FreeSurfer

Example workflow for FreeSurfer

This tutorial was created by Steffen Bollmann.

Github: @stebo85 Web: mri.sbollmann.net Twitter: @sbollmann_MRI

Getting Set Up with Neurodesk

FreeSurfer Example using module load (e.g. on an HPC)

Download data:

osf -p bt4ez fetch osfstorage/TOMCAT_DIB/sub-01/ses-01_7T/anat/sub-01_ses-01_7T_T1w_defaced.nii.gz sub-01_ses-01_7T_T1w_defaced.nii.gz

Setup FreeSurfer:

ml freesurfer/7.3.2
export SUBJECTS_DIR=$PWD/freesurfer-output
mkdir $SUBJECTS_DIR
export SINGULARITYENV_SUBJECTS_DIR=$SUBJECTS_DIR
export APPTAINERENV_SUBJECTS_DIR=$SUBJECTS_DIR

Run Recon all pipeline:

recon-all -subject test-subject -i sub-01_ses-01_7T_T1w_defaced.nii.gz -all

When using Freesurfer >8.0.0:

export FS_ALLOW_DEEP=1
export APPTAINERENV_FS_ALLOW_DEEP=$FS_ALLOW_DEEP
export SINGULARITYENV_FS_ALLOW_DEEP=$FS_ALLOW_DEEP

When running on a GPU, make sure to check if this is set:

export neurodesk_singularity_opts='--nv'

Alternative instructions for using Freesurfer via the Neurodesk application menu

Download demo data

Open a terminal and run:

pip install osfclient
osf -p bt4ez fetch TOMCAT_DIB/sub-01/ses-01_7T/anat/sub-01_ses-01_7T_T1w_defaced.nii.gz /neurodesktop-storage/sub-01_ses-01_7T_T1w_defaced.nii.gz

FreeSurfer License file:

Before using Freesurfer you need to request a license here (https://surfer.nmr.mgh.harvard.edu/registration.html) and store it in your homedirectory as ~/.license

FreeSurfer Example

Open FreeSurfer (Neurodesk -> Image Segmentation -> Freesurfer -> Freesurfer 7.1.1)

Setup FreeSurfer license (for example - replace with your license):

echo "Steffen.Bollmann@cai.uq.edu.au
> 21029
>  *Cqyn12sqTCxo
>  FSxgcvGkNR59Y" >> ~/.license

export FS_LICENSE=~/.license 

Setup FreeSurfer:

mkdir /neurodesktop-storage/freesurfer-output
source /opt/freesurfer-7.1.1/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/neurodesktop-storage/freesurfer-output

Run Recon all pipeline:

recon-all -subject test-subject -i /neurodesktop-storage/sub-01_ses-01_7T_T1w_defaced.nii.gz -all