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We do not run any registrations in FEAT at the first level. We do most of our pre-processing outside of FEAT as well, so our .fsf file at the first level handles only temporal filtering and modeling. We use epi_reg to calculate registration of the functional data to the T1 separately. We convert that matrix to a format ANTs will take using c3d. We then use ANTs to apply the affine and warp from T1 to template space and aforementioned functional to T1 converted matrix at the same time. We do that for all of the stats images as well as the mean, and mask images. The errors in your log file will be much more informative than the error you get in the terminal window. The error you reported before occurs for many different failures within FEAT, so the issue may be different each time. The log file will usually give you an error that you can use to troubleshoot. If you would like to provide a copy of a feat directory complete with your constructed reg_standard folder, I can compare it to the files we usually have. ________________________________________ From: Keren Lesinger <[log in to unmask]> Sent: Thursday, July 9, 2015 12:47 PM To: [log in to unmask]; Katie Askren Cc: Keren Lesinger Subject: Re: FEAT second level analysis with standard space from ants Thanks Katie, I tried to create all the files you mentioned. now when I ran the copes I at least don't get the box with registration error, but I get a simmilar error to the error which ocurred when I ran the second level analysis with feat directories as inputs.I would like to make sure my first level analysis was defined appropriately similar to your , did u ran registration stage in the first level analysis? can you walk me through your stages in the first level analysis ? Thanks! Keren