This CrossLong repository contains the raw manuscript files, data, scripts and other material associated with our work describing the ANTs longitudinal cortical thickness pipeline. An early version of this work was formally submitted to biorxiv:

Nicholas J. Tustison, Andrew J. Holbrook, Brian B. Avants, Jared M. Roberts, Philip A. Cook, Zachariah M. Reagh, Jeffrey T. Duda, James R. Stone, Daniel L. Gillen, and Michael A. Yassa for the Alzheimer’s Disease Neuroimaging Initiative. The ANTs Longitudinal Cortical Thickness Pipeline.

• Abstracts/: Rmd files for submitted abstracts.
• Data/: .csv files used for different analysis components.
  • RegionalPredictionPlots/: Prediction plots for MMSE for each of the regions (see Scripts/Analysis/doPrediction.R).
  • RegionalThicknessSlopeDistributions/: Various plots showing the thickness slope distributions for each pipeline in each of the 62 DKT regions (see Scripts/Analysis/plotSlopeDistributions.R).
  • RegionalThicknessSpaghettiPlots/: Spaghetti plots of the thickness values for each pipeline in each of the 62 DKT regions (see Scripts/Analysis/plotSpaghetti.R).
  • XmlFiles/: Original ADNI Xml files providing the demographics of the cohort used.
• Figures/: .png and .pdf files used in the manuscript.
• Manuscript/: Rmd files to create the manuscript submission. Also contains reviewer responses and cover letters to the editor.
  • Neuroimage/: Neuroimage submission (including reviews and our responses).
  • JAD/: Journal of Alzheimer's Disease submission (including reviews and our responses).
• Presentations/: Rmd files to create boomer presentations.
• Sandbox/: Outdated R scripts and .csv data files.
• Scripts/
  • Analysis/: R scripts to analyze the results.
  • RunStudy/: Perl scripts to run the FreeSurfer and ANTs pipelines, run DKT joint fusion, and parse files.
• Template/: ADNI template and auxiliary images used for the ANTs pipelines. Also, contains related .png files of the template with superimposed ratio values.