This directory is the default location for subject data files.

A different directory can be specified by setting the env var
SUBJECTS_DIR prior to the 'source $FREESURFER_HOME/FreeSurferEnv.csh'
statement in your .cshrc file.

Use the -i and -s flags in recon-all (see recon-all --help) to
import subject data and automatically create a new subject directory.

Two example input files are included, called sample-001.mgz and
sample-002.mgz.  Example usage of these files, to create a new subject,
called 'ernie', and to run the first stage (averaging, intensity 
normalization and skull-strip) would be:

  recon-all -s ernie \
    -i $SUBJECTS_DIR/sample-001.mgz \
    -i $SUBJECTS_DIR/sample-002.mgz \
    -autorecon1

Upon completion, you will find files in $SUBJECTS_DIR/ernie/mri:

  orig/001.mgz  - output of 'mri_convert sample-001.mgz 001.mgz' *
  orig/002.mgz  - output of 'mri_convert sample-002.mgz 002.mgz' *
  rawavg.mgz    - average of 001.mgz and 002.mgz
  orig.mgz      - rawavg.mgz conformed to 1^3mm dims by 256^3 voxels
  nu.mgz        - MNI's nu_correct intensity normalization
  T1.mgz        - Freesurfer's intensity normalization
  brainmask.mgz - skull-stripped T1.mgz

* Note that the input files can be Dicom, or Analyze, or many other
formats (see mri_convert --help).

The -i flags are no longer necessary after this first run.  They
are used only to 'pull' your input data from wherever it is kept.

For more info, see:

  http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable