[Simnibs-discuss] Recurring poor GM segementation/surface with charm pipeline

[Oula Puonti]

Hi Dan,

Looking at the attached screenshot I would not expect a GM surface like
that from charm, so I'm guessing something went wrong with the
segmentation here. 

If the data set is openly available I can process a few of the
problematic subjects and see if I can tweak some of the settings to
make this work better.

Best,
Oula

On Tue, 2023-01-17 at 20:41 +0000, Daniel McCalley wrote:
> Hi all, 
> 
> I've noticed that in many (almost all) of the scans I've put through
> the charm pipeline have returned really nice surface segmentations of
> the scalp, bone, WM, etc. However, the grey matter surface typically
> appears very poor (loses detail in sulci/gyri).
> 
> I've tried headreco and charm for 3 separate anatomical scan
> acquisitions and got the same result consistently (photo attached). 
> 
> I suspect something in the despiking/cleaning tetrahedra step in
> charm may be causing this, but I'm not sure. Any pointers or things
> to try for troubleshooting? 
> 
> Best,
> 
> Dan McCalley, Ph.D.
> Postdoctoral Scholar, Padula BRAVE lab
> Stanford University
> School of Medicine, Psychiatry and Behavioral Sciences 
> (he/him)
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