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.
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
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> <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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>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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