[tomoakiyama]

Hi everyone,

I’m new to Brainsuite and I’m interested in creating a brain surface mesh to compare vessel geometries. After loading the brain surface into Python from Brainsuite and displaying it using pyvista, I noticed that the mesh’s coordinates, scaling, and orientation differ significantly from those of the original image. Of course, the vessel mesh was created beforehand from the MRA co-registered with T1 images. Is there a way to bring it back to the same coordinate system as the original image?

Thanks!

[apatel98]

Hi,

I recently faced similar issue. I would suggest you to use “cortex.dewisp.mask.nii.gz” file,
1. Load it into 3D Slicer (or any other similar software). Open your T1w image as well and see if it matches coordinate space (it matched in my case).

2. In 3D Slicer, open segment editor and segment that mask. Finally, you should export segment as model, which will save segmentation as STL file. Again load saved stl and check for coordinate space.

It should work most likely!

Thanks!

[apatel98]

Of course, follow these steps after you finish cortical surface extraction steps (at least up to inner cortical surface).

[V2U-Services]

To resolve problems with orientation, scaling, and mesh coordinates:

To apply transformations, use software such as Blender (e.g., “Apply All Transforms”).
Verify the scale and rotation import settings in Unity/Unreal.
Assure uniform units for all tools.
Verify pivot points again to ensure proper mesh alignment.

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