PALM with Freesurfer and twins

[jmdk73]

Dear Anderson,

I am trying to use PALM with Freesurfer surface data like thickness
and volume because my sample consists of monozygotic twins. It is a
simple two group design, patients/non-patients with twin pairs that
could be both in the same group or across groups. I use FSL GLM tool
to generate the mat and con files. I encounter two issues:

1. While Palm runs fine, the output mgz files are corrupted, can’t be
   loaded in either freeview or fsleyes. The palm command I run is:

palm
-i mgh_g3/lh.volume.s5.g3.mgh
-i mgh_g3/lh.volume.s5.g3.mgh
-d palm/g3.mat
-t palm/PALM.con
-eb palm/g3_eb.csv -within
-n 1000
-tfce2D
-s fsaverage/surf/lh.white
-s fsaverage/surf/rh.white
-o palm/g3_n1000

2. I don’t manage to figure out how a good exchangeability file to
   restrict the permutations should look like. While I can’t find any
   information online, conceptually I would go for each twin pair should
   be considered a block and permutations should be performed between
   blocks. However, using the -whole option or (-1 as the first column,
   twinID as second), palm complains that the blocks are not the same
   size – which is correct since a lot of the twins don’t have their
   co-twin in the sample. For the above run, I split the sample into
   paired and unpaired twins just to be able to run but it is probably
   not optimal.

Kind regards,
Julian