Dear freesurfer experts,

I would like to restrict my surface analyses (cortical thickness and surface 
area) to a mask from an fMRI meta-analysis using my own subject-specific 
template that I created with ANTS. So far, I have used Qdec and wanted to 
correct for cluster size running the Monte Carlo (MC) simulation on my own 
template. 
Now I would like to restrict the simulation to my mask to do a small volume 
correction in my regions of interest. I mapped the mask to my own template (in 
volume space) using ANTS (WarpImageMultiTransform) but how can I get this mask 
to the surface space to run the MC simulation on my own template within this 
mask?

I was planning to do:
mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z 
--surface my_template ?h --nreps 10000 --mask mymask.mgz

How do I get mymask.mgz in the correct space for this?

And can I continue using Qdec or do I have to use glmfit for these analyses?

In addition: is it also possible to do a small volume correction using FDR 
rather than cluster-size correction?

Thanks for your help!

Charlotte
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