Hello
Thank you @tmedani, I will try tomorrow. For the T1 and T2, I guess I should import them in brainstorm and then register and reslice the T2 to the T1 image; and then launch the FEM or should I use the image created by fressurfer (eg after recon -all)? Especially, I saw that the output T2 of free surfer is cut to contains only the brain (eg no eye or skull)
However, even if it's looks great, I am not sure I will be able to use it since; right now, for nirs we need to have: -the head shape, the cortical surface, and the segmentation of the head in 5 tissue as generated by SPM (eg one value per voxel of the MRI). I will try t see if Mcxlab also support FEM mesh as input for the segmentation 
However, if we can improve the SPM segmentation easily (much faster and lighter in terms of dependencies), let's do it.
I actually generated the batch using the GUI of SPM and ask it to generate the Matlab script. This is actually similar to what is done at the beginning of process_fem_mesh (brainstorm3/toolbox/process/functions/process_fem_mesh.m at master · brainstorm-tools/brainstorm3 · GitHub). I think we can call this pipeline without creating the FEM mesh.
How did you evaluate the quality of the output?
That's the issue. It looks actually very similar and since we don't have any ground truth I find it very difficult to say this pipeline is better than another. Even Cat12 with just the T1 image seems to be giving very similar results. So I am very confused about what pipeline I should use. For now, I identified 3 main pipelines that would give me the head surface, cortical surface, and segmentation. (with the possibility to use BET from fsl to remove any suspicious skin that would appear in the background of the segmentation like in Noisy segmentation - #3 by edelaire)
1/ Cat12 on the T1 image
2/ Using Freesurfer on T1 and T2 to generate Head surface, and cortical surface; and SPM12 on T1 (and T2) to generate the segmentation. ( a variant is to use only the SPM segmentation result to complete the ASEG segmentation created by Freesurfer that only contains white matter; grey matter and CSF).
3/ Using one of the pipelines to generate a FEM mesh ( brain2mesh or SimNIBS)
But again, comparing the output seems complicated without ground truth. I will try to see if the developers of Mcxlab have any recommendations on how to generate this segmentation.
Edit: I tried Brain2mesh but tetgen is failing. From the tutorial, it means that I might have intersecting surfaces; but we cannot check when launching Brain2mesh directly from the T1 and T2 images.
Regards,
Édouard