data

Example of adding link to Google drive

• Edit the markdown file
• On Google drive, upload file, then create a globally readable link
• Include the link in the markdown
• Push updated markdown file, and any .png thumbnail images, to the repo
• Test link from the repo

Link	File Type	Image	File Size
nefetiti.obj	obj		3.5MB
T1_Utah_SCI.nii	NIfTI		109.1MB
IXI661-HH-2788-T1.nii	NIfTI		19.7MB
d2	e2	f2	g2

Common Data Models

Data sources, such as isosurfaces and meshes, either in repo (small files) or linked to Google drive (large files)

Name	Image	Size	vertices	faces/volumes
cube.stl		1 kB	8	12
sphere.stl		4.2 MB	8,447	16,890
bunny.stl		7.5 MB	14,290	28,576
igea.obj		9.6 MB	134,456	268,686
igea.stl		70.7 MB	134,456	268,686
igea.inp		48 MB	330,175	312,752

T1 Utah SCI brain

See folder containing T1_Utah_SCI_brain in format npy, stl and T1_Utah_SCI_outer in npy, stl, T1_Utah_SCI.nii, and T1_Utah_SCI.yaml.

RMU source files

• All_Hex_Dec.inp 212 MB (All-hexahedral created Dec 2021)
• Subject D
  • Sushan's original work
  • 18 year old female
  • 10 .stl files total:

Name	Image	Size	vertices	faces/volumes
brainstem Aseg_dura_falx_tent_BS.stl		862 kB	8,626	17,248
midbrain Aseg_dura_falx_tent_MB.stl		3.6 MB	35,522	71,092
ventricles Aseg_dura_falx_tent_V.stl		1.7 MB	17,174	34,328

2022-08-16: More to come.

Cubit>graphics perspective off  # orthogonal, not perspective view
Cubit>view iso # isometric x, y, z camera
Cubit>up 0 0 1  # z-axis points up

Simić brainstem

From GrabCAD

Brain (healthy), Slobodan Simić, April 2nd, 2019

Healthy human brain. Model shows complete brain with separated models for cerebellum, cerebrum, brain stem and corpus callosum. The model was segmented from MRI file downloaded at http://www.sci.utah.edu/sci-headmodel.html , model T1. "This project was supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant number P41 GM103545-18."

Six files:

• complete_brain.stl
• brainstem+corpus_callosum.stl
• corpus_callosum.stl
• brainstem.stl
• cerebrum.stl
• cerebellum.stl

See Also

• Spherical meshes used in
  • https://github.com/autotwin/mesh/blob/main/doc/octa_loop.md
  • https://github.com/autotwin/mesh/blob/main/doc/sphere_mesh_refinement.md

References:

• SCI Head model: https://www.sci.utah.edu/sci-headmodel.html
• IXI Dataset: https://brain-development.org/ixi-dataset/
• Alec Jacobson's commond 3D test models: https://github.com/alecjacobson/common-3d-test-models
• Philip Bayly, NeuroImaging Tools and Resources Collaboration (NITRC), Brain Biomechanics Imaging Resources (BBIR), accessed 28 Jun 2023.