# Lead-DBS

- [Overview](https://netstim.gitbook.io/leaddbs/lead-dbs/step0-overview.md)
- [Self-Tutoring with Lead-Tutor](https://netstim.gitbook.io/leaddbs/lead-dbs/self-tutoring-with-lead-tutor.md)
- [1. Load Patient Folder](https://netstim.gitbook.io/leaddbs/lead-dbs/step1-load-patient-folder.md)
- [Importing a classic Lead-DBS dataset to BIDS version](https://netstim.gitbook.io/leaddbs/lead-dbs/step1-load-patient-folder/importing-a-classic-lead-dbs-dataset-to-bids-version.md): We are happy to answer any questions related to BIDS migration in our Slack support channel.
- [2. Image Import](https://netstim.gitbook.io/leaddbs/lead-dbs/step2-image-import.md)
- [Converting NIfTI-images into BIDS](https://netstim.gitbook.io/leaddbs/lead-dbs/step2-image-import/converting-nifti-images-into-bids.md)
- [Converting DICOM files into BIDS](https://netstim.gitbook.io/leaddbs/lead-dbs/step2-image-import/converting-dicom-files-into-bids.md)
- [3. Volume Registrations](https://netstim.gitbook.io/leaddbs/lead-dbs/step3-volume-registrations.md): First steps in the LEAD-DBS pipeline.
- [Coregister Volumes](https://netstim.gitbook.io/leaddbs/lead-dbs/step3-volume-registrations/coregister-volumes.md)
- [Normalizing the Images](https://netstim.gitbook.io/leaddbs/lead-dbs/step3-volume-registrations/normalization-of-images.md)
- [Brainshift Correction](https://netstim.gitbook.io/leaddbs/lead-dbs/step3-volume-registrations/subcortical-refine-post-to-pre-transforms.md)
- [Checking the Coregistration and Normalization](https://netstim.gitbook.io/leaddbs/lead-dbs/step3-volume-registrations/checking-the-coregistration.md)
- [4. (optional) Surface Reconstruction](https://netstim.gitbook.io/leaddbs/lead-dbs/step4-optional-surface-reconstruction.md)
- [5. (optional) Reconstruction of Electrode Trajectories](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories.md)
- [Orientation of Directional Leads](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories/determining-the-orientation-of-directional-leads.md)
- [Prerequisites](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories/determining-the-orientation-of-directional-leads/prerequisites.md)
- [Automatic Algorithm](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories/determining-the-orientation-of-directional-leads/automatic-algorithm.md)
- [Possible Problems with the Automatic Algorithm](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories/determining-the-orientation-of-directional-leads/possible-problems-with-the-automatic-algorithm.md)
- [User-Assisted Algorithm (Manual Refine)](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories/determining-the-orientation-of-directional-leads/user-assisted-algorithm-manual-refine.md)
- [TRAC/CORE Details](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories/trac-core-details.md)
- [Manual Reconstruction](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories/manual-reconstruction.md)
- [Reconstruction File](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories/reconstruction-file.md): This page might be outdated. We continuously work on updating our documentation, thank you for your patience.
- [6. (optional) Perform Connectivity Analysis](https://netstim.gitbook.io/leaddbs/lead-dbs/step6-optional-perform-connectivity-analysis.md)
- [7. Visualization](https://netstim.gitbook.io/leaddbs/lead-dbs/step7-visualization.md)
- [MER Analysis](https://netstim.gitbook.io/leaddbs/lead-dbs/step7-visualization/mer-analysis.md)
- [Reconstruction Statistics](https://netstim.gitbook.io/leaddbs/lead-dbs/reconstruction-statistics.md)


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