README

vasst-dev repository


Add the following to your ~/.bashrc file to set-up paths:

VASST_DEV_HOME=<path to your repository>/vasst-dev
if [ -f $VASST_DEV_HOME/init_vasst_dev.sh ]
then
 . $VASST_DEV_HOME/init_vasst_dev.sh 
fi


Add the following to your ~/.octaverc file:

addpath(genpath('<path to your repository>/tools/matlab'));




pipelines/

Description:

These are scripts/programs that are aware of the standardized pipeline folder structure and read/write data from/to the standardized folder structure. Writes to and reads from the current project folder, thus working directory should be the one where the subject ID folders are sub-directories.

e.g.:  
  preprocT1 subject14



Required arguments:

Subject ID(s) / Subject List

Required documentation:

General description
Input/output arguments
Optional arguments
List of software dependencies (e.g. FSL, Freesurfer, other tools)
List of prerequisite pipelines (e.g. pipelines that need to be run prior to this)
Standardized data inputs
Standardized data outputs



tools/

Description:

Various command-line tools where input and output files must be specified -- i.e. does not assume standardized pipeline folder structure.
e.g.:  SegmentBrain <input brain nifti>  <output brain segmentation nifti>


e.g.:
  concatDWI in_dwi_shell1.nii.gz in_dwi_shell2.nii.gz out_dwi_multishell.nii.gz