Re: [Freesurfer] Figures for publication

I would use either the ocn (cluster annotation) or the cluster-wise corrected map: overlay as you generally don't want to show uncorrected data. As for the max, it is a personal choice, just what you think looks good or makes your point.

On 4/22/2024 7:52 AM, Asuka Toyofuku wrote:

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Dear Freesurfer experts,

Thanks to all the help from this community, we're finally done with GLM analysis(mri_glimfit) and the cluster-wise correction (mri_glmfit_sim), and now I'm making figures for publication.

My question is

1. Which output mgh files are commonly used for making figures for publication? Do people use, for example, cache.th40.abs.sig.cluster.mgh (cluster-wise corrected map: overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values masked by the clusters that survive correction) or even uncorrected ones, such as sig.mgh file in the contrast directory before running the correction? From my impression, not many people use e.g., cache.th40.abs.sig.cluster.mgh (which shows no colour gradation inside the clusters)...
2. How do you select the colour-bar cut-off and max values? Most publications I saw use min cut-off value: -log10(p) = 2.00 and max: -log10(p) = 5.00, but some uses min: p=0.05 and max: p=0.01. Obviously, if you set the max value (with the configure section) very low (e.g., 2.0), the size of the cluster gets bigger and looks more significant. Are there any suggestions for setting the configure/threshold for the figures?

Many thanks, Asuka

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