How to create mirror ROI in the other hemisphere?

Hello brainstorm expert,

I have a scout in the right hemisphere created in one hemisphere based on the group comparison t-map. How can I create a mirror scout in the left hemisphere? Thank you!

Yuhan

Hello
The is unfortunately no easy solution for this.
You can use the available anatomical atlases (if you used FreeSurfer) to make sure your left scout is in the same anatomical region.
Francois

Do you mean to manually draw the scout on the other hemisphere (original scout from the right hemisphere), and then use the template to check if the two scouts are in the same anatomical region?

Another question - is there a way to create the scout based on thresholding the t-map (or thresholding the map based on p<0.05), and constrain the ROIs by applying a mask from the region in anatomical atlases?

Thank you.
Yuhan

Do you mean to manually draw the scout on the other hemisphere (original scout from the right hemisphere), and then use the template to check if the two scouts are in the same anatomical region?

Yes, I cannot think of a better solution at the moment.

is there a way to create the scout based on thresholding the t-map (or thresholding the map based on p<0.05)

Display the thresholded t-map you are interested in, then create your scout with the button “Constrained” selected.

and constrain the ROIs by applying a mask from the region in anatomical atlases?

Not at the moment.

Thanks for the answers.

Sorry to keep extending the questions - If I can’t constrain the ROI by applying a mask, can I do a cluster thresholding to obtain a scout? For example, thresholding the t-map and do another cluster thresholding to get rid of the little clusters.

Thank you.
Yuhan

What do you mean with “cluster thresholding”?
If you select the button “Constrained” and then grow your scout, it won’t expand beyond the actual “cluster” or significant vertices.

I’m sorry. I thought by clicking “constrained” it will create scouts across the whole brain above the threshold. I see that it will only grow within the area where I first planted the scout seed.

I am still trying to find a better way to manually create mirror scout in the other hemisphere. Is there a way to control it so I can make it as similar to the scout in the original hemisphere? At the moment I can select a seed in the other hemisphere and click the arrows scout size to grow the mirror scout, but it’s hard to control the shape to be as similar as the original scout. How do I manually control the shape of the scouts, or is there a paint tool to manually erase and add vertices within the mirror scout?

Thank you.
Yuhan

Is there a way to control it so I can make it as similar to the scout in the original hemisphere?

Not at the moment. But I guess this is possible using the FreeSurfer registered spheres (http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects). The right sphere could be mirrored to match the left sphere, and then the region could be projected from one sphere to the other, like it is done when projecting scouts across surfaces or subjects (https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/math/bst_project_scouts.m).

This is already part of our infinite todo list (http://neuroimage.usc.edu/brainstorm/Next#Anatomy).
We currently do not have the resource necessary to develop this feature, but you are more than welcome to contribute to the project and help us developing it.

or is there a paint tool to manually erase and add vertices within the mirror scout?

Yes, there is: read the tooltip of the first button in the panel for instructions. Or read the instructions in section “Add vertex manually” in the tutorial:
http://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#Growing_a_scout
Click on the “Edge” button of the Surface tab to see the vertices that you can actually click.

Thanks for the solutions. My data is infant MEG data, and we don’t always have the baby’s MRI. So I registered everyone to the Oreilly 1-year-old template. We also don’t do freesurfer on the MRIs younger than 1 year old. So I think I can’t use the fredsurfer registered spheres. So at the moment I’m going to use the tools to grow scouts.

I also have another question about how to create scout for individual subject based on their top 50% of the activity centered from the peak vertex within a region. For example, all subjects activated temporal lobe+fusiform at a time window. I would like to select a big region based on the atlas as the boundary of the individual scout. Within this big region (temporal+FFG), can I grow a scout centered around the vertex of the maximum activity and grow or extend the scout to only vertices that have amplitude at top 50% of activity across all vertices within the temporal+FFG region.

Thank you!
Best, Yuhan

I’m sorry, we don’t have any tools beyond the ones already discussed.
If you want to develop additional tools for the design of ROIs, you are welcome to help us with the project. Here are the description of the cortex, source and scouts structures:
http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_Surface
http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#On_the_hard_drive
http://neuroimage.usc.edu/brainstorm/Tutorials/TimeFrequency#On_the_hard_drive
http://neuroimage.usc.edu/brainstorm/Tutorials/Scripting

Note that “50% activity” is not a meaningful criteria, it depends on the maximum of the current color bar: http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Display:_Cortex_surface

Thanks for clarifying this. I will keep it in mind the scout tool developing project. If I have something I’ll update to the group.

Thanks again.
Yuhan