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5. '''`recon-all -all -subjid `''your_subject_name''''' | 5. '''`recon-all -autorecon-all -subjid `''your_subject_name''''' |
[wiki:FreeSurferWorkFlows top] | [wiki:FreeSurferWorkFlows previous] | [wiki:TroubleshootingReconstruction next]
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
See the BasicReconTable for individual steps that will be run.
6. Check your surfaces and talairach transform. For examples of editing surfaces and troubleshooting, refer to:
- ["FsTutorial/Talairach"]