[Simnibs-discuss] Problem with editing segmentation results

[Gülce Lale]

Hello,

I’ve been editing my segmentation results with Freeview following the instructions on this page: https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html <https://simnibs.github.io/simnibs/build/html/documentation/command_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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