Dear Experts,

I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file.

I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI.

I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster?

Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary?

My calls to the two methods are as follows (for one hemisphere):

First the mcsim:

mri_mcsim --o “${subject}_mcsim_lh_${roi}" --base mc-z --surface ${subject} lh --nreps 10000 --label $roi

Then the mri_surfcluster:

mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \

--csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \

--clabel "${subject}/label/lh.${roi}.label" \

--cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \

--vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \

--sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \

--thmin 3 \

--surf white \

--subject ${subject } \

--hemi lh \

--ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \

--cwpvalthresh 0.05

In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p?

The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to.

Thank you,

Leonardo Tozzi, MD, PhD

Williams PanLab | Postdoctoral Researcher

Stanford University | 401 Quarry Rd

ltozzi@stanford.edu | (650) 5615738

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