Hi Ludovica,
thank you very much for the advice. I checked the mask and mask_All files and they are not empty. However, I think you are right that something went wrong with the registration since the subjects' masks don't look very well aligned and consequently the overlap mask only covers the middle of the brain. I am new to FSL so I might have made some basic mistake. The registration was done in MELODIC just with the standard options (linear warping, normal search, 12DOF). I didn't specify any structural images and selected the MNI template from the FSL library. I thought this would result in the functional images directly being registered to the template - am I mistaken? Looking at the MELODIC output report, the registration looks fine...
Best,
Janina
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