dcm2niix - DICOM to NifTI converter
dcm2niix [options] <sourcedir>
Most medical imaging devices save images in some variation of the
popular DICOM format. However, most scientific tools expect medical images
to be stored in the comparatively simpler NIfTI format. dcm2niix is
designed to perform such conversion from DICOM to NIfTI with a simple
command-line interface.
Please be advised that dcm2niix has been developed for
research purposes only and should not be considered a clinical tool.
-1..-9 gz compression level (1=fastest..9=smallest, default 6)
- -b <y/i/n>
- Save additional BIDS metadata to a side-car .json file (default y). The
"i"nput-only option reads DICOMs but saves neither BIDS nor
NIfTI.
- -f <format>
- Format string for the output filename(s). The following specifiers are
supported:
- %a, antenna (coil) name
- %b, basename (filename of 1st DICOM file)
- %c, comments
- %d, description
- %e, echo number
- %f, folder name
- %i, patient ID
- %j, series instance UID
- %k, study instance UID
- %m, manufacturer
- %n, patient name
- %o, media object instance UID
- %p, protocol
- %r, instance number (of 1st DICOM file)
- %s, series number
- %t, time
- %u, acquisition number
- %v, vendor
- %x, study ID
- %z, sequence name
The default format string is "%p_%e_%4s".
- -g <y/n/o/i>
- Generate defaults file (default n) If "y", create default file
on completion If "n", default will not be written If
"o", only reset and write defaults If "i", the values
of the defaults file are ignored : reset defaults], default n)
- -h
- Show help
- -i <y/n>
- Ignore derived, localizer and 2D images (default n)
- -l <y/n/o>
- Losslessly scale 16-bit integers to use maximal dynamic range (default o).
If "y", then intensity rescaled to use full 16-bit range. If
"n", data not scaled uint16 will be saved as int16. If
"o", original data and datatype preserved.
- -m <y/n/2>
- Merge slices from the same series regardless of study time, echo, coil,
orientation, etc. (default 2). If "2", automatic based on image
modality.
- -n <number>
- Only convert this series CRC number. Provide a negative number for listing
of series CRC numbers in input folder.
- -o <path>
- Output directory where the converted files should be saved. If
unspecified, the files are saved within the specified source
directory.
- -p <y/n>
- Use Philips precise float (rather than display) scaling.
- -r <y/n>
- Rename instead of convert DICOMs. Useful for organizing images.
- -s <y/n>
- Convert a single file only.
- -t <y/n>
- Save patient details as text notes.
- -u
- Update check: attempts to see if newer version is available.
- -v <2/y/n>
- Enable verbose output. "n" for succinct, "y" for
verbose, "2" for high verbosity
- -x <y/n/i>
- Crop images. This will attempt to remove excess neck from 3D acquisitions.
If "i", images are neither cropped nor rotated to canonical
space.
- -z <y/i/n>
- Desired compression method. The "y"es option uses the external
program pigz if available. The "i" option compresses the image
using the slower built-in compression routines.
- --big-endian <y/n/o>
- Byte order (default o). Optimal is machine native
- --progress
- Slicer format progress information (y/n, default n)
- --ignore_trigger_times
- Disregard values in 0018,1060 and 0020,9153
- --terse
- Omit filename post-fixes (can cause overwrites)
- --version
- Report version and terminate
- --xml
- Slicer format features
Copying and distribution of this file, with or without
modification, are permitted in any medium without royalty provided the
copyright notice and this notice are preserved. This file is offered as-is,
without any warranty. The dcm2niix project is distributed under the BSD
2-Clause License.
This manual was developed by Ghislain Antony Vaillant and is
maintained by the community
2022 The dcm2niix contributors