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-request@nmr.mgh.harvard.edu wrote:
Message: 16 Date: Thu, 27 Sep 2012 11:29:06 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails To: freesurfer@nmr.mgh.harvard.edu Message-ID: 506470C2.5060906@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
Hmmm, that's a lot, but I'm very surprised that the final FWHM is over 30. How many subjects do you have? There might be one that is messed up. You can check this by loading the y.mgh as a "time course" in tksurfer. It will give you a graph with each subject. Finally, you can run mri_glmfit with the --pca option to get a PCA of the residuals. This will create a folder called pca-eres. Look at the stats.dat and see how much variance is explained by the first component (first row, 4th column). doug
On 09/28/2012 03:31 AM, Ed Gronenschild wrote:
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-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 16
Date: Thu, 27 Sep 2012 11:29:06 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Message-ID: <506470C2.5060906@nmr.mgh.harvard.edu mailto:506470C2.5060906@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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Ed Gronenschild