This repository contains packages, scripts, and notebooks for the following article Consistency of resting-sta fMRI connectivity on a single individual over 2.5 years and 13 sites using the Canadian dementia imaging protocol (to add link and DOI).
Click the following link to reproduce the analysis on binder:
Here is a brief description of each item in the repository:
Matlab Scripts
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niak_pipeline_t1_average.m - Octave script averaging T1w images of a subject iteratively with linear registration inside a NIAK container.
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Csub_t1_average_all_scans_final.m - Octave script that calls niak_pipeline_t1_average.m and provides needed information.
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Csub_preprocess_all_scans.m - Octave script to run a preprocessing pipeline analysis on CDIP data inside a NIAK container.
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HNU1_preprocess_sll_scans.m - Octave script to run a preprocessing pipeline analysis on HNU1 data inside a NIAK container.
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connectome_test_retest.m - Octave script to run a connectome pipeline on preprocessed fMRI data to generate connectivity maps.
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connectome_HNU.m - Octave script to run a connectome pipeline on preprocessed fMRI data to generate connectivity maps.
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all_correlations_Csub.m -
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all_correlations_HNU.m -
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connectome_test_only.m -
Notebooks
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graphs.ipynb - Jupter notebook that continas graphs for Csub intra-site, inter-scan consistency over time (2.5 years),Csub vendor consistency and HNU intra-individual consistency per network, and across all networks
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stats_repro.ipynb - Jupyter notebook used for generating the statistics used to assess consistency of individual rsfMRI measures within/between sites
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stats_fingerprinting.ipynb - Jupyter notebook used to assess the ability of a simple data-driven cluster analysis to recover the identity of subjects based on connectivity maps of a single network
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Csub-intra_png - images used for average connectivity maps
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all_correlation_list.csv - spreadsheet with correlations for intra-site and inter-scan consistency
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HNU1_Csub.csv -
Dockerfile - defines the executable environment used for binder container
HNU1_dataset_with_Csub - dashboard that shows the consistency of brain connectivity maps generated using resting-state functional magnetic resonance imaging (rsfMRI) across 17 visits of a single individual
This repository has also been archived on Zenodo: (provide link and DOI)