Project lesion drawing to cortex

[Raymundo.Cassani]

Hi Adam,

@bakerdon

First, I ran FreeSurfer on the T1 to segment the brain. I imported FreeSurfer results into Brainstorm.
After this, outside of Brainstorm, I normalized the lesion drawing (and T1) to MNI space. Now, I have lesion drawing in MNI space. I used this script: (spmScripts/nii_enat_norm.m at master · rordenlab/spmScripts · GitHub).
Finally, back in Brainstorm with FreeSurfer results, I computed MNI normalization of the imported anatomy

In this approach, you need to ensure that the MNI normalization that is performed in Brainstorm uses the Segment method. As this is the method that is used in the nii_enat_norm.m script.

Moreover, you can import the normalized lesion volume, with right-click on the Subject, then Import MRI and the option Volume atlas (MNI space). By doing so, it will be possible to verify the alignment between the volumes in Brainstorm.

@bakerdon

My steps for this second part were as follows: atlas tab --> add scouts to atlas --> selected the normalized lesion mask under the settings volume mask or atlas (dilated, MNI space). When I got the warning (screenshot below), I said Yes, just to see what it would look like.

While using a volume mask to create cortical scouts is possible, results must be verified, as the warning points, the results are not optimal. This happens as to be assigned to a scout a cortical vertex must be INSIDE the volume parcellation, which is not always the case as the cortex vertices are often at the border of the the volume parcellation. See these examples, of cases where it goes wrong:

• Atlas image look different in template vs volume
• Connectivity between functional networks - #3 by saeedimanparast

In your case, you can use the resulting green scout as an started point and edit it to reflect what you expect.

@bakerdon

Then, I applied the MNI transformation as prompted (since I computed it in Brainstorm already, screenshot below), which I believe matches up the lesion drawing and Brainstorm anatomy to MNI space?

There is no MNI transformation happening, the transformation popup that you get is for MRI orientation only.

FYI, @EHill , I remember you've worked on something similar before — if you have a moment, your input here would be really appreciated!