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# interfaces.dcmstack

## CopyMeta

Link to code

Copy meta data from one Nifti file to another. Useful for preserving meta data after some processing steps.

Inputs:

    [Mandatory]
    dest_file: (an existing file name)
    src_file: (an existing file name)

    [Optional]
    exclude_classes: (a list of items which are any value)
            List of meta data classifications to exclude
    include_classes: (a list of items which are any value)
            List of specific meta data classifications to include. If not
            specified include everything.

Outputs:

    dest_file: (an existing file name)

## DcmStack

Link to code

Create one Nifti file from a set of DICOM files. Can optionally embed meta data.

### Example

    >>> from nipype.interfaces.dcmstack import DcmStack
    >>> stacker = DcmStack()
    >>> stacker.inputs.dicom_files = 'path/to/series/'
    >>> stacker.run()
    >>> result.outputs.out_file
    '/path/to/cwd/sequence.nii.gz'

Inputs:

    [Mandatory]
    dicom_files: (a list of items which are an existing file name or an
             existing directory name or a string)

    [Optional]
    embed_meta: (a boolean)
            Embed DICOM meta data into result
    exclude_regexes: (a list of items which are any value)
            Meta data to exclude, suplementing any default exclude filters
    force_read: (a boolean, nipype default value: True)
            Force reading files without DICM marker
    include_regexes: (a list of items which are any value)
            Meta data to include, overriding any exclude filters
    out_ext: (a string, nipype default value: .nii.gz)
            Determines output file type
    out_format: (a string)
            String which can be formatted with meta data to create the output
            filename(s)

Outputs:

    out_file: (an existing file name)

## GroupAndStack

Link to code

Create (potentially) multiple Nifti files for a set of DICOM files.

Inputs:

    [Mandatory]
    dicom_files: (a list of items which are an existing file name or an
             existing directory name or a string)

    [Optional]
    embed_meta: (a boolean)
            Embed DICOM meta data into result
    exclude_regexes: (a list of items which are any value)
            Meta data to exclude, suplementing any default exclude filters
    force_read: (a boolean, nipype default value: True)
            Force reading files without DICM marker
    include_regexes: (a list of items which are any value)
            Meta data to include, overriding any exclude filters
    out_ext: (a string, nipype default value: .nii.gz)
            Determines output file type
    out_format: (a string)
            String which can be formatted with meta data to create the output
            filename(s)

Outputs:

    out_list: (a list of items which are any value)
            List of output nifti files

## LookupMeta

Link to code

Lookup meta data values from a Nifti with embeded meta data.

### Example

    >>> from nipype.interfaces import dcmstack
    >>> lookup = dcmstack.LookupMeta()
    >>> lookup.inputs.in_file = 'functional.nii'
    >>> lookup.inputs.meta_keys = {'RepetitionTime' : 'TR',                                    'EchoTime' : 'TE'}
    >>> result = lookup.run()
    >>> result.outputs.TR
    9500.0
    >>> result.outputs.TE
    95.0

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            The input Nifti file
    meta_keys: (a list of items which are any value or a dictionary with
             keys which are any value and with values which are any value)
            List of meta data keys to lookup, or a dict where keys specify the
            meta data keys to lookup and the values specify the output names

    [Optional]

Outputs:

    None

## MergeNifti

Link to code

Merge multiple Nifti files into one. Merges together meta data extensions as well.

Inputs:

    [Mandatory]
    in_files: (a list of items which are any value)
            List of Nifti files to merge

    [Optional]
    merge_dim: (an integer)
            Dimension to merge along. If not specified, the last singular or
            non-existant dimension is used.
    out_ext: (a string, nipype default value: .nii.gz)
            Determines output file type
    out_format: (a string)
            String which can be formatted with meta data to create the output
            filename(s)
    sort_order: (a string or a list of items which are any value)
            One or more meta data keys to sort files by.

Outputs:

    out_file: (an existing file name)
            Merged Nifti file

## NiftiGeneratorBase

Link to code

Base class for interfaces that produce Nifti files, potentially with embeded meta data.

Inputs:

    [Mandatory]

    [Optional]
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run

Outputs:

    None

## SplitNifti

Link to code

Split one Nifti file into many along the specified dimension. Each result has an updated meta data extension as well.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            Nifti file to split

    [Optional]
    out_ext: (a string, nipype default value: .nii.gz)
            Determines output file type
    out_format: (a string)
            String which can be formatted with meta data to create the output
            filename(s)
    split_dim: (an integer)
            Dimension to split along. If not specified, the last dimension is
            used.

Outputs:

    out_list: (a list of items which are an existing file name)
            Split Nifti files

## `make_key_func()`

Link to code

## `sanitize_path_comp()`

Link to code