1DCM2NIIX(1)                        dcm2niix                        DCM2NIIX(1)
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NAME

6       dcm2niix - DICOM to NifTI converter
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SYNOPSIS

9       dcm2niix [options] <sourcedir>
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DESCRIPTION

12       Most medical imaging devices save images in some variation of the popu‐
13       lar DICOM format. However, most scientific tools expect medical  images
14       to  be  stored  in  the comparatively simpler NIfTI format. dcm2niix is
15       designed to perform such conversion from DICOM to NIfTI with  a  simple
16       command-line interface.
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18       Please  be  advised  that dcm2niix has been developed for research pur‐
19       poses only and should not be considered a clinical tool.
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OPTIONS

22       -1..-9          gz compression level (1=fastest..9=smallest, default 6)
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24       -b <y/i/n>
25              Save additional BIDS metadata to a  side-car  .json  file.   The
26              "i"nput-only  option  reads  DICOMs  but  saves neither BIDS nor
27              NIfTI.
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29       -ba <y/n>       anonymize BIDS
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31       -f <format>
32              Format string for the output filename(s). The  following  speci‐
33              fiers are supported:
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35              · %a, antenna (coil) name
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37              · %b, basename (filename of 1st DICOM file)
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39              · %c, comments
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41              · %d, description
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43              · %e, echo number
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45              · %f, folder name
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47              · %i, patient ID
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49              · %j, seriesInstanceUID
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51              · %k, studyInstanceUID
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53              · %m, manufacturer
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55              · %n, patient name
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57              · %p, protocol
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59              · %r, instance number (of 1st DICOM file)
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61              · %s, series number
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63              · %t, time
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65              · %u, acquisition number
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67              · %v, vendor
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69              · %x, study ID
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71              · %z, sequence name
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73              The default format string is "%p_%e_%4s".
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75       -i <y/n>
76              Ignore derived, localizer and 2D images.
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78       -l <y/n>
79              Losslessly scale 16-bit integers to use maximal dynamic range.
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81       -m <y/n>
82              Merge  slices  from  the  same  series regardless of study time,
83              echo, coil, orientation, etc...
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85       -n <number>
86              Only convert this series number. Provide a negative  number  for
87              listing of series numbers in input folder.
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89       -o <path>
90              Output  directory  where the converted files should be saved. If
91              unspecified, the files are saved  within  the  specified  source
92              directory.
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94       -p <y/n>
95              Use Philips precise float (rather than display) scaling.
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97       -r <y/n>
98              Rename instead of convert DICOMs. Useful for organizing images.
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100       -s <y/n>
101              Convert a single file only.
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103       -t <y/n>
104              Save patient details as text notes.
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106       -u     Update check: attempts to see if newer version is available.
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108       -v <h/y/n>
109              Enable  verbose  output.  "n" for succinct, "y" for verbose, "h"
110              for high verbosity
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112       -x <y/n>
113              Crop images. This will attempt to remove  excess  neck  from  3D
114              acquisitions.
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116       -z <y/i/n>
117              Desired  compression  method. The "y"es option uses the external
118              program pigz if available. The "i" option compresses  the  image
119              using the slower built-in compression routines.
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LICENSING

122       Copying  and  distribution  of this file, with or without modification,
123       are permitted in any medium  without  royalty  provided  the  copyright
124       notice and this notice are preserved. This file is offered as-is, with‐
125       out any warranty.  The dcm2niix project is distributed  under  the  BSD
126       2-Clause License.
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AUTHOR

129       This manual was developed by Ghislain Antony Vaillant and is maintained
130       by the community
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133       2020 The dcm2niix contributors
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1381.0                              Feb 01, 2020                      DCM2NIIX(1)
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