Separate cifti by structure in python

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.@effigies had a great presentation at NeuroHackademy this year that included a section on handling CIFTIs with spatial awareness in nibabel 3.x. You can find his notebook here.

In particular, I think this code segment might be useful:

import nibabel as nb
from nilearn import plotting as nlp

def surf_data_from_cifti(data, axis, surf_name):
    assert isinstance(axis, nb.cifti2.BrainModelAxis)
    for name, data_indices, model in axis.iter_structures():  # Iterates over volumetric and surface structures
        if name == surf_name:                                 # Just looking for a surface
            data = data.T[data_indices]                       # Assume brainmodels axis is last, move it to front
            vtx_indices = model.vertex                        # Generally 1-N, except medial wall vertices
            surf_data = np.zeros((vtx_indices.max() + 1,) + data.shape[1:], dtype=data.dtype)
            surf_data[vtx_indices] = data
            return surf_data
    raise ValueError(f"No structure named {surf_name}")

_ = nlp.plot_surf(str(data_dir / "conte69/Conte69.L.inflated.32k_fs_LR.surf.gii"),
                  surf_data_from_cifti(cifti_data, axes[1], 'CIFTI_STRUCTURE_CORTEX_LEFT').mean(axis=1),
                  cmap='plasma')

Hope that helps !

Elizabeth

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