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This workflow completes the entire reconstruction process without stopping. See the BasicReconTable for a list of all the steps run by this command. After the process finishes the user must check the final surfaces and talairach transform. Any manual intervention needed to fix problems that occurred during the process is done at the end, after which the necessary steps will have to be repeated. This can be both time-consuming and use a lot of computer power. Therefore, this workflow is recommended only for excellent data sets which have no anticipated problems (e.g. data acquired where the subject was perfectly aligned in the scanner, the subject has normal brain anatomy, there were no image artifacts or excessive movements during the scan, etc.).

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 for each scan to .mgz files in the $SUBJECTS_DIR/your_subjects_name/mri/orig directory:

If you have multiple scans from the same session, convert additional files like this example for a second set:

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: