Thank you Anderson,
Yes, I did mean 'respective' control. The controls are not family members, but subjects specifically recruited to match for sex age and a polymorphism, and otherwise unrelated. Can you elaborate a little on why this doesn't constitute a sample in which a paired t-test should be used? What I am proposing is a 'matched-pair analysis', which is not unusual, at least in 'non-imaging' statistics (see below, from the IBM SPSS Statistics webpage).
Are you concerned about the concept of a matched-pair analysis, or is there a specific assumptions FSL makes that makes a paired ttest not appropriate in matched-pair designs?
Thanks!
Marco
http://publib.boulder.ibm.com/infocenter/spssstat/v20r0m0/index.jsp?topic=%2Fcom.ibm.spss.statistics.help%2Fidh_ttpr.htm
Example. In a study on high blood pressure, all patients are measured at the beginning of the study, given a treatment, and measured again. Thus, each subject has two measures, often called before and after measures. An alternative design for which this test is used is a matched-pairs or case-control study, in which each record in the data file contains the response for the patient and also for his or her matched control subject. In a blood pressure study, patients and controls might be matched by age (a 75-year-old patient with a 75-year-old control group member).
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