path/to/patient/diris the directory of the patient. Multiple patients can be processed by entering all their directories.
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:
-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.
executecommand and specifying the file location:
.jsonformat. This option must be set in the exporting code dialog:
.jsonfile with a text editor and run the desired processes (without the need to specify every option as in the previous section).