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This workflow completes the reconstruction process in three different steps, allowing the user to check the outputs before proceeding. See the ReconAllDevTable for a list of the steps run with this command OtherUsefulFlags for a list of other flags that you can use with recon-all. Any manual intervention that is needed is done before moving on to the next step, which can save both time and use of computer power.

FreeSurfer Troubleshooting Reconstruction Work Flow

1. Source the correct version of FreeSurfer:

   • source your_freesurfer_dir/SetUpFreeSurfer.csh

2. Set your SUBJECTS_DIR variable to your subjects directory:

   • setenv SUBJECTS_DIR your_subjects_dir

3. Run the first step of recon-all. See the ReconAllDevTable for individual steps that will be run during the whole process.

   • recon-all -i invol1  -i invol2 -autorecon1 -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

4. Check the talairach transform:

   • tkregister2 --mgz --s your_subject_name --fstal

   • For intructions on how to fix bad talairachs tranforms, refer to:
     • ["FsTutorial/Talairach"]
5. 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

       • After adding control points run the step [wiki:OtherUsefulFlags -autorecon2-cp] (this will run -normalization, using control points, and everything else through the end of -autorecon2.)

     • FsTutorial/SkullStripFix

6. After you have an accurate brain volume, run the next step of recon-all:

   • recon-all -autorecon2 -subjid your_subject_name

7. Check the white and pial surfaces:

   • tkmedit your_subject_name wm.mgz rh.white -aux brainmask.mgz -aux-surface lh.white

   • For intructions on editing the final surfaces, refer to:

     • FsTutorial/WhiteMatterEdits

       • After editing the wm.mgz volume run the step [wiki:OtherUsefulFlags -autorecon2-wm] (this will run -fill, using new wm.mgz volume, and everything else through the end of -autorecon2.)

     • FsTutorial/PialEdits

       • After editing the brainmask.mgz volume run the step [wiki:OtherUsefulFlags -autorecon2-pial] (this will run -finalsurfs, using new brainmask.mgz volume, and everything else through the end of -autorecon2.)

     • FsTutorial/FinalSurfEx

8. After you have accurate pial and white surfaces run the final step of recon-all:

   • recon-all -autorecon3 -subjid your_subject_name