Cerebro-Viewer 0.0.9.1

Cerebro Viewer - A pythonic 3D viewer to visualize and plot brains

Cerebro_Viewer

A pythonic 3D viewer to visualize and plot brains and neuroimaging data

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Citing Cerebro:

Thanks for choosing Cerebro! We're honored to have you as a user. If you end up using our code in your project or research (which we hope you will!), we'd be grateful if you could give us a little shout-out by including a citation in your publication. This helps us spread the word, motivates us to keep making it better, and gives us warm and fuzzy feelings inside! 😊 Here's the reference you can use:

Sina Mansour L. (2023). Cerebro_Viewer A Pythonic 3D viewer to visualize and plot brains (v0.0.9). Zenodo. https://doi.org/10.5281/zenodo.7885669

Cerebro is a work in progress, and we're excited to share more with you soon! We're currently working on a manuscript that will explain how to use the software in your work. As soon as that's available, we'll let you know so you can cite it in your publication. Thanks for being part of our journey!

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Cerebro aims to provide a solution to advance the currently available methods for visualization of neuroimaging and brain connectivity data.

Installation

Cerebro is provided as a python package and requires Python 3. To install the package, simply run the following command:

pip install Cerebro-Viewer

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Motivation

Were you ever stuck when trying to visualize your study findings? Did you want to visualize different data formats and notice there’s no software to visualize them ALL in one place? Have you thought about a different way to present your findings but couldn’t find a tool to do it? Do you find limitations in current neuroimaging visualization software? And finally, did you ever want to generate nice brain visualizations within your script (without launching third-party software) and found the existing packages incapable/slow? Cerebro aims to provide a solution that tries to answer these needs.

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Development plan

Cerebro is currently under active development. The plan is to further develop exciting features through open-source contributions and discussions during hackathons, brainhacks, and other relevant opportunities. Checkout the contributors page to find out more.

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To try the package, run the following code after installation:

from cerebro import cerebro_brain_utils as cbu
from cerebro import cerebro_brain_viewer as cbv

my_brain_viewer = cbv.Cerebro_brain_viewer()

# render a surface
surface = 'pial'
surface_model = my_brain_viewer.load_template_GIFTI_cortical_surface_models(surface)

cifti_space = my_brain_viewer.visualize_cifti_space()

# render data over surface
dscalar_file = cbu.get_data_file(f'templates/HCP/dscalars/hcp.gradients.dscalar.nii')
dscalar_layer = my_brain_viewer.add_cifti_dscalar_layer(dscalar_file=dscalar_file,)

# enter interactive view
my_brain_viewer.show()