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
Hi Michael,
I can answer the subfield part - perhaps someone else (Bruce?) can chime in regarding aseg.
For the subfields, there isn't really a standard routine to go in and alter the segmentation results. You could try to alter the aseg hippocampus segmentation as this is what is used to initialize the subfield segmentation routine, but if you're out of luck the subfield segmentation might try to go on and produce the same type of error anyway, regardless of the initialization.
Sorry I don't have better news,
Koen
On Mon, Jul 23, 2012 at 5:21 PM, Murray, Michael mgmurray@wustl.edu wrote:
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
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Hi Michael
we have seen that occasionally, but that looks like a pretty bad example. If you upload the subject I'll take a look. We have some unreleased tools that can help with this (a relatively small manual intervention).
cheers Bruce
On Mon, 23 Jul 2012, Murray, Michael wrote:
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Koen Van Leemput -
Murray, Michael