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.labelIt 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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