nipype.interfaces.cmtk.parcellation module¶
Parcellate¶
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',)¶
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nipype.interfaces.cmtk.parcellation.
create_annot_label
(subject_id, subjects_dir, fs_dir, parcellation_name)¶
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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.
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nipype.interfaces.cmtk.parcellation.
create_wm_mask
(subject_id, subjects_dir, fs_dir, parcellation_name)¶
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nipype.interfaces.cmtk.parcellation.
crop_and_move_datasets
(subject_id, subjects_dir, fs_dir, parcellation_name, out_roi_file, dilation)¶
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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