Functional connectivity and group analysis

[Raymundo.Cassani]

Thanks for the explanation

@Francesca27

When I compute the sources and open the Cortex in the Scouts tab, I only see the default scouts and the Schaefer atlas isn’t listed.

This confirms that the surface Schaefer altas was not computed during the MRI segmentation. Otherwise, it would have been imported.

@Francesca27

However, if I import the atlas from the subject’s anatomy and then click on "Create surfaces"

If you use the option (in the Scout tab) Atlas > From subject anatomy > ANATOMICAL_PARCELLATION, it will create a surface scout atlas.

However, this is not recommended. Check the first image in the other post, to see how bad it can go: Atlas image look different in template vs volume

@Francesca27

Might one alternative be to compute unconstrained sources instead?

It's not about the orientation of the sources (constrained or unconstrained) but about the space (cortical surface or brain volume).

If sources have their positions on the cortex (surface sources), and you want to aggregate in Scouts, you need surface scouts, computed during the MRI segmentation.

If sources have their position on 3D grid that comprises the brain volume (volume sources), and you want to aggregate in Scouts, you need volume scouts. These volume scouts can be obtained from the anatomical parcellation.
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases

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1. The most accurate surface Schaefer atlas is the one obtained during the MRI segmentation

2. An alternative approach is to project the surface Schaefer scout atlas from the Default anatomy to the Subject anatomy. The Subject anatomy must be MNI normalized. This is not a good as the point 1.

3. Another way, that is not recommended, is to project the anatomical Schaefer parcellation, this is done by creating a scout atlas from the subject anatomy. This implies a projection from 3D anatomical parcellation to 2D scouts.