New subject: mri_glmfit-sim with pre-cached fails

1 Oct 2012


      Doug,
For the PCA residuals we found 37% for the first component.
The same analysis has been done for FreeSurfer v4.5.0,
and we found a residual FWHM of 15.27 and 30% for the
first PCA component. The time courses showed some outliers
for both versions, very much dependent on the position on
the surface, i.e., each time different subjects were outside
the confidence limits.
Summarizing:
v4.5.0: residualFWHM = 15.27; 1st PCA 30%
v5.0.0: residualFWHM = 34.00; 1st PCA 37%
(number of subjects is 53).
So, it is a puzzle why the residual FWHM is that large for v5.0.0.
Ed
On 1 Oct 2012, at 9:15, Ed Gronenschild wrote:
...
On 28 Sep 2012, at 18:00, freesurfer-request@nmr.mgh.harvard.edu  
wrote:
...
Message: 27
Date: Fri, 28 Sep 2012 10:03:47 -0400
From: Douglas N Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fmri_glmfit-sim with pre-cached fails
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 5065AE43.7060103@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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