Hi
This is more a theoretical question:
@Francois has posted several times that it is not useful nor accurate to use Broadman Atlas for defining Scouts, instead you should create a new one with the ROI
But I don't get what will be the best approach, I mean by example:
If my ROI is Inferior Frontal Sulcus , Can I use an atlas to locate and constrain the scout and then should I divide it in smaller regions? or Should I create a new and trace a smaller scout from the selected area?
How can I make it more objective, I mean, is not more subjective to pick up a small region and make it an scout, than use standarized scout atlas? (for the experiment to be comparable across subjects)
Thanks in advance!
You have two possible approaches:
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Atlas based / hypothesis driven: Your hypothesis is that the activity in a specific brain region is different between two experimental conditions. You can try to find a ROI in one of the anatomical atlases available in FreeSurfer/CAT/BrainSuite/BrainVISA that matches the brain region of your hypothesis. The scout should ideally not be too large (it would average too much different information), or too small (otherwise you might miss the target in some of the subjects in your study), and it should be relatively homogeneous in all the directions (eg. not a very long strip of isolated sources). In the Brodmann atlas, some regions are perfectly fine (eg. V1, V2, MT, perirhinal, BA44, BA45) others are not (eg. BA1, BA2, BA3, BA6)
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Data driven: In a grand average across all subjects (or in a pilot study), you find where your effect of interest seem to be located by the minimum norm method (eg. auditory cortex, motor regions, etc...), you create a scout that captures this activity, then project the scout from the template back to the individual subject spaces (in the Scout tab, menu Scout > Project to...)
Both approaches would give you equivalent scouts for all the subjects, and avoid the biases introduced by manual marking on each subject individually.
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Hello Tourette95,
What I've been doing is actually to manually create the scouts for my ROI. You can then follow the actual borders of your ROI as per described in the literature and recreate those within Brainstorm. It's... time consuming and maybe not the most pleasant experience, but I can give you a few tricks I discovered to make it not as bad.
First, you can create multiple scouts and use the merge tool. Because all new scouts are kinda-round-ish, you can start by covering as much as you want with multiple smaller scouts and then fuse them together in an approximative version of your final shape.
After that, you can manually add/remove vertex by vertex by holding the shift key. If you do that on an Vertex already part of that scout, it should remove it. A thing to keep in mind, is that the tool tries to add/remove the closest vertex from where you clicked.
Let me know if these instructions are not clear or if you would like to know more about my rationale behind this choice.
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You can also start the scout on a subject from some predefined MNI coordinates (from your hypothesis): use the menu "Scout > New: coordinates" and fill in the MNI coordinates.
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Really thank you both!
that information is so useful!
:)!
I'm gonna try it and I will let you know if it works!
Thank you!