Hi Anderson,
Thanks very much for getting back to me and for your suggestions & advice.
Unfortunately I don't think the problems are due to the overlapping nature of the lesions. The highest overlap I have is 6 subjects out of 63 who have lesions in the same voxel, so this shouldn't violate the assumption you mention.
Further, I get the same error of Rows >= Columns when running a test on just 10 subjects, all of whom have no lesions, hence the lesion maps are just blank nifti files.
Having discussed things with my colleagues, they have previously been able to run randomise on a setup_masks derived call with more columns that rows in the matrix file - but no longer. Could a bug have appeared in a recent update??
Thanks again for the help,
James
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