Creating conductivity with SimNIBS and Brainstorm

[michefabb]

Dear @tmedani ,

it took some work, however here it is:

@tmedani

in Brainstorm: the DTI-EIG in BST with (154 512 512 12), the first 3 values are the resolution of the reference MRI, and the 12 values are the eigenvectors (3 vectors => 9 values ) + eigenvalue at each voxel (3 scalars) => 9+3 =12.
I don't know how the SimNibs team handles these values in their algorithms, with 6 values it seems that they have either a reduced model or using an other file to save the data.

In SimNIBS it is the output of dtifit --save_tensor from FSL TBSS, or the same prepared by SimNIBS dwi2cond

@tmedani

Brainstorm has the leadfield in the format of Nch x Ndip*3. Please check this: https://neuroimage.usc.edu/brainstorm/Tutorials/HeadModel#On_the_hard_drive

However, you may need to apply transformation in space since BST and SimNbs do not use the same CS. [again, it needs to dive into the code and the data and check].

You are right, here I am plotting the "leadfield sensitivity": since this plots the constrained dipoles orientation, there is no difference from a Coordinate System standpoint.
The one on the top is the Leadfield Matrix calculated with SimNIBS using also the dwi2cond (anisotropic White Matter derived from FSL TBSS dtifit) and the 12 tissues of charm, I imported to BST after reconstructing the HeadModel variable in Matlab and then imported in the GUI after referencing to 1st electrode (as done by DunEuro).
The one on the bottom is the LF Matrix calculated with BST-DunEuro Isotropic 5 tissues. I had to discard the DUneuro 5tissues Anisotropic as the result from Brainsuite does not look reliable (results are 1000 times bigger than all the others, see picture at bottom of my first post above https://neuroimage.usc.edu/forums/t/creating-conductivity-with-simnibs-and-brainstorm/47423/3). They look very similar to my eyes even if the results from SimNIBS look to have a smaller range (I mean as min,max interval of the LF).

You can find the result for BEM model in my first post (top picture https://neuroimage.usc.edu/forums/t/creating-conductivity-with-simnibs-and-brainstorm/47423/3), this is different from these results but no so much.

Feel free to comment!

Mic