Everyone,
I am having problems with Freesurfer not seemingly appreciating the WM/GM boundary in the temporal lobe. I have attached a screenshot of the problem area which is in the bottom right of the pic.
A large portion of the grey matter is outside the pial surface and the inner boundary does not extend to the edge of the white matter. I have checked the white matter segmentation and edited the aseg volume to correct this problem but after running recon-all again I get the same result. Any ideas?
Chris.
Hi Chris,
check the intensity of the temporal lobe white matter that is missing. If it is significantly lower than 110, try adding some control points in the white matter (making sure it is not partial volumed - it must be completely wm), then run autorecon2-cp and autorecon3. You are probably losing surface from an incorrectly fixed topological defect, but the underlying cause is probably errors in the segmentation. If you find you can't fix it, tar and gzip the subject and send it to us and we'll show you how to correct this problem. It's pretty easy once you get the hang of it, but there is definitely a learning curve :)
cheers, Bruce
On Wed, 9 Sep 2009, Chris Adamson wrote:
Everyone,
I am having problems with Freesurfer not seemingly appreciating the WM/GM boundary in the temporal lobe. I have attached a screenshot of the problem area which is in the bottom right of the pic.
A large portion of the grey matter is outside the pial surface and the inner boundary does not extend to the edge of the white matter. I have checked the white matter segmentation and edited the aseg volume to correct this problem but after running recon-all again I get the same result. Any ideas?
Chris.
You can use defect-seg (see the --help) to help explore defects.
doug
Bruce Fischl wrote:
Hi Chris,
check the intensity of the temporal lobe white matter that is missing. If it is significantly lower than 110, try adding some control points in the white matter (making sure it is not partial volumed - it must be completely wm), then run autorecon2-cp and autorecon3. You are probably losing surface from an incorrectly fixed topological defect, but the underlying cause is probably errors in the segmentation. If you find you can't fix it, tar and gzip the subject and send it to us and we'll show you how to correct this problem. It's pretty easy once you get the hang of it, but there is definitely a learning curve :)
cheers, Bruce
On Wed, 9 Sep 2009, Chris Adamson wrote:
Everyone,
I am having problems with Freesurfer not seemingly appreciating the WM/GM boundary in the temporal lobe. I have attached a screenshot of the problem area which is in the bottom right of the pic.
A large portion of the grey matter is outside the pial surface and the inner boundary does not extend to the edge of the white matter. I have checked the white matter segmentation and edited the aseg volume to correct this problem but after running recon-all again I get the same result. Any ideas?
Chris.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Chris Adamson -
Douglas N Greve