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# 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()

> left_central_surfacesa list of items which are a pathlike object or string representing an existing file

>   Left and central surfaces files.

> areaa boolean

>   Extract area surface. (Nipype default value: `True`)

> deptha boolean

>   Extract sulcus depth based on euclidean distance between the central surface anf its convex hull. (Nipype default value: `False`)

> fractal_dimensiona boolean

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

> gmva boolean

>   Extract volume. (Nipype default value: `True`)

> gyrificationa 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_cmda string

>   Matlab command to use.

> mfilea boolean

>   Run m-code using m-file. (Nipype default value: `True`)

> pathsa list of items which are a pathlike object or string representing a directory

>   Paths to add to matlabpath.

> surface_filesa list of items which are a pathlike object or string representing an existing file

>   All surface files.

> use_mcra boolean

>   Run m-code using SPM MCR.

> use_v8structa boolean

>   Generate SPM8 and higher compatible jobs. (Nipype default value: `True`)

> lh_areaa list of items which are a pathlike object or string representing an existing file

>   Area of left Hemisphere.

> lh_deptha list of items which are a pathlike object or string representing an existing file

>   Depth of left Hemisphere.

> lh_extracted_filesa list of items which are a pathlike object or string representing an existing file

>   Files of left Hemisphere extracted measures.

> lh_fractaldimensiona list of items which are a pathlike object or string representing an existing file

>   Fractal Dimension of left Hemisphere.

> lh_gmva list of items which are a pathlike object or string representing an existing file

>   Grey matter volume of left Hemisphere.

> lh_gyrificationa list of items which are a pathlike object or string representing an existing file

>   Gyrification of left Hemisphere.

> rh_areaa list of items which are a pathlike object or string representing an existing file

>   Area of right Hemisphere.

> rh_deptha list of items which are a pathlike object or string representing an existing file

>   Depth of right Hemisphere.

> rh_extracted_filesa list of items which are a pathlike object or string representing an existing file

>   Files of right Hemisphere extracted measures.

> rh_fractaldimensiona list of items which are a pathlike object or string representing an existing file

>   Fractal Dimension of right Hemisphere.

> rh_gmva list of items which are a pathlike object or string representing an existing file

>   Grey matter volume of right Hemisphere.

> rh_gyrificationa 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.

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

>     >>> # 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()

> lh_roi_atlasa list of items which are a pathlike object or string representing an existing file

>   (Left) ROI Atlas. These are the ROI’s .

> lh_surface_measurea list of items which are a pathlike object or string representing an existing file

>   (Left) Surface data files. .

> matlab_cmda string

>   Matlab command to use.

> mfilea boolean

>   Run m-code using m-file. (Nipype default value: `True`)

> pathsa list of items which are a pathlike object or string representing a directory

>   Paths to add to matlabpath.

> rh_roi_atlasa list of items which are a pathlike object or string representing an existing file

>   (Right) ROI Atlas. These are the ROI’s .

> rh_surface_measurea list of items which are a pathlike object or string representing an existing file

>   (Right) Surface data files.

> surface_filesa 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_mcra boolean

>   Run m-code using SPM MCR.

> use_v8structa boolean

>   Generate SPM8 and higher compatible jobs. (Nipype default value: `True`)

> label_filesa list of items which are a pathlike object or string representing an existing file

>   Files with the measures extracted for ROIs.