zoom.prepare.process_SBP

zoom.prepare.process_SBP(SBP: PathLike | tuple | nibabel.gifti.gifti.GiftiImage, parcellation: PathLike | tuple | nibabel.gifti.gifti.GiftiImage, atlas: str, density: str, hemi: str, n_perm: int, seed: int) → Tuple[pandas.DataFrame, pandas.DataFrame][source]

Assign SBP image to parcellation image and perform spatial permutation test.

Parameters:

  • SBP (nibabel.Nifti1Image, tuple or dict) –

    Brain atlas specification. Can be: - A parcellation image in MNI space. - A tuple of GIFTI images in fsaverage5 space. - a dictionary where keys are donor IDs and values are parcellation

    images (or surfaces) in the native space of each donor.

  • parcellation (path_like str, tuple, nib.gifti.gifti.GiftiImage) –

    Recognized parcellation image - If hemi in [‘L’,’lh’,’left’]:

    • path_like str: Filepaths to .gii or .annot

    • nib.gifti.gifti.GiftiImage

    • Otherwise, use both hemisphere:
      • tuple: must be organized as L/R pair

        • (str, str): Filepaths to .gii or .annot

        • (nib.gifti.gifti.GiftiImage, nib.gifti.gifti.GiftiImage)

  • atlas ({'fsaverage', 'fSLR', 'civet'} optional,) – Name of surface atlas on which parcellation is defined.

  • density (str, optional) – Density of surface mesh on which parcellation is defined. Must becompatible with specified atlas.

  • hemi ({'L','lh','left','both'} optional,) – Hemisphere used to perform downstream analyses.

  • n_perm (int) – Number of permuation test to perform.

  • seed (int) – Random seed of spatial permutation test.

Returns:

  • df_SBP_parc (pd.DataFrame) – SBP values in parcellation labels.

  • df_surr_parc (pd.DataFrame) – Permutated SBP values in parcellation labels.

References

[1] Markello, R. D. et al. Neuromaps: structural and functional interpretation

of brain maps. Nat. Methods 19, 1472-1479 (2022)..

[2] Alexander-Bloch, A. F. et al. On testing for spatial correspondence between

maps of human brain structure and function. Neuroimage 178, 540-551 (2018).