FreeSurfer Basic Reconstruction Work Flow

1. source your_freesurfer_dir/SetUpFreeSurfer.csh

2. setenv SUBJECTS_DIR your_subjects_dir

3. mksubjdirs your_subject_name

4. mri_convert your_dicom_file your_subject_name/mri/orig/001.mgz

If you have multiple scans from the same session, convert additional scans like:
mri_convert your_other_dicom_file your_subject_name/mri/orig/002.mgz

5. recon-all -all -subjid your_subject_name

6. Check your surfaces and talairach transform. For examples of editing surfaces and troubleshooting, refer to:

-  ⇤ ← Revision 6 as of 2005-08-12 17:26:53 → 
  Size: 948
  Editor: EvelinaBusa
  Comment:
+   ← Revision 10 as of 2005-08-15 15:00:22 → ⇥
  Size: 1019
  Editor: NickSchmansky
  Comment: fixed-up FsTutorial/Talairach link
-Deletions are marked like this.
+Additions are marked like this.
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+   See the BasicReconTable for individual steps that will be run.
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-    * FsTutorial/Talairach
+    * ["FsTutorial/Talairach"]