# d2b-dcm2niix
Dcm2niix plugin for the d2b package
[](https://pypi.org/project/d2b-dcm2niix/)
## Installation
```bash
pip install d2b-dcm2niix
```
## Usage
After installation the `d2b run` command should have additional `dcm2niix`-specific flags:
```text
$ 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 the `d2b run` command if none of the dcm2niix flags are set)
- `--dcm2niix`: This will try to run `dcm2niix` on (copies of) each of the input directories prior to proceeding with BIDS-ification. **NOTE:** If any NIfTI files are found from a previous `d2b run --dcm2niix ...` run, then dcm2niix will not be invoked on that (copy of that) specific input directory.
- `--force-dcm2niix`: This will run `dcm2niix` on (copies of) each of the input directories _always_, regardless of files from previous `d2b run` runs.
Also, there should be a new subcommand `d2b dcm2niix` available:
```text
$ 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).
