FreeSurfer
Example workflow for FreeSurfer
This tutorial was created by Steffen Bollmann.
Github: @stebo85 Web: mri.sbollmann.net Twitter: @sbollmann_MRI
Getting Setup with Neurodesk
For more information on getting set up with a Neurodesk environment, see hereFreeSurfer 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
mkdir ~/freesurfer-output
export SINGULARITYENV_SUBJECTS_DIR=~/freesurfer-output
export APPTAINERENV_SUBJECTS_DIR=~/freesurfer-output
Run Recon all pipeline:
recon-all -subject test-subject -i ~/sub-01_ses-01_7T_T1w_defaced.nii.gz -all
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