### Topological correction step

Posted:

**Tue Jan 30, 2018 3:45 pm**Hi,

I'm working on algorithms of brain segmentation, in particular the cortex. My interest in using AIMS commands is to obtain a mesh of my results, which are usually fuzzy (values between 0 and 1, thus not binary). My inputs are a T2w MRI and its cortex segmentation. I have tried AimsMesh before a format conversion and a thresholding and it works but without topological correction, so I think that it could improve the final mesh.

Could you tell me please how can I add a topological correction step given my inputs ? Which commands allow us to correct it and which extra-parameters do they need ? I tried to reproduce the Morphologist pipeline without success and I don't know in which step it goes wrong.

Thank you.

I'm working on algorithms of brain segmentation, in particular the cortex. My interest in using AIMS commands is to obtain a mesh of my results, which are usually fuzzy (values between 0 and 1, thus not binary). My inputs are a T2w MRI and its cortex segmentation. I have tried AimsMesh before a format conversion and a thresholding and it works but without topological correction, so I think that it could improve the final mesh.

Could you tell me please how can I add a topological correction step given my inputs ? Which commands allow us to correct it and which extra-parameters do they need ? I tried to reproduce the Morphologist pipeline without success and I don't know in which step it goes wrong.

Thank you.