DICOM to NIfTI Converter (dcm2niix)¶
Library: dcm2niix | Docker Image: xnat/dcm2niix
Function¶
Converts DICOM medical images to NIfTI format with BIDS-compatible JSON sidecar files, preserving acquisition metadata.
Modality: DICOM image directory from any MRI acquisition.
Typical Use: First step in any neuroimaging pipeline: converting raw DICOM acquisitions to analysis-ready NIfTI.
Key Parameters¶
-o (output directory), -f (filename format), -z (compression: y/n/o/i), -b (BIDS sidecar: y/n/o)
Key Points¶
Generates BIDS-compatible JSON sidecars. Handles multi-echo, diffusion (bval/bvec), and Philips/Siemens/GE formats. Default filename format is %f_%p_%t_%s.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input_dir |
Directory |
Yes | Input DICOM directory | |
filename |
string |
No | Output filename format (default %f_%p_%t_%s) | -f |
compress |
enum |
No | Compression (y=pigz, o=optimal, i=internal, n=none, 3=save .nii and .gz) | -z |
merge |
enum |
No | Merge 2D slices (0=no, 1=yes, 2=auto) | -m |
single_file |
enum |
No | Single file mode for 4D (y/n) | -s |
bids |
enum |
No | BIDS sidecar (y=yes, n=no, o=only) | -b |
anonymize |
enum |
No | Anonymize BIDS sidecar (y/n) | -ba |
ignore_derived |
boolean |
No | Ignore derived/localizer/2D images | -i |
verbose |
enum |
No | Verbosity level (0=none, 1=some, 2=all) | -v |
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
nifti_files |
File[] |
*.nii.gz, *.nii |
json_sidecars |
File[] |
*.json |
bval_files |
File[] |
*.bval |
bvec_files |
File[] |
*.bvec |
log |
File |
dcm2niix.log |
Output Extensions¶
- nifti_files:
.nii,.nii.gz - json_sidecars:
.json - bval_files:
.bval - bvec_files:
.bvec
Docker Tags¶
Available versions: latest, 1.0.20240202
Categories¶
- Utilities > dcm2niix > Format Conversion