Is there a reason that you are not using mri_glmfit-sim to do this? It is fairly complicated, and so I spent a lot of time writing mri_glmfit-sim to make sure it does the right thing.
On 4/29/2021 6:16 PM, Leonardo Tozzi wrote:
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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}"--basemc-z --surface${subject}lh --nreps10000--label$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 mailto:ltozzi@stanford.edu | (650) 5615738
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