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Hi Mirko, what files exactly have you put into the reg directory? And what happens when you run FEAT? Do you get beyond the registration part at all? Note that you could still create the merged 4D file by command line and then proceed with the analysis (check the featwatcher output and report.logfor the necessary commands). See you in Wuerzburg, Cheers- Andreas ________________________________ Von: FSL - FMRIB's Software Library im Auftrag von M. Pham Gesendet: Di 22.05.2007 21:26 An: [log in to unmask] Betreff: [FSL] FEAT mice Hi, following the description in the FAQ on how to insert an own/custom registration in FEAT has not worked out for me yet. I am trying to obtain the necessary first-level FEAT files/folders to do a two-group paired comparison on 2D perfusion data of 11 mice. For all subjects there is a single 2D CBF map at each of the two time points (24h apart). The CBF maps were calculated from a modified CASL sequence and satisfactory 6dof registration to a common mouse space could be obtained by FLIRT (via a structural T2). How are these registered 2D maps presented correctly to FEAT as cope images and how do I produce the necessary first-level files to start right off with higher-level analysis? (Matrix is 64x64 and FoV adjusted to 140x140 as recommended for small animals) Thanks in advance for any help! Mirko