1DCM2NIIBATCH(1)                    dcm2niix                    DCM2NIIBATCH(1)
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NAME

6       dcm2niibatch - DICOM to NifTI batch converter
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SYNOPSIS

9       dcm2niixbatch <configuration-file>
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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       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.
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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.
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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.
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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
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37       The  configuration  file  should  be in yaml format as shown in example
38       batch_config.yaml
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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
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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.
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59       in_dir     Path to the dicom files
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61       out_dir    Path to save the nifti file
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63       filename   File name of nifti file to save
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SEE ALSO

66       dcm2niix(1)
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LICENSING

69       Copying  and  distribution  of this file, with or without modification,
70       are permitted in any medium  without  royalty  provided  the  copyright
71       notice and this notice are preserved. This file is offered as-is, with‐
72       out any warranty.
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AUTHOR

75       This  manual  was  developed  and  is  maintained  by  Benjamin  Irving
76       <mail@birving.com>
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79       2016 The dcm2niix contributors
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841.0                              Jan 31, 2019                  DCM2NIIBATCH(1)
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