Registered Report Reviewed and Accepted at PCI RR
Project Title:
Test-Retest Reliability in Functional Magnetic Resonance Imaging: Impact of Analytical Decisions on Individual and Group Estimates in the Monetary Incentive Delay Task_
Project Authors:
Michael I. Demidenko, Jeanette A. Mumford, Russell A. Poldrack
Respository & code maintained by: Michael Demidenko
This github repository contains the Python (.py) and R scripts (.rmd/.html) that are associated with the project.
This project is being submitted as a Registered Report. As described by the OSF, there are two stages to the
registered report. Stage 1 is the submission and review of introduction, methods and proposed analyses for the publication.
The Stage 2 is the completion of the analyses (as proposed), results and discussion section.
Note: The requirements file was generated using pipreqs
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Stage2_Code: Contains Python scripts, Jupyter notebooks, and cluster job files for stage 2 analysis.
- brain_mask: Folder containing brain mask files.
- cluster_jobs: Cluster job files for running analyses on Sherlock (AHRB/MLS) and MSI (ABCD).
- compute_icc_permutations.py: Script for computing ICC permutations (240 models).
- compute_icc_subsample.py: Script for computing ICC subsamples (Top ICC model).
- extract_values.py: Script for extracting values (Used to calculate mFD, % probe acc, probe response times.
- runs_withinrun_permutations.py: Script for within-run permutations, for each individual run 60 models * 4 contrasts.
- runs_withinrun_single.py: Script for single within-run analysis, top ICC model for subsampling.
- runs_withinsession_permutations.py: Script for within-session permutations, weighted fixed effect model for 60 models * 4 contrast.
- run-analyses.ipynb: Jupyter notebook for running summary (maps avgs, distributions) on group and ICC output files for between-run estimates.
- session-analyses.ipynb: Jupyter notebook for running summary (maps avgs, distributions) on group and ICC output files for between-session estimates.
- taskreliabilty-run_descriptives.Rmd: R markdown file for descriptive task reliability analysis.
- taskreliabilty-run_inferential.Rmd: R markdown file for inferential task reliability analysis.
- taskreliabilty-session_descriptives.Rmd: R markdown file for descriptive session reliability analysis.
- taskreliabilty-session_inferential.Rmd: R markdown file for inferential session reliability analysis.
- upload_neurovault.py: Script for uploading group derivatives to NeuroVault.
- output: folder contains the majority of estimates statistics used in the .Rmd analyses. Does not include ABCD data that includes subjects IDs (e.g. efficiencies, mFD, beh performance)
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Stage1_Code: Contains Python scripts and R markdown files from the Stage 1 Submission.
- designmat_regressors_define.py: Script for defining design matrix regressors.
- group_withinsession_permutations.py: Script for within-session group permutations.
- runs_withinrun_permutations.py: Script for within-run permutations.
- taskreliabilty_reporting.Rmd: R markdown file for reporting task reliability.
- taskreliabilty_reporting.html: HTML output of the task reliability report.