Attention: Confluence is not suitable for the storage of highly confidential data. Please ensure that any data classified as Highly Protected is stored using a more secure platform.
If you have any questions, please refer to the University's data classification guide or contact ict.askcyber@sydney.edu.au
Skip to end of banner
Go to start of banner

FreeSurfer

Skip to end of metadata
Go to start of metadata

You are viewing an old version of this content. View the current version.

Compare with Current View Version History

« Previous Version 5 Next »

FreeSurfer is a neuroimaging software package that is primarily used for processing and analysis of T1 weighted MRI. FreeSurfer is a great tool for surface-based morphometry, hippocampal and amygdala segmentations, and longitudinal analysis using linear mixed effects modelling.

The following documentation will outline FreeSurfer’s pre-processing steps, and general guidelines to analysis.

Before running anything on FreeSurfer on Artemis, you must:

  1. load the module. e.g.

module load freesurfer/7.0.1

2. Identify the directory in which your subject folders (in FreeSurfer format) are located

e.g. If your subjects are located in a structure that looks like this:

-scratch

-Project

-FreeSurferSubjectFolder

-subject_1

-subject_2

-subject_3

export SUBJECTS_DIR=/scratch/project/FreeSurferSubjectFolder

  • No labels