Relating Global and Local Connectome Changes to Dementia and Targeted Gene Expressions in Alzheimer’s Disease
This repo comprises the code for the manuscript:
- Elsheikh SSM, Chimusa ER, Alzheimer's Disease Neuroimaging Initiative, Mulder NJ and Crimi A (2021) Relating Global and Local Connectome Changes to Dementia and Targeted Gene Expression in Alzheimer's Disease. Front. Hum. Neurosci. 15:761424. doi: 10.3389/fnhum.2021.761424
For a brief summary of the paper, check out this video
This work uses data from the Alzheimer's Disease Neuroimaging Initiative publicly available
The image data are processed accoding to the pipeline reported in the script pre_process.sh Tractography, connectome creation and feature extraction is given in the scripts compute_conn_CSA.py, tracking_conn_ACT.py, metrics.py and metrics.py. Those scripts are inside the folder Scripts.
The main bioinformatics analyis is in the scipt analysis.py
The data extracted from MRI volumes needed in this analysis are accessable in the Data folder Those are the resulting connectomes, and the features. While the neuroimaging scripts are inside this folder