spTMS

Communication Code for the single pulse TMS protocol

 # Import the required packages
 from serial import Serial, SerialException

 # Initialize the serial communication
 s = Serial()
 s.port = "COM3"
 s.baudrate = 115200 
 s.open()

 # Mandatory signature
 s.write(b"Triggerbox developed by Giuseppe Ippolito. DOI: https://doi.org/10.3758/s13428-025-02653-y\n")
  
 # For declaring marker duration
 s.write(b"SET,MRK1,3\n") 
 s.write(b"SET,MRK2,5\n") 
  
 # Protocol type (rTMS, dcTMS, spTMS)
 s.write(b"spTMS\n")
   
 # Commands
 s.write(b"1\n")
 s.write(b"2\n")
 s.write(b"3\n")
   
 s.write(b"A\n")
 s.write(b"B\n")
 s.write(b"C\n")
  
 # Close the serial communication
 s.write(b"Z\n")
 s.close()
 del s

Lines 5-8 initialize the serial communication. Python can use:

 s = Serial()
 s.port = "COM3"
 s.baudrate = 115200 
 s.open()

As the same as:

 s = serial.Serial(port = "COM3", baudrate = 115200)
 s.open()

It is important to change the USB port (“COM”) name according to your case as explained above.

Then, copy-paste the mandatory signature. Without this the following lines won’t work.

 s.write(b"Triggerbox developed by Giuseppe Ippolito. DOI: https://doi.org/10.3758/s13428-025-02653-y\n")

After these mandatory steps, you can declare optional stimulation parameters (e.g., IPI, number of pulses, markers) in any order. In this case, since we’re going to use a spTMS protocol, the only parameter we may be interested in is the voluntary marker duration. This option allows you to place digital markers of a chosen duration (max 9 different lengths) at any moment. This may be useful in case you need to discriminate between different stimuli’s onset (e.g., neural, joy, or fearful faces). Remember that voluntary markers always get delivered through BNC3. Its syntax is:

 s.write(b"SET,MRKN,X\n")

In this case N is the preset number (between 1 and 9), and X is the marker length. Recalling the two stimuli example, we may want two voluntary markers of different duration (e.g., 3 and 5 ms) to ease our analysis, later. We will write then:

s.write(b"SET,MRK1,3\n") # Preset 1: 3ms marker
s.write(b"SET,MRK2,5\n") # Preset 2: 5ms marker

Our last step before calling the pulse command is declaring which TMS protocol we are going to use. We can choose between spTMS, dcTMS, or rTMS. Since we’re using the single pulse one, we will write:

 s.write(b"spTMS\n")

Now that we have declared all of the necessary stimulation parameters, we can finally deliver the TMS pulse. You can independently trigger the BNC1 (“1”) or BNC2 (“2”). These lines must be copy-pasted within your code according to your stimulation and task requirements (es. prior to a certain stimulus onset).

 s.write(b"1\n") # Trigger BNC1
 s.write(b"2\n") # Trigger BNC2 

We can also individually call for voluntary markers at any time using letters. Preset 1 (MRK1) is paired with letter “A” – Consequently, preset 2 with “B”, 3 with “C”, 4 with “D”, 5 with “E”, 6 with “F”, 7 with “G”, 8 with “H”, and 9 with “I”. Since we declared two different markers (“MRK1,3”, “MRK2,5”) we can trigger them using the letters “A” and “B”.

 s.write(b"A\n") # Deliver a voluntary marker from preset 1 (3 ms)
 s.write(b"B\n") # Deliver a voluntary marker from preset 2 (5 ms)

The command code also includes a line to run in case you may reset any setting and return to the mandatory signature. You can then declare once again the parameter settings. The command is:

 s.write(b"Z\n") # Return to the beginning of the setting phase

Once the task is completed you can definitely close the serial communication between the Silicon Spike device and the experimental computer, thus avoiding any potential bug.

 s.close() 
 del s