External Email - Use Caution Hi Doug
Thank you very much for the very helpful reply! It worked perfectly and was exactly what I needed. I assume that these are the clusters after cluster-level correction for multiple comparison since --csd is used? Thanks, Keri On Tue, Oct 15, 2019 at 4:17 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Sorry for the delay ... > > First, run selxavg3-sess with -fwhm ( you might need to delete the > bold/analysis folder to get it to re-run). > > cd session/bold/analyis > There will be a filed called fwhm.dat. Look in that. Depending upon how > much you smoothed it might be something like 10.395. This is the FWHM in > mm. Next, you can run something like the following command > > mri_surfcluster --in contrast/sig.nii.gz --hemi lh --csd > $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/thTT/mc-z.cdf > --mask mask.nii.gz --sum contrast.sum.dat --oannot ./lh.contrast.annot > --thmin T --sign abs --subject fsaverage --cwpvalthresh .05 > > Note that the subject must be fsaverage because the tables were computed > with fsaverage. Above, fwhmXX would be fwhm11 (because the FWHM is 10.395, > but round up to 11). TT refers to the cluster forming threshold (eg, p<.001 > would be 30), and so --thmin T would be 3. "abs" in the path to the CSD > file indicates that you want to use an unsigned (absolute) value; you can > also use pos and neg. --cwpvalthresh .05 means to filter out any clusters > that are not significant at p=0.05. The cluster table will be in > contrast.sum.dat > > doug > > > On 10/3/2019 7:52 AM, Keri Woods wrote: > > External Email - Use Caution > Hi > > From the 1st level analysis of an fMRI study I'm trying to extract the > size of the clusters of activation from each subject, but don't know how to > go about this. I know that for the group analysis you can get the cluster > sizes from the output from mri_glm-sim. Is there a way to run the multiple > comparison correction on the first level analysis in order to get this > table? Or is there another way of getting the cluster sizes? > > Any help would be much appreciated. > > Thank you, > Keri > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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