Hello Freesurfer Experts,

   I was running permutation simulations on cortical thickness data and I had an issue with non-orthogonal covariates with mri_glmfit-sim -perm.  I then tried FSL's PALM which is an extension of randomize to calculate threshold free stats.  I saved the output as logp(which is similar to qdec I believe), however I have not been able to load the stats files correctly.  The output of palm is lh.thickness_tfce.mgz for my various contrasts.

1) Is .mgz the proper format for the stats files or do I need to convert this to another type like .mgh etc? 

2) Can I display this in freeview or is another program needed?  I also tried tksurfer but when I loaded the stats file as an overlay nothing displayed.  I want to make sure that the stats is loaded as an overlay in freeview/tksurfer and if so, do I need to select anything special so that it scales the logp values correctly?

Thanks,

Ajay

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