All of the following scripts can be found on the head node under: /usr/local/sge_templates/

If you are modifying any of the scripts, check for syntax errors before submitting a job.

> sh -n script.sh

• bxh2analyze - Create Analyze or NIFTI files from BXH files
• qa - Run fmri QA analyses on the cluster

• BET - Brain Extraction Tool
• FEAT Level 1
• FEAT Level 2
• FDR - Calculate the false discovery rate (FDR) on 3rd Level/group FSL analysis

• freesurfer - Freesurfer Segmentation