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()
subject_ida string

Subject ID.

dilationa boolean

Dilate cortical parcels? Useful for fMRI connectivity. (Nipype default value: False)

freesurfer_dira pathlike object or string representing an existing directory

Freesurfer main directory.

out_roi_filea 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_dira pathlike object or string representing an existing directory

Freesurfer subjects directory.

aseg_filea pathlike object or string representing an existing file

Automated segmentation file converted from Freesurfer “subjects” directory.

cc_unknown_filea pathlike object or string representing an existing file

Image file with regions labelled as unknown cortical structures.

dilated_roi_file_in_structural_spacea pathlike object or string representing a file

Dilated ROI image resliced to the dimensions of the original structural image.

ribbon_filea pathlike object or string representing an existing file

Image file detailing the cortical ribbon.

roi_filea pathlike object or string representing an existing file

Region of Interest file for connectivity mapping.

roi_file_in_structural_spacea pathlike object or string representing an existing file

ROI image resliced to the dimensions of the original structural image.

roiv_filea pathlike object or string representing a file

Region of Interest file for fMRI connectivity mapping.

white_matter_mask_filea 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