https://github.com/brain-to/gecs
Science Score: 13.0%
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Low similarity (7.4%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: BRAIN-TO
- Language: Python
- Default Branch: main
- Size: 48.8 KB
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- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Codes for Generative Embedding (using DCM-based connectivity features) with Clustering Solution (GECS). In this repository, we specifically use P-DCM [1] which is a state-of-the-art DCM framework.
The overall generative embedding process comprises of:
Step 1. Computation of connectivity features for task-fMRI data of several subjects in an iterative manner using the DCM framework(s).
P-DCM was initially developed on Matlab. For S-DCM [2], one may refer to the standard SPM package which involves the code for running S-DCM on task fMRI data.
Alternatively, one may also use the python implementation of both P-DCM and S-DCM which are available in the src/utilities folder in this repository.
Step 2. Obtain the clusters based on the estimated connectivity features.
Once, the connectivity estimates are obtained it is recommended to store them in a pandas dataframe as a '.pt' file with subjects in rows and connectivity between different regions in the columns.
This dataframe is to be used in the src/EC_cluster.py script to obtain the clusters by utilizing k-means and leave-one-out-cross validation strategy.
The Accuracy and Cluster Membership Index (CMI) scores are also computed simultaneously.
References:
``` [1] Havlicek, M., Roebroeck, A., Friston, K., Gardumi, A., Ivanov, D., & Uludag, K. (2015). Physiologically informed dynamic causal modeling of fMRI data. Neuroimage, 122, 355-372.
[2] Friston, K. J., Harrison, L., & Penny, W. (2003). Dynamic causal modelling. Neuroimage, 19(4), 1273-1302. ```
Owner
- Name: Brain Research in Advanced Imaging and Neuromodeling - Toronto
- Login: BRAIN-TO
- Kind: organization
- Repositories: 4
- Profile: https://github.com/BRAIN-TO
GitHub Events
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- Public event: 1
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Last Year
- Public event: 1
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Dependencies
- pipinstallnetworkx *