Correct
On 10/15/2019 9:38 AM, Keri Woods wrote:
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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.
<dgr...@mgh.harvard.edu<mailto: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
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