Hello Anderson

Sorry for my delayed response and thank you so much for your answer! It was very educational.

Just to be sure I understand this correctly: For this kind of twinship (or sibship) correlation I need to use the approached you have described in PALM, and is it correctly understood that randomise cannot handle this kind of correlation? And that randomize and PALM both can handle paired analyses and longitudinal designs? We do have some experience with randomise in our group, but not PALM… JThanks again!

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 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]> 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

 

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