Hello all, 

I am new to Freesurfer and learning as I go/encounter problems. This might be an obvious question, but has anyone had issues with black holes in their subcortical segmentation runs? The wiki page it suggests contacting the freesurfer mailing list before attempting to manually fix the issue to see if there is an automatic procedure that could fix it.

The second part of my issue is that the black voxels are not incorrectly labeled as another structure/region. When I place the cursor over the black holes, the TkMedit Tools window reads "Sgmtn label: none" . If I do any of the suggested manual fixes (brushing, flood filling, linear selections) on the "none" voxels and label them as hippocampus, would that assign voxels to a structure, increasing the volume of that structure, when those voxels are not actually there? 

To be more clear, I am worried that these "none" voxels are the result of movement during the scan or an error in how the scan was read by the computer. I do not want to 'fix' this problem by manually labeling those voxels as part of the hippocampus and find out down the line that this scan was actually unusable. That would mean that the data collected from this scan on hippocampal volume would be erroneous and make the final cross-sectional data analysis invalid/inaccurate. 

Thank you for your help!