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Using this workflow will perform all the steps of the entire volume and surface reconstruction stream without stopping. Upon completeion the user is able to check the final surfaces and if any manual intervention is needed to correct any of the steps those processes must be repeated.

FreeSurfer Basic Reconstruction Work Flow

1. Source the correct version of FreeSurfer:

2. Set your SUBJECTS_DIR variable to your subjects directory:

3. Make a subjects directory within your SUBJECTS_DIR:

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

If you have multiple scans from the same session, convert additional scans like:

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

6. Check your surfaces and talairach transform.

For intructions on how to fix bad talairachs tranforms, refer to:

For examples of editing surfaces, refer to:

For instructions on how to fix poor normalizations or skull strips, refer to: