> For the complete documentation index, see [llms.txt](https://netstim.gitbook.io/leaddbs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://netstim.gitbook.io/leaddbs/appendix.md).

# Appendix

- [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)