Convert DICOM folders to NIfTI (and optional BIDS sidecars) using dcm2niix.
Usage
ni_dcm2niix_convert(
in_folder,
args = NULL,
compression_level = NULL,
adjacent = NULL,
bids_sidecar = NULL,
anon_bids = NULL,
bids_subject = NULL,
bids_session = NULL,
comment = NULL,
depth = NULL,
export_format = NULL,
filename = NULL,
ignore_derived = NULL,
lossless_scale = NULL,
merge_2d_slices = NULL,
series_crc = NULL,
out_dir = NULL,
philips_float = NULL,
search_only = NULL,
rename = NULL,
single_file = NULL,
verbose = NULL,
write_conflicts = NULL,
crop = NULL,
compression = NULL,
big_endian = NULL,
progress = NULL,
ignore_trigger_times = NULL,
terse = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_folder
Character; directory path. Folder with DICOM images to convert. Required.
- args
Character. Additional parameters to the command
- compression_level
Integer. Gzip compression level (1=fastest..9=smallest).
- adjacent
Character; one of: "n", "y". Assume adjacent DICOMs from a series are stored in the same folder (n/y).
- bids_sidecar
Character; one of: "y", "n", "o". BIDS sidecar mode (y/n/o; o=JSON only, no NIfTI).
- anon_bids
Character; one of: "y", "n". Anonymize BIDS sidecars (y/n).
- bids_subject
Character. Set BIDS subject label (equivalent to -bi).
- bids_session
Character. Set BIDS session label (equivalent to -bv).
- comment
Character. Comment stored in NIfTI aux_file (up to 24 characters).
- depth
Integer. Directory search depth for recursive discovery (0..9).
- export_format
Character; one of: "n", "y", "o", "j", "b". Export format (n=NIfTI, y=NRRD, o=MGH, j=JNIfTI, b=BJNIfTI).
- filename
Character. Output filename template (e.g. %p_%t_%s).
- ignore_derived
Character; one of: "y", "n". Ignore derived/localizer/2D images (y/n).
- lossless_scale
Character; one of: "y", "n", "o". Lossless scaling for 16-bit integers (y/n/o).
- merge_2d_slices
Character; one of: "0", "1", "2", "n", "y". Merge slices from same series despite differing properties (0/1/2 or n/y).
- series_crc
Character or numeric vector. Only convert specific series CRC numbers; repeatable.
- out_dir
Character; directory path. Output directory (omit to write into input directory).
- philips_float
Character; one of: "y", "n". Use Philips precise floating-point scaling (y/n).
- search_only
Character; one of: "y", "l", "n". Directory search mode (y=count, l=list, n=off).
- rename
Character; one of: "y", "n". Rename DICOMs instead of converting (y/n).
- single_file
Character; one of: "y", "n". Single-file mode: convert only one file in folder (y/n).
- verbose
Character; one of: "0", "1", "2", "n", "y". Verbosity (0/1/2 or n/y).
- write_conflicts
Character; one of: "0", "1", "2". Name conflict behavior (0=skip, 1=overwrite, 2=add suffix).
- crop
Character; one of: "y", "n", "i". Crop 3D acquisitions (y/n/i where i=ignore crop and rotate).
- compression
Character; one of: "y", "o", "i", "n", "3". Compression mode (y/o/i/n/3).
- big_endian
Character; one of: "y", "n", "o". Output byte order (y=big-endian, n=little-endian, o=native/optimal).
- progress
Character; one of: "y", "n". Progress reporting (y/n).
- ignore_trigger_times
Logical. Ignore trigger time DICOM fields (0018,1060 and 0020,9153).
- terse
Logical. Omit filename postfixes (can increase overwrite risk).
- .cwd
Working directory override.
- .env
Named character vector of environment variables.
- .engine
Execution engine override.
- .profile
Runtime profile override.
- dry_run
Logical; preview command without executing.
- echo
Logical; echo stdout/stderr in real time.