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    '''`mri_convert `''your_dicom_file'' ''your_subject_name''`/mri/orig/001.mgz`'''
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    '''`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:
If you have multiple scans from the same session, convert additional scans like:
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5. '''`recon-all -autorecon-all -subjid `''your_subject_name'''''
   See the BasicReconTable for individual steps that will be run.
5. Start the script recon-all. See the BasicReconTable for individual steps that will be run.
    '''`recon-all -autorecon-all -subjid `''your_subject_name'''''
   

[wiki:FreeSurferWorkFlows top] | [wiki:FreeSurferWorkFlows previous] | [wiki:TroubleshootingReconstruction next]

FreeSurfer Basic Reconstruction Work Flow

1. Source the correct version of FreeSurfer:

  • source your_freesurfer_dir/SetUpFreeSurfer.csh

2. Set your SUBJECTS_DIR variable to your subjects directory:

  • setenv SUBJECTS_DIR your_subjects_dir

3. Make a subjects directory within your SUBJECTS_DIR:

  • mksubjdirs your_subject_name

4. Convert the DICOM files to .mgz files in the $SUBJECTS_DIR/your_subjects_name/mri/orig directory:

  • 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. Start the script recon-all. See the BasicReconTable for individual steps that will be run.

  • recon-all -autorecon-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)