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1. Run FAST. 2. Make sure you have already performed functional to structural registration. 3. Apply FLIRT transform (i.e. highres2example_func.mat) to the partial volume estimate for CSF. This takes the highres pve and puts it into lowres functional space. Use the FLIRT apply transform utility. 4. Then at the command line do this on the pve: fslmaths unthreshCSFpve -thr .99 -bin threshCSFmask 5. To get the time series: fslmeants myfunctionaldata -m threshCSFmask -o myCSFtimeseries jack