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 <gr...@nmr.mgh.harvard.edu> > *To:* Antonella Kis <ator...@yahoo.com> > *Cc:* "freesurfer@nmr.mgh.harvard.edu" > <freesurfer@nmr.mgh.harvard.edu>; "fis...@nmr.mgh.harvard.edu" > <fis...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > Hi Doug, > > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
