This is the code used for data processing and statistical analyses in Flaherty R, Sui YV, Masurkar AV, Betensky RA, Rusinek H, Lazar M. Diffusion imaging markers of accelerated aging of the lower cingulum in subjective cognitive decline. Frontiers in Neurology. 2024;15. doi: 10.3389/fneur.2024.1360273.
Running this code requires the following dependencies:
- RStudio >= 2023.09.1+494 with the following packages:
- base >= 4.3.2
- tidyverse >= 2.0.0
- arsenal >= 3.6.3
- ggpmisc >= 0.5.4-1
- interactions >= 1.1.5
- ggtext >= 0.1.2
- FreeSurfer == 7.4.1
- FSL == 6.0.4
- MRTrix3 == 3.0
- python == 3.7 with package dmri-amico == 1.5.4 (more detailed installation instructions for AMICO are available on their github)
- zsh
- MatLab >= 2023a with Image Processing Toolbox
Scripts with .sbatch extensions are written for submission to a SLURM batch processing system on an HPC. It is highly recommended to conduct this analysis on an HPC. Scripts with .sh extensions are written for Mate Desktop and can be run with either bash or zsh. Scripts with .zsh extensions can only be run with zsh.
Run each numbered script in order. Unnumbered scripts are called by the numbered scripts and do not need to be called manually. Wait until the script finishes before starting the next numbered script.
The original analysis was conducted on Red Hat Enterprise Linux Server release 7.4.
The Cam-CAN data is available at https://camcan-archive.mrc-cbu.cam.ac.uk/dataaccess/
Shield:
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
