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FreeSurfer

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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. export subjects directory (the directory where your subject folders are located)

export SUBJECTS_DIR=/scratch/project/FreeSurferSubjectFolder

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