Dear Doug,
Seems that this will never end...It is so painful already.
I was running the --sim as you told me and it worked out for my Sample data formed by controls and patients with Abnormal side Left.
Now, I am doing the same thing but I am getting an error for both lh and rh. Here is what I was running: mri_glmfit-sim \ --glmdir lh_qdec_AbnormalSide_R.glmdir \ --cache 2 neg \ --cwpvalthresh .99 \ --overwrite
and the ERROR: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/june2011/_orig_ FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/y.mgh --fsgd /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/qdec.fsgd dods --glmdir /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir --surf fsaverage lh --label /usr/local/freesurfer/subjects/june2011/_orig_/fsaverage/label/lh.aparc.label --C /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/contrasts/lh-Avg-Intercept-thickness.mat --C /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/contrasts/lh-Diff-Class1-Class2-Intercept-thickness.mat
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 31.843147
ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd
PLEASE HELP!
THANKS! AK