Hi everyone,
I'm working on source localization from participants with individual MRIs and EEGs.
In looking at scout options, I'm visualizing the templated atlas's onto cortex. The templated ones look great (e.g., DKT_1, attached here). However, when I try to create from the subject's anatomy, the image looks less complete (DKT_2). Smoothing the image looks better, but I'm worried that I am doing something wrong. ANy thoughts? THank you!
Brian
The approach of creating surface scouts From subject anatomy is not is not recommended. This option is designed mostly for volume source models to create volume scouts.
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource
If the MRI segmentation method that was used did not return the cortical parcellations that you want, a way to get them would be to project them from the Default anatomy to the Subject anatomy.
Example of results:
DK atlas imported from MRI segmented with FreeSurfer
DK atlas from Default anatomy projected to subject anatomy
Hi Raymundo,
Thank you! That makes sense, although I'm confused by the alternative.
I'm trying to use brainnectome_leadDBS to identify scouts, but I can't see it within the 'scouts' tab unless I use the 'from subject anatomy' option.
Is there a way to get the non-templated (e.g., schaefer, brainnectome) to be options within the scout tab alongside the templated (e.g., DKT, brodmann, etc)?
I had previously added the brainnectome_leadDBS parcellation in the anatomy tab.
Thanks Raymundo!
Brian
In Brainstorm, the term Atlas is often used for two different things:
An anatomical atlas. These are volumes where each voxel has a label. This type of atlas are shown in the Anatomy view with this icon: 
A collection of scouts. First, a scout is a set of vertices that were used to estimate sources. There are surface and volume scouts, since sources can be computed in surface or volume grids. Thus there are surface and volume Atlases. More details in the head model tutorial (below). Scout and These are save inside surface files. Even if source space is a volume grid, there is not a one-to-one equivalence between a voxel (anatomy volume) and a vertex (volume grid).
https://neuroimage.usc.edu/brainstorm/Tutorials/HeadModel
This is an anatomical atlas. So, when you try to import it as an surface Atlas (made of surface scouts), the surface vertex are converted to MNI coordinates, and the label is search in the anatomical atlas. As you saw this does not always give good results. You could try to do it directly in the Scout tab as Atlas > Load atlas... and select the anatomical atlas .nii file as Volume mask or atlas.
These are computed when doing MRI segmentation. So it depends on which software was used.
Cortical segmentation (e.g. *.annot files from FreeSurfer and CAT12) are sucessfully imported as they are defined in the extracted cortical surface, not in the MRI volume.
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Cortical_parcellations
https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12#Cortical_parcellations
Ohhh! Okay, this was incredibly helpful. I see my error. Thanks Raymundo.
Follow-up re brainnetome atlas. I see in this post a few years ago (below), if we download and use FSAverage_2020 as a template, I now see multiple other scouts available (including brainnectome). these appear to be cortical and not volumetric. is this an appropriate approach?
Now I'm realizing that this approach just overrides the individual's MRI with the FSAverage MRI. I believe I need to map the brainnetome atlas onto the individual's MRI in free surfer, prior to brainstorm, and then when i upload anatomy to brainstorm, the brainnetome atlas should be available. right?
Yes, after that the .annot file for the brainnetome atlas will be automatically imported in Brainstorm>
This info in the Cortical parcellations section of the FreeSurfer tutorial. Check the example code, and the info from FreeSurfer function mri_surf2surf
Additional parcellations can be computed from FreeSurfer with mri_surf2surf (example):
this worked perfectly, thank you again Raymundo!
