What threshold are you using in tksurfer? It should be the same as -log10(cwp), where cwp is the --cwp threshold you used in mri_glmfit-sim. If it is different, then it might not show all the cluster

On 3/29/19 6:48 AM, Giuliana Klencklen wrote:

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Hi FS experts,

I use tksurfer (e.g., tksurfer fsaverage/ lh inflated -gray) to open the overlays (i.e., something.sig.cluster.mgh) I generated with the permutation simulation correction. It goes perfectly well for most of them expect for some, where the overlay does not show at all the significant clusters summarized in the something.sig.cluster.summary.

I run the mri_glmfit-sim command again but the problem persists.

Does anyone have a clue about what is going wrong?

Many thanks,
Giuliana Klencklen


--
Giuliana Klencklen, Ph.D.
Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall 
Berkeley, CA 94720-3190
510-395-0040

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