Hi,
Just to add to this - there is a utility called updatefeatreg.
So do as Eugene says and do a standard registration
in your first level directory. Then take your FLIRT matrices
created elsewhere and copy over the relevant files in the
reg directory. Once this is done, just run updatefeatreg
and everything will be appropriately adjusted to take into
account your new registration matrices. Note that only
example_func2highres.mat or highres2standard.mat
(or ones involving *initial* if you are using an Initial
structural image) are important. All other files are
derived from these - and that is what updatefeatreg
actually does.
Also note that you can update the non-linear reg
in the same way if you wish.
All the best,
Mark
On 13 May 2010, at 23:36, Eugene Duff wrote:
> 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
>
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>
> 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.
>
>
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