Surface shape is the way I would characterize it.  We would at times segment the white/gray/other differently than Freesurfer along that boundary.  But at the same time it is hard to tell exactly how it should be segmented, but could possibly be improved by manual edits.

--
Stephen Tyree
Neuroimaging Computer Scientist
Laureate Institute for Brain Research
Tulsa, OK, USA


On Wed, Jul 29, 2009 at 10:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
do you mean noise in the surface placement or in the parcellation labels?

On Wed, 29 Jul 2009, Stephen Tyree wrote:

Rahul, thanks for the ref to the atlas definitions.  Is there a similar
definition for the cortex mask (?h.cortex.label)?

Bruce, yes we are using the latest version.  Some of our surfaces seem to
exhibit a lot of noise between the anterior cingulate and the corpus
callosum, sometimes encroaching on the ac.  We are trying to determine if
manual editing of the surfaces will improve that region sufficiently to
justify the time spent and the introduction of human bias to surface
reconstruction.  Any advice?

--
Stephen Tyree
Neuroimaging Computer Scientist
Laureate Institute for Brain Research
Tulsa, OK, USA


On Tue, Jul 28, 2009 at 6:20 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:

sure, you could edit it. You'll want to look at the volume as well. What
version are you using? I think we improved this sometime in the past year
(using the improved callosum labels)

cheers
Bruce



On Tue, 28 Jul 2009 rahul@nmr.mgh.harvard.edu wrote:

 Hi Stephen,

For the ?h.aparc.annot atlas, the boundary definitions are included in the
Desikan et al., 2006 paper (Neuroimage).

Best,

Rahul

 One of the regions we are investigating using a surface-based analysis is
the anterior cingulate.  In some of our surface reconstructions, parts of
this region are excluded from the ?h.cortex.label files.  What are the
criteria that Freesurfer uses to determine those boundaries?  Could
manual
editing around the boundary reliably extend the usable surface in that
area?  Thanks.

--
Stephen Tyree
Neuroimaging Computer Scientist
Laureate Institute for Brain Research
Tulsa, OK, USA
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