Orientation of view in 3d viewer an issue?

Hi Francois & Brainstorm team,

I have imported a lesioned brain into Brainstorm after segmenting in FreeSurfer. However, now I have a question about the various views able to be selected in the 3D viewer (by right clicking the image and selecting "views").

When viewing the reconstructed cortex (lower # of vertices) with the scalp, I click the "view" button, select "back" and get the attached screenshot, which shows that the view is coming from the back but not beginning below the neck.

Next, I click the same view (back) with only cortex (again, lower # vertices) and it looks fine. Note that curve at the back of the brain interhemispheric fissure is present in the raw T1w MRI, so this is expected).

Next, I can view from the top with the Desikan atlas, and segmentation looks ok. Still lower # cortical vertices.

My question: is how Brainstorm registers the default "back" view with cortex an issue if we're doing sEEG source localization? If so, how do we alleviate this?I want to ensure that FreeSurfer/Brainstorm has registered our brains correctly so we may correctly do our analyses. Please let me know any thoughts. Thank you very much!!


Hey Adam,

I'm not sure that I got your issue.

Can you share a lateral/sagittal view of the head and the brain?

You can also plot the surfaces + the MRI, and then you can check the orientation of all the surfaces with the MRI.


But the alignment of the head and the brain of the same subject will be in the same coordinate system and with have the same orientation.

Brainstorm use different approaches to estimate the scalp surface (from a simple to a more realistic shape). Still, all of them are based on the orientation of the cortex, which is obtained from any segmentation tools and then reorientation to the SCS coordinate system when you load the MRI or compute the MNI coordinates.


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Hi Adam,

The views Left, Bottom, Right, From, Top and Back are with respect to the: Subject Coordinate System (SCS / CTF) https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Subject_Coordinate_System_.28SCS_.2F_CTF.29

SCS is based on: Nasion, left pre-auricular point (LPA), and right pre-auricular point (RPA).

  • Origin: Midway on the line joining LPA and RPA.
  • Axis X: From the origin towards the Nasion (exactly through).
  • Axis Y: From the origin towards LPA in the plane defined by (NAS,LPA,RPA), and orthogonal. to X axis.
  • Axiz Z: From the origin towards the top of the head.

In the figures, you can show the SCS axes with right-click > Figure > View axis (only the positive side of the axis is shown). X:red, Y:green, Z:blue. As such, the Back view corresponds to the view from a point from the -X axis (top figures); the Left view is the view from +Y axis (bottom figures), etc.

EDIT: added image

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