Hi,
It sounds like your registration has not worked.
If both your whole brain EPI and your T1-weighted
structural image have a full FOV then anything from
your functional activations should show up on either
of these scans. Have you checked all the registration
page results? This would be the first thing to do. If
these are not clear then load the corresponding
images from the reg directory (within the .feat
directory) into FSLView and check them that way.
Once you've found something which is wrong then
we can help more. Until then there isn't much that
we can do.
All the best,
Mark
On 3 Mar 2010, at 17:07, Hongyu Yang wrote:
> Hi Mark,
>
> Let me explain it. For each subject, we got a 2-sec full-brain epi,
> two runs
> data for fMRI, and one t1 structure image. Our TR of 1.7 seconds for
> fMRI
> data requires that the cerebellum is cut off. We learned that FSL
> does better
> if we have a whole brain epi to register to before it registers to
> the T1 image.
> We feed the full-brain epi (after BET) into the initial image for
> registration, and
> the t1 structure image (after BET) for main image. I did not find
> the problem
> for basic results of run1 and run2, however it may have happened.
> After I
> cimbined the two runs with fixed effect, I found for some post-stats
> results,
> some red activated areas were beyond the background brain image, which
> were obvious in OFC and occipital areas. We think something must
> have been
> wrong, and registration part should be the first part we need to
> concern.
> BTW, I just ran Renderstats - GUI with the basic feat result for
> run1, found
> the activated areas were beyond the background brain image too. So,
> something was wrong for the first analysis. We need your help for
> this issue.
>
>
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