Try it without the --no-sim. The --no-sim was from before I stored the cached data and you either had to run a simulation or not.

On 4/12/16 9:10 PM, Pedro Rosa wrote:

Dear list,

I want to limit my vertex-wise group analysis to a smaller spatial region, then I ran my own Monte-Carlo simulation on fsaverage for the superior temporal gyrus:

mri_mcsim --o lh/superiortemporal --base mc-z --surface /fsaverage lh --nreps 10000 --label superiortemporal

After 36 hours, it finished and I pasted the resulting into $FREESURFER_HOME/average/mult-comp-cor/fsaverage, and ran glmfit:

mri_glmfit --glmdir glmdir --y lh.thickness.5.mgh --fsgd table.fsgd --C contrast.mtx --surface fsaverage lh --label /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label

It seems it ran only on the label, as expected.

However I am not able touse this pre-cached simulation in mri_glmfit-sim.

I tried: mri_glmfit-sim --glmdir glmdir --sim-sign abs --cache-dir $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/superiortemporal --no-sim mc-z.abs.th13 --cache-label /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label

...but I get an error although the csd files are in /average/mult-comp-cor/fsaverage... path : ERROR: cannot find any csd files

I tried several combinations of the text specified after --no-sim, but all I got is the error above. I though I should refer to my own simulation using --cache-dir, but it requires the --no-sim flag.

Can anyone help me?

Best,

Pedro Rosa.

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