Hello Freesurfers,

My ultimate goal is a MLE analysis of 2 groups (n~25) at 2 time points. 

I have followed the longitudinal processing stream (cross, base, long) although only ran -qcache at the cross stage. Do I need to add this flag to the base and/or long recon-all command? Or is the same thing achieved by running this code (described in the LME wiki page under Preparing your data):

mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.stack.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.stack.mgh --tval lh.thickness.stack.fwhm10.mgh --fwhm-trg 10 --cortex --noreshape

I'm using Freesurferv5.3.0 on OS X El Capitan although about to move to a Linux system.

Thanks kindly,

Linette Savage

University of Calgary

Brain Training Study

www.braintrainingstudy.ca