Connecting FSM 1 to Bonsai

Panagiota

Hi,

I have a Bpod State Machine r1 (Firmware v 23) and can't figure out how to connect it to Bonsai. When I press on the Bpod System Info (lens button on the GUI), it shows:
App Serial Port: - None

I also tried connecting using the bonsai button on the GUI and running the APP_SoftCodeExample.bonsai at the same time but this didn't seem to be working either.

Josh

Hi Panagiota,

Unfortunately State Machine r1 does not have the app serial port, so you'll have to use the TCP/IP link configured from the settings menu, following the instructions here.

What error are you seeing when you try this?

Thanks,
Josh

Panagiota

I get the following error message:

TCPCom: Created a socket on port 11235. Waiting 10s for client connection...
Error using TCPCom
Error using TCPCom
TCPCom: Could not connect to server at localhost on port 11235

Error in ConfigureBonsaiSocket>ConnectToBonsai (line 58)
BpodSystem.BonsaiSocket = TCPCom(11235);

Error while evaluating UIControl Callback.

Josh

Hi Panagiota,

From the error, it looks like you're using an old version of Bpod_Gen2.
In the latest version of ConfigureBonsaiSocket.m,
BpodSystem.BonsaiSocket = TCPCom(11235);
is on line 76.

Please let me know if updating fixes the issue.

One thing to ensure is that Bonsai is running the workflow before you click the 'connect' button in Bpod. If the workflow is not running yet, there is no TCP server to connect to.

Which version of Windows and MATLAB are you using? Is MATLAB running with administrator privileges?

Thanks,
Josh

Panagiota

I have updated my Bpod_Gen2 and ran MATLAB with administrator privileges but I still get the same error:

TCPCom: Created a socket on port 11235. Waiting 10s for client connection...
Error using TCPCom
Error using TCPCom
TCPCom: Could not connect to server at localhost on port 11235

Error in ConfigureBonsaiSocket>connect2bonsai (line 76)
BpodSystem.BonsaiSocket = TCPCom(11235);

Error while evaluating UIControl Callback.

Is there anything I need to change on the Bonsai side? Like the PortNames, maybe? I've tried different options, but none of them seem to be working.

Josh

Hello Panagiota,

I had a closer look at the issue. It looks like our Bonsai example code no longer works with the latest version of Bonsai!

I reworked the example code to simplify it. Please try the example workflow on the develop branch of Bpod_Gen2, here. You don't need other files from the develop branch. Unlike the previous example, this one does not require a webcam. It simply sends Soft Code 5 to the state machine once per second.

Please run the example, following the updated instructions here.

Please let me know if this works for you!

Thanks,
Josh

Panagiota

Hi again,

The new examples work great for getting information from Bonsai to Bpod.
Could you give me some more details on how to get information from Bpod to Bonsai? I am not sure about how to configure Bonsai to receive messages from Bpod.

This is what I currently have in my loop to send softCode1 to bonsai:

sma = AddState(sma, 'Name', 'Port2LightOn', ...
'Timer', 1,...
'StateChangeConditions', {'Tup', 'exit'},...
'OutputActions', {'PWM2', 255, 'SoftCode', 1});

Josh

Hello Panagiota,

Unfortunately Bonsai integration via TCP/IP for State Machine r1.0 and earlier only supports inbound messages from Bonsai to Bpod. The state machine's SoftCode output actions are routed to your selected soft code handler function in MATLAB, not Bonsai. One workaround may be to code your soft code handler to send messages to Bonsai via MATLAB's tcpclient class (or Bpod's TCPCom class if PsychToolbox is installed). You'd have to use a port other than 11235 for the second connection.

Josh

Panagiota

I see thank you!
How do you suggest I synchronize Bonsai timestamps with the Bpod timestamps?
I use Bonsai to capture imaging and behavior videos and Bpod to deliver rewards. I don't use any TDT device.
Could I maybe use the timestamps of a Soft Code sent from Bonsai to Bpod to synchronize the Bpod timestamps and the Bonsai timestamps after the experiment is done?

Josh

Hello Panagiota,

If you want to accurately synchronize each video frame with an acquisition system like Bpod, the standard solution is to use a camera (e.g. FLIR) that can output a TTL pulse with each frame capture. You'd patch the TTL directly from the camera into one of Bpod's digital input channels. You'll need to use the TrialManager class instead of RunStateMachine() on the Bpod side for continuous acquisition (example protocol here).

Alternatively you can send a soft code from Bonsai to Bpod at some point(s) during each trial to synchronize the two clocks. This method carries the theoretical risk of unexpected jitter, as the operating system running Bonsai is not real-time, and the OS will ultimately decide when to write the soft code to the TCP port.

Please let me know if you run into any issues implementing these.

Thanks,
Josh