Contributions:NeuroOmegaADC - Revision history

Wengelhardt at 21:30, 13 November 2024

2024-11-13T21:30:14Z

← Older revision		Revision as of 21:30, 13 November 2024
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	* William Engelhardt (engelhardt@neurotechcenter.org)		* William Engelhardt (engelhardt@neurotechcenter.org)
	* Alexander Belsten (belsten@neurotechcenter.org)		* Alexander Belsten (belsten@neurotechcenter.org)

	~~{{warning}} This is my warning~~

	===Version History===		===Version History===

Wengelhardt at 17:50, 3 September 2024

2024-09-03T17:50:00Z

← Older revision		Revision as of 17:50, 3 September 2024
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	* William Engelhardt (engelhardt@neurotechcenter.org)		* William Engelhardt (engelhardt@neurotechcenter.org)
	* Alexander Belsten (belsten@neurotechcenter.org)		* Alexander Belsten (belsten@neurotechcenter.org)

			{{warning}} This is my warning

	===Version History===		===Version History===
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	[[User Reference:Filters]], [[Contributions:ADCs]], [[User Reference:NeuroStimulationParamsGUI]]		[[User Reference:Filters]], [[Contributions:ADCs]], [[User Reference:NeuroStimulationParamsGUI]]

	[[Category:Contributions]][[Category:Data Acquisition]]		[[Category:Contributions]][[Category:Data Acquisition]][[Category:Video]]

Wengelhardt: /* StimulationTriggers */

2024-07-23T18:28:09Z

StimulationTriggers

← Older revision		Revision as of 18:28, 23 July 2024
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	'''Additional Notes:'''		'''Additional Notes:'''
	* NeuroOmega has a bug where '''a channel cannot immediately switch from being a cathode to anode, or vice versa'''. To overcome this restriction, you can introduce a sham stimulation to a channel you are not using. This means you can set both the stimulation amplitudes to 0, and trigger it in-between the two stimulations. For example, if you did bipolar stimulation with Ch 1 and Ch 8 and wanted to switch which channel is the return channel. You could do the first stimulation to Ch 1 (with Ch 8 as the return channel), the sham stimulation, then the second stimulation to Ch 8 (with Ch 1 as the return channel).		* NeuroOmega has a bug where '''a channel cannot immediately switch from being a cathode to anode, or vice versa'''. To overcome this restriction, you can introduce a sham stimulation to a channel you are not using. This means you can set both the stimulation amplitudes to 0, and trigger it in-between the two stimulations. For example, if you did bipolar stimulation with Ch 1 and Ch 8 and wanted to switch which channel is the return channel. You could do the first stimulation to Ch 1 (with Ch 8 as the return channel), the sham stimulation, then the second stimulation to Ch 8 (with Ch 1 as the return channel).
	* Channel Names are set by the NeuroOmega system. They can be found by following the steps resulting in Figure 1.		* Channel Names are set by the NeuroOmega system. They can be found by following the steps resulting in Figure 1.
			* If multiple stimulation channels are specified, ''each'' will be delivered with the current specified in the stimulation configuration. For example, if you want a total of 3mA with 2 channels, you should specify 1 mA as your current, which will be delivered at each electrode.

	===DynamicStimulation===		===DynamicStimulation===

Wengelhardt: DynamicStimulation update

2024-01-30T19:11:44Z

DynamicStimulation update

← Older revision		Revision as of 19:11, 30 January 2024
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	===Version History===		===Version History===
			* 2024/01/30: Enable DynamicStimulation to use BCI2000 States as stimulation parameters.
	* 2022/10/18: Changed to BufferedADC to prevent data loss.		* 2022/10/18: Changed to BufferedADC to prevent data loss.
	* 2022/07/18: StimMarker 1 and Ports 1 and 2 are written to BCI2000 States.		* 2022/07/18: StimMarker 1 and Ports 1 and 2 are written to BCI2000 States.
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	===StimulationConfigurations===		===StimulationConfigurations===
	<gallery mode="packed" widths=800px heights=~~800px~~>		<gallery mode="packed" widths=800px heights=500px>
	File:NOStimulationFigure.png\|Figure 2: Stimulation pulse shape and train shape definition. The stimulation pulses on the left would take place during the "Stimulation duration" phase on the right.		File:NOStimulationFigure.png\|Figure 2: Stimulation pulse shape and train shape definition. The stimulation pulses on the left would take place during the "Stimulation duration" phase on the right.
	</gallery>		</gallery>
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	* NeuroOmega has a bug where '''a channel cannot immediately switch from being a cathode to anode, or vice versa'''. To overcome this restriction, you can introduce a sham stimulation to a channel you are not using. This means you can set both the stimulation amplitudes to 0, and trigger it in-between the two stimulations. For example, if you did bipolar stimulation with Ch 1 and Ch 8 and wanted to switch which channel is the return channel. You could do the first stimulation to Ch 1 (with Ch 8 as the return channel), the sham stimulation, then the second stimulation to Ch 8 (with Ch 1 as the return channel).		* NeuroOmega has a bug where '''a channel cannot immediately switch from being a cathode to anode, or vice versa'''. To overcome this restriction, you can introduce a sham stimulation to a channel you are not using. This means you can set both the stimulation amplitudes to 0, and trigger it in-between the two stimulations. For example, if you did bipolar stimulation with Ch 1 and Ch 8 and wanted to switch which channel is the return channel. You could do the first stimulation to Ch 1 (with Ch 8 as the return channel), the sham stimulation, then the second stimulation to Ch 8 (with Ch 1 as the return channel).
	* Channel Names are set by the NeuroOmega system. They can be found by following the steps resulting in Figure 1.		* Channel Names are set by the NeuroOmega system. They can be found by following the steps resulting in Figure 1.

			===DynamicStimulation===
			* '''DynamicStimulation''': Enable to skip Preflight checks and change stimulation parameters during the run. This can easily be done with [[Technical Reference:State Definition\|BCI2000 States]]. The State's value is evaluated when the StimulationTrigger Expression is true. This can be useful if you have a custom application which modifies States, then you can set one of the parameters as that State.

	==[[User Reference:StimulationConfigurationIntegrativeTool (SCIT)\|SCIT]]==		==[[User Reference:StimulationConfigurationIntegrativeTool (SCIT)\|SCIT]]==
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	====NeuroOmegaStimulation====		====NeuroOmegaStimulation====
	*'''EnableNeuroOmegaStimulation''' - If disabled, no stimulation will be performed.		*'''EnableNeuroOmegaStimulation''' - If disabled, no stimulation will be performed.
			*'''DynamicStimulation''' - [[#DynamicStimulation\|Described above.]]
	*'''StimulationConfigurations''' - [[#StimulationConfigurations\|Described above.]]		*'''StimulationConfigurations''' - [[#StimulationConfigurations\|Described above.]]
	*'''StimulationTriggers''' - [[#StimulationTriggers\|Described above.]]		*'''StimulationTriggers''' - [[#StimulationTriggers\|Described above.]]
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	Two tests were performed to measure the Stimulation Latency: 1) the latency of the [[#StimMarker1\|StimMarker]] (the response from the Neuro Omega), and 2) the latency of the actual stimulation.		Two tests were performed to measure the Stimulation Latency: 1) the latency of the [[#StimMarker1\|StimMarker]] (the response from the Neuro Omega), and 2) the latency of the actual stimulation.

	<gallery mode="packed" widths=~~450px~~ heights=~~450px~~>		<gallery mode="packed" widths=400px heights=400px>
	File:NO StimMarkerLatency SourceTime.png \| Figure 6: The latency of the StimMarker, sent from the Neuro Omega to a BCI2000 state. The average is '''97 ± 1 ms'''.		File:NO StimMarkerLatency SourceTime.png \| Figure 6: The latency of the StimMarker, sent from the Neuro Omega to a BCI2000 state. The average is '''97 ± 1 ms'''.
	File:NO StimulationLatency SourceTime.png \| Figure 7: The latency of stimulation. The beginning of stimulation was measured by the first peak recorded. The average is '''200 ± 1 ms'''.		File:NO StimulationLatency SourceTime.png \| Figure 7: The latency of stimulation. The beginning of stimulation was measured by the first peak recorded. The average is '''200 ± 1 ms'''.

Wengelhardt: /* Stimulation Parameter GUI */

2023-10-03T15:23:24Z

Stimulation Parameter GUI

← Older revision		Revision as of 15:23, 3 October 2023
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	* Channel Names are set by the NeuroOmega system. They can be found by following the steps resulting in Figure 1.		* Channel Names are set by the NeuroOmega system. They can be found by following the steps resulting in Figure 1.

	==[[User Reference:~~NeuroStimulationParamsGUI~~\|~~Stimulation Parameter GUI~~]]==		==[[User Reference:StimulationConfigurationIntegrativeTool (SCIT)\|SCIT]]==
	To help out with creating the BCI2000 parameters, a GUI has been made which should make it easy to translate your stimulation specifications into BCI2000 parameter files. The GUI also visualizes the stimulation from three different perspectives, making it easy to tell if your parameters are really what you want. There is a [[User Reference:~~NeuroStimulationParamsGUI~~\|~~NeuroStimulationParamsGUI~~ user reference]] which will further tell you how to use this tool.		To help out with creating the BCI2000 parameters, a GUI has been made which should make it easy to translate your stimulation specifications into BCI2000 parameter files. The GUI also visualizes the stimulation from three different perspectives, making it easy to tell if your parameters are really what you want. There is a [[User Reference:StimulationConfigurationIntegrativeTool (SCIT)\|Stimulation Configuration tool user reference]] which will further tell you how to use this tool.

	<gallery mode="packed" widths=500px heights=500px>		<gallery mode="packed" widths=500px heights=500px>

Wengelhardt: Updated for BufferedADC

2022-10-18T19:55:02Z

Updated for BufferedADC

← Older revision		Revision as of 19:55, 18 October 2022
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	==Versioning==		==Versioning==
	===Authors===		===Authors===
			* William Engelhardt (engelhardt@neurotechcenter.org)
	* Alexander Belsten (belsten@neurotechcenter.org)		* Alexander Belsten (belsten@neurotechcenter.org)
	* William Engelhardt (engelhardt@neurotechcenter.org)

	===Version History===		===Version History===
			* 2022/10/18: Changed to BufferedADC to prevent data loss.
	* 2022/07/18: StimMarker 1 and Ports 1 and 2 are written to BCI2000 States.		* 2022/07/18: StimMarker 1 and Ports 1 and 2 are written to BCI2000 States.
	* 2021/06/17: Initial working release R6310.		* 2021/06/17: Initial working release R6310.
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	===Source Code Revisions===		===Source Code Revisions===
	*Initial development: 6274		*Initial development: 6274
	*Known to compile under: ~~6843~~		*Known to compile under: 6969
	*Broken since: --		*Broken since: --
	===Known Issues/Important Things to Know===		===Known Issues/Important Things to Know===
	*Recording from channels with different sampling rates is not possible.		*Recording from channels with different sampling rates is not possible.
	*The Neuro Omega is not able to immediately switch stimulating an electrode as a cathode to an anode. If this is desired, you must introduce a sham stimulation in-between, which can be done to a channel that is not used		*The Neuro Omega is not able to immediately switch stimulating an electrode as a cathode to an anode. If this is desired, you must introduce a sham stimulation in-between, which can be done to a channel that is not used
	*It has been seen with the [[#PC Specifications\|computer used for Certification Testing ]], that if it has been powered on for more than a couple of days, it fails to ~~connect~~ to the Neuro Omega. This ~~can be~~ fixed by ~~just~~ restarting the computer.		*It has been seen with the [[#PC Specifications\|computer used for Certification Testing ]], that if it has been powered on for more than a couple of days (or perhaps another reason, we are not totally sure), it fails to stream consistent data to the Neuro Omega. This creates an irregular block size timing, loss of data, and occasional crashing. '''This was fixed by restarting the computer.''' The theory for the source of the problem is that something was wrong with the AO driver, and restarting fixed it.


	==Functional Description==		==Functional Description==
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	<youtube alignment="center" dimensions="700">https://youtu.be/icyllz5G55U</youtube>		<youtube alignment="center" dimensions="700">https://youtu.be/icyllz5G55U</youtube>
	<br>		<br>
			'''Edits since the video creation'''
			* You no longer need the BCI2000 computer's MAC address, you only need the Neuro Omega's.

	==Integration into BCI2000==		==Integration into BCI2000==
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	*'''Configuring IPv4 address''' - Now that the two systems are connected physically, the BCI2000 PC's IPv4 address can be configured such that it is on the same subnet as the Neuro Omega. This can be done by checking the IPv4 address and subnet mask on the Neuro Omega system ethernet adapter and setting the BCI2000 PC's ethernet adapter to the same subnet mask and setting an appropriate IPv4 address.		*'''Configuring IPv4 address''' - Now that the two systems are connected physically, the BCI2000 PC's IPv4 address can be configured such that it is on the same subnet as the Neuro Omega. This can be done by checking the IPv4 address and subnet mask on the Neuro Omega system ethernet adapter and setting the BCI2000 PC's ethernet adapter to the same subnet mask and setting an appropriate IPv4 address.
	*'''Installation of SDK''' - Alpha Omega provides an SDK installer for the Neuro Omega that must be installed. Acquire this installer and carry out the installation process.		*'''Installation of SDK''' - Alpha Omega provides an SDK installer for the Neuro Omega that must be installed. Acquire this installer and carry out the installation process.
	*'''Setting MAC addresses''' - Now that the two systems are configured, and everything is installed, launch your batch file that has the NeuroOmegaADC as the source module. Open the ''Config'' window and navigate to the source tab. You will need to enter the Alpha Omega's MAC address into the ''NeuroOmegaMAC'' parameter. This can be located by looking at the sticker on the bottom of the Alpha Omega, near where ethernet ports are. Next, you will need to set the ''HostMAC'' parameter to the BCI2000 PC's MAC address. You can find this by opening the command prompt on the BCI2000 PC and entering the command <code>ipconfig /all</code>. In the output of this command, find ''physical address'' in the ethernet adapter section. This is the BCI2000 PC's MAC address.		*'''Setting MAC addresses''' - Now that the two systems are configured, and everything is installed, launch your batch file that has the NeuroOmegaADC as the source module. Open the ''Config'' window and navigate to the source tab. You will need to enter the Alpha Omega's MAC address into the ''NeuroOmegaMAC'' parameter. This can be located by looking at the sticker on the bottom of the Alpha Omega, near where ethernet ports are.
	*'''Setting Recording Channels''' - On the Neuro Omega, launch the data acquisition software. Press <code>Ctrl-Shift-M</code> to show the menu bar. In the Options tab, open the settings dialog box for the channel type you want to record from. You should see a box like this:		*'''Setting Recording Channels''' - On the Neuro Omega, launch the data acquisition software. Press <code>Ctrl-Shift-M</code> to show the menu bar. In the Options tab, open the settings dialog box for the channel type you want to record from. You should see a box like this:
	<gallery class="center" mode="nolines" widths=600px heights=600px>		<gallery class="center" mode="nolines" widths=600px heights=600px>
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	*'''NeuroOmegaMAC''' - This parameter should be the MAC address of the Neuro Omega system.		*'''NeuroOmegaMAC''' - This parameter should be the MAC address of the Neuro Omega system.

	*'''~~HostMAC~~''' - ~~This parameter should be~~ the ~~MAC address~~ of the ~~BCI2000 recording computer~~.		====MPX file====
			*'''SaveMPX''' - Enabling will save a data file on the Neuro Omega system using their own data format.
			*'''FilePath''' - Where to save the file on the Neuro Omega system. A tested path has been "C:\Surgeries_Data\<patient ID>"
			*'''FileName''' - Name of the file on the Neuro Omega system. Will saved where the File Path specifies.

	====Digital Ports====		====Digital Ports====
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	===NeuroOmegaTimeStamp===		===NeuroOmegaTimeStamp===
	The 32-bit time at which the channels are read from the Neuro Omega.		The 32-bit time at which the channels are read from the Neuro Omega.
	===~~NeuroOmegaStimulation~~===		===AOConnectionPercentage===
	~~A boolean state showing whether or not~~ the ~~Neuro Omega is stimulating~~. It is ~~important to note it only has one value per block~~, so it ~~cannot~~ be ~~updated more frequently than~~ the ~~block size~~.		From 0 - 100, the quality of the connection between the systems in percentage. Higher is better, and it might be useful for determining the cause of an issue if data isn't able to be streamed.
	===StimMarker1===		===StimMarker1===
	A state that contains the number of the channel that is being stimulated. It will only be triggered when stimulation is occurring, otherwise it will be zero.		A state that contains the number of the channel that is being stimulated. It will only be triggered when stimulation is occurring, otherwise it will be zero.

Wengelhardt at 16:39, 6 September 2022

2022-09-06T16:39:28Z

← Older revision		Revision as of 16:39, 6 September 2022
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	*Recording from channels with different sampling rates is not possible.		*Recording from channels with different sampling rates is not possible.
	*The Neuro Omega is not able to immediately switch stimulating an electrode as a cathode to an anode. If this is desired, you must introduce a sham stimulation in-between, which can be done to a channel that is not used		*The Neuro Omega is not able to immediately switch stimulating an electrode as a cathode to an anode. If this is desired, you must introduce a sham stimulation in-between, which can be done to a channel that is not used
			*It has been seen with the [[#PC Specifications\|computer used for Certification Testing ]], that if it has been powered on for more than a couple of days, it fails to connect to the Neuro Omega. This can be fixed by just restarting the computer.

	==Functional Description==		==Functional Description==

Wengelhardt: /* Additional Information */

2022-08-01T23:13:30Z

Additional Information

← Older revision		Revision as of 23:13, 1 August 2022
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	There are currently three timestamps logged: NeuroOmega timestamp, StimMarker timestamp, and the Ports 1 and 2 timestamps. The NeuroOmega timestamp is 32 bits, and corresponds to the time at which each block of data is read. Since both the StimMarkers and the Ports are read asynchronously to the signal source, they each have their own timestamps to accurately mark when the event occurred. These states are 16-bit, and increase twice as fast as the NeuroOmegaTimeStamp. To align them, shift every other peak up by 2^15.		There are currently three timestamps logged: NeuroOmega timestamp, StimMarker timestamp, and the Ports 1 and 2 timestamps. The NeuroOmega timestamp is 32 bits, and corresponds to the time at which each block of data is read. Since both the StimMarkers and the Ports are read asynchronously to the signal source, they each have their own timestamps to accurately mark when the event occurred. These states are 16-bit, and increase twice as fast as the NeuroOmegaTimeStamp. To align them, shift every other peak up by 2^15.

	~~[[File:AlignNeuroOmegaStimMarkerTime.pdf \|~~ Here is a published Matlab script that aligns the data for you! ]]. The pdf shows an example of how it should look like, but to use it yourself '''you must change the file path'''.		Here is a published Matlab script that aligns the data for you: '''[[File:AlignNeuroOmegaStimMarkerTime.pdf]]'''. The pdf shows an example of how it should look like, but to use it yourself '''you must change the file path'''.

	The units of the NeuroOmega time are currently unknown, however you can easily convert it to milliseconds by using the SourceTime state at the same index.		The units of the NeuroOmega time are currently unknown, however you can easily convert it to milliseconds by using the SourceTime state at the same index.

Wengelhardt: /* Additional Information */

2022-08-01T23:11:46Z

Additional Information

← Older revision		Revision as of 23:11, 1 August 2022
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	==Additional Information==		==Additional Information==
	===TimeStamps===		===TimeStamps===
	There are currently three timestamps logged: NeuroOmega timestamp, StimMarker timestamp, and the Ports 1 and 2 timestamps. The NeuroOmega timestamp is 32 bits, and corresponds to the time at which each block of data is read. Since both the StimMarkers and the Ports are read asynchronously to the signal source, they each have their own timestamps to accurately mark when the event occurred. These states are 16-bit, and increase twice as fast as the NeuroOmegaTimeStamp. To align them, shift every other peak up by 2^15.		There are currently three timestamps logged: NeuroOmega timestamp, StimMarker timestamp, and the Ports 1 and 2 timestamps. The NeuroOmega timestamp is 32 bits, and corresponds to the time at which each block of data is read. Since both the StimMarkers and the Ports are read asynchronously to the signal source, they each have their own timestamps to accurately mark when the event occurred. These states are 16-bit, and increase twice as fast as the NeuroOmegaTimeStamp. To align them, shift every other peak up by 2^15.

			[[File:AlignNeuroOmegaStimMarkerTime.pdf \| Here is a published Matlab script that aligns the data for you! ]]. The pdf shows an example of how it should look like, but to use it yourself '''you must change the file path'''.

			The units of the NeuroOmega time are currently unknown, however you can easily convert it to milliseconds by using the SourceTime state at the same index.

	==Certification Results==		==Certification Results==

Wengelhardt: /* Certification Results */

2022-07-30T00:08:41Z

Certification Results

← Older revision		Revision as of 00:08, 30 July 2022
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	The individual task breakdown can be found commented out in the Wiki code below, for additional information.		The individual task breakdown can be found commented out in the Wiki code below, for additional information.

	====Acquisition Latency====		===Acquisition Latency===

	To measure the acquisition latency, the Audio and Video Latency were compared between the Neuro Omega and the g.USBAmp, which is considered to have an acquisition latency of 0. Performing this comparison, the Neuro Omega was found to have an average acquisition latency of '''10.6 ± 5.4 ms'''.		To measure the acquisition latency, the Audio and Video Latency were compared between the Neuro Omega and the g.USBAmp, which is considered to have an acquisition latency of 0. Performing this comparison, the Neuro Omega was found to have an average acquisition latency of '''11 ± 5 ms'''.

			===Stimulation Latency===

			Two tests were performed to measure the Stimulation Latency: 1) the latency of the [[#StimMarker1\|StimMarker]] (the response from the Neuro Omega), and 2) the latency of the actual stimulation.

			<gallery mode="packed" widths=450px heights=450px>
			File:NO StimMarkerLatency SourceTime.png \| Figure 6: The latency of the StimMarker, sent from the Neuro Omega to a BCI2000 state. The average is '''97 ± 1 ms'''.
			File:NO StimulationLatency SourceTime.png \| Figure 7: The latency of stimulation. The beginning of stimulation was measured by the first peak recorded. The average is '''200 ± 1 ms'''.
			</gallery>

			The two tests were performed at a block size of 100 ms, while stimulating the ECOG High Frequency channel #2 (numbered 10272). As you can observe, the StimMarker recognizes the stimulation before the stimulation actually occurs, by almost half the time.

	==See also==		==See also==