• BasicReconstruction

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:

• FsTutorial/FixingDefects

• FsTutorial/PialEdits

• FsTutorial/Talairach

• FsTutorial/ControlPoints

• FsTutorial/SkullStripTutorial