Converts and organises source MR image data-sets in accordance with the Brain Imaging Data Structure (BIDS)
Project description
convert_source
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.
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