lyman.utils.image_to_matrix

lyman.utils.image_to_matrix(img, mask_img, use=None)

Extract image data from voxels using segmentation mask.

Parameters

imgnifti image

3D or 4D nifti image with data to extract.

mask_img3D nifti image

Image defining the voxels where data will be extracted. Must be 3D.

useint, list of ints, or None, optional

Value(s) within mask_img to use. If None, use all nonzero.

Returns

datan_vox or n_tp, n_vox numpy array

Array with voxel data from img matching the mask. Note that when the input image is a time series, the time dimension is the first axis of the matrix (corresponding to the structure of a GLM).