d2b-dcm2niix
Dcm2niix plugin for the d2b package
Installation
pip install d2b-dcm2niixUsage
After installation the d2b run command should have additional dcm2niix-specific flags:
$ d2b run --help
usage: d2b run [-h] -c CONFIG_FILE -p PARTICIPANT -o OUT_DIR [-s SESSION] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--no-dcm2niix | --dcm2niix | --force-dcm2niix] in_dir [in_dir ...]
Organize data in the BIDS format
positional arguments:
in_dir Directory(ies) containing files to organize
required arguments:
-c CONFIG_FILE, --config CONFIG_FILE
JSON configuration file (see example/config.json)
-p PARTICIPANT, --participant PARTICIPANT
Participant ID
-o OUT_DIR, --out-dir OUT_DIR
Output BIDS directory
--no-dcm2niix Don't run dcm2niix on the input directories. (This is the default)
--dcm2niix Run dcm2niix on each of the input directories before organization code executes. dcm2niix execution will be skipped for directories for which converted results from a previous run are found.
--force-dcm2niix Run dcm2niix on each of the input directories before organization code executes. Previous dcm2niix results will be overwritten
optional arguments:
-s SESSION, --session SESSION
Session ID
-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set logging level
Specifically, the following new (mutually exclusive) options are available:
-
--no-dcm2niix: This is the default behaviour (i.e. the behaviour of thed2b runcommand if none of the dcm2niix flags are set) -
--dcm2niix: This will try to rundcm2niixon (copies of) each of the input directories prior to proceeding with BIDS-ification. NOTE: If any NIfTI files are found from a previousd2b run --dcm2niix ...run, then dcm2niix will not be invoked on that (copy of that) specific input directory. -
--force-dcm2niix: This will rundcm2niixon (copies of) each of the input directories always, regardless of files from previousd2b runruns.
Also, there should be a new subcommand d2b dcm2niix available:
$ d2b dcm2niix --help
usage: d2b dcm2niix [-h] in_dir [in_dir ...] out_dir
Run dcm2niix with the options used by d2b
positional arguments:
in_dir DICOM directory(ies)
out_dir Output BIDS directory
optional arguments:
-h, --help show this help message and exit
This command is the equivalent of dcm2bids's dcm2bids_helper command. In particular it's serves as a way to run dcm2niix in the exact same way that d2b run --[force-]dcm2niix would run the command (i.e. potentially useful to see what the resulting sidecars/filenames would look like).
