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
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
rahul＠nmr.mgh.harvard.edu -
Stephen Tyree