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Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into a volume and then into a surface with 1s inside the label and 0s outside the label. I want to make a connectivity map surface overlay with values only within my label overlay. However when I run it, it creates a surface overlay with only zeros. There is definitely values within the label surface overlay (I triple checked). Code I used: Mri_mask original_surface_overlay label_mask new_masked_output
It doesn’t output any errors. Here is what it looks like in freeview: Original surface overlay (label is outlined in green) [cid:image001.png@01D5821A.1324B130] The label made into a surface overlay (same as the one shown in green above): [cid:image002.png@01D5821A.1324B130] But this is the output: all zeros even though there was data within the mask. [cid:image003.png@01D5821A.1324B130]
Help! Sara A. Sims
