I have been using fslmeants to extract mean intensity values for my experimental conditions within a mask that I derived from one of the FSL-supplied atlases. When I extract stats/cope1 values at the 2nd level (single subject) and 3rd (all subjects) levels of analysis, I do not get the same averages (i.e. the extracted 3rd level mean values do not match the mean values for the 2nd level when I calculate them in Excel). I have tried to figure out if there is something incorrect with how I am processing my data as a colleague of mine did the same type of extraction on an unrelated set of data and was able to get the 3rd level extracted values to match the mean calculated 2nd level values. Any ideas on what might be happening or what I might be doing wrong?
Thank you,
Jill
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