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

This workflow completes the entire reconstruction process without stopping. See the BasicReconstructionTable for a list of all the steps run by this command. After the process finishes the user should check the final surfaces and talairach transform. Any manual intervention needed to fix problems that occurred during the process are done at the end. Then the necessary steps are repeated, which can be both time-consuming and use a lot of compute power.

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 recon-all script:

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: