Calling SPM segentation with T1 and T2

[tmedani]

Hi @edelaire

sorry for late reply,

@edelaire

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)

I have started an advanced FEM tuto here, you can have a look
https://neuroimage.usc.edu/brainstorm/Tutorials/tutoFEMadvanced?highlight=(FEM)

@edelaire

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).

Once the FEM mesh with SimNIbs is done, you will have the tissues in the database, and you can extract the surfaces of the FEM mesh easily (right click> extract surfaces). Then you can build any model you want.

@edelaire

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.

You can also have a look at the headreco.py script from where the SPM-CAT batch is called, I think it can help you to reproduce and adapt your code from there.

@Francois

@Francois

I don't know whether the T2 should be resliced on the T2 for the various segmentation methods. This might result in a loss of resolution...
@tmedani?

If I remember well, with SimNibs we don't need to reslice the volume, even more we don't need to co-register the T2 to the T1 from Braintorm, all these steps are handeled by SimNibs Headreco.
However, if we use the roast pipeline, I think reslicing is required either from Brainstorm or with adding an argument to the roast command line.