---

From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Friday, September 30, 2011 11:40 AM
Subject: Re: [Freesurfer] Default for fwhm while running mri_glmfit


There is no one smoothing level that is right. In general, people tend
to just go with a default value. I think that 20 is pretty high, I
usually go with 5-15. You might examine your data to see if you have an
outlier. I think it is unusual for you to get an output fwhm of over 30
when the smoothing level is only 20.
doug

Antonella Kis wrote:
>
>
> Hi Doug,
>
>
> Thanks for helping again.  I used  smoothing level of 20 because I was
> told to use this smoothing.  If I use the 15 I am not getting the
> error but I need to use the 20.Is there a way that I can make it
> work/correct this error and get my tables cached in this case?
>
> Is fwhm= 15  the default in FS while running the mri_gmlfit
> (mri_surfcluster? What if my data was smoothed at 10 while running the
> mris_preproc --cache-in thickness.fwhm20.fsaverage \
>
>
> Please advise.
> Thank you.
> AK
>
> ------------------------------------------------------------------------
> *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *To:* Antonella Kis <atorok9@yahoo.com>
> *Cc:* "freesurfer@nmr.mgh.harvard.edu"
> <freesurfer@nmr.mgh.harvard.edu>; "fischl@nmr.mgh.harvard.edu"
> <fischl@nmr.mgh.harvard.edu>
> *Sent:* Friday, September 30, 2011 10:52 AM
> *Subject:* Re: Error due to fwhm
>
> That exceeds the valued for which the tables are cached. What
> smoothing level did you use?
> doug
>
> Antonella Kis wrote:
> >
> > Hi,
> >
> > When I ran the QDEC on patients with abnormal side right, the fwhm
> for the clusters at thresh 2 is fwhm = 31.843147.
> > Then, I ran mri_glmfit-sim on the QDEC output and it gives me the
> following  error (cannot find fwhm 32):
> >
> > ERROR: cannot find
> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd
> >
> > Is there a way that I can change the fhwm while running
> mri_glmfit-sim from 32 to 31.843147 or how I can correct this error?
> >
> >
> > Many thanks.
> > AK
> >
> >
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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>
>
>
> Hi Doug,
>
>
>
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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