[Simnibs-discuss] ***Suspected SPAM*** Re: Problem with editing segmentation results

[Oula Puonti]

Hi Gülce,

If the file called <subid>_final_contr.nii changes according to your
edits then you have succesfully managed to propagate the manual edits
to the mesh file. 

The two other files, namely head_contr.fsmesh and brain_contr.fsmesh,
are generated by the headreco --check call. You should be able to re-
create those by first removing them and then re-running the check call.
You might have to also remove the .msh file and re-run the
volumemeshing step for the changes to propagate to the fsmesh files.

The editing in headreco works *only* when the --no-cat flag is used. In
the newest version of SimNIBS manual edits are easier to make, but note
that the new version is not backwards compatible, i.e., you need to use
the new headmodel generation pipeline called charm in that case.

Best,
Oula


On Fri, 2022-12-30 at 15:13 +0100, Gülce Lale wrote:
> Hello,
> I’ve been editing my segmentation results with Freeview following the
> instructions on this
> page: https://simnibs.github.io/simnibs/build/html/documentation/comm
> and_line/headreco.html My aim is to correct the CSF since it
> overflows to bone in some of the segmentations. After I edit the
> segmentation on the binary mask in the /mask_prep folder (in this
> case MASK_CSF.nii.gz), I run headreco surfacemesh and headreco
> volumemesh, the colors of the segmentation changes, these are saved
> in , SubID_final_contr.nii file. However, the lines saved in
> head_contr.fmesh and brain_contr.fmesh that define the boundary
> between bone and CSF are not changing.
> I tried to do these steps with CAT12 as well as without CAT12, with -
> -no -cat command. However, both of them resulted in the same way. Am
> I successfully editing the segmentation so that the magnetic field
> simulation done by SimNIBS will use the correct tissue borders? Or,
> do I have to apply something else in order to edit the line
> boundaries as well?
> Thank you for your help and answers in advance.
> Best wishes,
> Gülce
> 
> Gülce Lale
> MSc Neurosciences
> 
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