Installation
Prerequisite
Recommended RAM size: 32GB or more
MATLAB: R2022b or later
MATLAB Image Processing Toolbox
MATLAB Signal Processing Toolbox
MATLAB Statistics and Machine Learning Toolbox
MATLAB Curve Fitting Toolbox (optional)
MATLAB Parallel Computing Toolbox (optional)
Normal installation
Download Lead-DBS from here.
Extract the downloaded zip into your MATLAB toolbox folder. For example, it can be in your home folder under
Documents/MATLAB/toolbox. Please avoid extracting Lead-DBS into MATLAB installation folder or other folder which requiressudooradministratorpermission. An installation directory path with spaces should also be avoided.Add SPM12 in your MATLAB search path: right-click on the SPM12 folder and choose
Add to Path->Selected Folders(NOTSelected Folders and Subfolders).Add Lead-DBS in your MATLAB search path: right-click on the Lead-DBS folder and choose
Add to Path->Selected Folders and Subfolders.
Once Lead-DBS is added to your MATLAB search path, you can start it by running lead dbs in MATLAB Command Window.
Installation via GitHub
For more experienced users or developers who'd also wish to modify the code and potentially improve Lead-DBS, there is an alternative way of installation:
Clone (NOT download) the Lead-DBS repository from here and switch to
developbranch.Download the necessary data and unzip it into the cloned git repository.
Add SPM12 in your MATLAB search path: right-click on the SPM12 folder and choose
Add to Path->Selected Folders(NOTSelected Folders and Subfolders).Add Lead-DBS in your MATLAB search path: right-click on the Lead-DBS folder, choose
Add to Path->Selected Folders(NOTSelected Folders and Subfolders) and then runea_setpathin MATLAB Command Window to set the path.
This alternative way of installation can also make it easy to receive quicker (most often daily) hotfixes or updates and helps us to assist you in a more flexible way.
If you have the GitHub installation of Lead-DBS and need to switch between the develop branch and the classic branch, you must also download the classic data and unzip it into the Lead-DBS installation folder. To switch branches, you can utilize the MATLAB helper functionsea_switch2classic and ea_switch2dev (ensure Git is installed on your system. While it often comes preinstalled on Linux and macOS, Windows users typically need to install it manually). This will ensure that the prefs and recent histories for both branches are preserved correctly.
We'd love to implement your improvements into Lead-DBS – feel free to submit pull requests or contact us for direct push access.
Installing additional content
Several add-ons are available which can be installed manually from inside Lead-DBS. For most cases, Lead-DBS will try to auto-install these when needed. You can also take a look at the Install menu within the main Lead-DBS GUI to install custom items.
Update Lead-DBS
If you have a normal installation of Lead-DBS, you can use the menu
Install->Install development version of Lead-DBS. It will download and apply the latest hotfix before a new release is available.If you have Lead-DBS installed via GitHub, simply
pullfrom GitHub (in the terminal or any Git client you prefer).
Troubleshooting
If you have used previous versions of Lead-DBS, but encounter errors when running a new version, you can run ea_restoreprefs(1,1) in MATLAB Command Window to reset the preferences and try again.
If Lead-DBS subfolders are somehow not completely added to MATLAB search path (in such case you may see Unrecognized function or variable error), you can run ea_setpath in MATLAB Command Window to update the search path.
On macOS, Lead-DBS version < 3.0 and the classic branch on GitHub only support MATLAB version <= R2023a.
If you encounter permission issue when running Lead-DBS on macOS, can run ea_clear_xattr to fix it.
Disclaimer
We try to maintain compatibility to Linux, masOS and Windows, but given our small team, not all functions are well tested on all OSs (fork us on GitHub and join our team to improve that).
Useful tools
DICOM viewer Aliza
DTI-TK Quicklook plugin (macOS)
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