So, when I use the function
masker = NiftiLabelsMasker(labels_img=yeo['thick_17'], standardize=True,
memory='nilearn_cache')
x = masker.fit_transform(processed_file_path) # processed_file_path: skull-stripped or gray matter images.
x will be all zero.
Now when I use masker
on the raw image (i.e., no masks were applied), it does return non-zero elements:
x = masker.fit_transform(raw_path)
Why is that?