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Hi Anja again, I've just written a script (attached) hopefully doing what you're after. Just call it from a command line: ./areg.sh x x: name of your 4D image; e.g. filtered_func_data; outputs: reg_x image + split volumes which are moved to VOL directory whichthe script creates in your working dir (similalrly reg_ volums are moved to REGG dir). Mind: it's a beta version; tested only once. If you have any problems/questions please let me know. Good luck, 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