Autorecon2

The -autorecon2 directive tells Freesurfer to convert the cubic voxel-based T1 (high-resolution anatomical) image into a triangular mesh surface model. If you checked your data carefully after autorecon1 has finished you should find that the second step goes fairly smoothly.

There is a script, autorecon2.sh that is a wrapper for the recon-all command with the -autorecon2 directive. It simply requires you to specify a valid subjectid within your $SUBJECTS_DIR. Note that a valid subjectid will be the name of the directory generated by Freesurfer when executing the -autorecon1 directive. For example, if my source data prior to running Freesurfer came from:

• /home
  • /mydirectory
    • /fmri
      • /sub_001
        • /MPRAGE

My $SUBJECTS_DIR might be set to be /home/mydirectory/fmri. After running autorecon1.sh, depending on the value given for the -subjid flag, a new directory might now exist containing all the resulting outputs, e.g.:

• /home
  • /mydirectory
    • /fmri
      • /FS_001

For all subsequent processing steps, the subject id is FS_001 for this data set, and not 001.