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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. <DGREVE@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:

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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

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