Did you check the registration (tkregister-sess)? My guess is that the partial field of view messed up the registration. If so, you can probably get around this by adding -init-header to preproc-sess

On 8/19/2019 8:11 AM, Hang Zeng wrote:

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Hi Freesurfers,

when I collected the fMRI data, I set the slices to cover part of the brain (only cover the occipital and the temporal lobe).

The anatomy scan was of course whole brain.

After analysing the data with the pipeline (preproc mkanalysis selxavg3), I overlaid the results on the surf, it looked so weird.

So I analysed the data using spm, and used bbregister to register the functional volume to the anatomical data (which also looked weird). The result looked different but doesn't make sense. Because I should see the activations on the occipital and the temporal lobe surf, but instead it appeared on the upper part of the brain surf. I guess this is because of the registration?

So how to analyse the data in this situation and how to view the results?

Thanks! Zoe

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