[Simnibs-discuss] Brainstem visualization

[Oula Puonti]

Hi Atsushi,

In gmsh if you select Tools -> Visibility, and then select WM in the
tissues list (along with GM if you like) you should be able to see the
brain stem.

Best,
Oula


On Tue, 2023-01-17 at 13:15 +0900, Atsushi Shima wrote:
> Dear Oula,
> 
> Thank you for your reply.
> I wanted to display the results of the simulation on the brainstem,
> instead of creating labels for the brainstem.
> Similarly in Ernie, the brainstem was not displayed in the results.
> Do I need to process to display of the white matter in gmsh?
> I appreciate your help.
> 
> Best,
> Atsushi
> BS.pngBS2.png
> 
> 2023年1月17日(火) 7:59 Oula Puonti <oulap at drcmr.dk>:
> > Hi Atsushi,
> > 
> > Are you trying to create a separate label for the brain stem? It
> > should
> > be part of the white matter in the standard charm output.
> > 
> > You said that you can see the brain stem on ernie, so I'm wondering
> > if
> > something went wrong when you ran the specific subject where you
> > cannot
> > see the brain stem. 
> > 
> > Could you maybe send us a screenshot showing the problem?
> > 
> > Thanks,
> > Oula
> > 
> > 
> > On Sun, 2023-01-15 at 21:20 +0900, Atsushi Shima wrote:
> > >  Dear SimNIBS Team,
> > > 
> > > Thank you for the wonderful program. I have a couple of
> > > questions.
> > > 
> > > I would like to visualize the brainstem.
> > > The pipeline of "charm" seems working well. However, when we see
> > > the
> > > results with gmsh, there is a lack of the brainstem.
> > > I also tried the test data (ernie m2m), however, I could see the
> > > brainstem.
> > > 
> > > Is it possible to visualize the brainstem in SimNIBS version
> > > 4.0.0?
> > > (I could see the previous papers describing the brainstem by v2
> > > or
> > > 3.)
> > > I appreciate your help.
> > > 
> > > Sincerely,
> > > Atsushi Shima
> > > _______________________________________________
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> > > Simnibs-discuss at drcmr.dk
> > > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
> >