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If you are trying to quantify resting perfusion from pASL data then the easiest thing to do is use oxford_asl (or the new user interface Asl_gui) - I would recommend that you make sure you are using FSL 5.0.3 for this, since it handles single TI data better. In essence what you need to do if you want absolute perfusion are three steps (all carried out by the GUI now): 1. Tag-control subtraction (asl_file). 2. Kinetic model inversion (oxford_asl does this) 3. Calibration (estimation of M0a) (oxford_asl or asl_calib) If you can live with relative perfusion then the first step might be all you want to start with. I think that correction for partial volume effects is a good idea, but this is not widely used as of yet in the community so it can currently be harder to interpret the results since there is less literature to refer to. Motion correction is generally a good idea and mcflirt can be used as a first step. Motion correction can be problematic with ASL data though. Michael On 9 May 2013, at 14:00, Dídac Vidal <[log in to unmask]> wrote: > Hi everybody!. > > I am trying to preprocess fMRI perfusion data with BASIL toolset scripts for first time in a pASL with single TI data and I am getting a little confused. > > I think I would use > a) asl_reg for registration, > b) asl_file in order to get a CBF quantification, > and then I woul use c) asl_calib in order to get an absolute quantification of CBF. > > My questions are: > 1) is that correct? > 2) I am missing something? > Is PVE recommended /necessary? > I guess some motion correction should be carried out before asl_file? Probably mcflirt should work fine. > > Thanks in advance >