nipype.interfaces.cmtk.parcellation module

Parcellate

Link to code

Bases: LibraryBaseInterface

Subdivides segmented ROI file into smaller subregions

This interface implements the same procedure as in the ConnectomeMapper’s parcellation stage (cmp/stages/parcellation/maskcreation.py) for a single parcellation scheme (e.g. ‘scale500’).

Example

>>> import nipype.interfaces.cmtk as cmtk
>>> parcellate = cmtk.Parcellate()
>>> parcellate.inputs.freesurfer_dir = '.'
>>> parcellate.inputs.subjects_dir = '.'
>>> parcellate.inputs.subject_id = 'subj1'
>>> parcellate.inputs.dilation = True
>>> parcellate.inputs.parcellation_name = 'scale500'
>>> parcellate.run()                 # doctest: +SKIP
subject_id : a string
Subject ID.
dilation : a boolean
Dilate cortical parcels? Useful for fMRI connectivity. (Nipype default value: False)
freesurfer_dir : a pathlike object or string representing an existing directory
Freesurfer main directory.
out_roi_file : a pathlike object or string representing a file
Region of Interest file for connectivity mapping.
parcellation_name : ‘scale33’ or ‘scale60’ or ‘scale125’ or ‘scale250’ or ‘scale500’
(Nipype default value: scale500)
subjects_dir : a pathlike object or string representing an existing directory
Freesurfer subjects directory.
aseg_file : a pathlike object or string representing an existing file
Automated segmentation file converted from Freesurfer “subjects” directory.
cc_unknown_file : a pathlike object or string representing an existing file
Image file with regions labelled as unknown cortical structures.
dilated_roi_file_in_structural_space : a pathlike object or string representing a file
Dilated ROI image resliced to the dimensions of the original structural image.
ribbon_file : a pathlike object or string representing an existing file
Image file detailing the cortical ribbon.
roi_file : a pathlike object or string representing an existing file
Region of Interest file for connectivity mapping.
roi_file_in_structural_space : a pathlike object or string representing an existing file
ROI image resliced to the dimensions of the original structural image.
roiv_file : a pathlike object or string representing a file
Region of Interest file for fMRI connectivity mapping.
white_matter_mask_file : a pathlike object or string representing an existing file
White matter mask file.
Parcellate.imports = ('scipy',)
nipype.interfaces.cmtk.parcellation.create_annot_label(subject_id, subjects_dir, fs_dir, parcellation_name)
nipype.interfaces.cmtk.parcellation.create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation)

Creates the ROI_%s.nii.gz files using the given parcellation information from networks. Iteratively create volume.

nipype.interfaces.cmtk.parcellation.create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name)
nipype.interfaces.cmtk.parcellation.crop_and_move_datasets(subject_id, subjects_dir, fs_dir, parcellation_name, out_roi_file, dilation)
nipype.interfaces.cmtk.parcellation.extract(Z, shape, position, fill)

Extract voxel neighbourhood

Parameters:
  • Z (array-like) – the original data
  • shape (tuple) – tuple containing neighbourhood dimensions
  • position (tuple) – tuple containing central point indexes
  • fill (float) – value for the padding of Z
Returns:

R – the neighbourhood of the specified point in Z
Return type:

ndarray