nipype.interfaces.dcmstack module¶
dcmstack allows series of DICOM images to be stacked into multi-dimensional arrays.
CopyMeta¶
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¶
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, 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 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¶
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, 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 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¶
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
¶
MergeNifti¶
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-existant 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¶
Bases: BaseInterface
Base class for interfaces that produce Nifti files, potentially with embedded meta data.
SplitNifti¶
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)¶