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# interfaces.dcm2nii

## Dcm2nii

Link to code

Wraps command dcm2nii

Uses MRIcron’s dcm2nii to convert dicom files

### Examples

    >>> tmp = getfixture('tmpdir')
    >>> old = tmp.chdir() # changing to a temporary directory

    >>> from nipype.interfaces.dcm2nii import Dcm2nii
    >>> converter = Dcm2nii()
    >>> converter.inputs.source_names = [os.path.join(datadir, 'functional_1.dcm'), os.path.join(datadir, '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'

    >>> os.chdir(old.strpath)

Inputs:

    [Mandatory]
    source_dir: (an existing directory name)
            flag: %s, position: -1
            mutually_exclusive: source_names
    source_names: (a list of items which are an existing file name)
            flag: %s, position: -1
            mutually_exclusive: source_dir

    [Optional]
    anonymize: (a boolean, nipype default value: True)
            Remove identifying information
            flag: -a
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    collapse_folders: (a boolean, nipype default value: True)
            Collapse input folders
            flag: -c
    config_file: (an existing file name)
            Load settings from specified inifile
            flag: -b %s
    convert_all_pars: (a boolean, nipype default value: True)
            Convert every image in directory
            flag: -v
    date_in_filename: (a boolean, nipype default value: True)
            Date in filename
            flag: -d
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    events_in_filename: (a boolean, nipype default value: True)
            Events (series/acq) in filename
            flag: -e
    gzip_output: (a boolean, nipype default value: False)
            Gzip output (.gz)
            flag: -g
    id_in_filename: (a boolean, nipype default value: False)
            ID in filename
            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)
            Save as .nii - if no, create .hdr/.img pair
            flag: -n
    output_dir: (an existing directory name)
            Output dir - if unspecified, source directory is used
            flag: -o %s
    protocol_in_filename: (a boolean, nipype default value: True)
            Protocol in filename
            flag: -p
    reorient: (a boolean)
            Reorient image to nearest orthogonal
            flag: -r
    reorient_and_crop: (a boolean, nipype default value: False)
            Reorient and crop 3D images
            flag: -x
    source_in_filename: (a boolean, nipype default value: False)
            Source filename
            flag: -f
    spm_analyze: (a boolean)
            SPM2/Analyze not SPM5/NIfTI
            flag: -s
            mutually_exclusive: nii_output
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    bvals: (a list of items which are an existing file name)
    bvecs: (a list of items which are an existing file name)
    converted_files: (a list of items which are an existing file name)
    reoriented_and_cropped_files: (a list of items which are an existing
             file name)
    reoriented_files: (a list of items which are an existing file name)

## Dcm2niix

Link to code

Wraps command dcm2niix

Uses Chris Rorden’s dcm2niix to convert dicom files

### Examples

    >>> from nipype.interfaces.dcm2nii import Dcm2niix
    >>> converter = Dcm2niix()
    >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
    >>> converter.inputs.compress = 'i'
    >>> converter.inputs.single_file = True
    >>> converter.inputs.output_dir = '.'
    >>> converter.cmdline
    'dcm2niix -b y -z i -x n -t n -m n -f %t%p -o . -s y -v n functional_1.dcm'

    >>> flags = '-'.join([val.strip() + ' ' for val in sorted(' '.join(converter.cmdline.split()[1:-1]).split('-'))])
    >>> flags
    ' -b y -f %t%p -m n -o . -s y -t n -v n -x n -z i '

Inputs:

    [Mandatory]
    source_dir: (an existing directory name)
            flag: %s, position: -1
            mutually_exclusive: source_names
    source_names: (a list of items which are an existing file name)
            flag: %s, position: -1
            mutually_exclusive: source_dir

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    bids_format: (a boolean, nipype default value: True)
            Create a BIDS sidecar file
            flag: -b
    compress: (u'y' or u'i' or u'n', nipype default value: i)
            Gzip compress images - [y=pigz, i=internal, n=no]
            flag: -z %s
    crop: (a boolean, nipype default value: False)
            Crop 3D T1 acquisitions
            flag: -x
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    has_private: (a boolean, nipype default value: False)
            Flag if text notes includes private patient details
            flag: -t
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    merge_imgs: (a boolean, nipype default value: False)
            merge 2D slices from same series
            flag: -m
    out_filename: (a unicode string, nipype default value: %t%p)
            Output filename
            flag: -f %s
    output_dir: (an existing directory name)
            Output directory
            flag: -o %s
    single_file: (a boolean, nipype default value: False)
            Convert only one image (filename as last input
            flag: -s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean, nipype default value: False)
            Verbose output
            flag: -v

Outputs:

    bids: (a list of items which are an existing file name)
    bvals: (a list of items which are an existing file name)
    bvecs: (a list of items which are an existing file name)
    converted_files: (a list of items which are an existing file name)