Skip to content

Module 3 FreeSurfer on HiPerGator

Jump to bottom
Jared Tanner edited this page Feb 1, 2025 · 15 revisions

Complete the following

The video linked to below will walk you through setting up and processing the sample data. If you follow along, you should have everything completed for the homework assignment other than uploading the requested files. Remember that subject names, paths, directories, and more might be different. For example, in the video the Module3 directory was in /blue/clp7934/share/Module3 but in 2025 it was in /blue/clp7934/share/clp7934/Module3. Make changes as appropriate.

I did much of the copying and organizing on one of the login nodes. What I recommend is you not do that. It's within the acceptable use of HiperGator to do that, but it's better to do the work in a Console session, a HiPerGator Desktop session, or a SLURM interactive session.

To switch to a SLURM interactive session, you can paste the following for a 2 hour session with 4 GB of RAM. Note that if you close the browser window, it's possible the session will end.

srun --mem=4gb --time=02:00:00 --pty bash -i

Also, this video requests 6 CPU cores. Some students ran out of memory requesting 6 cores and 24GB of RAM. You can request 2-4 cores and keep the amount of RAM (just change the recon-all command to mirror the number of cores: recon-all .... --openmp 4). Or, you can request more RAM. 36GB should be fine but at least one student ran out of RAM with that much, so maybe 48GB. The easiest fix is to cut the number of requested cores down.

NIfTI, BIDS, and FreeSurfer

NOTE: You can load older versions of FreeSurfer. We won't get into why you might but you can do it by specifying a particular version.

The example script you copy (please don't move or delete it!) is in the Module3 directory on the class share.

Process 2 T1 images with FreeSurfer

Use the ADNI_T1_dicom directory in the Module3 directory.

  1. Format the T1 files into a simple BIDS format.
  2. Process a set of 2 brains using FreeSurfer.

Sample script to process (this is requesting fewer cores [CPUs])

Be aware that you will need to update this script to work for you.

  1. Put your email address in the appropriate line.
  2. Update the sub_dir variable to match where your data are
  3. Change this line to fit where your data are: cd /blue/clp7934/share/jjtanner
  4. Update the recon-all -s sub-6303 -i command to input the data to where yours are.
#!/bin/bash
#SBATCH --job-name=recon-all_sub-6303    # Job name
#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=user@email.domain     # Where to send mail	
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --cpus-per-task=4            # Use 6 cores on node
#SBATCH --mem=24gb                     # Job memory request
#SBATCH --time=12:00:00               # Time limit hrs:min:sec
#SBATCH --account=clp7934            # Allocation name (req'd if you have more than 1)
#SBATCH --qos=clp7934-b                 # QOS selecting burst allocation
#SBATCH --output=recon-all_sub-6303_%j.log   # Standard output and error log
pwd; hostname; date

module load freesurfer/7.4.1

# Define the output subjects directory
sub_dir="/blue/clp7934/share/jjtanner/ADNI_T1w/ADNI_bids/derivatives/freesurfer"

# Check if the directory exists. If not, create it
if [ ! -d "$sub_dir" ]; then
  echo "Directory $sub_dir does not exist. Creating it now."
  mkdir -p "$sub_dir"
else
  echo "Directory $sub_dir already exists."
fi

# Export the variable
export SUBJECTS_DIR=$sub_dir

cd /blue/clp7934/share/jjtanner

recon-all -s sub-6303 -i /blue/clp7934/share/jjtanner/ADNI_T1w/ADNI_bids/sub-6303/ses-01/anat/sub-6303_ses-01_T1w.nii.gz -all -qcache -parallel -openmp 4

date

What you will turn in

  1. screenshot of your BIDS directory.
  2. The recon-all.log files for the brains

Please verify that the jobs completed. The end of the log file should have something like this: recon-all -s sub-011S6303 finished without error

If you don't see that, the job did not complete appropriately, even if you did not receive an error message. I recommend deleting all files created by the script (the .nii or .nii.gz input files and the output directory for the subject) and trying again. You might need to give the script more RAM (try 36 GB if using 4 or 6 CPUs) or time.

Clone this wiki locally