You can click on “Configure Overlay” button on the left pane to adjust threshold for the overlay display.

Ruopeng

On Jun 29, 2021, at 9:53 AM, Jacoby, John <JJACOBY@mgh.harvard.edumailto:JJACOBY@mgh.harvard.edu> wrote:

Hi all,

I've used mri_glmfit to run some GLMs on surface data. Now I would like to visualize the "gamma.mgh" output in freeview, but only with vertices colored if they're above or below a certain value according to the "z.mgh" output of mri_glmfit. In other words, visualize the gamma file normally but keep non-significant vertices uncolored.

So far, I tried using mri_binarize on z.mgh to create a file with ones on the significant vertices and zeros everywhere else. Then I used mris_calc "masked" option to mask the gamma file by the binarized z file. This sort of works, but by "masking" it just sets the output file to zero outside the mask, and zero is still colored like any other number in freeview. I want non-significant areas to be entirely un-colored. Is this possible? Thanks in advance for any help.

Best, John _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer