running freesurfer-v3.0
SUBJECTS_DIR=/home/gkirk/freesurfer-v3.0/freesurfer/subjects/sickle_cell
glm is at /home/gkirk/freesurfer-v3.0/freesurfer/subjects/sickle_cell
and contains
age.mat lh.sickle.glmdir mris_preproc.surface.lh.log rh.sickle.thickness.10.mgh
FSGDstudy.txt lh.sickle.thickness.10.mgh mris_preproc.surface.rh.log rh.sickle.thickness.mgh
FSGDstudy.txt~ lh.sickle.thickness.mgh rh.sickle.glmdir surfer.log
lh.sickle.glmdir contains
age ar1.mgh beta.mgh eres.mgh fsgd.X.mat mri_glmfit.log rstd.mgh rvar.mgh Xg.dat y.fsgd
age/ contains
C.dat F.mgh gamma.mgh maxvox.dat sig.mgh
SUBJECTS_DIR has average directory with the group av surf & vol stuff
I run
mri_surfcluster --src lh.sickle.glmdir/age/sig.mgh --sum lh.sickle.glmdir/age/sig.cluster.sum --ocp lh.sickle.glmdir/age/ sig.cluster.mgh ( on same line of course ) and get ERROR: hemi must be supplied I add --hemi lh and get ERROR: srcsubjid must be supplied etc. can't seem to make it happy.
thanks
Greg.