I added an extra check for this error:
Please update Brainstorm and try again.
Note that importing surface scouts volume atlases is not recommended.
This menu Import from subject anatomy in the Scout tab is designed mostly for volume source models:
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource
After reloading the atlas, I tried to run the "Down Sample to Atlas" function in the pipeline but I got an error output:
Probably because you have some empty scouts in there...
We don't really recommend using this process "Downsample to atlas" anymore.
Instead: extract the scouts time series and then call the process " Full source maps from scouts":
https://neuroimage.usc.edu/brainstorm/Tutorials/Simulations#Generate_full_source_maps_from_scouts
The atlas in the anatomy folder:
It looks like there is a scaling issue here: your ROIs cover most of the skull and skin, and don't look at all aligned with the cortex.
The atlas in after reloading in the drop-down manu:
This looks pretty ugly in my opinion. Use surface-based atlases for surface-based source modeling.
My file structures:
I can see here that you are using a linear MNI normalization.
If you are using MNI-based parcellations, it is highly recommended to use a non-linear MNI registration. Use SPM Segment, or even better: run CAT12 on your MRI.
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#MNI_coordinates
https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12