Hi,
The process you need is described here:
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/FAQ?highlight=%28updatefeatreg%29#How_can_I_insert_a_custom_registration_into_a_FEAT_analysis.3F
In essence you need to:
- Run the first-level analyses with registration turned ON.
- Replace the appropriate mat or warp files inside the reg directory with the ones you made yourself with FLIRT.
- Run updatefeatreg in the feat directory. This will then calculate all the necessary combinations of registrations and get the feat directory into a consistent state, ready for higher level analysis.
It is possible to populate a reg directory yourself, without initially running the first-level analysis with registration turned ON, but it is more difficult so I advise you to follow the process above.
All the best,
Mark
On 29 Oct 2014, at 22:14, Laura Banu <[log in to unmask]> wrote:
> Dear Experts,
>
> I am attempting to use FLIRT registration with FEAT. I am using FSL 5.0.5 with Ubuntu. I took the following steps:
>
> 1. Ran first-level analyses with registration turned OFF (all boxes in the Registration tab unchecked)
> 2. Attempted to run registration with FLIRT through the terminal by following the instructions on the FLIRT UserGuide: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide
>
> I used the commands under the "Registration" heading exactly as they are written for all first-level FEAT outputs, except I added a few options to the first three FLIRT commands (-dof 9 -cost normmi -interp sinc). When I tried to run a higher-level analysis, I got a Fatal Error message saying "registration has not been run." Any insight into this problem would be greatly appreciated!
>
> ~Laura
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