Meisler_ReadingInt_DWI

Code and data used in the Meisler, Gabrieli, and Christodoulou 2024 paper on DWI correlates of reading intervention. To cite: Meisler, Steven L., John DE Gabrieli, and Joanna A. Christodoulou. "White matter microstructural plasticity associated with educational intervention in reading disability." Imaging Neuroscience (2024).

If using code in this study, please note the following:

• You need a FreeSurfer license (register here: https://surfer.nmr.mgh.harvard.edu/registration.html)
• The code assumes a Slurm job scheduler with access to Singularity.
  • The image is amirro/tracula:latest https://hub.docker.com/r/amirro/tracula
• Your data must be organized in BIDS, and this code assumes there are ses-pre and ses-post data
• We cannot share the raw data used in this study, but we share all of the code used to reproduce it, as well as a CSV with necessary data to rerun the statistical analyses

preproc-code

First, run the longitudinal recon-all pipeline by invoking the job array submission script. In submit_recon_all_job_array.sh, change the bids variable and add the path to the recon_all_longitudinal.sh script in the last line. In recon_all_longitudinal.sh update the scratch (working direcory) and fs_img (container) variables to match your data.

Then, run the longitudinal tracula pipeline by invoking the job array submission script. In submit_job_array_tracula.sh, change the bids variable and add the path to the single_subject_tracula.sh script in the last line. In single_subject_tracula.sh update the IMG (container), license (FS license), and preproc_dev (path to trac-preproc in this repo) variables to match to your data directory.

stats

In this folder you will find the data frame with necessary subject data as well as a jupyter notebook for running statistical analyses and creating figures. Please refer to comments in the notebook for instructions.

Questions?

Please open an issue in this repository or email Steven Meisler at smeisler@g.harvard.edu