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Hi Higher level FEAT analyses use various images in the /reg directory, so the best thing to do is to run the basic reg in your first level analysis and then replace the necessary files in the /reg directory with those obtained from your own registration (e.g. example_func2highres.mat, highres2standard_warp.nii.gz etc.). Make sure to check that things work. Importantly, I'm pretty sure you need to delete any reg_standard directories in the first level directories (which are created by any prior higher level analyses run on these dirs), or the high level FEAT just uses the data in those. Eugene -- Centre for Functional MRI of the Brain (FMRIB) | University of Oxford John Radcliffe Hospital | Headington OX3 9DU | Oxford | UK Ph: +44 (0) 1865 222 523 | Mob: +44 (0) 7946 362 059 | Fax: +44 (0) 1865 222 717 -- On 13 May 2010 22:55, Catherine Hanson <[log in to unmask]> wrote: > Hi, all. Because the FEAT GUI registration tab (first level analysis) > doesn't offer advanced settings (e.g. cost function), which can produce much > better registration results for some data, I use FLIRT independent of FEAT > to register 4D BOLD files. I then turn off the "registration" when running > a first level analysis. However, when I then try to use FEAT to do the > higher level analysis, it exits prematurely with the "can't find > filtered_func header files" - Not surprising given there is no first level > reg directory. So, the conundrum is how to run a higher level analysis on > first level feat directories that don't contain a reg directory? I've > looked through the forum archives and the use of the CLI "flameo" may be one > answer, but I'm not clear about how to set that up for a higher order > analysis; e.g., can two cope files be fed in? What would a tcontrastsfile or > a designfile look like? Another possibility would be to edit the design.fsf > file to incorporate the advanced registration function(s) that I'm > interested in during the first level analysis, but I'm not sure if I'd > simply add the FLIRT CLI lines to the design.fsf file or if this is even an > option. Any clarification of either option -- or a different one -- would > be greatly appreciated. > >