Hello,
In several of our subjects, we've noticed on the aseg that the hippocampus extends into the fusiform gyrus. I've attached an image showing this in the left hippocampus. Looking at the wm.mgz volume, there seem to be wm voxels in that region that shouldn't be there (image attached). Could these be what are causing the incorrect segmentation (in which case the voxels can just be removed from wm.mgz)? If not, do you have any other ideas as to how to fix this problem? Otherwise, it seems as though the aseg would have to be edited, which would be a large and tedious edit to make in our very large set of subjects.
This is particularly a problem because we are interested in the subfields, and the issue carries over when that processing is performed. In the same subject as discussed above, the CA1 subfield of the left hippocampus also overextends into the fusiform gyrus (image attached). Since we are primarily interested in using the total subfield volume (rather than the aseg volume), it would also work if we could just specifically edit whatever the input to the subfield stream is. Would this just be aseg, or are there other volumes that would need to be edited before running the subfields flag? That may be a question for Koen, but any advice that anyone could offer would be very helpful.
Thank you,
Michael Murray