- Week 2 (9/10) course material by Jiwoong Park.
- See for more info about ActFlowToolbox by ColeLab: https://github.com/ColeLab/ActflowToolbox
- You can find the original version of activity flow tutorial here: https://colelab.github.io/ActflowToolbox/HCP_example.html
- Cole, M. W., Ito, T., Bassett, D. S., & Schultz, D. H. (2016). Activity flow over resting-state networks shapes cognitive task activations. Nature Neuroscience, advance online publication. https://doi.org/10.1038/nn.4406
- Ito, T., Hearne, L., Mill, R., Cocuzza, C., & Cole, M. W. (2020). Discovering the Computational Relevance of Brain Network Organization. Trends in Cognitive Sciences, 24(1), 25–38.
- Sanchez-Romero, R., & Cole, M. W. (2020). Combining multiple functional connectivity methods to improve causal inferences. Journal of Cognitive Neuroscience, 1-15.
You may need to install additional packages to proceed the tutorial.
- Jupyter:
pip install jupyterfor development environment - Numpy:
pip install numpyfor numerical calculation - Matplotlib:
pip install matplotlibfor data visualization - scipy:
pip install scipyfor statistics - h5py:
pip install h5pyfor HDF data read/write
You can download and install ActflowToolbox by run below command and it's recommended for end-users. but in this course tutorial, I won't use ActflowToolbox but I will proceed the tutorial by using basic scientific computing packages only.
- ActflowToolbox:
git clone --recurse-submodules https://github.com/ColeLab/ActflowToolbox.git
Some files are from ActflowToolbox by ColeLab (https://github.com/ColeLab/ActflowToolbox)
Tutorial.ipynb: Notebook file forActivityFlowtutorialHCP_example_data/: HCP cognitive-task, resting-state fMRI data used in the tutorialHCPMMP1_on_MNI152_ICBM2009a_nlin.nii.gz: Cortical atlas by Glasser et al., 2016img/: supplementary figurescortex_parcel_network_assignments.txt: Assigned labels of large-scale functional network for each ROIs