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Dear Anderson In your original answer to my question concerning permutation of a sample of twins you wrote: I assume all sibships are complete and have size (cardinality) = 2 In our sample this is not the case, of 39 twinships are incomplete (only one twin in a twin-pair have been scanned). Is this a problem in group level inference using PALM? Thanks in advance! Best Iselin Fra: FSL - FMRIB's Software Library [mailto:[log in to unmask]] På vegne af Anderson M. Winkler Sendt: 6. oktober 2016 09:43 Til: [log in to unmask] Emne: Re: [FSL] fMRI analysis of non-independent groups Hi Iselin, This can be done using permutation tests, although not yet in randomise. It is available in PALM though. You'd proceed as this: 1) Assemble a design matrix as usual for a 3-group comparison: EV1: Control group, coded as 0 if not control, or 1 if control. EV2: High-risk group, coded as 0 if not high-risk, 1 if high-risk. EV3: Affected group, coded as 0 if not affected, 1 if affected. EV4, etc: Additional nuisance variables as needed, e.g., age, sex, etc. 2) Define the contrasts also as a 3-group comparison. For instance: C1: [1 -1 0 0 ...], for Con > HR C2: [1 0 -1 0 ...], for Con > Aff C3: [0 1 -1 0 ...], for HR > Aff C4: [-1 1 0 0 ...], for Con < HR C5: [-1 0 1 0 ...], for Con < Aff C6: [0 -1 1 0 ...], for HR < Aff 3) Define a file with the exchangeability blocks, one such block per sibship. I assume all sibships are complete and have size (cardinality) = 2. If the subjects are entered in the design in pairs, the EB file would be something as: 1 1 2 2 3 3 4 4 ... etc 4) Run PALM with the desired options, making sure to use the options "-eb <EB file>", "-within" and "-whole". Something as this: palm -i 4d_copes.nii.gz -d design.mat -t design.con -eb design.grp -within -whole -n 2000 -corrcon -logp -o myresults [other options] The way as the permutations are created for these cases is described in this<http://www.sciencedirect.com/science/article/pii/S105381191500508X> paper. Subjects will be permuted within sibship, then the sibships will be permuted as a whole. Interestingly, this design isn't properly seeking either "within-pair" or "between-pair" effects. Yet, it will inform about group differences while respecting the family relationships. Hope this helps! All the best, Anderson On 5 October 2016 at 17:23, Iselin Meluken <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear Experts I want to compare fMRI activity between three groups consisting of twins. I want to be able to account for both non-independence between and within groups and unequal group size. We have performed fMRI using four paradigms assessing different domains of emotional processing. The individual twins are grouped according to personal and co-twin history of affective disorders: 1) Control Group: Both twins have no personal history of affective disorders. Both twins in a twin pair are in the same group. N=29. 2) High Risk group: The healthy co-twins of twins with affective disorder. Only one twin from a twin pair is eligible in this group. N=33. 3) Affected Group: Twins with a personal history of affective disorder. Either the affected twin form a pair discordant for affective disrders or both twins from a twin pair concordant for affective disorders. N=63. Would randomise/permutation testing be the best method of comparing these groups or would you recommend another approach? Is it possible to account for non-independence in traditional FEAT group analysis? Looking forward to you response! Best Regards Iselin Meluken ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den.