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dcm2niix - Man Page

DICOM to NifTI converter

Synopsis

dcm2niix [options] <sourcedir>

Description

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.

Options

-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.

-ba <y/n> anonymize BIDS (default y).

If "n"o, side-car may report patient name, age and weight.

-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

Licensing

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.

Author

This manual was developed by Ghislain Antony Vaillant and is maintained by the community

Referenced By

dcm2niibatch(1).

Feb 06, 2024 1.0