On 4/6/2020 10:57 AM, s7675...@stud.uni-frankfurt.de wrote:
> External Email - Use Caution
> Hi Douglas,
>
> thanks a lot for your quick response. I wanted to use Monte Carlo sim
> as all other analyses in our project include a monte carlo simulation
> and I try to keep things consistent. Am I getting you right - there is
> no way to run a monte carlo simulation with LGI data? And why exactly
> would you not recommend it in this case (even if it worked)?
Yes, you can do the MCZ simulation yourself with mri_mcsim, something like
mri_mcsim --o /your/space/mcsim/fsaverage/lh/cortex --base mc-z
--save-iter --surf fsaverage lh --nreps 1000 --fwhm 37
Then run mri_glmfit-sim as you did before, but specify --mczsim-dir
/your/space/mcsim
>
> I did try permutations with freesurfer in the past, but it never
> really worked out for me, to be honest. They kept running for ages and
> I stopped them after 6-7 days...
Not sure what happened, but if you want to debug it, I can help
>
> Thanks in advance,
>
> Doro
> Zitat von "Douglas N. Greve" <dgr...@mgh.harvard.edu>:
>
>> The problem is that mri_glmfit-sim is looking for a entry in the
>> table that does not exist. The table only goes up to a smoothness
>> level of 35. LGI data tend to bed very smooth. I would strongly
>> recommend that you use permutation instead. See
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>>
>> On 4/6/2020 7:42 AM, s7675...@stud.uni-frankfurt.de wrote:
>>> External Email - Use Caution
>>> Dear Freesurfer experts,
>>>
>>> I'm trying to run a simulation (--> mri_glmfit-sim) with cached LGI
>>> data (fwhm10), but get an error due to the estimated fwhm kernel.
>>> The folder corresponding to the fwhm value (-->37) does not exist, I
>>> guess because it's a pretty unusual value...?
>>>
>>> DoSim = 0
>>> UseCache = 1
>>> DoPoll = 0
>>> DoPBSubmit = 0
>>> DoBackground = 0
>>> DiagCluster = 0
>>> gd2mtx = dods
>>> fwhm = 36.855100
>>> ERROR: cannot find
>>> /apps/prod/x86_64/freesurfer-6.0.1/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/abs/th20/mc-z.csd
>>>
>>> I've seen mails describing similar issues in the archive and from
>>> your explanation I more or less understand that you cannot define
>>> this value as it is estimated in the process...? However, I did not
>>> see if there is a solution to this problem. What could I do about it
>>> now?
>>>
>>> I attached the logfiles and would be very grateful for your help,
>>>
>>> thanks a lot and stay healthy,
>>>
>>> Doro
>>>
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>>> Freesurfer@nmr.mgh.harvard.edu
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>
>
>
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