Convert source DICOM, PAR REC or NIFTI image data to BIDS directory layout.
The YAML configuration file used as input dictates the search terms used to find and rename files. Please see config/config.default.yml or config/config.example.yml for examples.
Requires dcm2niix and pydicom.
usage: study_proc [-h] [-s STUDY_DIR] [-o OUT_DIR] [-c CONFIG.yml] [--no-gzip]
[--compress INT] [--zero-pad INT] [--append-dwi-info]
[--verbose] [--version] [--path-env PATH_VAR]
Convert source data of a study's imaging data to BIDS NIFTI data.
optional arguments:
-h, --help show this help message and exit
Required Argument(s):
-s STUDY_DIR, -study STUDY_DIR, --study-dir STUDY_DIR
Parent study image directory for all subjects.
-o OUT_DIR, -out OUT_DIR, --out-dir OUT_DIR
Output directory.
Optional Argument(s):
-c CONFIG.yml, -config CONFIG.yml, --config-file CONFIG.yml
Input YAML configuration file. If no configuration
file is provided, then the default configuration file
is used.
--no-gzip DO NOT gzip the resulting BIDS NIFTI files [default:
False].
--compress INT Compression level [1 - 9] - 1 is fastest, 9 is
smallest [default: 6].
--zero-pad INT The amount of zeropadding to pad the run numbers of
the BIDS NIFTI files (e.g. '--zero-pad=2' corresponds
to '01') [default: 2].
--append-dwi-info RECOMMENDED: Appends DWI acquisition information
(unique non-zero b-values, and TE, in msec.) to BIDS
acquisition filename of diffusion weighted image files
[default: False].
--verbose Enables verbose output to the command line.
--version Prints the version of 'convert_source', then exits.
Expert Option(s):
--path-env PATH_VAR Environmental path variable or variables for
dependencies (e.g. the path to 'dcm2niix'). NOTE: This
option is repeatable, and can thus be specified
multiple times.