Hi, I've been using freesurfer with only one run (image) pers subject and have generally been obtaining good results. I've just noticed a few quirks in the estimation of the pial surface that I was seeking some clarification. 1 - the algorithm consistently misses portions of grey matter in the medial temporal lobes (amygdala/hippocampus). I've noticed that this "missed" area becomes part of the "medial wall" region when parcellate_subject is run. Does the algorithm intentionally avoid estimatiung the grey/csf surface in the medial temporal lobes?
2 - Sometimes a portion of the other hemisphere gets included in estimates of the pial surface. Any tips for dealing with this? I was thinking of manually deleting a thin line of voxels through the midline of the T1 to emphasise the medial surface in areas where the algorithm has trouble?
As an aside, where can I find the average7? I thought it would be in /usr/local/freesurfer/average/, but all I have is .gcs, .tif, and .txt files.
Thanks as always, Alex