There is currently not a way to mask for anything but the brain. I just found out that that did not work (and never had). That has been fixed. I also added the ability to specify an FDR mask using an environment variable, like

setenv TKM_FDR_MASK yourfdrmask.mgz

This will look in the $SUBJECTS_DIR for subject/mri/yourfdrmask.mgz. Note that you must check the "mask to brain" option next to the FDR button.

This two changes will be live in both dev and stable upon the next update.

You can make the mask you want from aparc+aseg.mgz using mri_binarize with the --match option to choose the structures you want to include in the mask.

doug

Yigal Agam wrote:

Hi,

Is it possible to restrict FDR correction to gray matter in tkmedit?

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