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# interfaces.dcm2nii

## Dcm2nii

Link to code

Wraps command dcm2nii

Uses MRICRON’s dcm2nii to convert dicom files

### Examples

    >>> from nipype.interfaces.dcm2nii import Dcm2nii
    >>> converter = Dcm2nii()
    >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
    >>> converter.inputs.gzip_output = True
    >>> converter.inputs.output_dir = '.'
    >>> converter.cmdline
    'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'
    >>> converter.run()

Inputs:

    [Mandatory]
    source_dir: (an existing directory name)
            flag: %s, position: -1
            mutually_exclusive: source_names
    source_names: (an existing file name)
            flag: %s, position: -1
            mutually_exclusive: source_dir
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    anonymize: (a boolean, nipype default value: True)
            flag: -a
    args: (a string)
            Additional parameters to the command
            flag: %s
    collapse_folders: (a boolean, nipype default value: True)
            flag: -c
    config_file: (an existing file name)
            flag: -b %s
    convert_all_pars: (a boolean, nipype default value: True)
            flag: -v
    date_in_filename: (a boolean, nipype default value: True)
            flag: -d
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    events_in_filename: (a boolean, nipype default value: True)
            flag: -e
    gzip_output: (a boolean, nipype default value: False)
            flag: -g
    id_in_filename: (a boolean, nipype default value: False)
            flag: -i
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    nii_output: (a boolean, nipype default value: True)
            flag: -n
    output_dir: (an existing directory name)
            flag: -o %s
    protocol_in_filename: (a boolean, nipype default value: True)
            flag: -p
    reorient: (a boolean)
            flag: -r
    reorient_and_crop: (a boolean, nipype default value: False)
            flag: -x
    source_in_filename: (a boolean, nipype default value: False)
            flag: -f
    spm_analyze: (a boolean)
            flag: -s
            mutually_exclusive: nii_output

Outputs:

    bvals: (an existing file name)
    bvecs: (an existing file name)
    converted_files: (an existing file name)
    reoriented_and_cropped_files: (an existing file name)
    reoriented_files: (an existing file name)