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Hi Anja, You can write a bash script with the following workflow: 1) you can split your time series into individual time point images using the fslsplit command 2) Then you can register one volume only (for instance the middle one) and output a *.mat parameters file . Using these parametrs you can loop over all time series images outputing registered images with some prefix, eg: reg_ 3) merge all registered slices with the command fslmerge and a wild card, e.g.: fslmerge -t <output name: reg_*> This is just a brief overlook of the workflow I don't know if it was clear enough? Best wishes, Iwo ________________________________ From: SUBSCRIBE FSL Anonymous <[log in to unmask]> To: [log in to unmask] Sent: Monday, 11 March 2013, 11:58 Subject: [FSL] Flirt command line Hi, I am trying to register my filtered_func data by using a flirt command line in the working space. I have noticed that this line only works by registering on volume-by-volume basis, which means I need to run it for every single volume in my functional data. Is there a quicker way to register filtered_func data by normalising all the volumes at once? Thanks very much, Anja