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Siemens Physio
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Logging Physio Data
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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 
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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.

.. image:: images/siemens_physio/CFMRIPhysioLog_pic1.PNG
  :width: 800

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

.. image:: images/siemens_physio/CFMRIPhysioLog_pic2.PNG
  :width: 800

4. **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.

.. image:: images/siemens_physio/CFMRIPhysioLog_pic3.PNG
  :width: 800


Transferring Physio Data
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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?
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Coming soon.


Simulating Physio Signal - ECG, PULSE, RESP 
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To simulate a physio signal, you must enter the command prompt:
* Control-ESC
* Choose the "Command Prompt" application from the list

.. image:: images/siemens_physio/physsig1.PNG
  :width: 800

Open the "ideacmdtool" application

.. image:: images/siemens_physio/physsig2.PNG
  :width: 800

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

.. image:: images/siemens_physio/physsig3.PNG
  :width: 800

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

.. image:: images/siemens_physio/physsig4.PNG
  :width: 800

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

.. image:: images/siemens_physio/physsig5.PNG
  :width: 800

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

.. image:: images/siemens_physio/physsig6.PNG
  :width: 800

To stop the simulation, enter "5" into the command window

.. image:: images/siemens_physio/physsig7.PNG
  :width: 800

.. image:: images/siemens_physio/physsig8.PNG
  :width: 800