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
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