1DCM2NIIX(1)                        dcm2niix                        DCM2NIIX(1)
2
3
4

NAME

6       dcm2niix - DICOM to NifTI converter
7

SYNOPSIS

9       dcm2niix [options] <sourcedir>
10

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.
17
18       Please  be  advised  that dcm2niix has been developed for research pur‐
19       poses only and should not be considered a clinical tool.
20

OPTIONS

22       -1..-9          gz compression level (1=fastest..9=smallest, default 6)
23
24       -b <y/n>
25              Save additional BIDS metadata to a side-car .json file.
26
27       -ba <y/n>       anonymize BIDS
28
29       -f <format>
30              Format string for the output filename(s). The  following  speci‐
31              fiers are supported:
32
33              · %a, antenna (coil) number
34
35              · %c, comments
36
37              · %d, description
38
39              · %e, echo number
40
41              · %f, folder name
42
43              · %i, patient ID
44
45              · %j, seriesInstanceUID
46
47              · %k, studyInstanceUID
48
49              · %m, manufacturer
50
51              · %n, patient name
52
53              · %p, protocol
54
55              · %s, series number
56
57              · %t, time
58
59              · %u, acquisition number
60
61              · %v, vendor
62
63              · %x, study ID
64
65              · %z, sequence name
66
67              The default format string is "%p_%e_%4s".
68
69       -i <y/n>
70              Ignore derived, localizer and 2D images.
71
72       -m <y/n>
73              Merge  slices  from  the  same  series regardless of study time,
74              echo, coil, orientation, etc...
75
76       -n <number>
77              Only convert this series number. Provide a negative  number  for
78              listing of series numbers in input folder.
79
80       -o <path>
81              Output  directory  where the converted files should be saved. If
82              unspecified, the files are saved  within  the  specified  source
83              directory.
84
85       -p <y/n>
86              Use Philips precise float (rather than display) scaling.
87
88       -s <y/n>
89              Convert a single file only.
90
91       -t <y/n>
92              Save patient details.
93
94       -v <h/y/n>
95              Enable  verbose  output.  "n" for succinct, "y" for verbose, "h"
96              for high verbosity
97
98       -x <y/n>
99              Crop images.
100
101       -z <y/i/n>
102              Desired compression method. The "y"es option uses  the  external
103              program  pigz  if available. The "i" option compresses the image
104              using the slower built-in compression routines.
105

LICENSING

107       Copying and distribution of this file, with  or  without  modification,
108       are  permitted  in  any  medium  without royalty provided the copyright
109       notice and this notice are preserved. This file is offered as-is, with‐
110       out any warranty.
111

AUTHOR

113       This manual was developed and is maintained by Ghislain Antony Vaillant
114       <ghisvail@gmail.com>
115

117       2016 The dcm2niix contributors
118
119
120
121
1221.0                              Nov 09, 2018                      DCM2NIIX(1)
Impressum