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 de‐
15       signed 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  (default
26              y).  The "i"nput-only option reads DICOMs but saves neither BIDS
27              nor NIfTI.
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29       -ba <y/n> anonymize BIDS (default y).
30              If "n"o, side-car may report patient name, age and weight.
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32       -f <format>
33              Format string for the output filename(s). The  following  speci‐
34              fiers are supported:
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36              • %a, antenna (coil) name
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38              • %b, basename (filename of 1st DICOM file)
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40              • %c, comments
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42              • %d, description
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44              • %e, echo number
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46              • %f, folder name
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48              • %i, patient ID
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50              • %j, series instance UID
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52              • %k, study instance UID
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54              • %m, manufacturer
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56              • %n, patient name
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58              • %o, media object instance UID
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60              • %p, protocol
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62              • %r, instance number (of 1st DICOM file)
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64              • %s, series number
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66              • %t, time
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68              • %u, acquisition number
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70              • %v, vendor
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72              • %x, study ID
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74              • %z, sequence name
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76              The default format string is "%p_%e_%4s".
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78       -g <y/n/o/i>
79              Generate  defaults  file (default n) If "y", create default file
80              on completion If "n", default will not be written If  "o",  only
81              reset and write defaults If "i", the values of the defaults file
82              are ignored : reset defaults], default n)
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84       -h     Show help
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86       -i <y/n>
87              Ignore derived, localizer and 2D images (default n)
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89       -l <y/n/o>
90              Losslessly scale 16-bit integers to use  maximal  dynamic  range
91              (default o).  If "y", then intensity rescaled to use full 16-bit
92              range.  If "n", data not scaled uint16 will be saved  as  int16.
93              If "o", original data and datatype preserved.
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95       -m <y/n/2>
96              Merge  slices  from  the  same  series regardless of study time,
97              echo, coil, orientation, etc. (default 2).   If  "2",  automatic
98              based on image modality.
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100       -n <number>
101              Only  convert  this series CRC number. Provide a negative number
102              for listing of series CRC numbers in input folder.
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104       -o <path>
105              Output directory where the converted files should be  saved.  If
106              unspecified, the files are saved within the specified source di‐
107              rectory.
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109       -p <y/n>
110              Use Philips precise float (rather than display) scaling.
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112       -r <y/n>
113              Rename instead of convert DICOMs. Useful for organizing images.
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115       -s <y/n>
116              Convert a single file only.
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118       -t <y/n>
119              Save patient details as text notes.
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121       -u     Update check: attempts to see if newer version is available.
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123       -v <2/y/n>
124              Enable verbose output. "n" for succinct, "y"  for  verbose,  "2"
125              for high verbosity
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127       -x <y/n/i>
128              Crop images. This will attempt to remove excess neck from 3D ac‐
129              quisitions.  If "i", images are neither cropped nor  rotated  to
130              canonical space.
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132       -z <y/i/n>
133              Desired  compression  method. The "y"es option uses the external
134              program pigz if available. The "i" option compresses  the  image
135              using the slower built-in compression routines.
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137       --big-endian <y/n/o>
138              Byte order (default o). Optimal is machine native
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140       --progress
141              Slicer format progress information (y/n, default n)
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143       --ignore_trigger_times
144              Disregard values in 0018,1060 and 0020,9153
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146       --terse
147              Omit filename post-fixes (can cause overwrites)
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149       --version
150              Report version and terminate
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152       --xml  Slicer format features
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LICENSING

155       Copying  and  distribution  of this file, with or without modification,
156       are permitted in any medium without royalty provided the copyright  no‐
157       tice and this notice are preserved. This file is offered as-is, without
158       any warranty.  The  dcm2niix  project  is  distributed  under  the  BSD
159       2-Clause License.
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AUTHOR

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

166       2022 The dcm2niix contributors
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1711.0                              Aug 07, 2022                      DCM2NIIX(1)