Higher resolution labelled anatomical regions

[hiimwilson]

Is there any chance you have the .ply files for the substructures of the brain? for example, within the lh.pial.Mice.Striatum.ply file, having subvolumes for the caudate and putamen. In the infralimbic cortex, subvolumes for the dlPFC, mPFC, etc.

I know that all these components are annotated in the Allen atlas. but it looks like .ply files in this repository only exist for the higher level brain structures. Having access to the lower level structures in Blender would be super helpful for scientific animation purposes.

[razvanmarinescu]

I'm afraid we don't have those models in higher resolution, but it can be done. Essentially, you need to run a segmentation algorithm on an MRI scan, and then convert the volumetric segmentations to cortical meshes as ply files that can be imported by Blender. You can then add those meshes to BrainPainter easily.

if you're interested, @vmallela0 has done this process for mice and can elaborate further

[razvanmarinescu]

Alternatively, you can also start right from a template/atlas segmentation .nii file, and convert each mask-id to a cortical surface mesh .ply file

[hiimwilson]

would love to hear @vmallela0 's processes a little further. Depending on how far i get, i'm happy to share the results.

[williamscotton]

Hi all. Did you ever get any further with this? Keen to modify the brainstem.ply to a medulla / pons / midbrain .ply based on the new(ish) freesurfer brainstem segementation..

[vmallela0]

hi @williamscotton , we retrieved the ply files we use for the mice brain renders from the allen institute (https://mouse.brain-map.org/). We applied transforms for these files that enable them to run on Blender and link with our BrainPainter platform. We only used the polygon files for the larger structures, because we felt that having all of the regions might cause for confusion when users fill in the biomarker data. If you think that having more detailed structures would be helpful, however, I would be more than happy to add them to them to the platform. Could you just let me know what regions specifically might be helpful (for example would you like to see pons divided into pons-motor, pons-sensory and pons-behavior state related or something similar)?

[williamscotton]

Hi @vmallela0 thanks so much for getting back to me. So the regions specfically interested in are the medlla oblongata / pons / midbran and superior cerebellar peduncle from Freesurfer (details below) https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Given the brainstem mesh is already there (have used this already to render brainstem) was hoping that relatively easy to generate these meshes? Thanks for your help with this it is greatly appreciated! Will

[vmallela0]

@williamscotton , we would likely have to apply the same transforms to the allen institute files and use the files corresponding with those regions. I just checked and found the superior cerebellar peduncle at https://connectivity.brain-map.org/3d-viewer?v=1&types=PLY&PLY=752 for example. Would using the allen files in lieu of the freesurfer generated ones be ok? It shouldn't take more than a couple of hours to add I think.

[williamscotton]

not at all - so long as it is similar / equivalent regions would be great! These regions are really important for movement disorders including PD / MSA / CBD and PSP in which our group and others are looking at now so would be fantastic if brainpainter able to incorporate! thanks again

[williamscotton]

@vmallela0 just to be clear this would be for human atlas!

[vmallela0]

@williamscotton my mistake, I thought you were referring to the mice atlas. I'm not sure entirely sure how it would work for the human atlas, we would probably have to run freesurfer then like you mentioned earlier. I can take a look and let you know if that's possible, but the files we have for the human atlases were actually acquired from brainder, so we would need to find the nifti atlases that they use and run the new freesurfer brainstem segmentation on them.

[williamscotton]

Thanks for this..

Yes if possible would be great but if too much I understand

Will

On 26 Jan 2022, at 18:24, Vedu Mallela @.***> wrote:

@williamscotton https://github.com/williamscotton my mistake, I thought you were referring to the mice atlas. I'm not sure entirely sure how it would work for the human atlas, we would probably have to run freesurfer then like you mentioned earlier. I can take a look and let you know if that's possible, but the files we have for the human atlases were actually acquired from brainder https://brainder.org/, so we would need to find the nifti atlases that they use and run the new freesurfer brainstem segmentation on them.

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