[FieldTrip] Between-condition permutation analysis

Raghavan Gopalakrishnan gopalar.ccf at gmail.com
Thu May 14 17:50:06 CEST 2020

Dear Fieldtrippers,


I have a scenario as depicted below with a oversimplified example.

Condition-1 has subjects-A (n=30),B (n=45),C(n=100)and D(n=50)

Condition-2 has subjects-X (n=90), Y(n=75) and Z(n=60)


Basically there are two conditions with 

1. totally different subjects (ABCD in condition-1, XYZ in condition-2)

2. different number of subjects (4 in condition-1, 3 in condition-2)

3. different number of trials per subject (as indicated by n next to each


I would like to perform cluster based time frequency comparisons between the
two conditions.

I have come across studies where same subjects are studied over two
conditions and have differing trial numbers. But, here I have different
subjects in each condition, different number of subjects percondition and
different number of trials per subject. 

Does group comparison of condition-1 vs condition-2 using cluster based
permutation analysis based on differing t-statistic hold valid in the above
mentioned experimental design? Any input would be of great help.


I was following some advice from a previous thread and paper from Groppe et
al. that permutation statistics are insensitive to population variance.




Thank you.


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