1DCM2NIIBATCH(1)                    dcm2niix                    DCM2NIIBATCH(1)
2
3
4

NAME

6       dcm2niibatch - DICOM to NifTI batch converter
7

SYNOPSIS

9       dcm2niixbatch <configuration-file>
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       dcm2niibatch  acts as a wrapper around dcm2niix and allows the process‐
19       ing of multiple DICOM sequences by specifying the  list  of  files  and
20       settings  in a yaml text file.  The makes processing a dataset of DICOM
21       scans simpler and more easily repeatable.
22
23       In addition, yaml files are designed to be both human and machine read‐
24       able  and  a script can easily be written in many programming languages
25       to automatically create a yaml file based on an existing folder  struc‐
26       ture.
27
28       Please  be  advised  that dcm2niix and dcm2niibatch have been developed
29       for research purposes only and should  not  be  considered  a  clinical
30       tool.
31

CONFIGURATION FILE FORMAT

33       Perform a batch conversion of multiple dicoms using dcm2niibatch, which
34       is run by passing a  configuration  file  e.g  dcm2niibatch  batch_con‐
35       fig.yml
36
37       The  configuration  file  should  be in yaml format as shown in example
38       batch_config.yaml
39
40          Options:
41            isGz:             false
42            isFlipY:          false
43            isVerbose:        false
44            isCreateBIDS:     false
45            isOnlySingleFile: false
46          Files:
47              -
48                in_dir:           /path/to/first/folder
49                out_dir:          /path/to/output/folder
50                filename:         dcemri
51              -
52                in_dir:           /path/to/second/folder
53                out_dir:          /path/to/output/folder
54                filename:         fa3
55
56       You can add as many files as you want to convert as long as this struc‐
57       ture stays consistent.  Note that a dash must separate each file.
58
59       in_dir     Path to the dicom files
60
61       out_dir    Path to save the nifti file
62
63       filename   File name of nifti file to save
64

SEE ALSO

66       dcm2niix(1)
67

LICENSING

69       Copying  and  distribution  of this file, with or without modification,
70       are permitted in any medium without royalty provided the copyright  no‐
71       tice and this notice are preserved. This file is offered as-is, without
72       any warranty.
73

AUTHOR

75       This  manual  was  developed  and  is  maintained  by  Benjamin  Irving
76       <mail@birving.com>
77
79       2023 The dcm2niix contributors
80
81
82
83
841.0                              Jul 19, 2023                  DCM2NIIBATCH(1)
Impressum