Usage

The software is a script run from the command line, currently tested on Ubuntu 18.04.

The main script is qias_brain_atrophy.sh located in the qiasbrainatrophy/scripts subdirectory of the qias project. At the command line while in the scripts directory, type ./qias_brain_atrophy.sh and include required and any desired optional arguments. Use the -h or --help flag for a description of script usage.

Dependencies for the script include:

• Freesurfer, version 6.0 or greater

  • Freeview, included with Freesurfer

• DCMTK

• R

  • gamlss

• Python, version 3.0 or greater

  • numpy

  • itk

• Latex and pdfLatex

The entire program takes approximately 4 hours to run on a standard desktop computer. The majority of this run time is due to the FreeSurfer segmentation.