Notes
- Any words that are in red font need to substituted for your own data set i.e. directory or file names.
1. Make a directory where you will navigate to each time you run any analysis, this could be a 'FreeSurfer' directory or the directory where your data is stored.
e.g.
% mkdir /home/mydata_dir
2. The following steps will set up FreeSurfer and instruct it to navigate all information to your subjects directory. You will need to set up your subjects directory into the directory that you have just created to ensure that information is all kept together.
e.g.
% setenv FREESURFER_HOME /software/system/freesurfer/freesurfer-5.1.0
% source $FREESURFER_HOME/SetUpFreeSurfer.csh
% setenv SUBJECTS_DIR /home/mydata_dir
These steps will need to be followed each time a new terminal is opened and you wish to run FreeSurfer; if you are running FreeSurfer often it may be beneficial to set up an alias to run these commands.
3. The next step performs automated cortical surface reconstruction, which prepares the data for surface-based analysis. In addition, to process data with the QDEC module of FreeSurfer each subjects needs to have pre-computed smoothed data for the target surface, 'fsaverage' is the default for this. Reconstruction can take many hours, it may be best to run this command overnight. The following command can be used to perform reconstruction and smoothing for all of the data in a set:
e.g.
% foreach file (mydata*)
recon-all -s $file -qcache
end
To perform reconstruction on one subject at a time:
e.g.
% recon-all -autorecon-all -subjid subject_name
For information on the reconstruction workflow see http://freesurfer.net/fswiki/BasicReconstruction
For more information on how FreeSurfer performs cortical reconstruction see http://freesurfer.net/fswiki/FreeSurferAnalysisPipelineOverview
