3 d(@sddlZddlmZddlmZmZmZmZmZddl m Z m Z ddl m Z ddlmZddlmZGdd d eZGd d d eZGd d d e ZGdddeZGdddeZGddde ZGddde ZdS)N)Path)FileInputMultiPath TraitedSpectraits isdefined) NestedCellCell) SPMCommand)SPMCommandInputSpec)split_filenamec@seZdZeedddddddZeeddddddZejdd dd d Z ejdd dd d Z ejddddd Z ejddddd Z ejddddd Z dS)+ExtractAdditionalSurfaceParametersInputSpecT)existsZ data_surfzLeft and central surfaces filesF)fielddesc mandatorycopyfilezAll surface files)rrrZGIzExtract gyrification index (GI) based on absolute mean curvature. The method is described in Luders et al. Neuroimage, 29:1224-1230, 2006)rZ usedefaultrgmvzExtract volumeareazExtract area surfaceZSDzaExtract sulcus depth based on euclidian distance between the central surface anf its convex hull.ZFDztExtract cortical complexity (fractal dimension) which is described in Yotter ar al. Neuroimage, 56(3): 961-973, 2011N)__name__ __module__ __qualname__rrleft_central_surfaces surface_filesrZBool gyrificationrrdepthfractal_dimensionrrA/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/cat12/surface.pyr s2r c@seZdZejeddddZejeddddZejeddddZejeddddZ ejeddddZ ejeddd dZ ejeddd dZ ejeddd dZ ejeddd dZejeddd dZejeddddZejeddddZdS),ExtractAdditionalSurfaceParametersOutputSpecT)rz+Files of left Hemisphere extracted measures)rz,Files of right Hemisphere extracted measureszGyrification of left Hemispherez Gyrification of right Hemispherez%Grey matter volume of left Hemispherez&Grey matter volume of right HemispherezArea of left HemispherezArea of right HemispherezDepth of left HemispherezDepth of right Hemispherez$Fractal Dimension of left Hemispherez%Fractal Dimension of right HemisphereN)rrrrListrZlh_extracted_filesZrh_extracted_filesZlh_gyrificationZrh_gyrificationZlh_gmvZrh_gmvZlh_areaZrh_areaZlh_depthZrh_depthZlh_fractaldimensionZrh_fractaldimensionrrrrr0s(rcs<eZdZdZeZeZfddZddZ fddZ Z S)"ExtractAdditionalSurfaceParametersav 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 indeces * 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() # doctest: +SKIP c s2tj}|r d|kr d|_d|_tjf|dS)Nz12.toolszcat.stools.surfextract)r version_jobtype_jobnamesuper__init__)selfinputs_local_version) __class__rrr'ts  z+ExtractAdditionalSurfaceParameters.__init__cCs|jj}|jjdf|jjdf|jjdf|jjdf|jjdfg}x|jjD]}t |\}}}|j ddd }x|D]\}} |rtxdD]} | d } | d | } t || sg|| <t || sg|| <dj | | |g} || j tjj || || j tjj || qWqtWqLW|S)NrrrrZfractaldimension.rhlhZ_extracted_files_)r/r0)_outputsgetr)rrrrrrr splitrjoinappendospath)r(outputsZ names_outputsfilenamepthbaseextZoriginal_filenameZextracted_parameterZparameter_nameZ hemisphereZall_files_hemisphereZname_hemisphereZgenerated_filenamerrr _list_outputs|s2          z0ExtractAdditionalSurfaceParameters._list_outputscs$|dkrt|Stt|j|||S)Nr)Cell2Strr&r! _format_arg)r(optspecval)r+rrrAs z.ExtractAdditionalSurfaceParameters._format_arg) rrr__doc__r input_specr output_specr'r?rA __classcell__rr)r+rr!Ts  'r!c@s~eZdZeeddddddZeedddddddZeeddd dddZeeddd d dddZeeddd dddZ d S)'ExtractROIBasedSurfaceMeasuresInputSpecT)rz;Surface data files. This variable should be a list with allF)rrrZrdataz&(Left) ROI Atlas. These are the ROI's )rrrrz'(Right) ROI Atlas. These are the ROI's cdataz(Left) Surface data files. z(Right) Surface data files.N) rrrrrr lh_roi_atlasZ rh_roi_atlaslh_surface_measureZrh_surface_measurerrrrrIs6rIc@s eZdZejeddddZdS)(ExtractROIBasedSurfaceMeasuresOutputSpecT)rz+Files with the measures extracted for ROIs.)rN)rrrrr r label_filesrrrrrMsrMcs8eZdZdZeZeZddZfddZ ddZ Z S)ExtractROIBasedSurfaceMeasuresac 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 Examples -------- >>> # 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() # doctest: +SKIP cKs2tj}|r d|kr d|_d|_tj|f|dS)Nz12.r"zcat.stools.surf2roi)r r#r$r%r')r(r)r*rrrr's  z'ExtractROIBasedSurfaceMeasures.__init__cs4|dkrt|S|dkr t|Stt|j|||S)NrLrK)rr@r&rOrA)r(rBrCrD)r+rrrAs z*ExtractROIBasedSurfaceMeasures._format_argcCsB|jj}t|jjd\}}}ddt|jdD|d<|S)NrcSsg|]}|jrt|qSr)is_filestr).0labelrrr sz@ExtractROIBasedSurfaceMeasures._list_outputs..zlabel/*rN)r3r4r r)rLrglob)r(r:r<r=r>rrrr?s z,ExtractROIBasedSurfaceMeasures._list_outputs) rrrrErIrFrMrGr'rAr?rHrr)r+rrOs  rOc@seZdZddZdS)r@cCs d|jS)z-Convert input to appropriate format for cat12z{%s})Z to_string)r(rrr__str__szCell2Str.__str__N)rrrrVrrrrr@sr@)r8ZpathlibrZnipype.interfaces.baserrrrrZnipype.interfaces.cat12.baserr Znipype.interfaces.spmr Znipype.interfaces.spm.baser Znipype.utils.filemanipr r rr!rIrMrOr@rrrrs    %$W(8