Differences between revisions 5 and 6
Deletions are marked like this. Additions are marked like this.
Line 9: Line 9:
3. '''`mksubjdirs `''your_subject_name''`''' 3. '''`mksubjdirs `''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 -all -subjid your_subject_name

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

BasicReconstruction (last edited 2008-04-29 11:45:31 by localhost)