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.TH "DCM2NIIBATCH" "1" "Jun 03, 2017" "1.0" "dcm2niix"
.SH NAME
dcm2niibatch \- DICOM to NifTI batch converter
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.SH SYNOPSIS
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\fBdcm2niixbatch\fP <\fIconfiguration\-file\fP>
.SH DESCRIPTION
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Most medical imaging devices save images in some variation of the popular DICOM
format. However, most scientific tools expect medical images to be stored in
the comparatively simpler NIfTI format. \fBdcm2niix\fP is designed to perform
such conversion from DICOM to NIfTI with a simple command\-line interface.
.sp
\fBdcm2niibatch\fP acts as a wrapper around \fBdcm2niix\fP and allows the processing of
multiple DICOM sequences by specifying the list of files and settings in a yaml text file.
The makes processing a dataset of DICOM scans simpler and more easily repeatable.
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In addition, yaml files are designed to be both human and machine readable and a
script can easily be written in many programming languages to automatically create a
yaml file based on an existing folder structure.
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Please be advised that \fBdcm2niix\fP and \fBdcm2niibatch\fP have been developed for research
purposes only and should not be considered a clinical tool.
.SH CONFIGURATION FILE FORMAT
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Perform a batch conversion of multiple dicoms using \fBdcm2niibatch\fP, which is run by passing a
configuration file e.g \fIdcm2niibatch batch_config.yml\fP
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The configuration file should be in yaml format as shown in example \fIbatch_config.yaml\fP
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Options:
  isGz:             false
  isFlipY:          false
  isVerbose:        false
  isCreateBIDS:     false
  isOnlySingleFile: false
Files:
    \-
      in_dir:           /path/to/first/folder
      out_dir:          /path/to/output/folder
      filename:         dcemri
    \-
      in_dir:           /path/to/second/folder
      out_dir:          /path/to/output/folder
      filename:         fa3
.ft P
.fi
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You can add as many files as you want to convert as long as this structure stays consistent.
Note that a dash must separate each file.
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in_dir     Path to the dicom files
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out_dir    Path to save the nifti file
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filename   File name of nifti file to save
.SH SEE ALSO
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\fBdcm2niix(1)\fP
.SH LICENSING
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Copying and distribution of this file, with or without modification, are
permitted in any medium without royalty provided the copyright notice and this
notice are preserved. This file is offered as\-is, without any warranty.
.SH AUTHOR
This manual was developed and is maintained by Benjamin Irving <mail@birving.com>
.SH COPYRIGHT
2017 The dcm2niix contributors
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