Command line interface
Lead-DBS can now also be accessed from the command-line in the standalone version.
To run lead, open a terminal in the application folder of the standalone release and run the
run_lead.shscript specifying the path to Matlab Runtime (currently v96). For example, in Mac:
It is also possible to execute a process without the lead GUI by specifying further options. For example, in order to run coregistration and normalization using the Segment algorithm:
./run_lead.sh /Applications/MATLAB/MATLAB_Runtime/v97 dbs -coreg_checkbox -normalize_checkbox -normmethod 2 /path/to/patient/dir
path/to/patient/diris the directory of the patient. Multiple patients can be processed by entering all their directories.
Command line options are defined the same way as the handles name in the GUI. It is possible to query them opening the
lead_dbs.figin GUIDE and clicking the desired component. A non extensive list of options is also listed in the Command line options page.
-processoption the basic Lead-DBS pipeline is executed: coregistration, normalization, brain shift correction and electrode reconstruction (PaCER). For example:
./run_lead.sh /Applications/MATLAB/MATLAB_Runtime/v97 dbs -process /path/to/patient/dir
When using the
-processoption it is also possible to specify BIDS subject directory(s). In this case the subject images will be processed in a derivates (Lead_DBS-like) folder. If a BIDS root directory is set, then all of its subjects will be processed.
Exported jobs created with the Export Code button can be run from the command line using the
executecommand and specifying the file location:
./run_lead.sh /Applications/MATLAB/MATLAB_Runtime/v97 execute /path/to/lead_job.json
It's important to remark that the file is in
.jsonformat. This option must be set in the exporting code dialog:
Finally, it is also possible to edit this
.jsonfile with a text editor and run the desired processes (without the need to specify every option as in the previous section).