Module 6 FSL ANAT

FSL fsl_anat Assignment on HiPerGator

Purpose

FSL is a widely used software suite for analyzing structural and functional MRI data. In this assignment, you will run one T1-weighted structural scan through the fsl_anat pipeline on HiPerGator.

Reference overview of FSL tools: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslOverview

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What you will do

1. Choose one subject from your ADNI BIDS dataset.
2. Identify a single T1-weighted NIfTI file to use as input (.nii.gz).
3. Run fsl_anat on HiPerGator (either via SBATCH or a HiPerGator Desktop session).
4. Submit the pipeline log file (log.txt).

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Requirements

• Input file: a valid structural MRI NIfTI file: something.nii.gz (typically a T1w image).
• Compute request (minimum):
  • RAM: 6 GB or more
  • Time: 2 hours or more
• Output naming: use a clear subject identifier for the output folder name (e.g., your BIDS subject ID).

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Command(s) to run

Run these commands on HiPerGator from the directory where you want outputs saved:

module load fsl
fsl_anat -i /path/to/input_T1w.nii.gz -o sub-XXXX

Notes:

• Replace /path/to/input_T1w.nii.gz with the full path to your input file.
• Replace sub-XXXX with your subject ID (or another clear label). This becomes the output directory name.

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How to run it (choose one)

Option A — SBATCH script

• Create an SBATCH script that:
  • requests ≥ 6 GB RAM and ≥ 2 hours
  • loads the fsl module
  • runs the fsl_anat command above

Option B — HiPerGator Desktop session

• Start a Desktop session with ≥ 6 GB RAM and ≥ 2 hours
• Open a terminal
• Run the commands above

You are expected to use the skills you have already practiced in this course to set up either option.

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What to submit

Upload the log.txt file produced by your run.

Typical locations:

• It should be inside the output directory created by -o sub-XXXX.anat/ (possibly within subfolders depending on how fsl_anat ran).