Module 6 FSL ANAT

FSL is a set of structural and functional MRI tools to analyze data. It is one of the most popular and well-supported MRI software suites.

Here is an overview of included tools: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslOverview

For this assignment you will run one subject (use your ADNI bids data) and then run that through the fsl_anat pipeline using HiPerGator. Instructions are in the slides but after you have the input .nii.gz file run in an SBATCH script (make sure to module load fsl):

fsl_anat -i [file].nii.gz -o [subID]

This can also be done live on a HiPerGator Desktop session or in an interactive "development" session. Make sure you request at least 6 GB of RAM and at least a couple hours.

You will upload the log.txt file. We will look at results in class but you are welcome to look at them on your own.