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Hello all, I am trying to remove CSF and white matter signals from resting state data, and I was hoping someone could take a look at the steps I took and the resulting image. I have completed the following based on previous messages in the FSL archive: -running FAST on the T1 image to obtain CSF and WM masks and then eroding and thresholding at 80% with fslmaths -running FEAT prestats to preprocess functional runs (motion correction, slice timing correction, and highpass filtering set on, spatial filtering set off) -transforming masks to the functional space with FLIRT and rebinarising them with fslmaths -extracting the average time courses from the CSF and WM of filtered_func_data.nii.gz with fslmeants -concatenating the resulting CSF and WM text files into a single text file with two columns (av CSF time course in one column, WM in the other) -fsl_glm with the concatenated text file as the design file The residual from fsl_glm should be the functional image with the CSF and WM signals regressed out, but it doesn’t look quite right… I don’t have much experience in working with functional data and I would appreciate some feedback/suggestions. I’ve attached a screenshot of the residual in fslview. Thank you in advance, Jack [cid:4FE2DA6C-A10D-4E1B-ADD7-B5909656FDC8@campus.MCGILL.CA]