Hi Doug,
For mri_glmfit I used a cortical thickness smoothed with a FWHM of 20,
resulting from using the -qcache option in recon-all.
Ed
On 27 Sep 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 16
Date: Thu, 27 Sep 2012 11:29:06 -0400
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <506470c2.5060...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ed, when I created the cache, I only went up to 30mm FWHM thinking
that no one would ever go above it, or maybe should never go above
it. I
can create tables at higher smoothing levels, but 34mm is a lot of
smoothing. How much did you apply to the data?
doug
On 09/27/2012 05:48 AM, Ed Gronenschild wrote:
Hi,
I want to apply a cluster correction with mri_glmfit-sim with
the --cache option:
mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs
It fails with the error message that it can't find the file:
FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc-
z.csd
(FSDir is the directory where FreeSurfer is located,
version 5.0.0, Mac OSX10.5)
Looking at the content of the ....fsaverage/lh/cortex directory
than indeed, only the directories fwhm01, fwhm02, ..., fwhm30
are present.
In the log file from mri_glmfit I can read that the residualFWHM
is 34.005014. Since this FWHM is automatically derived by
mri_glmfit, does it mean that I can never use the --cache option
in this case?
Cheers,
Ed
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