Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR threshold from tksurfer and will use that as my -thmin.

One last thing, how would I view the results of mri_surfclluster in tksurfer? Would I load the  ocn.mgh file? If so, I can't seem to find it.


On Thu, Jan 23, 2014 at 2:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
just add "--subject fsaverage_sym"

btw, that command does not perform FDR

doug

On 01/23/2014 01:41 PM, krista kelly wrote:
> Hi all,
>
> I have obtained laterality indices using xhemi analyses and would like
> to use FDR instead of the mri_glmfit-sim suggested in the xhemi
> instructions. I know to get the FDR threshold from tksurfer, but I
> want to restrict the clusters to a certain cluster size. Based on a
> previous thread (
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html
> ) I think this should be done using mri_surfcluster but I am having
> trouble with the actual commands. I've tried this but it doesn't seem
> to work:
>
> mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54
> --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf
> fsaverage_sym --hemi lh
>
> the error = srcsubjid must be supplied
>
> If I'm performing this on a group file (not individual subject), what
> would I even input as the subjid? Or do I have this totally wrong?
>
> Thanks!
> Krista
>
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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