Hi! I am new to brainstorm and I am trying to visualize an MRI mask (based on AAL2 atlas and resampled to mni template) that I would like to plot on a 3d cortex. However, whenever I overlay the mask, it will give me the orthogonal slices including the skull and scalp. Is there a way in brainstorm to get rid of the orthogonal slices themselves or at least the skull and scalp without getting rid of the mask in the image? Thanks!
Hi @princessamygdala, you can plot the AAL2 atlas alone without overlaying on the MRI, and then add the 3D cortex on it.
- Right-click on the anatomical atlas, then Display > 3D orthogonal slices
- Then, on the Surface tab (right side on the main Brainstorm in), click on Add surface (
), and select the cortex
P.S. Nice user name
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Dear Raymundo,
Thanks for the quick reply! I tried this step but unfortunately, it doesn't work (still shows the orthogonal slices and not just the mask and cortex). Could it be that it's because of my imported nifti mask file itself (maybe because it's resampled)?
Kind regards,
Marla
PS: Thanks 
What is going on here is that the AAL2 atlas is an anatomical atlas, it is defined in the MRI volume space, each parcellation is a set of voxels that include not only the cortex for white-matter; while the cortex is a surface, a set of dots in the space that delimits the cortex, and it is not defined a as set of voxels.
It is possible to set of surface parcellations (Scouts in Brainstorm jargon), from the anatomy atlas, the results are not often great. See option From subject anatomy https://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#Scout_toolbar_and_menus