Hi Håkon,
editing will probably be a *lot* easier than generating a parcellation from scratch, and probably more reproducible as well, but of course it depends on your background and experience. If you've done a lot of manual parcellating maybe you can do better.
cheers, Bruce
On Fri, 4 Apr 2008 hakon.grydeland@psykologi.uio.no wrote:
Hi Bruce,
I am trying to parcellate the cortex following the normal processing stream (recon-all) in order to get estimations of cortical thickness and volume in the cortical labels/annotations (?h.aparc.annot).
As you can see from the attached files the automatic cortical parcellation works fairly well, but there seem to be some errors in the parcellation due to the discrepancy between the labels used and the "corresponding" brain tissue (i.e. the labels for the anterior temporal lobe are superfluous because of the loss of brain tissue in this area, but parts of the cortex is still labeled with these labels because of the probabilistic atlas). In addition there also seem to be displacements of some labels for which the brain tissue is intact.
I am therefore wondering what would be the best way of doing the cortical parcellation in order to label the cortex outside of the temporal lobe in a precise manner; modifying the automatic cortical parcellation, by doing some of it manually, etc.? I hope this made things clearer!??
Thanks again!
Håkon
Hi Håkon,
could you give us more detail about what you are trying to achieve?
cheers, Bruce On Fri, 4 Apr 2008 hakon.grydeland@psykologi.uio.no wrote:
Dear FreeSurfers, I am analyzing data from a few patients with quite severe unilateral
temporal lobe damage (no or little brain tissue left both medially and laterally). The cortical parcellation in the damaged hemispheres seem - compared to the presumably unaffected contralateral hemisphere and other
"normal" brains - all right in some parts, while other labels are
misplaced due to the placing of temporal lobe labels which no longer exist. I was looking for some advice as to how to proceed:
Is it advicable to use the labels from the original (recon-all)
cortical
parcellation that seem well parcellated, and create ROIs manually by
drawing in tksurfer/tkmedit the parts of the brain where the labels have
been misplaced? Or should I create ROIs manually and don't use the
automated cortical parcellation? Or is yet another approach more appropriate, for example changing the input used in the parcellation so that Freesurfer don't expect to find and label temporal lobe structures in
the damaged hemisphere? Thanks! Håkon Grydeland _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer