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
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