nipype.interfaces.dcmstack module

dcmstack allows series of DICOM images to be stacked into multi-dimensional arrays.

CopyMeta

Link to code

Bases: BaseInterface

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

Mandatory Inputs:

• dest_file (a pathlike object or string representing an existing file)

• src_file (a pathlike object or string representing an existing file)

Optional Inputs:

• 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 (a pathlike object or string representing an existing file)

DcmStack

Link to code

Bases: NiftiGeneratorBase

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'

Mandatory Inputs:

dicom_files (a list of items which are a pathlike object or string representing an existing file or a pathlike object or string representing an existing directory or a string)

Optional Inputs:

• embed_meta (a boolean) – Embed DICOM meta data into result.

• exclude_regexes (a list of items which are any value) – Meta data to exclude, supplementing any default exclude filters.

• force_read (a boolean) – Force reading files without DICM marker. (Nipype default value: True)

• include_regexes (a list of items which are any value) – Meta data to include, overriding any exclude filters.

• out_ext (a string) – Determines output file type. (Nipype default value: .nii.gz)

• out_format (a string) – String which can be formatted with meta data to create the output filename(s).

• out_path (a pathlike object or string representing a directory) – Output path, current working directory if not set.

Outputs:

out_file (a pathlike object or string representing an existing file)

GroupAndStack

Link to code

Bases: DcmStack

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

Mandatory Inputs:

dicom_files (a list of items which are a pathlike object or string representing an existing file or a pathlike object or string representing an existing directory or a string)

Optional Inputs:

• embed_meta (a boolean) – Embed DICOM meta data into result.

• exclude_regexes (a list of items which are any value) – Meta data to exclude, supplementing any default exclude filters.

• force_read (a boolean) – Force reading files without DICM marker. (Nipype default value: True)

• include_regexes (a list of items which are any value) – Meta data to include, overriding any exclude filters.

• out_ext (a string) – Determines output file type. (Nipype default value: .nii.gz)

• out_format (a string) – String which can be formatted with meta data to create the output filename(s).

• out_path (a pathlike object or string representing a directory) – Output path, current working directory if not set.

Outputs:

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

LookupMeta

Link to code

Bases: BaseInterface

Lookup meta data values from a Nifti with embedded 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

Mandatory Inputs:

• in_file (a pathlike object or string representing an existing file) – 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.

LookupMeta.output_spec

alias of DynamicTraitedSpec

MergeNifti

Link to code

Bases: NiftiGeneratorBase

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

Mandatory Inputs:

in_files (a list of items which are any value) – List of Nifti files to merge.

Optional Inputs:

• merge_dim (an integer) – Dimension to merge along. If not specified, the last singular or non-existent dimension is used.

• out_ext (a string) – Determines output file type. (Nipype default value: .nii.gz)

• out_format (a string) – String which can be formatted with meta data to create the output filename(s).

• out_path (a pathlike object or string representing a directory) – Output path, current working directory if not set.

• 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 (a pathlike object or string representing an existing file) – Merged Nifti file.

NiftiGeneratorBase

Link to code

Bases: BaseInterface

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

SplitNifti

Link to code

Bases: NiftiGeneratorBase

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

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Nifti file to split.

Optional Inputs:

• out_ext (a string) – Determines output file type. (Nipype default value: .nii.gz)

• out_format (a string) – String which can be formatted with meta data to create the output filename(s).

• out_path (a pathlike object or string representing a directory) – Output path, current working directory if not set.

• 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 a pathlike object or string representing an existing file) – Split Nifti files.

nipype.interfaces.dcmstack.make_key_func(meta_keys, index=None)

nipype.interfaces.dcmstack.sanitize_path_comp(path_comp)