
--debug, --no-debug: Debug mode, print all commands to stdout (off by default)
--dry-run, --no-dry-run: Dry run, don't run any commands, implies debug (off by default)