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-requ...@nmr.mgh.harvard.edu > <mailto: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 >> <mailto:gr...@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: <506470c2.5060...@nmr.mgh.harvard.edu >> <mailto: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 >>> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 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.
