[wiki:FreeSurferWorkFlows top] | [wiki:FreeSurferWorkFlows previous] | [wiki:IntermediateReconstruction 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

5. recon-all -all -subjid your_subject_name

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