NAME

       dcm2niibatch - DICOM to NifTI batch converter

SYNOPSIS

       dcm2niixbatch <configuration-file>

DESCRIPTION

       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. dcm2niix is designed to perform such conversion from DICOM to NIfTI
       with a simple command-line interface.

       dcm2niibatch acts as a wrapper around dcm2niix 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.

       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.

       Please be advised that dcm2niix and dcm2niibatch have been developed for research purposes
       only and should not be considered a clinical tool.

CONFIGURATION FILE FORMAT

       Perform  a batch conversion of multiple dicoms using dcm2niibatch, which is run by passing
       a configuration file e.g dcm2niibatch batch_config.yml

       The configuration file should be in yaml format as shown in example batch_config.yaml

          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

       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.

       in_dir     Path to the dicom files

       out_dir    Path to save the nifti file

       filename   File name of nifti file to save

SEE ALSO

       dcm2niix(1)

LICENSING

       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.

AUTHOR

       This manual was developed and is maintained by Benjamin Irving <mail@birving.com>

COPYRIGHT

       2018 The dcm2niix contributors