Hello Iwo,
var_filtered_func_data is a concatenation of the lower level variance data. It can contain zero values within the masked region due to differences in how we calculate the group statistic mask, and the overlap of the registered variance images. This does not affect the lower-level as each run is in the subject's own functional space. This warning is common and can be safely ignored - it is there to tell you that there are voxels for which not all subjects have valid information and so will be excluded from the analysis.
Kind regards
Matthew
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