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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
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
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