Warning: This document is for an old version of niworkflows. The main version is master.

niworkflows.interfaces.surf module

Handling surfaces.

class niworkflows.interfaces.surf.CSVToGifti(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Converts CSV files back to GIfTI, after moving vertices with antsApplyTransformToPoints.

input_spec

alias of niworkflows.interfaces.surf._CSVToGiftiInputSpec

output_spec

alias of niworkflows.interfaces.surf._CSVToGiftiOutputSpec

class niworkflows.interfaces.surf.GiftiNameSource(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Construct a new filename for a GIFTI file.

Construct a new filename based on an input filename, a matching pattern, and a related template, with optionally additional keywords.

This interface is intended for use with GIFTI files, to generate names conforming to Section 9.0 of the GIFTI Standard.

Patterns are expected to have named groups, including one named “LR” that matches “l” or “r”. These groups must correspond to named format elements in the template.

Examples

>>> surf_namer = GiftiNameSource()
>>> surf_namer.inputs.pattern = r'(?P<LR>[lr])h.(?P<surf>\w+).gii'
>>> surf_namer.inputs.template = r'{surf}.{LR}.surf'
>>> surf_namer.inputs.in_file = 'lh.pial.gii'
>>> res = surf_namer.run()
>>> res.outputs.out_name
'pial.L.surf'

>>> func_namer = GiftiNameSource()
>>> func_namer.inputs.pattern = r'(?P<LR>[lr])h.(?P<space>\w+).gii'
>>> func_namer.inputs.template = r'space-{space}.{LR}.func'
>>> func_namer.inputs.in_file = 'rh.fsaverage.gii'
>>> res = func_namer.run()
>>> res.outputs.out_name
'space-fsaverage.R.func'

>>> namer = GiftiNameSource()
>>> namer.inputs.pattern = r'(?P<LR>[lr])h.(?P<space>\w+).gii'
>>> namer.inputs.template = r'space-{space}_density-{density}_hemi-{LR}.func'
>>> namer.inputs.in_file = 'rh.fsaverage.gii'
>>> namer.inputs.template_kwargs = {'density': '10k'}
>>> res = namer.run()
>>> res.outputs.out_name
'space-fsaverage_density-10k_hemi-R.func'

>>> import os
>>> os.unlink('lh.pial.gii')
>>> os.unlink('rh.fsaverage.gii')

input_spec

alias of niworkflows.interfaces.surf._GiftiNameSourceInputSpec

output_spec

alias of niworkflows.interfaces.surf._GiftiNameSourceOutputSpec

class niworkflows.interfaces.surf.GiftiSetAnatomicalStructure(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Set AnatomicalStructurePrimary attribute of GIFTI image based on filename.

For files that begin with lh. or rh., update the metadata to include:

{
    AnatomicalStructurePrimary: (CortexLeft | CortexRight),
}

If AnatomicalStructurePrimary is already set, this function has no effect.

input_spec

alias of niworkflows.interfaces.surf._GiftiSetAnatomicalStructureInputSpec

output_spec

alias of niworkflows.interfaces.surf._GiftiSetAnatomicalStructureOutputSpec

class niworkflows.interfaces.surf.GiftiToCSV(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Converts GIfTI files to CSV to make them ammenable to use with antsApplyTransformsToPoints.

input_spec

alias of niworkflows.interfaces.surf._GiftiToCSVInputSpec

output_spec

alias of niworkflows.interfaces.surf._GiftiToCSVOutputSpec

class niworkflows.interfaces.surf.NormalizeSurf(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Normalize a FreeSurfer-generated GIFTI image.

FreeSurfer includes an offset to the center of the brain volume that is not respected by all software packages. Normalization involves adding this offset to the coordinates of all vertices, and zeroing out that offset, to ensure consistent behavior across software packages. In particular, this normalization is consistent with the Human Connectome Project pipeline (see AlgorithmSurfaceApplyAffine and FreeSurfer2CaretConvertAndRegisterNonlinear), although the the HCP may not zero out the offset.

GIFTI files with midthickness/graymid in the name are also updated to include the following metadata entries:

{
    AnatomicalStructureSecondary: MidThickness,
    GeometricType: Anatomical
}

This interface is intended to be applied uniformly to GIFTI surface files generated from the ?h.white/?h.smoothwm and ?h.pial surfaces, as well as externally-generated ?h.midthickness/?h.graymid files. In principle, this should apply safely to any other surface, although it is less relevant to surfaces that don’t describe an anatomical structure.

input_spec

alias of niworkflows.interfaces.surf._NormalizeSurfInputSpec

output_spec

alias of niworkflows.interfaces.surf._NormalizeSurfOutputSpec

class niworkflows.interfaces.surf.PLYtoGifti(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Convert surfaces from PLY to GIfTI

input_spec

alias of niworkflows.interfaces.surf._PLYtoGiftiInputSpec

output_spec

alias of niworkflows.interfaces.surf._PLYtoGiftiOutputSpec

class niworkflows.interfaces.surf.Path2BIDS(pattern=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Extract BIDS entities from paths using a pattern.

Default pattern is given for Gifti surfaces.

>>> Path2BIDS(in_file='_fix_surfs0/rh.pial.surf.gii').run().outputs

extension = .surf.gii
hemi = R
suffix = pial

>>> Path2BIDS(in_file='_fix_surfs0/rh.pial.gii').run().outputs

extension = .gii
hemi = R
suffix = pial

>>> Path2BIDS(in_file='_fix_surfs0/rh.smoothwm_converted.gii').run().outputs

extension = .gii
hemi = R
suffix = smoothwm

>>> Path2BIDS(in_file='_fix_surfs0/rh.smoothwm_converted.func.gii').run().outputs

extension = .func.gii
hemi = R
suffix = smoothwm

input_spec

alias of niworkflows.interfaces.surf._Path2BIDSInputSpec

output_spec

alias of niworkflows.interfaces.surf._Path2BIDSOutputSpec

class niworkflows.interfaces.surf.PoissonRecon(command=None, terminal_output=None, **inputs)

Bases: nipype.interfaces.base.core.CommandLine

Runs Poisson Reconstruction on a cloud of points + normals given in PLY format. See https://github.com/mkazhdan/PoissonRecon

input_spec

alias of niworkflows.interfaces.surf._PoissonReconInputSpec

output_spec

alias of niworkflows.interfaces.surf._PoissonReconOutputSpec

class niworkflows.interfaces.surf.SurfacesToPointCloud(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Converts multiple surfaces into a pointcloud with corresponding normals to then apply Poisson reconstruction

input_spec

alias of niworkflows.interfaces.surf._SurfacesToPointCloudInputSpec

output_spec

alias of niworkflows.interfaces.surf._SurfacesToPointCloudOutputSpec

class niworkflows.interfaces.surf.UnzipJoinedSurfaces(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Unpack surfaces by identifier keys

input_spec

alias of niworkflows.interfaces.surf._UnzipJoinedSurfacesInputSpec

output_spec

alias of niworkflows.interfaces.surf._UnzipJoinedSurfacesOutputSpec

niworkflows.interfaces.surf.get_gii_meta(in_file)

niworkflows.interfaces.surf.load_transform(fname)

Load affine transform from file

Parameters

fname (str or None) – Filename of an LTA or FSL-style MAT transform file. If None, return an identity transform

Returns

affine

Return type

(4, 4) numpy.ndarray

niworkflows.interfaces.surf.normalize_surfs(in_file, transform_file, newpath=None)

Re-center GIFTI coordinates to fit align to native T1w space.

For midthickness surfaces, add MidThickness metadata

Coordinate update based on: https://github.com/Washington-University/workbench/blob/1b79e56/src/Algorithms/AlgorithmSurfaceApplyAffine.cxx#L73-L91 and https://github.com/Washington-University/Pipelines/blob/ae69b9a/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh#L147

niworkflows.interfaces.surf.ply2gii(in_file, metadata, out_file=None)

Convert from ply to GIfTI

niworkflows.interfaces.surf.pointcloud2ply(vertices, normals, out_file=None)

Converts the file to PLY format

niworkflows.interfaces.surf.vertex_normals(vertices, faces)

Calculates the normals of a triangular mesh