You can adjust overlay thresholds in Configure Overlay window.
Ruopeng
On Oct 6, 2022, at 10:49 AM, Jun Yeon Won <won25@umd.edumailto:won25@umd.edu> wrote:
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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.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.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.png>
I saw somebody posted the same issue here (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg46328.htmlhttps://secure-web.cisco.com/1OHcN_bRSEDk0roNAjIAfufCwrh4xf7rzgQtoclY3flDVpCe2znW_Z-NEpNRC5ahFScfL8n7RZ7746EG5EibldfK0DyeuD8DOWxlEyzUiN6n_d2y4MRqLtRR8U2w2JQKD1dWyZjSMMQFhQKdnQGw_18koHPTGIRMmENF2G45P9aleWGnIh9S5DkSuIB8fqjPlWZZf9mEfzCdZl1dfoU5zRunt_p6sTDDJbI1pdAK_fiffsZyrD7IoVFSicGxBcz_6P8d2ROKxTtCbnNCmdL3Cw_CbU505e2Yr2rrdrRUWeHs1bWHNGTWzCNfcxGeiA2Zd/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg46328.html), 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
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