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Hello, I have multiple perfusion datasets. Up to this point, I have been performing the subtraction in Matlab prior to feeding the data to FSL. However, the Matlab subtraction produces very grainy images, preventing both motion correction and registration from working properly since - to the best of my understanding - these are both based on image intensity. Given this problem, I am trying to use FSL's perfusion subtraction. I have read the relevant documentation, and am opting for the Perfusion Subtraction rather than the Full Model, since I'm using a TE of 3ms. Hence, I have formatted my data into a single timecourse, with datapoints alternating between tagged and control. I've attached my NIFTI file. My most significant issue is that there is no activation when using the perfusion subtraction in FSL. When I had been performing the subtraction in Matlab, then processing in FSL, I had clear motor activation and well-formed time courses. I have tried looking at the perfusion_subtract script, but unfortunately, I cannot follow it. I realize this is a broad issue to be asking about, but I really do not know where I'm going wrong. Other than this most prominent problem, I was also wondering why your images do not turn out grainy as mine do, and why in the FSL output, there are black areas around the edges of my images. Finally, I question how one can perform motion correction on perfusion data at all, given the alternation between tag and control. Thanks so much, Nicole P.S.: Please let me know if any images (to show graininess, blackened areas, time courses, etc.) would be useful; they are too large in their current state.