MR Hardware - Revision history

Huawu: /* Coils */

2026-04-22T19:25:05Z

Coils

← Older revision		Revision as of 19:25, 22 April 2026
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	* [http://www.novamedical.com/ Nova Medical] 32-channel head coil (interior coil dimensions - 18.5 cm width, 21 cm length, 24 cm height to nose bridge, 21 cm height to forehead)		* [http://www.novamedical.com/ Nova Medical] 32-channel head coil (interior coil dimensions - 18.5 cm width, 21 cm length, 24 cm height to nose bridge, 21 cm height to forehead)
	* [http://www.novamedical.com/ Nova Medical] 16-channel visual array. This is similar to the Nova 32-channel coil, but with the front half removed to allow a completely unobstructed field of view for visual studies. (interior coil dimensions - 18.5 cm width, 21 cm length, 10 cm height)		* [http://www.novamedical.com/ Nova Medical] 16-channel visual array. This is similar to the Nova 32-channel coil, but with the front half removed to allow a completely unobstructed field of view for visual studies. (interior coil dimensions - 18.5 cm width, 21 cm length, 10 cm height)
	* Custom built 32-channel infant head coil. This coil was [https://onlinelibrary.wiley.com/doi/10.1002/mrm.28791 designed and built by Dr. Boris Keil] for imaging infants up to 12 months of age. The top portion is split into left and right halves that can slide open, allowing adjustment to accommodate different head sizes. Indentations on both sides are designed to accommodate the infant’s ~~ear~~ protection.		* Custom built 32-channel infant head coil. This coil was [https://onlinelibrary.wiley.com/doi/10.1002/mrm.28791 designed and built by Dr. Boris Keil] for imaging infants up to 12 months of age. The top portion is split into left and right halves that can slide open, allowing adjustment to accommodate different head sizes. Indentations on both sides are designed to accommodate the infant’s hearing protection.
	* Custom built 32-channel toddler head coil. This coil features a design and performance similar to the infant coil but offers a slightly larger imaging volume, enabling imaging of infants up to 24 months of age.		* Custom built 32-channel toddler head coil. This coil features a design and performance similar to the infant coil but offers a slightly larger imaging volume, enabling imaging of infants up to 24 months of age.

Huawu: /* Coils */

2026-04-22T19:19:43Z

Coils

← Older revision		Revision as of 19:19, 22 April 2026
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	* [http://www.novamedical.com/ Nova Medical] 32-channel head coil (interior coil dimensions - 18.5 cm width, 21 cm length, 24 cm height to nose bridge, 21 cm height to forehead)		* [http://www.novamedical.com/ Nova Medical] 32-channel head coil (interior coil dimensions - 18.5 cm width, 21 cm length, 24 cm height to nose bridge, 21 cm height to forehead)
	* [http://www.novamedical.com/ Nova Medical] 16-channel visual array. This is similar to the Nova 32-channel coil, but with the front half removed to allow a completely unobstructed field of view for visual studies. (interior coil dimensions - 18.5 cm width, 21 cm length, 10 cm height)		* [http://www.novamedical.com/ Nova Medical] 16-channel visual array. This is similar to the Nova 32-channel coil, but with the front half removed to allow a completely unobstructed field of view for visual studies. (interior coil dimensions - 18.5 cm width, 21 cm length, 10 cm height)
			* Custom built 32-channel infant head coil. This coil was [https://onlinelibrary.wiley.com/doi/10.1002/mrm.28791 designed and built by Dr. Boris Keil] for imaging infants up to 12 months of age. The top portion is split into left and right halves that can slide open, allowing adjustment to accommodate different head sizes. Indentations on both sides are designed to accommodate the infant’s ear protection.
			* Custom built 32-channel toddler head coil. This coil features a design and performance similar to the infant coil but offers a slightly larger imaging volume, enabling imaging of infants up to 24 months of age.

	= Peripheral Devices =		= Peripheral Devices =

Huawu: /* Additional Information */

2026-04-20T19:20:41Z

Additional Information

← Older revision		Revision as of 19:20, 20 April 2026
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	== Tektronix oscilloscope ==		== Tektronix oscilloscope ==
	The CNI has a [[https://www.tek.com/en/oscilloscope/tds2022b-manual/tds2022b-and-tds2024b Tektronix TDS2024B]] 4 channel oscilloscope for debugging pulse sequences.		The CNI has a [https://www.tek.com/en/oscilloscope/tds2022b-manual/tds2022b-and-tds2024b Tektronix TDS2024B] 4 channel oscilloscope for debugging pulse sequences.

	==The magnetic field==		==The magnetic field==

Huawu: /* Additional information */

2026-04-20T19:20:21Z

Additional information

← Older revision		Revision as of 19:20, 20 April 2026
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	To use the fORP response box system to receive timing pulses from the scanner, set up the system as described in the 'Response Box' section above. Note that timing pulses will be received via the same USB connection as subjects' responses, and that no additional USB cables need be plugged into your testing computer. If you have selected a numeric mapping between button presses and keys, the timing pulses sent to your testing laptop will be in the form of a '5'. (Note that use of the 5-button diamond-shaped response box will include the numbers 1-4 and 6, and thus will not include the number 5). Use caution when editing experimental scripts while using this method--if your script is open while the scanner sends pulses, a long series of 5's will be inserted into your script!		To use the fORP response box system to receive timing pulses from the scanner, set up the system as described in the 'Response Box' section above. Note that timing pulses will be received via the same USB connection as subjects' responses, and that no additional USB cables need be plugged into your testing computer. If you have selected a numeric mapping between button presses and keys, the timing pulses sent to your testing laptop will be in the form of a '5'. (Note that use of the 5-button diamond-shaped response box will include the numbers 1-4 and 6, and thus will not include the number 5). Use caution when editing experimental scripts while using this method--if your script is open while the scanner sends pulses, a long series of 5's will be inserted into your script!

	= Additional ~~information~~ =		= Additional Information =
	== ~~Additional equipment~~ ==		== CNI laptops ==
	* CNI Laptops: CNI has one MacBook and one Windows PC for users to use during their experiments. The MacBook is running OS 10.12 and has MATLAB R2014b with PsychToolbox and PsychoPy 3 installed. The Windows PC is running Windows 11 and has E-Prime 3 installed (CNI also has a license for E-Prime 3). You could also checkout out [[Stimulus\|some (old) notes]] shared by previous CNI users on how to set up experiments with these toolboxes.		The CNI has one MacBook and one Windows PC for users to use during their experiments. The MacBook is running OS 10.12 and has MATLAB R2014b with PsychToolbox and PsychoPy 3 installed. The Windows PC is running Windows 11 and has E-Prime 3 installed (CNI also has a license for E-Prime 3). You could also checkout out [[Stimulus\|some (old) notes]] shared by previous CNI users on how to set up experiments with these toolboxes.
	* Tektronix TDS2024B: 4 channel oscilloscope ~~to debug~~ pulse sequences.
			== Tektronix oscilloscope ==
			The CNI has a [[https://www.tek.com/en/oscilloscope/tds2022b-manual/tds2022b-and-tds2024b Tektronix TDS2024B]] 4 channel oscilloscope for debugging pulse sequences.

	==The magnetic field==		==The magnetic field==

Huawu at 19:17, 20 April 2026

2026-04-20T19:17:02Z

← Older revision		Revision as of 19:17, 20 April 2026
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	For step-by-step operation instructions, please see this [[Media:Optoacoustics_How-To.pdf \| How-To Guide]], clearly summarized by Prof. Cameron Ellis and Emily Chen.		For step-by-step operation instructions, please see this [[Media:Optoacoustics_How-To.pdf \| How-To Guide]], clearly summarized by Prof. Cameron Ellis and Emily Chen.

	~~== CNI Laptops ==~~
	The CNI has one MacBook and one Windows PC for users to use during their experiments. The MacBook is running OS 10.12 and has MATLAB R2014b with PsychToolbox and PsychoPy 3 installed. The Windows PC is running Windows 11 and has E-Prime 3 installed (CNI also has a license for E-Prime 3). You could also checkout out [[Stimulus\|some (old) notes]] shared by previous CNI users on how to set up experiments with these toolboxes.

	== Subject measurement ==		== Subject measurement ==
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	To use the fORP response box system to receive timing pulses from the scanner, set up the system as described in the 'Response Box' section above. Note that timing pulses will be received via the same USB connection as subjects' responses, and that no additional USB cables need be plugged into your testing computer. If you have selected a numeric mapping between button presses and keys, the timing pulses sent to your testing laptop will be in the form of a '5'. (Note that use of the 5-button diamond-shaped response box will include the numbers 1-4 and 6, and thus will not include the number 5). Use caution when editing experimental scripts while using this method--if your script is open while the scanner sends pulses, a long series of 5's will be inserted into your script!		To use the fORP response box system to receive timing pulses from the scanner, set up the system as described in the 'Response Box' section above. Note that timing pulses will be received via the same USB connection as subjects' responses, and that no additional USB cables need be plugged into your testing computer. If you have selected a numeric mapping between button presses and keys, the timing pulses sent to your testing laptop will be in the form of a '5'. (Note that use of the 5-button diamond-shaped response box will include the numbers 1-4 and 6, and thus will not include the number 5). Use caution when editing experimental scripts while using this method--if your script is open while the scanner sends pulses, a long series of 5's will be inserted into your script!

	= ~~Other General~~ information =		= Additional information =
			== Additional equipment ==
			* CNI Laptops: CNI has one MacBook and one Windows PC for users to use during their experiments. The MacBook is running OS 10.12 and has MATLAB R2014b with PsychToolbox and PsychoPy 3 installed. The Windows PC is running Windows 11 and has E-Prime 3 installed (CNI also has a license for E-Prime 3). You could also checkout out [[Stimulus\|some (old) notes]] shared by previous CNI users on how to set up experiments with these toolboxes.
			* Tektronix TDS2024B: 4 channel oscilloscope to debug pulse sequences.

	==The magnetic field==		==The magnetic field==
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	When positioning equipment in the scan room, it's useful to be aware of the magnetic field lines. All equipment in the CNI scan room is MR-safe, but not all equipment functions properly in very high-field regions. The diagrams show the estimated field lines in the MR suite area.		When positioning equipment in the scan room, it's useful to be aware of the magnetic field lines. All equipment in the CNI scan room is MR-safe, but not all equipment functions properly in very high-field regions. The diagrams show the estimated field lines in the MR suite area.

	==~~Additional/~~Legacy hardware information==		==Legacy hardware information==
	See the [[Hardware configuration]] page for some additional and legacy hardware information.		See the [[Hardware configuration]] page for some additional and legacy hardware information.

Huawu at 19:11, 20 April 2026

2026-04-20T19:11:20Z

Show changes

Huawu: /* MR Scanner */

2026-04-20T19:06:37Z

MR Scanner

@@ Line 1: / Line 1: @@
-= MR Scanner =
+= Scanner =
-The MR scanner is in room 065 of the CNI suite in Building 420. It has its [[MR Scanner|own wiki page]].
+The CNI scanner is a GE 3T Ultra-High Performance (UHP) MR system. It is a whole body MR scanner with 60 cm bore, gradient strengths at 100 mT/m (constant mode) and 110 mT/m (burst mode) and a slew rate of 250 T/m/s. The scanner is currently running the latest GE operating system, MR30.1 R01. It is equipped with the latest imaging features and pulse sequences such as multi-band EPI/DWI, DL (deep learning) recon, and compressed sensing etc. To compile custom EPIC PSD's for the scanner, we also have a dedicated server with the necessary software environment installed. Just contact us for details.
 = Peripheral Device Rack (Laima Box) =

Huawu: /* Parsing the physio files */

2026-03-18T20:20:32Z

Parsing the physio files

← Older revision		Revision as of 20:20, 18 March 2026
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	** stop at the same time as the scan		** stop at the same time as the scan

	To reiterate-- the physio data stored in the physio files starts 30 seconds '''before''' you press the 'Scan' button (yes, it's psychic ;), which is almost always more than 30 seconds before scanning actually starts. It could be substantially longer if you do external triggering. In that case, you'll get some extra physio data recorded during the time between when you press start scan and you send your trigger. But the recording does stop when the scan stops. So, to synchronize physio and scan data, you can take the end of the physio data and count backward the number of data points to keep using the duration of MR ~~acquisiton~~ and sampling rate of the physio data.		To reiterate-- the physio data stored in the physio files starts 30 seconds '''before''' you press the 'Scan' button (yes, it's psychic ;), which is almost always more than 30 seconds before scanning actually starts. It could be substantially longer if you do external triggering. In that case, you'll get some extra physio data recorded during the time between when you press start scan and you send your trigger. But the recording does stop when the scan stops. So, to synchronize physio and scan data, you can take the end of the physio data and count backward the number of data points to keep using the duration of MR acquisition and sampling rate of the physio data.

	The physio files are zipped and uploaded to Flywheel. A simple Flywheel gear "CNI GE Physio File Converter" is available to help extract, visualize, and summarize the data.		The physio files are zipped and uploaded to Flywheel. A simple Flywheel gear "CNI GE Physio File Converter" is available to help extract, visualize, and summarize the data.

Huawu: /* Parsing the physio files */

2026-03-18T20:19:28Z

Parsing the physio files

← Older revision		Revision as of 20:19, 18 March 2026
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	To reiterate-- the physio data stored in the physio files starts 30 seconds '''before''' you press the 'Scan' button (yes, it's psychic ;), which is almost always more than 30 seconds before scanning actually starts. It could be substantially longer if you do external triggering. In that case, you'll get some extra physio data recorded during the time between when you press start scan and you send your trigger. But the recording does stop when the scan stops. So, to synchronize physio and scan data, you can take the end of the physio data and count backward the number of data points to keep using the duration of MR acquisiton and sampling rate of the physio data.		To reiterate-- the physio data stored in the physio files starts 30 seconds '''before''' you press the 'Scan' button (yes, it's psychic ;), which is almost always more than 30 seconds before scanning actually starts. It could be substantially longer if you do external triggering. In that case, you'll get some extra physio data recorded during the time between when you press start scan and you send your trigger. But the recording does stop when the scan stops. So, to synchronize physio and scan data, you can take the end of the physio data and count backward the number of data points to keep using the duration of MR acquisiton and sampling rate of the physio data.

	The physio files are zipped and uploaded to Flywheel. A simple Flywheel gear "CNI GE Physio File Converter" is ~~avalible~~ to help extract, visualize, and summarize the data.		The physio files are zipped and uploaded to Flywheel. A simple Flywheel gear "CNI GE Physio File Converter" is available to help extract, visualize, and summarize the data.

	===Biopac measures===		===Biopac measures===

Huawu: /* Subject video */

2026-03-18T20:18:31Z

Subject video

← Older revision		Revision as of 20:18, 18 March 2026
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	==Subject video==		==Subject video==
	You can monitor and record the subject's face or body using the [https://mrc-systems.de/en/products/mr-compatible-cameras MRI ~~compatable~~ video camera from MRC Systems]. The camera is always on and streaming video to the linux box next to the scan console. An analog video signal is also sent to the large-screen tv in the control room (use the 'A/v input'). To use the camera, you can attach it to the head coil using the loc-line connectors. When not in use, the camera should be hung on the side of the scanner along with the response devices. To see the video feed, run the following from the command line: "ffplay -f video4linux2 /dev/video0". To record the video feed, you can use our video recording scripts. From the command line run "recordSubject 310", this will record subject video for 5 minutes and 10 seconds; to synchronize the recording to the start of the scan, run "recordSubjectTrigger 310" instead. The data files are saved to the "video" directory.		You can monitor and record the subject's face or body using the [https://mrc-systems.de/en/products/mr-compatible-cameras MRI compatible video camera from MRC Systems]. The camera is always on and streaming video to the linux box next to the scan console. An analog video signal is also sent to the large-screen tv in the control room (use the 'A/v input'). To use the camera, you can attach it to the head coil using the loc-line connectors. When not in use, the camera should be hung on the side of the scanner along with the response devices. To see the video feed, run the following from the command line: "ffplay -f video4linux2 /dev/video0". To record the video feed, you can use our video recording scripts. From the command line run "recordSubject 310", this will record subject video for 5 minutes and 10 seconds; to synchronize the recording to the start of the scan, run "recordSubjectTrigger 310" instead. The data files are saved to the "video" directory.

	Troubleshoot: if you get an error "/dev/device0: busy or resource unavailable", then run "fuser /dev/device0" and you'll get the PID of the process that is currently occupying the video device. Then run "kill -9 [PID]". This should kill the process and you should be able to use the video camera again. Occasionally the camera feed fails and the recorded video files are empty. If this happens, check the video device setting with "v4l2-ctl -d /dev/video0 --all" and look for the "Video Standard" section. If it's something like "Video Standard = 0x000000ff PAL-B/B1/G/H/I/D/D1/K", then you'll need to change it to NTSC standard with "v4l2-ctl -d /dev/video0 -s ntsc". The returned message should be "Standard set to 0000b000 NTSC-M/M-JP/M-KR".		Troubleshoot: if you get an error "/dev/device0: busy or resource unavailable", then run "fuser /dev/device0" and you'll get the PID of the process that is currently occupying the video device. Then run "kill -9 [PID]". This should kill the process and you should be able to use the video camera again. Occasionally the camera feed fails and the recorded video files are empty. If this happens, check the video device setting with "v4l2-ctl -d /dev/video0 --all" and look for the "Video Standard" section. If it's something like "Video Standard = 0x000000ff PAL-B/B1/G/H/I/D/D1/K", then you'll need to change it to NTSC standard with "v4l2-ctl -d /dev/video0 -s ntsc". The returned message should be "Standard set to 0000b000 NTSC-M/M-JP/M-KR".


	= Scan Triggers =		= Scan Triggers =