Siemens Physio

Logging Physio Data

Physiological data can be logged on the Siemens platform either via manual logging or built-in sequence logging. Manual physio logging is performed via bash CFMRI_physiolog.bash. Built-in sequence logging can be much more convenient, but is not generally available and depends on programming of the pulse sequence build that feature. At CFMRI, the scans with built-in physio logging capabilities are the BOLD fMRI scans from the HCP and ABCD packages. All other scans will need to manually log physio if physio data is desired.

Manually Logging Physio Signal

  1. Open up a Command Prompt. You can do so by clicking Ctrl+Esc on the keyboard. This is a hotkey combination to open up the Start menu on the monitor, where you can select Command Prompt.

  2. Type bash CFMRI_physiolog.bash as shown below. This is a wrapper script around Siemen’s ideacmdtool, and will log both pulse ox and respiration data. (Please see instructions further below for logging other types of physio.) Enter a base filename for logging the physio data. For example, if the filename is 20220225_TestFilename, then the files 20220225_TestFilename.puls and 20220225_TestFilename.resp will be logged for pulse oximeter respiration data, respectively.

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  1. Enter the filename to start logging. You will see prompts indicating START OF LOGGING and LOGGING IN PROGRESS.

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  1. Keep the window open (you can move it to an unused corner of the screen, or minimize it and retrieve it later) until you are ready to stop recording. To stop the recording, press Enter twice. This will stop the physio recording and automatically send the files over to the neighboring workstation. Later, when using cfmricp on the neighboring workstation to transfer your data, your physio files will be gathered and included in your session data.

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Transferring Physio Data

To manually transfer physio data, open up a Command Prompt and type bash CFMRI_physioxfer.bash. This will send all physio files currently on the scanner to neighboring workstation, where they will be ready for transfer via cfmricp.

How can I identify my physio files?

Coming soon.

Simulating Physio Signal - ECG, PULSE, RESP

To simulate a physio signal, you must enter the command prompt: * Control-ESC * Choose the “Command Prompt” application from the list

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Open the “ideacmdtool” application

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Select “1” from the list of available options to open “PMU Control”

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Select “1” from the list of available options to run the “PMU Signal simulation”

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Enter “4” in the command prompt to “StartSignalSimulation”

Enter the desired ECG, Respiration, Pulse, and External Signal period duration

  • Hit enter for default values * ECG period - 1000 ms * Respiration period - 3000 ms * Pulse period - 1000 ms * External signal period - 2000 ms

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Signal will be shown in the physio display on the scanner GUI

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To stop the simulation, enter “5” into the command window

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