# Lead-DBS User Guide ## Lead-DBS User Guide - [Introduction](https://netstim.gitbook.io/leaddbs/readme.md) - [How to contribute to Lead-DBS](https://netstim.gitbook.io/leaddbs/ways-to-contribute-to-lead-dbs.md) - [Installation](https://netstim.gitbook.io/leaddbs/installation.md) - [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) - [Group analyses with Lead-DBS](https://netstim.gitbook.io/leaddbs/lead-group/group-analyses-with-lead-dbs.md) - [Setup Analysis](https://netstim.gitbook.io/leaddbs/lead-group/setup-analysis.md) - [General Settings](https://netstim.gitbook.io/leaddbs/lead-group/general-settings.md): This page is under construction. - [Group Visualization](https://netstim.gitbook.io/leaddbs/lead-group/group-visualization.md): Adapted from the Walkthrough Tutorial by Svenja Treu. - [Calculate VTA and Stats](https://netstim.gitbook.io/leaddbs/lead-group/calculate-vta-and-stats.md) - [Sweetspot Explorer](https://netstim.gitbook.io/leaddbs/lead-group/sweetspot-explorer.md) - [Connectomics](https://netstim.gitbook.io/leaddbs/connectomics/connectomic-analyses.md) - [Diffusion MRI: Patient Specific Processing](https://netstim.gitbook.io/leaddbs/connectomics/connectomic-analyses/dmri.md) - [fMRI-Analysis: Patient Specific Processing](https://netstim.gitbook.io/leaddbs/connectomics/connectomic-analyses/fmri.md) - [Using Normative Connectomes](https://netstim.gitbook.io/leaddbs/connectomics/connectomic-analyses/using-normative-connectomes.md) - [Network Mapping Explorer](https://netstim.gitbook.io/leaddbs/connectomics/connectomic-analyses/network-mapping-explorer.md) - [Discriminative Fibertracts analysis](https://netstim.gitbook.io/leaddbs/connectomics/connectomic-analyses/discriminative-fibertracts-analysis.md) - [Fiber Filtering Explorer](https://netstim.gitbook.io/leaddbs/connectomics/connectomic-analyses/fiber-filtering-explorer.md) - [Lead Connectome Mapper](https://netstim.gitbook.io/leaddbs/connectomics/lead-mapper.md) - [Imaging setup](https://netstim.gitbook.io/leaddbs/lead-or/imaging-setup.md): Imaging setup to use the Lead-OR platform - [Electrophysiology setup](https://netstim.gitbook.io/leaddbs/lead-or/electrophysiology-setup.md): Electrophysiology setup to use the Lead-OR platform - [Using the platform](https://netstim.gitbook.io/leaddbs/lead-or/using-the-platform.md) - [Code Backbone](https://netstim.gitbook.io/leaddbs/appendix/code-backbone.md) - [Acquiring and Installing Atlases](https://netstim.gitbook.io/leaddbs/appendix/acquiring-and-setting-atlases.md) - [Customizing Atlas Visualization](https://netstim.gitbook.io/leaddbs/appendix/acquiring-and-setting-atlases/customizing-atlas-visualization.md) - [Troubleshooting / Specific Help](https://netstim.gitbook.io/leaddbs/appendix/troubleshooting-specific-help.md) - [Adding Fortran dependencies for VTA modeling](https://netstim.gitbook.io/leaddbs/appendix/troubleshooting-specific-help/adding-fortran-dependencies-for-vta-modeling.md) - [VTA Calculation Troubleshoot](https://netstim.gitbook.io/leaddbs/appendix/troubleshooting-specific-help/vta-calculation-troubleshoot.md): Troubleshooting VTA Generation - [Command line interface](https://netstim.gitbook.io/leaddbs/appendix/command-line-interface.md) - [Command line options](https://netstim.gitbook.io/leaddbs/appendix/command-line-interface/command-line-options.md) - [Matlab scripting examples](https://netstim.gitbook.io/leaddbs/appendix/useful-command-line-tools.md) - [Installing an atlas from an online repository](https://netstim.gitbook.io/leaddbs/appendix/useful-command-line-tools/installing-an-atlas-from-a-repository.md) - [Warping a normative connectome to native subject space](https://netstim.gitbook.io/leaddbs/appendix/useful-command-line-tools/warping-a-normative-connectome-to-native-subject-space.md): This example shows how to warp the fibertracts represented in a normative connectome to the space of the "anat\_t1.nii" (anchor space) of a subject and to convert the result to a .trk file. - [Plotting atlas structures onto 3D slices](https://netstim.gitbook.io/leaddbs/appendix/useful-command-line-tools/plotting-atlas-structures-onto-3d-slices.md) - [Using Slicer](https://netstim.gitbook.io/leaddbs/appendix/using-slicer.md) - [Sweet-sour spot](https://netstim.gitbook.io/leaddbs/appendix/using-slicer/sweet-sour-spot.md)