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 -autorecon-all -subjid your_subject_name

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

-  ⇤ ← Revision 1 as of 2005-08-11 18:59:04 → 
  Size: 1052
  Editor: BrianQuinn
  Comment:
+   ← Revision 11 as of 2005-08-20 03:09:26 → ⇥
  Size: 1029
  Editor: JenniPacheco
  Comment:
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-## Note: This page was created with the WorkFlowTemplate
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## If you're modifying this page please take a look at the
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+[wiki:Self:FreeSurferWorkFlows top] | [wiki:Self:FreeSurferWorkFlows previous] | [wiki:Self:TroubleshootingReconstruction next]

= FreeSurfer Basic Reconstruction Work Flow =
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-. '''`mksubjdirs `''your_subject_name''`'''
+. '''`mksubjdirs `''your_subject_name'''''
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-. '''`recon-all -all -subjid `''your_subject_name'''''
+. '''`recon-all -autorecon-all -subjid `''your_subject_name'''''
   See the BasicReconTable for individual steps that will be run.
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-    * FsTutorial/Talairach
+    * ["FsTutorial/Talairach"]