class fmriprep.interfaces.NormalizeSurf(from_file=None, resource_monitor=None, **inputs)[source]

Normalizes 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.