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 de‐
15       signed 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/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.
28
29       -ba <y/n>       anonymize BIDS
30
31       -f <format>
32              Format string for the output filename(s). The  following  speci‐
33              fiers are supported:
34
35              • %a, antenna (coil) name
36
37              • %b, basename (filename of 1st DICOM file)
38
39              • %c, comments
40
41              • %d, description
42
43              • %e, echo number
44
45              • %f, folder name
46
47              • %i, patient ID
48
49              • %j, seriesInstanceUID
50
51              • %k, studyInstanceUID
52
53              • %m, manufacturer
54
55              • %n, patient name
56
57              • %p, protocol
58
59              • %r, instance number (of 1st DICOM file)
60
61              • %s, series number
62
63              • %t, time
64
65              • %u, acquisition number
66
67              • %v, vendor
68
69              • %x, study ID
70
71              • %z, sequence name
72
73              The default format string is "%p_%e_%4s".
74
75       -i <y/n>
76              Ignore derived, localizer and 2D images.
77
78       -l <y/n>
79              Losslessly scale 16-bit integers to use maximal dynamic range.
80
81       -m <y/n>
82              Merge  slices  from  the  same  series regardless of study time,
83              echo, coil, orientation, etc...
84
85       -n <number>
86              Only convert this series number. Provide a negative  number  for
87              listing of series numbers in input folder.
88
89       -o <path>
90              Output  directory  where the converted files should be saved. If
91              unspecified, the files are saved within the specified source di‐
92              rectory.
93
94       -p <y/n>
95              Use Philips precise float (rather than display) scaling.
96
97       -r <y/n>
98              Rename instead of convert DICOMs. Useful for organizing images.
99
100       -s <y/n>
101              Convert a single file only.
102
103       -t <y/n>
104              Save patient details as text notes.
105
106       -u     Update check: attempts to see if newer version is available.
107
108       -v <h/y/n>
109              Enable  verbose  output.  "n" for succinct, "y" for verbose, "h"
110              for high verbosity
111
112       -x <y/n>
113              Crop images. This will attempt to remove excess neck from 3D ac‐
114              quisitions.
115
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.
120

LICENSING

122       Copying  and  distribution  of this file, with or without modification,
123       are permitted in any medium without royalty provided the copyright  no‐
124       tice and this notice are preserved. This file is offered as-is, without
125       any warranty.  The  dcm2niix  project  is  distributed  under  the  BSD
126       2-Clause License.
127

AUTHOR

129       This manual was developed by Ghislain Antony Vaillant and is maintained
130       by the community
131

133       2022 The dcm2niix contributors
134
135
136
137
1381.0                              Jan 20, 2022                      DCM2NIIX(1)
Impressum