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.

dest_file : a pathlike object or string representing an existing file src_file : a pathlike object or string representing an existing file

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.

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() # doctest: +SKIP
>>> result.outputs.out_file # doctest: +SKIP
'/path/to/cwd/sequence.nii.gz'

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 unicode string

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
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 unicode string
Determines output file type. (Nipype default value: .nii.gz)
out_format : a unicode 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.

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.

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 unicode string

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
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 unicode string
Determines output file type. (Nipype default value: .nii.gz)
out_format : a unicode 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.
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() # doctest: +SKIP
>>> result.outputs.TR # doctest: +SKIP
9500.0
>>> result.outputs.TE # doctest: +SKIP
95.0
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 nipype.interfaces.base.specs.DynamicTraitedSpec

MergeNifti

Link to code

Bases: NiftiGeneratorBase

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

in_files : a list of items which are any value
List of Nifti files to merge.
merge_dim : an integer (int or long)
Dimension to merge along. If not specified, the last singular or non-existant dimension is used.
out_ext : a unicode string
Determines output file type. (Nipype default value: .nii.gz)
out_format : a unicode 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 unicode string or a list of items which are any value
One or more meta data keys to sort files by.
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.

in_file : a pathlike object or string representing an existing file
Nifti file to split.
out_ext : a unicode string
Determines output file type. (Nipype default value: .nii.gz)
out_format : a unicode 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 (int or long)
Dimension to split along. If not specified, the last dimension is used.
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)