Hi Isabel,
if dura is left around you are *much* better off than if brain is stripped.
In the latter case we will never recover, while if there is some dura we
generally can avoid including it in the surfaces. Note that in the
screenshots you attached that the dura was labeled as cortex by the aseg,
but that is irrelevant as we don't use the aseg for cortical analysis, but
rather the ?h.white and ?h.pial surfaces. Avoiding dura in general is an
extremely difficult, and in fact unsolved problem, as it can be physically
adjacent to the cortex and has similar contrast properties on most
T1-weighted images. In locations where there is some spatial separation
we usually avoid it, but if not you can manually erase it in the
brainmask.mgz.
cheers,
Bruce
On Mon, 17 Jul 2006, Dziobek, Isabel wrote:
Hi Everybody,
I have a question in regard to the skull stripping and subsequent grey and
white matter segmentation. The skull stripping process is faulty with almost
all my subjects, leaving large parts of the dura and sagittal sinus. I tried
changing the watershed parameters but that did not work (it seems that once
parts of the dura are removed, other parts of the more inferior aspects of
the brain are removed too). It would be good to have the option to e.g. only
eat up some pixels from the top, is that possible? Also, on what is the
subsequent segmentation in gray and white matter dependent? It seems that in
some cases, although dura and sagittal sinus are still thee after the skull
strip, they are correctly not segmented into gray (or white) matter. So I am
wondering if the skull strip does not have to be perfect but instead ohter
subsequent steps are more important. Is it possible to influence these
steps? I am attaching a snapshot of a slide, in which the dura is
misclassified as gray matter and the sagittal sinus is not classified at
all.
Thanks in advance for your help!! Best,
Isabel
PS. Are there any example scans (other than bert) where I can see how a very
good (or good enough) skull strip and segmentation look like?
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