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Computational-Neuroscience

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Using computational tools to explore the networks underlying cognitive neuroscience

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# Computational Neuroscience
This repo showcases some work I have done using computational tools to explore the networks underlying cognitive neuroscience.

### Utils

1. A Docker image to run NetPyNE with python3 [here](https://github.com/karnigili/NetworksNeuroscience/tree/master/docker/docker_python)
2. A Docker image to run NetPyNE on jupyter notebook [here](https://github.com/karnigili/NetworksNeuroscience/tree/master/docker/docker_jupyter)

### Tutorials

1. This tutorial discusses rs-fMRI preprocessing using mriQC, fMRIprep, and freesurfer & feature exctraction using nilearn and python. Read more on medium at my post [Identifying resting-state networks from fMRI data using ICAs](https://medium.com/@gili.karni/exploring-cognitive-differences-via-resting-state-networks-2112bf5291e2). Or find the python notebook [here](https://github.com/karnigili/NetworksNeuroscience/blob/master/rs_fmri_networks_ICA.ipynb).

2. This tutorial, following the previous one, explores using LSTMs for classifying preprocessed rs-fMRI data of ADHD patients from healthy controls. Read more on medium at my post  [Classifying ADHD from healthy controls using LSTMs with rs-fMRI data](https://medium.com/@gili.karni/classifying-adhd-from-healthy-controls-using-lstms-with-rs-fmri-data-300c1f3e9697). Or find the python notebook [here](https://github.com/karnigili/NetworksNeuroscience/blob/master/rs_fmri_LSTM_classification.ipynb).

3. This tutorial presents exploring biological neural netwrok via a simple simulation using NEURUON and NetPyNE. I present a docker image that runs the software in an isolated environment (See [here](https://github.com/karnigili/NetworksNeuroscience/tree/master/docker)) and an example of how to use it. Read more on medium at my post [Simulating Biological Neural Networks with NetPyNE](https://medium.com/@gili.karni/simulating-biological-neural-networks-with-netpyne-d1744c1f4a02?sk=a89822f7c03e3b7eddc72386d069c913). Find the full code [here](https://github.com/karnigili/NetworksNeuroscience/blob/master/netpyne_simulation_synchronization.ipynb).

Computational-Neuroscience

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