Hi Mike
we expect the cortex to have the topology of a sheet, and pathologies that
change that will cause unpredictable results. If you can segment the
pathology you would typically want to fill it in in the wm.mgz. As for the
deep segmentation, again it will be a case-by-case basis. The nonlineear
warp used in the segmentation is extremely flexible so it should be able to
handle relatively large deformations, but at some point of course it will
fail.
cheers
Bruce
On Tue, 1 Jan 2019, Michael Sughrue wrote:
External Email - Use Caution
I see... what does the fix topology step expect from the wm.mgz meaning how is
it testing it and
what are the values it would accept... for example if we were to script an auto
fill step which
calls a program which works on wm.mgz between steps what would it have to do to
make this work
With the second point about the location mattering in gliomas...I assume this
has an impact on areas
like the cingulate ....and hippocampus where the hemispheres and brainstem are
separated ....if so
can this be addressed....also are there other tricky areas....does the deep
segmentation work if the
brain is shifted ....and the basal ganglia are not near their atlas
positions.....
Thanks in advance
Mike
On Tue, 1 Jan. 2019, 3:18 am Bruce Fischl <fis...@nmr.mgh.harvard.edu wrote:
I see. Getting FS working is going to be a case-by-case thing then. For
holes extending into the ventricles you will probably need to fill the
hole in the wm.mgz to make the topology closer to what we expect it to be.
For the gliomas it depends on where they are
cheers
Bruce
On
Tue, 1 Jan 2019, Michael Sughrue wrote:
>
> External Email - Use Caution
>
> In some cases this is a hole in the cortex extending to the
ventricle...in others it
8s a low grade
> glioma which substantially enlarges ....and distorts the cortex
>
> On Tue, 1 Jan. 2019, 2:54 am Bruce Fischl <fis...@nmr.mgh.harvard.edu
wrote:
> Hi Matt
>
> yes, we have done this a number of times but of course it depends
a lot
> on the details of the abnormality so it is hard to give generic
advice
>
> cheers
> Bruce
>
> On Fri, 28 Dec 2018, Michael Sughrue
> wrote:
>
> >
> > External Email - Use Caution
> >
> > Has anyone had success extracting surfaces of brains with
obviously abnormal
> > surfaces....post-surgical or very distorted cortices from tumor
etc....even if
the
> extraction is
> > imperfect, is it possible to do with freesurfer and get
something imperfect
but
> useable.
> > ....typically this gets hung up at the fix tesselation step.....
> > if this isnt possible presently, any suggestions about how to
create modify
the source
> code to
> > create such a tool?
> >
> > On Fri, Dec 28, 2018 at 8:49 PM Matthieu Vanhoutte
<matthieuvanhou...@gmail.com>
> wrote:
> > External Email - Use Caution
> >
> > Dear Freesurfer’s experts,
> >
> > I used mri_coreg command to coregister PET image onto T1
volume.
Basically, this
> command
> > coregister PET image onto orig.mgz volume (default
target). However, I
wonder if
> T1.mgz
> > wouldn’t be a better target since it has been corrected
for
inhomogeneities and
> > intensity normalized ?
> >
> > Thanks for helping !
> >
> > Best,
> > Matt
> >
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> >
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