CNI Wiki - User contributions [en]

Setting up protocols page

2026-04-03T21:41:30Z

Akerr:

=Screenshots =
The following set of slides remind you about how to start a scanning session with entering subject information, entering information correctly into the "Patient ID" field for automatic data transfer to NIMS, continuing on by running a protocol with both anatomical and fMRI sequences, and ending the scanning session.

[[Image:Slide02.png|thumb|200px|none|Subject Data Entry]]
'''Subject Data Entry'''
When you first arrive at the scanner, you will see the interface shown in this slide. This is the subject information data entry form. In order to enter information the cells must be white. If they are not, clicking the icon in the upper left hand corner (circled in red) will turn them into enterable fields.

[[Image:Slide03.png|thumb|200px|none|Subject Data Entry]]
'''Subject Data Entry'''
Key data fields that must be entered include: Patient ID, Subject Weight, and Operator Name.
The format requirements for the "Patient ID" field are as follows (and are also posted by the GE console):[Anonymous Subject ID]@[SUNet ID of faculty PI] [slash] [description] (all lower case, no spaces, alphanumeric only)
Examples are:
s101@gross/study1,
sub_345@wandell/abc,
kalanit/xyz754.
The subject’s weight must be included in the weight field for SAR calculations otherwise the scanner will not run.
Please do NOT include any PHI for the subject in any of the fields (e.g. Name, Date of Birth, any identifying numbers-other than weight.)
For data retrieval and archiving please make sure that your data is stored in the your correct lab folder.

Click on Start Exam (circled in red) to proceed to protocol list.

[[Image:Slide04.png|thumb|200px|none|Protocol Retrieval]]
'''Protocol Retrieval'''
Click on the protocol you wish to run (highlighted protocol will appear in yellow). To move it into the “protocol basket” click on the arrow to the right of the protocol list (circled in red). By double clicking on the protocol you can view all the sequences in the protocol., You can also move individual sequences to the ‘protocol basket” from other protocols.

[[Image:Slide05.png|thumb|200px|none|Protocol Retrieval]]
'''Protocol Retrieval'''
Once you have collected a protocol, click accept (circled in red) to move to the next display.

[[Image:Slide06.png|thumb|200px|none|Choosing dB/dt and SAR Limits]]
'''Choosing dB/dt and SAR Limits'''
You will need to choose either Normal Mode or First Level before proceeding further. To accept First Level click accept (circled in red) or you can choose Normal Mode by clicking that box.

[[Image:Slide07.png|thumb|200px|none|The Localizer]]
'''The Localizer'''
Every protocol will have a localizer as its first sequence. The purpose of the localizer is to verify the land marking of the subject and to provide coronal, sagittal, and axial images onto which prescription geometries can be determined for subsequent sequences in the protocol. The designation ”InRx” (circled in red) to the left of the sequence name indicates that either the parameters and/or geometry must be checked by the user for the sequence to be executable. In the case of the localizer there are no parameter adjustments needed. In order to run the sequence the “Save Rx” (circled in red) must be clicked. This will turn the “InRx” to “ACT”. The localizer can now be run by clicking on the “Scan” button (circled in red, above the “Save Rx” button), which now will be highlighted.

[[Image:Slide08.png|thumb|200px|none|Asset Calibration]]
'''Asset Calibration'''
All imaging sequences include parallel imaging techniques to speed up data acquisition. GE sequences use either ARC or ASSET. All sequences in your protocol that use ASSET need to use data from the ASSET calibration sequence. It a good practice to run this sequence after the localizer. Proceed as follows:
Highlight the sequence with a single mouse click. By clicking Setup (circled in red) The designation “InRx” will appear to the left of the sequence name. Clicking in the left upper window (circled in red). will result in a grid appearing. Position the grid as shown in the screen shot to the right, making sure that the grid covers the image and also covers space outside the image as shown in the screen shot. As with the localizer first click “SaveRx” and click “Scan” to run the sequence.

[[Image:Slide09.png|thumb|200px|none|3D Anatomical Sequences]]
'''3D Anatomical Sequences'''
Depending on your method of data analysis, you will have at least one anatomical sequence in addition to the fMRI sequences as part of your protocol. These sequences can be either 2D or 3D. 3D Anatomical sequences are prescribed with slabs, shown in this slide rather than slice grids as seen with the localizer and Asset calibration, and are manipulated the same way. In the “Setup” mode parameters can be adjusted. The full parameter tab can be viewed by using the toggle button (circled in red) to display the full parameter page or the axial image views. Depending on the study it is sometimes preferable to run a 3D T1 weighted sequence first, which will then allow prescribing of the functional MRI sequences. After the geometry has been prescribed in this 3D anatomical sequence clicking “SaveRx” and “Scan” allow the sequence to run.

[[Image:Slide10.png|thumb|200px|none|fMRI Sequences]]
'''fMRI Sequences'''
fMRI sequences can be set up and run similarly to other sequences previously described by using the “Setup”, “SaveRx”, and “Scan”(circled in red)
The screen shot on the right shows where a geometry has been prescribed by clicking first on the upper left image. You can then move the grid by using the mouse and can rotate it by placing the mouse on either of the two dots on the grid. Parameters can be adjusted also and they can be viewed by clicking on the pointer (circled in red) to hide the third image window.

[[Image:Slide11.png|thumb|200px|none|fMRI Sequences]]
'''fMRI Sequences'''
Parameters may be adjusted on each of the available tabs (circled in red): Details, Multi-Phase, Acceleration, Advanced.

[[Image:Slide12.png|thumb|200px|none|fMRI Sequences]]
'''fMRI Sequences'''
The parameter in the Multi-Phase tab “Phases per Location”( circled in red) can be used to change the length of time fMIR sequence is run to match the length of the paradigm.

[[Image:Slide13.png|thumb|200px|none|fMRI Sequences]]
'''fMRI Sequences'''
The parameter “ Start Scan Trigger” (circled in red) determines how the fMRI sequence is triggered relative to the paradigm.
Prior to running the fMRI sequence it is important to adjust the high order shims. There is a dedicated sequence to do this and shown In the next slide. Is is also important to remember that the shimming program will use the last sequence prescribed for high order shimming.

[[Image:Slide14.png|thumb|200px|none|High Order Shims (HOS)]]
'''High Order Shims (HOS)'''
There are no parameters that need to be adjusted in the HOS sequence. The sequence is run by clicking on “SaveRx” and “Scan” and following the pop-up window choices. Clicking “Calculate Shims” and “Done” in the pop-up shim window allows the optimized shim values to be entered into the system.

After the completing the shim program. The fMRI sequence is run. Multiple copies of the sequence can be obtained by using the cutting and pasting options via the right mouse button when used over the sequence list.

[[Image:Slide15.png|thumb|200px|none|Ending the Exam]]
'''Ending the Exam'''
Exams are ended following the drop down window choices after clicking on “End” (circled in red)

Setting up protocols page

2026-04-03T21:24:56Z

Akerr:

=Screenshots =
The following set of slides remind you about how to start a scanning session with entering subject information, entering information correctly into the "Patient ID" field for automatic data transfer to NIMS, continuing on by running a protocol with both anatomical and fMRI sequences, and ending the scanning session.

[[Image:Slide02.png|thumb|200px|none|Subject Data Entry]]
'''Subject Data Entry'''
When you first arrive at the scanner, you will see the interface shown in this slide. This is the subject information data entry form. In order to enter information the cells must be white. If they are not, clicking the icon in the upper left hand corner (circled in red) will turn them into enterable fields.

[[Image:Slide03.png|thumb|200px|none|Subject Data Entry]]
'''Subject Data Entry'''
Key data fields that must be entered include: Subject Name, Subject Weight, Subject Date of Birth, and Operator Name
The subject’s weigh must be included in the weight field for SAR calculations otherwise the scanner will not run.
For data retrieval and archiving please make sure that your data is stored in the your correct lab folder.
The format requirements for the "Patient ID" field are as follows (and are also posted by the GE console):[Anonymous Subject ID]@[SUNet ID of faculty PI] [slash] [description] (all lower case, no spaces, alphanumeric only)
Examples are:
s101@gross/study1,
sub_345@wandell/abc,
kalanit/xyz754.
Click on Start Exam (circled in red) to proceed to protocol list.

[[Image:Slide04.png|thumb|200px|none|Protocol Retrieval]]
'''Protocol Retrieval'''
Click on the protocol you wish to run (highlighted protocol will appear in yellow). To move it into the “protocol basket” click on the arrow to the right of the protocol list (circled in red). By double clicking on the protocol you can view all the sequences in the protocol., You can also move individual sequences to the ‘protocol basket” from other protocols.

[[Image:Slide05.png|thumb|200px|none|Protocol Retrieval]]
'''Protocol Retrieval'''
Once you have collected a protocol, click accept (circled in red) to move to the next display.

[[Image:Slide06.png|thumb|200px|none|Choosing dB/dt and SAR Limits]]
'''Choosing dB/dt and SAR Limits'''
You will need to choose either Normal Mode or First Level before proceeding further. To accept First Level click accept (circled in red) or you can choose Normal Mode by clicking that box.

[[Image:Slide07.png|thumb|200px|none|The Localizer]]
'''The Localizer'''
Every protocol will have a localizer as its first sequence. The purpose of the localizer is to verify the land marking of the subject and to provide coronal, sagittal, and axial images onto which prescription geometries can be determined for subsequent sequences in the protocol. The designation ”InRx” (circled in red) to the left of the sequence name indicates that either the parameters and/or geometry must be checked by the user for the sequence to be executable. In the case of the localizer there are no parameter adjustments needed. In order to run the sequence the “Save Rx” (circled in red) must be clicked. This will turn the “InRx” to “ACT”. The localizer can now be run by clicking on the “Scan” button (circled in red, above the “Save Rx” button), which now will be highlighted.

[[Image:Slide08.png|thumb|200px|none|Asset Calibration]]
'''Asset Calibration'''
All imaging sequences include parallel imaging techniques to speed up data acquisition. GE sequences use either ARC or ASSET. All sequences in your protocol that use ASSET need to use data from the ASSET calibration sequence. It a good practice to run this sequence after the localizer. Proceed as follows:
Highlight the sequence with a single mouse click. By clicking Setup (circled in red) The designation “InRx” will appear to the left of the sequence name. Clicking in the left upper window (circled in red). will result in a grid appearing. Position the grid as shown in the screen shot to the right, making sure that the grid covers the image and also covers space outside the image as shown in the screen shot. As with the localizer first click “SaveRx” and click “Scan” to run the sequence.

[[Image:Slide09.png|thumb|200px|none|3D Anatomical Sequences]]
'''3D Anatomical Sequences'''
Depending on your method of data analysis, you will have at least one anatomical sequence in addition to the fMRI sequences as part of your protocol. These sequences can be either 2D or 3D. 3D Anatomical sequences are prescribed with slabs, shown in this slide rather than slice grids as seen with the localizer and Asset calibration, and are manipulated the same way. In the “Setup” mode parameters can be adjusted. The full parameter tab can be viewed by using the toggle button (circled in red) to display the full parameter page or the axial image views. Depending on the study it is sometimes preferable to run a 3D T1 weighted sequence first, which will then allow prescribing of the functional MRI sequences. After the geometry has been prescribed in this 3D anatomical sequence clicking “SaveRx” and “Scan” allow the sequence to run.

[[Image:Slide10.png|thumb|200px|none|fMRI Sequences]]
'''fMRI Sequences'''
fMRI sequences can be set up and run similarly to other sequences previously described by using the “Setup”, “SaveRx”, and “Scan”(circled in red)
The screen shot on the right shows where a geometry has been prescribed by clicking first on the upper left image. You can then move the grid by using the mouse and can rotate it by placing the mouse on either of the two dots on the grid. Parameters can be adjusted also and they can be viewed by clicking on the pointer (circled in red) to hide the third image window.

[[Image:Slide11.png|thumb|200px|none|fMRI Sequences]]
'''fMRI Sequences'''
Parameters may be adjusted on each of the available tabs (circled in red): Details, Multi-Phase, Acceleration, Advanced.

[[Image:Slide12.png|thumb|200px|none|fMRI Sequences]]
'''fMRI Sequences'''
The parameter in the Multi-Phase tab “Phases per Location”( circled in red) can be used to change the length of time fMIR sequence is run to match the length of the paradigm.

[[Image:Slide13.png|thumb|200px|none|fMRI Sequences]]
'''fMRI Sequences'''
The parameter “ Start Scan Trigger” (circled in red) determines how the fMRI sequence is triggered relative to the paradigm.
Prior to running the fMRI sequence it is important to adjust the high order shims. There is a dedicated sequence to do this and shown In the next slide. Is is also important to remember that the shimming program will use the last sequence prescribed for high order shimming.

[[Image:Slide14.png|thumb|200px|none|High Order Shims (HOS)]]
'''High Order Shims (HOS)'''
There are no parameters that need to be adjusted in the HOS sequence. The sequence is run by clicking on “SaveRx” and “Scan” and following the pop-up window choices. Clicking “Calculate Shims” and “Done” in the pop-up shim window allows the optimized shim values to be entered into the system.

After the completing the shim program. The fMRI sequence is run. Multiple copies of the sequence can be obtained by using the cutting and pasting options via the right mouse button when used over the sequence list.

[[Image:Slide15.png|thumb|200px|none|Ending the Exam]]
'''Ending the Exam'''
Exams are ended following the drop down window choices after clicking on “End” (circled in red)

Facilities and Resources

2026-02-18T17:09:17Z

Akerr:

==Facilities and Resources==

The Stanford Center for Cognitive and Neurobiological Imaging (CNI, http://cni.stanford.edu/), a shared facility dedicated to research and teaching, opened in 2011. The center co-directors are Prof. Kawin Setsompop and Dr. Adam Kerr, and Dr. Laima Baltusis is the Facility Manager. The CNI supports scientific investigations into the brain that make rigorous connections between neuroscience and society. The CNI mission is to (1) Support neuroscience discovery for enhancing society, (2) Develop and disseminate cognitive and neurobiological imaging methods and (3) Create a structured, safe, and innovative environment for human neuroscience research.

The CNI is equipped with a 3T GE Ultra-High Performance MR system and and EGI 256-channel MR-compatible EEG system. It is maintained by a dedicated staff who oversee daily operations and maintenance. The CNI is a GE research partner and is supported by an MR Physicist from GE who is partially dedicated to the center. Further MR Physics support is provided by Dr. Hua Wu, a full-time MR Physicist on staff at the CNI, as well as collaborations with the [http://www-mrsrl.stanford.edu/ Stanford Magnetic Resonance Systems Research Lab (MRSRL)]. In addition to the basic imaging equipment, the CNI has a wide array of state-of-the-art peripheral equipment.

The system is equipped with several standard coils from GE: a 48-channel head coil, a 28-channel head and neck coil, and several coils by NOVA Medical Inc including a 32 channel brain array (dimensions: 18.5 cm wide, 21 cm high) for collection of MRI images of the whole brain, and a 16 channel visual array for fMRI of visual cortex (dimensions: 18.5 wide, 10 cm high).

Visual display of stimuli during scan is achieved through one of two systems: a 47" 3D display by Resonance Technology which provides the ability to easily present different stimuli to each eye, and a data projector that provides a brighter stimulus with a larger field of view than the possible with the LCD displays. Eye movements can be tracked using an MR-compatible SR Research EyeLink 1000 with remote optics.

Auditory stimuli can be presented by low-profile MR-compatible headphones from Resonance Technology or through a custom system that uses bone-conduction transducers.

For collecting subject responses, we have a modular response box system (fORP 932) from [http://www.curdes.com/ Current Designs]. This system allows users to swap out various response devices. The output from any of these devices is available from the fORP box via USB keyboard emulation. We have confirmed that the fORP 932 USB interface is polled at 1kHz, allowing response time measurement with 1 millisecond resolution.The response devices that we currently have include a scroll-wheel device, bimanual button boxes, a 5-button response pad, a joystick, and a 4-button stick-style response device.

MRI Simulator (mock scanner): The MRI simulator (Psychology Software Tools, Inc.) is designed to parallel the experience an individual will encounter during an actual MRI scan. The simulator consists of a 12-foot mock scanner with 6-foot tapered bore, head coil, head stabilizer system, visual and auditory presentation systems, and equipment for monitoring the subject's response to the training procedure. Two speakers are placed within the bore in order to deliver simulated MR gradient sounds to the subject. Behavior analysis and therapy techniques are used to counter conditioned fear or anxiety experienced in response to the imaging equipment and procedures. In brief, this process involves careful control of the salient stimuli in the imaging environment, systematic gradual exposure to the equipment, personnel and sensations involved in image acquisition. The simulator apparatus is housed in a separate room within the CNI facility.

The simulator allows researchers to train subjects to inhibit body motion during scanning. Typically, the subject will to listen to music, hear a story or watch a movie during the training. This "entertainment" serves as both distraction and immediate reinforcement for inhibiting movement. If the subject exceeds a pre-set movement criterion, the entertainment is automatically interrupted for a brief interval to provide a contingent consequence for body motion. The entertainment resumes when movement is again inhibited below the established criterion. The movement criterion can be adjusted according to the subject's current ability and gradually made more stringent as training progresses. The entire training process usually can be accomplished in one to three 30 minute sessions.

Data Collection: Data collected at the CNI are archived in a permanent database using software provided by [//flywheel.io Flywheel]. Flywheel stores and organizes the raw data from the MR scanner as well as physiological measurements from the subject (synchronized with the MR data). Flywheel allows data to be shared within the CNI community, in accordance with regulations set forth by the Stanford IRB and the usage policies that apply to each investigator. Flywheel is securely hosted within a Google Cloud Project, provisioned for this specific use by Stanford's IT. Flywheel data are stored within a multi-regional object storage bucket to safeguard against natural disaster. The Flywheel database, as well as the data objects, are backed up hourly. User's authenticate to Flywheel using their Stanford University credentials. Authentication is handled via Stanford Login, backed by a Stanford/Google SAML 2.0 integration, which works across organizations and supports federation as well as multi-factor authentication protocols.

Data Processing: Data preprocessing is handled by Flywheel within its scalable cloud compute platform. Flywheel provides several pre-packaged processing algorithms (Gears), some of which were custom-developed at CNI. Gears are configured to run automatically on CNI data as they are ingested into Flywheel. These algorithms include extraction of metadata, data classification, DICOM-to-NIfTI conversion, reconstruction of raw k-space data, calculation of regressors from physiological recordings, and generation of automated [[QA|quality assurance reports]]. The Flywheel platform is extensible and several other algorithms can be run on data once they are in the platform. Data can be downloaded from Flywheel using the Flywheel CLI, SDKs, or user-interface.

Skope system: The CNI is also equipped with a Skope Dynamic Field Camera that can be used by researchers to accurately measure the time-varying magnetic fields. The system includes 16 field probes and software that fits up to 3rd order spherical harmonics of the magnetic field with one-microsecond temporal resolution. The CNI also has a license to the Skope software package that uses these measurements for iterative image reconstruction and can support a wide number of acquisition strategies including SMS, MUSE, non-Cartesian and inplane accelerated scans. Use of the Skope requires researchers to be competent with making modifications to their MRI sequences of interest and requires special training. Please contact the CNI Research Director for more information.

Facilities and Resources

2026-02-17T20:25:53Z

Akerr:

Facilities and Resources

2026-02-17T20:25:22Z

Akerr:

==Facilities and Resources==

The Stanford Center for Cognitive and Neurobiological Imaging (CNI, http://cni.stanford.edu/), a shared facility dedicated to research and teaching, opened in 2011. The center co-directors are Prof. Brian Wandell and Dr. Adam Kerr, and Dr. Laima Baltusis is the Facility Manager. The CNI supports scientific investigations into the brain that make rigorous connections between neuroscience and society. The CNI mission is to (1) Support neuroscience discovery for enhancing society, (2) Develop and disseminate cognitive and neurobiological imaging methods and (3) Create a structured, safe, and innovative environment for human neuroscience research.

The CNI is equipped with a 3T GE Ultra-High Performance MR system and and EGI 256-channel MR-compatible EEG system. It is maintained by a dedicated staff who oversee daily operations and maintenance. The CNI is a GE research partner and is supported by an MR Physicist from GE who is partially dedicated to the center. Further MR Physics support is provided by Dr. Hua Wu, a full-time MR Physicist on staff at the CNI, as well as collaborations with the [http://www-mrsrl.stanford.edu/ Stanford Magnetic Resonance Systems Research Lab (MRSRL)]. In addition to the basic imaging equipment, the CNI has a wide array of state-of-the-art peripheral equipment.

The system is equipped with several standard coils from GE: a 48-channel head coil, a 28-channel head and neck coil, and several coils by NOVA Medical Inc including a 32 channel brain array (dimensions: 18.5 cm wide, 21 cm high) for collection of MRI images of the whole brain, and a 16 channel visual array for fMRI of visual cortex (dimensions: 18.5 wide, 10 cm high).

Visual display of stimuli during scan is achieved through one of two systems: a 47" 3D display by Resonance Technology which provides the ability to easily present different stimuli to each eye, and a data projector that provides a brighter stimulus with a larger field of view than the possible with the LCD displays. Eye movements can be tracked using an MR-compatible SR Research EyeLink 1000 with remote optics.

Auditory stimuli can be presented by low-profile MR-compatible headphones from Resonance Technology or through a custom system that uses bone-conduction transducers.

For collecting subject responses, we have a modular response box system (fORP 932) from [http://www.curdes.com/ Current Designs]. This system allows users to swap out various response devices. The output from any of these devices is available from the fORP box via USB keyboard emulation. We have confirmed that the fORP 932 USB interface is polled at 1kHz, allowing response time measurement with 1 millisecond resolution.The response devices that we currently have include a scroll-wheel device, bimanual button boxes, a 5-button response pad, a joystick, and a 4-button stick-style response device.

MRI Simulator (mock scanner): The MRI simulator (Psychology Software Tools, Inc.) is designed to parallel the experience an individual will encounter during an actual MRI scan. The simulator consists of a 12-foot mock scanner with 6-foot tapered bore, head coil, head stabilizer system, visual and auditory presentation systems, and equipment for monitoring the subject's response to the training procedure. Two speakers are placed within the bore in order to deliver simulated MR gradient sounds to the subject. Behavior analysis and therapy techniques are used to counter conditioned fear or anxiety experienced in response to the imaging equipment and procedures. In brief, this process involves careful control of the salient stimuli in the imaging environment, systematic gradual exposure to the equipment, personnel and sensations involved in image acquisition. The simulator apparatus is housed in a separate room within the CNI facility.

The simulator allows researchers to train subjects to inhibit body motion during scanning. Typically, the subject will to listen to music, hear a story or watch a movie during the training. This "entertainment" serves as both distraction and immediate reinforcement for inhibiting movement. If the subject exceeds a pre-set movement criterion, the entertainment is automatically interrupted for a brief interval to provide a contingent consequence for body motion. The entertainment resumes when movement is again inhibited below the established criterion. The movement criterion can be adjusted according to the subject's current ability and gradually made more stringent as training progresses. The entire training process usually can be accomplished in one to three 30 minute sessions.

Data Collection: Data collected at the CNI are archived in a permanent database using software provided by [//flywheel.io Flywheel]. Flywheel stores and organizes the raw data from the MR scanner as well as physiological measurements from the subject (synchronized with the MR data). Flywheel allows data to be shared within the CNI community, in accordance with regulations set forth by the Stanford IRB and the usage policies that apply to each investigator. Flywheel is securely hosted within a Google Cloud Project, provisioned for this specific use by Stanford's IT. Flywheel data are stored within a multi-regional object storage bucket to safeguard against natural disaster. The Flywheel database, as well as the data objects, are backed up hourly. User's authenticate to Flywheel using their Stanford University credentials. Authentication is handled via Stanford Login, backed by a Stanford/Google SAML 2.0 integration, which works across organizations and supports federation as well as multi-factor authentication protocols.

Data Processing: Data preprocessing is handled by Flywheel within its scalable cloud compute platform. Flywheel provides several pre-packaged processing algorithms (Gears), some of which were custom-developed at CNI. Gears are configured to run automatically on CNI data as they are ingested into Flywheel. These algorithms include extraction of metadata, data classification, DICOM-to-NIfTI conversion, reconstruction of raw k-space data, calculation of regressors from physiological recordings, and generation of automated [[QA|quality assurance reports]]. The Flywheel platform is extensible and several other algorithms can be run on data once they are in the platform. Data can be downloaded from Flywheel using the Flywheel CLI, SDKs, or user-interface.

Skope system: The CNI is also equipped with a Skope Dynamic Field Camera that can be used by researchers to accurately measure the time-varying magnetic fields. The system includes 16 field probes and software that fits up to 3rd order spherical harmonics of the magnetic field with one-microsecond temporal resolution. The CNI also has a license to the Skope software package that uses these measurements for iterative image reconstruction and can support a wide number of acquisition strategies including SMS, MUSE, non-Cartesian and inplane accelerated scans. Use of the Skope requires researchers to be competent with making modifications to their MRI sequences of interest and requires special training. Please contact the CNI Research Director for more information.

Flywheel

2026-02-02T18:59:38Z

Akerr: /* Protected Health Information */

The CNI uses [//flywheel.io Flywheel] for data and computational management. Data from the scanner are automatically uploaded to the Flywheel database. The Flywheel system is on the Google Cloud Platform. Users download data either using a web-browser or another of the [//docs.flywheel.io/hc/en-us/articles/360008410994-Getting-Started-Downloading-Data methods provided by Flywheel] (e.g., command-line-interface or software-development-kit).

At the CNI, as data come into the Flywheel they are automatically processed according to rules determined by the CNI staff. For example, upon ingest PHI data are removed, DICOM and raw PFile data are converted to NIfTI format, and metadata about the scan parameters are read and inserted into the database. Some labs may configure initial processing of the data for individual projects differently. For help with customization groups can contact Flywheel directly or ask Michael Perry (see below).

This page describes Flywheel features that are specific to the CNI. You can learn more about Flywheel using the links below:

* A 5 minute video overview of Flywheel is available [//youtu.be/JUoSejTxXUw on YouTube]
* Manual pages and basic material about the system are maintained by Flywheel [//docs.flywheel.io/hc/en-us at this site].
* Links to videos and webinars are on the [//docs.flywheel.io/hc/en-us Flywheel Docs site]

'''Log in to CNI's Flywheel site here: [//cni.flywheel.io cni.flywheel.io]'''

= Authentication =

Authentication to Flywheel at the CNI requires a valid (full-account) SUNetID.

New users should ask the CNI staff to create an account.

= Data upload =
The CNI scanner produces DICOM, P-File, and Physio data. The sequence you are using along with your scan parameters will determine which of those data are generated. Regardless of the type, those data will make their way into Flywheel automatically via one of the Connectors, described next.

== Connectors ==
At the CNI data are uploaded to Flywheel automatically via Connectors (aka Reapers). CNI has multiple Flywheel Connectors running, one for each of the types of data that must make their way into Flywheel.

The connectors running at CNI are:
* DICOM connector - communicates directly with the scanner's DICOM server to "discover" new data, package those data, and upload those data to Flywheel
* P-File connector - packages and transfers raw P-File data from the console to Flywheel.
* Physio connector - packages and transfers physio data from the console to Flywheel. This connector attempts to match the physio data to the correct series/acquisition within Flywheel, however if the scan is ended early, or if the prescribed duration is off from the actual duration, the physio data may not be transferred or it may end up in the wrong series. Please be sure to check your physio data and report any issues to CNI staff right away.

== Getting your data to the right place ==
The Flywheel Connectors determine where to place data in the hierarchy using information entered into the MR console by the user and obtained from the DICOM or PFile data.

We refer to the information provided by the user to help Flywheel understand where the data belong as the "Sort String". It is important to understand how to provide this information correctly so that your data find their way to your project without delay.

If a mistake is made here, worry not, those data will still be uploaded to Flywheel, however they will go to a group and project which only CNI staff have access to. If you believe this has happened to you, please feel free to reach out to CNI staff and we will help get your data where it belongs.

=== Flywheel Sort String (Good) ===

To make sure the data you collect is sent to the correct Flywheel project for your lab, you must enter a "Flywheel sort string" on the console.

Enter this string into the '''Patient ID''' field on the scanner console.

The string format is:

<subject_label>@<group>/<project>

=== Flywheel Sort String (Bad) ===
If you do not enter the sort string correctly, the data will still be sent to Flywheel, but it will not be routed to the correct project. Instead, it will be assigned to the "unknown" group or "Unsorted" project, depending on what Flywheel can determine.

* If the data are sent to the unknown group, you must ask the Site Admins to retrieve your data. (Michael, Laima).
* If the data are sent to the "Unsorted" project (case sensitive), you can find it and move it yourself.

Thus, for a given piece of data coming in through a Connector:

No Group, No Project --> group_id = "unknown", project = "Unsorted"
No Group, Project --> group_id = "unknown", project = <Project>
Group, No Project --> group_id = <Group>, project = "Unsorted"

=== Session Labels and Tags ===
In some cases, users want to set the name of the session rather than have Flywheel use the default name (which is the exam number).

You can control the session name/label by placing information in the ''AdditionalPatientHistory'' section on the console, like so:

To set the '''session label'' using the following format (without the "<>"):

label_<your_desired_session_label>

You may also '''tag a session''' to make it easier to find later. You can '''set a session tag''' by inserting this string in the ''AdditionalPatientHistory'' section.

tag_<tag_name>

= Protected Health Information =

Protected Health Information (PHI) is considered High Risk Data according to the Stanford Data Classification Guidelines. PHI is defined as any information that can be used to identify an individual and may relate to their past, present, or future health. By law, this information must be encrypted by law and must be (a) stored in encrypted form, and (b) transmitted only through secure means.

Anonymized research data for publication can be shared without harm. See [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this Stanford site]. Although CNI participants are not medical patients, we treat human subject data with the same PHI status as if they were patients.

It is our policy that users '''never''' use any PHI identifiers when conducting an MRI exam. We further strip out any field that may inadvertently include PHI before it is uploaded to Flywheel. This includes:

* Patient ID field
* Date of Birth
* Medical Record Number
* Subject Name (first and last)
* Anything else that clearly identifies the human subject

'''Our standard however is to never use any PHI identifiers when entering data into the scanner!'''

Be careful also about what you enter in these fields - over the years we have found (and deleted) PHI from these fields:

* Subject code (part of Patient ID)
* Exam description
* Series description

It is permissible to include the subject's weight which is needed for scanner safety calculations.

At present, to describe the PHI methods in your publications, you might find this summary paragraph helpful.

''Data at Stanford's Center for Cognitive and Neurobiological Imaging are securely transferred from the MR scanner directly to a data management system (Flywheel.io) that is running within a Google platform space that is approved for research data. Prior to transfer the data file headers are stripped of fields that may contain subject information (patient id, DOB, MRN, name fields). These procedures meet the Stanford standard for anonymized research data for publication and can be shared without harm. See: [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this Stanford site].

= Data Processing =

Once data are uploaded to Flywheel those data are automatically processed according to a given Project's "[//docs.flywheel.io/hc/en-us/articles/360008553133-Project-Gear-Rules Gear Rules]". The Rules define which Gear will be run on a given piece of data when it lands in Flywheel. These rules do everything from metadata extraction from DICOM headers to execution of QA algorithms.

== Gear Rules (Default) ==

At CNI we have defined a default set of rules that are applied to every new project. Each rule defines the logic that must be satisfied in order for a given gear to be run on a data file.

The image below shows the default rules that every new project is provided with.

[[File:GearRules.png|600px|thumb|center|Gear Rule Template]]

=== A special note on DICOM to NIfTI Conversion (dcm2niix & dcm-convert) ===

Historically at CNI we have provided a tool that was developed in-house for DICOM to NIfTI conversion (dcm-convert). Recently users have expressed interest in having a very widely used and popular tool, dcm2niix, serve as the default tool to perform DICOM to NIfTI conversion in Flywheel. We are happy to say that Flywheel does provide a dcm2niix Gear and we have incorporated this into our default rule set. As of today the default is still dcm-convert, however for projects created recently you will see this rule available and in a disabled state. You can easily enable this rule, however it should be noted that if you do enable this rule you need to disable the existing dcm-convert rule so that you don't introduce a race condition which would result in a situation where you would not be able to predict which tool would be used to generate the NIfTI data.

=== Re-running DICOM to NIfTI conversion across a project ===

There are special considerations to be made if you desire to re-run DICOM to NIfTI conversion across an entire project, namely you need to ignore DICOM data that was generated by any of the MUX sequences, as those data are aliased and running either of the DICOM to NIfTI tools on those data will result in aliased NIfTI data. Special care is taken within the Gear rules to avoid this situation by specifically ignoring data that were collected with a mux sequence.

The best idea here is to coordinate with CNI staff (e.g., Michael Perry) prior to doing this.

= Downloading Data =
There are several ways to download data from Flywheel, including via the [//flywheelio.zendesk.com/hc/en-us/articles/360008622994-Downloading-sessions-or-acquisitions-from-the-Web-UI WEB UI], the [//flywheelio.zendesk.com/hc/en-us/sections/360001596834-Command-Line-Interface command line interface (CLI)], and the Flywheel SDK (which is available for both [//flywheel-io.github.io/core/branches/master/python/getting_started.html Python] and [//flywheel-io.github.io/core/branches/master/matlab/getting_started.html MATLAB]). The links below can help you get started with the various methods of export:

=== UI Downloads ===
* [//flywheelio.zendesk.com/hc/en-us/articles/360009256973-Downloading-a-file Download individual Files]
* [//flywheelio.zendesk.com/hc/en-us/articles/360008622994-Downloading-sessions-or-acquisitions-from-the-Web-UI Download session or acquisition containers]
* [//flywheelio.zendesk.com/hc/en-us/articles/360008629794-Downloading-an-entire-project Download a Project]

=== Flywheel SDK ===
* [//flywheel-io.gitlab.io/product/backend/sdk/branches/master/matlab/index.html MATLAB]
* [//flywheel-io.gitlab.io/product/backend/sdk/branches/master/python/index.html Python]
* [//gitlab.com/flywheel-io/public/flywheel-tutorials Support materials SDK examples (Jupyter notebooks)]

=== Flywheel CLI ===
* [//docs.flywheel.io/hc/en-us/search?utf8=%E2%9C%93&query=CLI Flywheel CLI Documentation]

=== CLI: Tips and Best Practices for CNI Users ===

This section focuses on a few tips for using the CLI to download your data. For a complete overview of the Flywheel CLI, including how to get started, please look through the [//docs.flywheel.io/hc/en-us/search?utf8=%E2%9C%93&query=CLI Flywheel CLI Documentation].

''Tip:'' ''' Download only the files you need'''
When downloading data from Flywheel using the CLI you can greatly speed up your downloads by excluding data types which are not needed for your analysis.

''Example: '''''Exclude pfile and DICOM data from a container download''': Most users do not need to download the raw scanner files (PFILES) or raw DICOM data. You can exclude certain data types from your downloads by using the `-e` flag with your CLI download, like so:
fw download "cni/testproject/subject1/session1" -e pfile -e dicom

This tells the CLI to exclude any pfile and dicom files in the container. Note that you can use consecutive -e flags to exclude multiple data types.

''Example:'' '''Download only NIfTI, BVEC, and BVAL files''': 
Most users are only interested in the data that will be input to their analysis pipelines. This is most often limited to three data types (nifti, bvec, and bval). You can use the following command with multiple include flags (`-i`) to accomplish exactly that:
fw download "cni/testproject/subject1/session1" -i nifti -i bvec -i bval

This will generate an archive (.tar) file containing the requested hierarchy with only those files you explicitly need.

''Example:'' '''Using quotes'''
Often times your source-path (that is the ''group/project/subject/session'' string the describes the location of your data in Flywheel) will have one or more spaces or special characters in it. To properly address that location using the CLI it's important to use quotes around the source path, like so:
fw download "cni/testproject/subject1/session1"

''Example'' ''Download a single file with the CLI''
So you have navigated to a container and your only desire is to download a single file from that container, the best way to do that is using the CLI with the 'files' spec filter.

''Example:'' '''Download a single NIfTI file from an acquisition container:'''
fw download "test/Unsorted/s001/18591/T1w 1mm/files/18591_13_1.nii.gz"

''The important bit here is the inclusion of "files" prior to the file name.''

= Using Sherlock and other Computers =
We suggest that you use the Flywheel Command Line Interface (CLI) to transfer data to other compute resources, like Sherlock.

To download and install the CLI on Sherlock we use the `wget` tool, then `unzip` to extract the CLI resource package, and finally modify our `.bashrc` file to add the fw binary as an alias in our environment.

'''Step 1:''' Get the URL for the CLI package, which can be found on the "Profile" page within the Flywheel interface. To grab the URL, find the CLI section on the Profile page, right-click the Linux CLI Download link, and choose "Copy Link Address" (or similar). Once you have the download link address move to the next step.

'''Step 2: ''' Log in to Sherlock and run the `wget` command, using the URL from ''Step 1'' to download the CLI package.
mkdir -p flywheel/cli
cd flywheel/cli
wget //storage.googleapis.com/flywheel-dist/cli/<version>/fw-linux_amd64.zip

'''Step 3:''' Unpack the CLI archive and cleanup the downloaded package.
unzip fw-linux_amd64.zip
mv linux_amd64/fw .
rmdir linux_amd64
rm -f fw-linux_amd64.zip

'''Step 4:''' Modify your `.bashrc` file to add the fw CLI command to your environment, and source it to make the alias active. ''Note that this only needs to be done once.''
echo -e "alias fw='$HOME/flywheel/cli/fw'" >> $HOME/.bashrc
source $HOME/.bashrc

'''Step 5:''' Once the above steps are complete, you should be able to log in using the CLI and use it as described in the official documentation: //flywheelio.zendesk.com/hc/en-us/sections/360001596834-Command-Line-Interface. The best way to do this is navigate to your [//cni.flywheel.io/#/profile profile page] in Flywheel, make sure that you have generated an API Key, and use the login command text that is provided for you there.

fw login <your API key>

= Data Migration from NIMS =
Before there was Flywheel, there was NIMS. Data have been preserved in NIMS and they can be migrated to Flywheel on an as-needed basis. Please inquire with Michael Perry for more information.

= Support =

Michael can help with most CNI Flywheel issues. If support is needed for Flywheel issues not related to the CNI, please email their help line: support@flywheel.io.

Getting Started

2025-11-09T21:07:28Z

Akerr:

The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.

If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).

== User Access/Onboarding & Training ==

The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.

All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.

=== Access/Onboarding ===

As of September 2025 new CNI users must complete the following three step onboarding process.
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below.
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.

*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-11AM. Registration links for those sessions are found in "CNI New User Orientation Session Registration Forms" section below.

*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.

New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .

''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.

Any questions regarding the on-boarding process should be directed to the CNI facility manager.

Access status to CNI is organized into three categories:
<ul>
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li> 
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li> 
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li>
</ul>

'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''

===CNI New User Orientation Session Registration Forms===
New user CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI.

The next CNI new user orientation will be on November 20, 2025, 9:00AM to 10:30AM.

The registration form for this session is here https://docs.google.com/forms/d/e/1FAIpQLSf-D-p4hqv70aHo0o3HdxPUc4XwmQ_MeexEdtn8uSggnM8vjw/viewform?usp=header

Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.

===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/hiv/testing/nonclinical/clia.html]
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]

===Late night scan sessions approval policy===

Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.

== IRB Approval for Project ==
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval.
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites].
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]].

Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.

== Setting up a CNI account for research studies ==

To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].

<ul>
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)
<li> Funding source (ex. NIH, NSF)
<li> PTA assigned to this project
<li> Grant (PTA) Expiration Date
<li> IRB approval letter
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.
<li> Name, e-mail, and SUnetID of the person, who will be receiving the invoice notice for this grant each month. The invoice contains the listing of all the bookings to the grant. This can be either the PI, finance manager for the grant, or any other designated person for these funds. Please note that only one person can be set up in the system to receive the invoice. The invoice e-mail can, however, be forwarded to others to additionally to review if needed.
</ul>

The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.

== Scheduling MRI Scanner Time ==

All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system].

Only researchers who have completed Level 2 training can make bookings.

== Scheduling Policy ==

'''Overview:''' We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours.

The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.

The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors.

'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.

If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible.

'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully.

Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant.

Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted.

Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant.

Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.

'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.

To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability.

We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials.

'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed.

Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.

== Billing Policies ==
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.

'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''

8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour

6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour

8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour

8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour

8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour

EEG usage has no charge currently (see CNI staff for more info)

Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.

'''Cancellation Policies'''

See above

== User Etiquette ==

Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:

 
<ol>
<li>Please show up for scan time that you have booked, and start and stop your scan session on time.
<ul>
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li>
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li>
<li>Please book your scans with valid grants.</li>
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li>
</ul>
</li>
 
<li>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.
<ul>
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li>
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li>
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li>
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li>
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li>
</ul>
</li>
 
<li>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.
<ul>
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li>
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li>
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li>
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li>
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li>
</ul>
</li>
</ol>

To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].

Getting Started

2025-09-18T21:27:05Z

Akerr:

The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.

If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).

== User Access/Onboarding & Training ==

The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.

All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.

=== Access/Onboarding ===

As of September 2025 new CNI users must complete the following three step onboarding process.
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below.
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.

*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-11AM. Registration links for those sessions are found in "CNI New User Orientation Session Registration Forms" section below.

*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.

New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .

''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.

Any questions regarding the on-boarding process should be directed to the CNI facility manager.

Access status to CNI is organized into three categories:
<ul>
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li> 
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li> 
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li>
</ul>

'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''

===CNI New User Orientation Session Registration Forms===
New user CNI orientation sessions are held on Thursdays 8:30AM to 11:00AM at CNI.

The next CNI new user orientation will be on October 2, 2025, 9:00AM to 11:00AM.
The registration form for this session is here https://docs.google.com/forms/d/e/1FAIpQLSdkffe1N9pkCicBKeBtLNvIFH7ismv6j4acgEYVFhx3JDN8AQ/viewform?usp=header

Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.

===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/hiv/testing/nonclinical/clia.html]
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]

===Late night scan sessions approval policy===

Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.

== IRB Approval for Project ==
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval.
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites].
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]].

Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.

== Setting up a CNI account for research studies ==

To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].

<ul>
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)
<li> Funding source (ex. NIH, NSF)
<li> PTA assigned to this project
<li> Grant (PTA) Expiration Date
<li> IRB approval letter
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.
<li> Name, e-mail, and SUnetID of the person, who will be receiving the invoice notice for this grant each month. The invoice contains the listing of all the bookings to the grant. This can be either the PI, finance manager for the grant, or any other designated person for these funds. Please note that only one person can be set up in the system to receive the invoice. The invoice e-mail can, however, be forwarded to others to additionally to review if needed.
</ul>

The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.

== Scheduling MRI Scanner Time ==

All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system].

Only researchers who have completed Level 2 training can make bookings.

== Scheduling Policy ==

'''Overview:''' We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours.

The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.

The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors.

'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.

If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible.

'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully.

Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant.

Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted.

Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant.

Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.

'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.

To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability.

We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials.

'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed.

Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.

== Billing Policies ==
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.

'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''

8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour

6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour

8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour

8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour

8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour

EEG usage charge is an additional $50/hour at any time

Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.

'''Cancellation Policies'''

See above

== User Etiquette ==

Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:

 
<ol>
<li>Please show up for scan time that you have booked, and start and stop your scan session on time.
<ul>
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li>
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li>
<li>Please book your scans with valid grants.</li>
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li>
</ul>
</li>
 
<li>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.
<ul>
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li>
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li>
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li>
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li>
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li>
</ul>
</li>
 
<li>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.
<ul>
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li>
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li>
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li>
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li>
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li>
</ul>
</li>
</ol>

To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].