.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.dcm2nii
==================


.. _nipype.interfaces.dcm2nii.Dcm2nii:


.. index:: Dcm2nii

Dcm2nii
-------

`Link to code <file:///build/nipype-4pzbZR/nipype-1.1.3/nipype/interfaces/dcm2nii.py#L103>`__

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  # doctest: +ELLIPSIS
'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'

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
        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

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)

.. _nipype.interfaces.dcm2nii.Dcm2niix:


.. index:: Dcm2niix

Dcm2niix
--------

`Link to code <file:///build/nipype-4pzbZR/nipype-1.1.3/nipype/interfaces/dcm2nii.py#L358>`__

Wraps command **dcm2niix**

Uses Chris Rorden's dcm2niix to convert dicom files

Examples
~~~~~~~~

>>> from nipype.interfaces.dcm2nii import Dcm2niix
>>> converter = Dcm2niix()
>>> converter.inputs.source_dir = 'dicomdir'
>>> converter.inputs.compression = 5
>>> converter.inputs.output_dir = 'ds005'
>>> converter.cmdline
'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n dicomdir'
>>> converter.run() # doctest: +SKIP

# In the example below, we note that the current version of dcm2niix
# converts any files in the directory containing the files in the list. We
# also do not support nested filenames with this option. Thus all files
# should have a common root directory.
>>> converter = Dcm2niix()
>>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
>>> converter.inputs.compression = 5
>>> converter.inputs.output_dir = 'ds005'
>>> converter.cmdline
'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n .'
>>> converter.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        source_dir: (an existing directory name)
                A directory containing dicom files to be converted
                flag: %s, position: -1
                mutually_exclusive: source_names
        source_names: (a list of items which are an existing file name)
                A set of filenames to be converted. Note that the current version
                (1.0.20180328) of dcm2niix converts any files in the directory. To
                only convert specific files they should be in an isolated directory
                flag: %s, position: -1
                mutually_exclusive: source_dir

        [Optional]
        anon_bids: (a boolean)
                Anonymize BIDS
                flag: -ba
                requires: bids_format
        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
        comment: (a unicode string)
                Comment stored as NIfTI aux_file
                flag: -c %s
        compress: (u'y' or u'i' or u'n' or u'3', nipype default value: y)
                Gzip compress images - [y=pigz, i=internal, n=no, 3=no,3D]
                flag: -z %s
        compression: (1 or 2 or 3 or 4 or 5 or 6 or 7 or 8 or 9)
                Gz compression level (1=fastest, 9=smallest)
                flag: -%d
        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 include private patient details
                flag: -t
        ignore_deriv: (a boolean)
                Ignore derived, localizer and 2D images
                flag: -i
        merge_imgs: (a boolean, nipype default value: False)
                merge 2D slices from same series
                flag: -m
        out_filename: (a unicode string)
                Output filename template (%a=antenna (coil) number, %c=comments,
                %d=description, %e=echo number, %f=folder name, %i=ID of patient,
                %j=seriesInstanceUID, %k=studyInstanceUID, %m=manufacturer, %n=name
                of patient, %p=protocol, %s=series number, %t=time, %u=acquisition
                number, %v=vendor, %x=study ID; %z=sequence name)
                flag: -f %s
        output_dir: (an existing directory name, nipype default value: .)
                Output directory
                flag: -o %s
        philips_float: (a boolean)
                Philips precise float (not display) scaling
                flag: -p
        series_numbers: (a list of items which are a unicode string)
                Selectively convert by series number - can be used up to 16 times
                flag: -n %s...
        single_file: (a boolean, nipype default value: False)
                Single file mode
                flag: -s
        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)
