Functional MRI analysis scripts for the Neuroplasticity and Development Lab.

• Clone the scripts directory to your machine:

git clone https://github.com/NPDL/NPDL-scripts

• Modify the configuration script: NPDL-config.sh.
• Source the configuration script in your shell startup file (e.g. in ~/.bashrc).

Required (with recommended versions):

• FSL (5.0.9)
• Freesurfer (5.3.0)
• HCP Workbench (1.2.0)
• Mricron (2014-08-04)
• Python (2.7) [with docopt, matplotlib, nibabel, numpy, scipy, gdist]
• Imagemagick

Optional:

• FSL-Fix (1.062 beta)
  • R (>3.2.0) [with kernlab, ROCR, class, party, e1071, randomForest]
  • MATLAB (R2014a)
• ICA-AROMA (0.3_beta)
• FSL PALM (alpha97)