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Although the reconstruction process is broken down into three different stages, this workflow suggests that the user run all these steps at once before beginning to inspect the data. This allows the user to see the final complete output before deciding on any interventions. Any manual intervention needed can be all done at once (with the exception of the talairach and the skullstrip) which can save both time and use of computer power. See the ReconAllDevTable for a list of all the steps associated with each recon stage, or ReconAllBlockDiagram for a different presentation, and OtherUsefulFlags for a list of other flags that you can use with recon-all.

= FreeSurfer Troubleshooting Reconstruction Work Flow =
 1. Source the correct version of FreeSurfer:
  . '''`source `''your_freesurfer_dir''`/SetUpFreeSurfer.csh`'''

 1. Set your SUBJECTS_DIR variable to your subjects directory:
  . '''`setenv SUBJECTS_DIR `''your_subjects_dir'''''

 1. Import your data and create a subject data directory.  This is done '''once''' using the following command:
  . '''`recon-all -i `''invol1''`  -i `''invol2''` -subjid `''your_subject_name'''''
  where ''invol1'' and ''invol2'' are paths to your input files.  You can use as many as necessary (i.e., '''-i ''invol3'' -i ''invol4''''') and they can be in any format that is accepted by mri_convert (i.e. DICOM, MGZ, NIFTI, etc.).  The command above will create an empty directory named ''your_subject_name'', except the mri/orig directory will contain files named 001.mgz and 002.mgz, which are your imported structurals.  Once your input files are imported, you do not need to use the -i flags again.

 1. Run the all the steps of recon-all. See the ReconAllDevTable for individual steps that will be run during the whole process.
  . '''`recon-all  -all -subjid `''your_subject_name'''''
  .  After your subject finishes running, check the recon to make sure that it was successful.
== If recon is inaccurate ==

 1. Check the skull strip:
  . '''`tkmedit `''your_subject_name''` brainmask.mgz -aux T1.mgz`'''
  . For instructions on how to fix poor normalizations or skull strips, refer to:
   * [[FsTutorial/ControlPoints_tktools]]
    . After adding control points run the steps [[OtherUsefulFlags|-autorecon2-cp]] (this will run -normalization, using control points, and everything else through the end of -autorecon2) and -autorecon3 (this will update all your stat tables with the new changes).
   * [[FsTutorial/SkullStripFix_tktools]]
    . After adjusting the skullstrip, run the steps -autorecon2 and -autorecon3.

 1. Check the white and pial surfaces:
  . '''`tkmedit `''your_subject_name''` brainmask.mgz -aux wm.mgz -surfs`'''
  . For instructions on editing the final surfaces, refer to:
   * [[FsTutorial/WhiteMatterEdits_tktools]]
    . After editing the wm.mgz volume run the steps [[OtherUsefulFlags|-autorecon2-wm]] (this will run -fill, using new wm.mgz volume, and everything else through the end of -autorecon2) and -autorecon3.
   * [[FsTutorial/PialEdits_tktools]]
    . After editing the brainmask.mgz volume to adjust the pial surface, run the steps [[OtherUsefulFlags|-autorecon-pial]] (this will run -finalsurfs, using new brainmask.mgz volume, and everything else through the end of -autorecon3.)
   * FsTutorial/FinalSurfEx

 1. Next, check the segmentations:
  . '''`tkmedit `''your_subject_name''` brainmask.mgz -surfs -aseg`'''
  . For instructions on editing the aseg, refer to:
   * TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations
    . After editing the wm.mgz volume run the following steps: -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3.