Below is a table of scripts contained in this repository alongside a short written description. The scripts or organized in the order in which they were intended to be run. This is because some scripts, for example, depend on the output of previous scripts.
| Script | Type | Description | Key Output |
|---|---|---|---|
0_tidy.R |
R | Creates a tidyverse compatible data frame from available data from the raw CamCan data and from MRIQC outputs | data.rds, motion.rds |
1_subject_numbers.Rmd |
R markdown | Illustrates subject numbers based on various selection criteria. | |
1_inclusion_criteria.Rmd |
R markdown | Alternative to previous script, this time using a parameterized report format. | |
1_subjects_to_prep.R |
R | Based on a selection of inclusion criteria, writes out a text file with a list of CamCan subject IDs to preprocess in fmriprep | subjects_to_prep.txt |
2_fix_bids.R |
R | Script that fixes the formatting of the raw BIDS data to comply with BIDS formatting | |
2_fix_fmaps.R |
R | Script that fixes the formatting of the fieldmaps to comply with BIDS formatting | |
A_write_conditions.m |
MATLAB | Script for writing out conditions text file for use by the conn toolbox | conditions.csv |
A_write_covariates.m |
MATLAB | Script for writing out covariates text files for use by the conn toolbox | sub-###_task-TASK_standard_motion.txt |
B_conn.m |
MATLAB | Script for running conn toolbox on preprocessed fMRI data. | |
C_tidy_conn.m |
MATLAB | script for importing scan run specific connectivity matrices into a tidy format | ConnTbl.mat |
D_tidy.m |
MATLAB | Script for further tidying connectivity data. Calculates within, between, extra, and hipp means. | PredictTbl.mat, PredictTbl.csv |
E_bayesModels.R |
R | Script for running Bayesian regression models to test hy hypotheses of interest | |
E_linearModels.Rmd.m |
R | Script for further tidying connectivity data. Calculates within, between, extra, and hipp means. | |
F_cbpm.m |
MATLAB | Script for running the CBPM analysis | analysis-cbpm_outcome-%s_connections-%s_connectome-%s_thresh-%.03f_partialCor-%s.csv; .mat |
F_cbpm.slurm |
bash | Script for submitting a CBPM analysis to the SLURM batch queuing system | |
F_cbpm_nullsim.m |
MATLAB | Script for running a single null simulation for a CBPM analysis | analysis-cbpm_outcome-%s_connections-%s_connectome-%s_thresh-%.03f_partialCor-%s_nullsim-%04d.mat |
F_cbpm_nullsim.slurm |
bash | Script for running a CBPM analysis null simulation using the SLURM batch queing system. | |
F_cbpm_nullsim_jobarray.slurm |
bash | Script for running a CBPM analysis null simulation using the SLURM batch queing system using a job array. | |
F_corr_with_behav.m |
MATLAB | Script that correlates the strength of every connection with memory ability. | networks.txt, total.txt, pos.txt, neg.txt, diff.txt, count.txt, thesholded_mat.txt, downsampled_corr_with_behav_mat.txt |
F_delayed_submit.sh |
bash | Script for submitting CBPM analysis jobs to the SLURM batch queuing system. Designed to pause breifly to avoid MATLAB parallel computing bug. | |
F_howsimilar.R |
R | How similar are the functional connectomes calculated using the movie-watching, resting-staate, and sensorimotor tasks? | restmovie.csv, restsmt.csv, moviesmt.csv |
F_null_sim.m |
MATLAB | Function for performing a single CBPM null simulation. | cbpm_memoryability_randperms_%04d.mat |
F_predict_behavior.m |
MATLAB | MATLAB script for running hypothsized linear regressions. Prints the results directly to the MATLAB console. | |
F_visualize.m |
MATLAB | MATLAB script for visualizing the functional connectome. Calculates the grand mean connectome and connection variability. | downsampled_grand_connectome.txt, gradmean_networks.txt |
G_CreateFigure2.R |
R | Creates Figure 2 from the manuscript. | Figure2.png |
G_CreateFigure3.R |
R | Creates Figure 3 from the manuscript. | Figure3.png |
G_CreateFigureS1.R |
R | Creates Figure S1 from the manuscript. | FigureS1.png |
G_CreateFigureS23.R |
R | Creates Figure S2 and Figure S3 from the manuscript. | FigureS2.png, FigureS3.png |
G_CreateFigureS4.R |
R | Creates Figure S4 from the manuscript. | FigureS4.png |
G_CreateFigureS5.R |
R | Creates Figure S5 from the manuscript. | FigureS5.png |
G_Table1.R |
R | Creates Table 1 from the manuscript. Note: further formatting by hand performed prior to publication. | Table1.docx |
G_Table2.R |
R | Creates Table 2 from the manuscript. Note: further formatting by hand performed prior to publication. | Table2.docx |
G_CreateTableS5.R |
R | Creates Table S5 from the manuscript. | TableS5.docx |