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It should be pretty similar - the mean of the raw data will be very similar to the control images. Either way with the newer versions of oxford_asl you need to do your own skull stripping. Michael On 24 Feb 2015, at 09:11, Matthieu Vanhoutte <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear FSL experts, I ran oxford_asl command on single pCASL data to compute partial volume corrected CBF : bash oxford_asl -i diffdata -o pvc --tis 3.175 --bolus 1.650 --casl -c control_brain -s T1_brain --tr 4.05 --te 14 --regfrom control_brain --pvcorr Here I used skull-stripped control images for calibration (-c control_brain) and registration (--regfrom control_brain). However, I saw in BASIL tutorial (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BASIL/Tutorial#Exercise_1.4:_Improving_the_registration_and_other_options) that in order to improve registration it should be interesting to use the mean of the raw data (--regfrom datamean_brain) and reuse the mask from before (--csf ex1_3/calib/refmask) to save repeating the identification of the ventricles. So my question is : Is it better to use skull-stripped control images or the mean of the raw data to improve the registration ? Best regards, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France