Thanks again!

Pedro Rosa.

On Apr 14, 2016, at 19:25, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

yes, assuming you ran mri_glmfit with that label as a mask

On 04/14/2016 06:06 PM, Pedro Rosa wrote:
Hi,
Many many thanks. It worked:

mri_glmfit-sim --glmdir teste2 --cache-dir
/$FREESURFER_HOME/average/mult-comp-cor/ --cache 1.3 abs --cache-label
superiortemporal

I had so specify --cache-label as well, or it would try to find the
default fsaverage/cortex label.

The summary table is named as the deafault ones
(cache.th13.abs.sig.cluster.summary), but I found this in it:

# SearchSpace_mm2 65416.6  ## against 65020.8 for deafult ones

# SearchSpace_vtx 7271 ## against 149926 for default ones

Does this mean that both GLM and Monte-Carlo ran in the label
exclusively? By the way, no cluster survived the correction.

Best,

Pedro.


On Thu, Apr 14, 2016 at 6:49 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   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>
   <mailto: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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