External Email - Use Caution Thanks.
On Tue, Oct 15, 2019 at 5:00 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Correct > > On 10/15/2019 9:38 AM, Keri Woods wrote: > > 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 > > > _______________________________________________ > 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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