dzhi1993 / brainhack_western Goto Github PK

Brainhack 2019 in Western University, Diedrichsen Lab (Ongoing)

This project aims to show cortical surface flatmap using python-based opengl programming. The first version features to allow users to change underlay, add multiple overlays and borders, etc. Eventually, we want to make it as a handy package for lab use to achieve several neuroimaging tasks and involves the 3D volume viewer along with the flatmap as an interactive image viewer, similar to the AtlasViewer.

Install OpenGL library of python version through standard pip installation:

pip install PyOpenGL PyOpenGL_accelerate

Or you can install the source repository by branching/cloning and running setup.py:

git clone https://github.com/mcfletch/pyopengl.git
cd pyopengl
python setup.py develop
cd accelerate
python setup.py develop

Please follow the instruction in the raw pyopengl repository

Install below dependencies:

pip install nibabel numpy matplotlib glfw

the default setting has two overlays (test.func.gii, test2.func.gii), which can be found in onlineAtlas folder.

python main.py

All data stored in onlineAtlas folder
The flatmap topology file is fs_LR.164k.L.flat.surf.gii
The default left hemisphere underlay is fs_LR.164k.LR.sulc.dscalar.nii
The borders information can be loaded via

`fs_LR.164k.L.border-CS.func.gii` 
`fs_LR.164k.L.border-IPS.func.gii` 
`fs_LR.164k.L.border-PoCS.func.gii` 
`fs_LR.164k.L.border-SF.func.gii`

The default loaded overlays are test.func.gii and test2.func.gii.