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Dear Douglas, Yes, I mean fMRI. I am currently using MATLAB to fit a GLM to the timeseries and then export the p-values as a MGH file of the cortical surface. Best,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, May 10, 2021 at 9:59 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
when you say time series, do you mean like fMRI? What are you using to do the time series analysis? On 5/10/2021 12:56 PM, Leonardo Tozzi wrote:
External Email - Use Caution Dear Douglas,
The reason is that I am running a GLM at the subject level on 4D fMRI timeseries. Thus, I obtain a parameter estimate on each vertex, which I can then enter in a contrast to obtain a p-value per vertex. These are the p-values I want to correct. From what I understand, the mri_glmfit does not work on timeseries data, am I wrong in this? So at the moment I am fitting the GLM in matlab and using the mcsim to correct the p-values I obtain. Best,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, May 10, 2021 at 8:32 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
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:
External Email - Use Caution 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.edumailto:ltozzi@stanford.edu | (650) 5615738
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