Re: [Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)

You will need to also specify a voxel-wise threshold and sign, eg,

--cache 2 abs

On 04/13/2016 07:37 PM, Pedro Rosa wrote:

Thanks, Doug. When I do it, I get the following error: ERROR: must spec --sim I am using FreeSurfer 5.3 in a Mac OS. I read in the wiki that mri_mcsim got an atualization for Linux. Should I get that atualization for Mac Os? Best, Pedro.

On Wed, Apr 13, 2016 at 11:43 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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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