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Dear Freesurfer experts,
I am running a linear regression analysis and found a significant result showing below (cache.th20.abs.sig.cluster.summary file).
[image: image.png]
I ran the below script to get this result. Right hemisphere was focused for this analysis.
mri_glmfit-sim --glmdir rh.thickness.10.glmdir \ --cache 2 abs \ --cwp 0.05
But, when visualizing the cache.th20.abs.sig.cluster.mgh file, it shows below - the hemisphere is in yellow.
[image: image.png]
The below is a visualization of sig.mgh. The underlay should be gray but I am not sure why the underlay looks yellow when overlaying the thresholded result.
[image: image.png]
I saw somebody posted the same issue here ( https://secure-web.cisco.com/1OHcN_bRSEDk0roNAjIAfufCwrh4xf7rzgQtoclY3flDVpC...), but I was not able to find the solution from here. Could you please let me know what is an issue and how to resolve this?
Best, Jun
