nipype.interfaces.cat12.surface module

class nipype.interfaces.cat12.surface.Cell2Str(arg)

Bases: nipype.interfaces.cat12.base.Cell

ExtractAdditionalSurfaceParameters

Link to code

Bases: SPMCommand

Additional surface parameters can be extracted that can be used for statistical analysis, such as:

  • Central surfaces

  • Surface area

  • Surface GM volume

  • Gyrification Index

  • Sulcus depth

  • Toro’s gyrification index

  • Shaer’s local gyrification index

  • Laplacian gyrification indices

  • Addicional surfaces

  • Measure normalization

  • Lazy processing

http://www.neuro.uni-jena.de/cat12/CAT12-Manual.pdf#page=53

Examples

>>> # Set the left surface files, both will be processed
>>> lh_path_central = 'lh.central.structural.gii'
>>> # Put here all surface files generated by CAT12 Segment, this is only required if the this approach is putted in
>>> surf_files = ['lh.sphere.reg.structural.gii', 'rh.sphere.reg.structural.gii', 'lh.sphere.structural.gii', 'rh.sphere.structural.gii', 'rh.central.structural.gii', 'lh.pbt.structural', 'rh.pbt.structural']
>>> extract_additional_measures = ExtractAdditionalSurfaceParameters(left_central_surfaces=lh_path_central, surface_files=surf_files)
>>> extract_additional_measures.run()
Mandatory Inputs:

left_central_surfaces (a list of items which are a pathlike object or string representing an existing file) – Left and central surfaces files.

Optional Inputs:

  • area (a boolean) – Extract area surface. (Nipype default value: True)

  • depth (a boolean) – Extract sulcus depth based on euclidean distance between the central surface anf its convex hull. (Nipype default value: False)

  • fractal_dimension (a boolean) – Extract cortical complexity (fractal dimension) which is described in Yotter ar al. Neuroimage, 56(3): 961-973, 2011. (Nipype default value: False)

  • gmv (a boolean) – Extract volume. (Nipype default value: True)

  • gyrification (a boolean) – Extract gyrification index (GI) based on absolute mean curvature. The method is described in Luders et al. Neuroimage, 29:1224-1230, 2006. (Nipype default value: True)

  • matlab_cmd (a string) – Matlab command to use.

  • mfile (a boolean) – Run m-code using m-file. (Nipype default value: True)

  • paths (a list of items which are a pathlike object or string representing a directory) – Paths to add to matlabpath.

  • surface_files (a list of items which are a pathlike object or string representing an existing file) – All surface files.

  • use_mcr (a boolean) – Run m-code using SPM MCR.

  • use_v8struct (a boolean) – Generate SPM8 and higher compatible jobs. (Nipype default value: True)

Outputs:

  • lh_area (a list of items which are a pathlike object or string representing an existing file) – Area of left Hemisphere.

  • lh_depth (a list of items which are a pathlike object or string representing an existing file) – Depth of left Hemisphere.

  • lh_extracted_files (a list of items which are a pathlike object or string representing an existing file) – Files of left Hemisphere extracted measures.

  • lh_fractaldimension (a list of items which are a pathlike object or string representing an existing file) – Fractal Dimension of left Hemisphere.

  • lh_gmv (a list of items which are a pathlike object or string representing an existing file) – Grey matter volume of left Hemisphere.

  • lh_gyrification (a list of items which are a pathlike object or string representing an existing file) – Gyrification of left Hemisphere.

  • rh_area (a list of items which are a pathlike object or string representing an existing file) – Area of right Hemisphere.

  • rh_depth (a list of items which are a pathlike object or string representing an existing file) – Depth of right Hemisphere.

  • rh_extracted_files (a list of items which are a pathlike object or string representing an existing file) – Files of right Hemisphere extracted measures.

  • rh_fractaldimension (a list of items which are a pathlike object or string representing an existing file) – Fractal Dimension of right Hemisphere.

  • rh_gmv (a list of items which are a pathlike object or string representing an existing file) – Grey matter volume of right Hemisphere.

  • rh_gyrification (a list of items which are a pathlike object or string representing an existing file) – Gyrification of right Hemisphere.

ExtractROIBasedSurfaceMeasures

Link to code

Bases: SPMCommand

Extract ROI-based surface values While ROI-based values for VBM (volume) data are automatically saved in the label folder as XML file it is necessary to additionally extract these values for surface data (except for thickness which is automatically extracted during segmentation). This has to be done after preprocessing the data and creating cortical surfaces.

You can extract ROI-based values for cortical thickness but also for any other surface parameter that was extracted using the Extract Additional Surface Parameters such as volume, area, depth, gyrification and fractal dimension.

>>> # Template surface files
>>> lh_atlas = 'lh.aparc_a2009s.freesurfer.annot'
>>> rh_atlas = 'rh.aparc_a2009s.freesurfer.annot'
>>> surf_files = ['lh.sphere.reg.structural.gii', 'rh.sphere.reg.structural.gii', 'lh.sphere.structural.gii', 'rh.sphere.structural.gii', 'lh.central.structural.gii', 'rh.central.structural.gii', 'lh.pbt.structural', 'rh.pbt.structural']
>>> lh_measure = 'lh.area.structural'
>>> extract_additional_measures = ExtractROIBasedSurfaceMeasures(surface_files=surf_files, lh_surface_measure=lh_measure, lh_roi_atlas=lh_atlas, rh_roi_atlas=rh_atlas)
>>> extract_additional_measures.run()
Mandatory Inputs:

  • lh_roi_atlas (a list of items which are a pathlike object or string representing an existing file) – (Left) ROI Atlas. These are the ROI’s .

  • lh_surface_measure (a list of items which are a pathlike object or string representing an existing file) – (Left) Surface data files. .

Optional Inputs:

  • matlab_cmd (a string) – Matlab command to use.

  • mfile (a boolean) – Run m-code using m-file. (Nipype default value: True)

  • paths (a list of items which are a pathlike object or string representing a directory) – Paths to add to matlabpath.

  • rh_roi_atlas (a list of items which are a pathlike object or string representing an existing file) – (Right) ROI Atlas. These are the ROI’s .

  • rh_surface_measure (a list of items which are a pathlike object or string representing an existing file) – (Right) Surface data files.

  • surface_files (a list of items which are a pathlike object or string representing an existing file) – Surface data files. This variable should be a list with all.

  • use_mcr (a boolean) – Run m-code using SPM MCR.

  • use_v8struct (a boolean) – Generate SPM8 and higher compatible jobs. (Nipype default value: True)

Outputs:

label_files (a list of items which are a pathlike object or string representing an existing file) – Files with the measures extracted for ROIs.