3T GE Training Session UCSD Center for Functional Magnetic Resonance Imaging March 2004.

3T GE Training Session3T GE Training Session

UCSD Center for Functional UCSD Center for Functional Magnetic Resonance ImagingMagnetic Resonance Imaging

March 2004March 2004

IntroductionIntroduction SafetySafety Magnetic Room EquipmentMagnetic Room Equipment Console Room Overview Console Room Overview

• DesktopDesktop• KeyboardKeyboard• Scan Rx DesktopScan Rx Desktop• Selecting a ProtocolSelecting a Protocol• Graphical PrescriptionGraphical Prescription

fMRI StudyfMRI Study Data ManagementData Management Reset the TPSReset the TPS

SafetySafety Eliminate Magnet HazardsEliminate Magnet Hazards

• Keep metal out of the magnet roomKeep metal out of the magnet room

Subject PreparationSubject Preparation• ScreeningScreening• Provide informationProvide information• Test intercomTest intercom• Enter the correct subject weightEnter the correct subject weight• Turn on the bore light and fanTurn on the bore light and fan• Show the subject how to turn on the patient alert systemShow the subject how to turn on the patient alert system• Provide ear protection for the subjectProvide ear protection for the subject• Instruct subject to close his or her eyes when the alignment Instruct subject to close his or her eyes when the alignment

light is on.light is on.

Bore TemperatureBore Temperature

EXCITE PlatformEXCITE Platform EXCITE: Ultra-fast, scalable, data acquisition and EXCITE: Ultra-fast, scalable, data acquisition and

reconstruction hardware.reconstruction hardware. Scalable from low end to ultra-high end (rBW and Scalable from low end to ultra-high end (rBW and

channels).channels). Rapid, parallel processingRapid, parallel processing Reconstruction: 100-400 frames/sec.Reconstruction: 100-400 frames/sec.

• Architectural support for up to 1600 frames/sec.Architectural support for up to 1600 frames/sec. Hardware: Hardware:

• HP x 8000 WorkstationHP x 8000 Workstation• Dual 2.66 GHz/533 MHz Bus Intel Xeon CPU’sDual 2.66 GHz/533 MHz Bus Intel Xeon CPU’s• 108 GB Disk108 GB Disk• Host Operating System: Red Hat Linux 7.3Host Operating System: Red Hat Linux 7.3

Magnetic Room EquipmentMagnetic Room Equipment 3T magnet labels: fmri3tw (host computer), fmri3tww 3T magnet labels: fmri3tw (host computer), fmri3tww

(Advantage workstation). (Advantage workstation). The 3T magnet is equipped with:The 3T magnet is equipped with:

• Physiological Acquisition Controller (PAC)Physiological Acquisition Controller (PAC) Respiratory compensation bellowsRespiratory compensation bellows A six pin connection for a high impedance ECG leadsA six pin connection for a high impedance ECG leads Peripheral gating: a fiber optic connection for the peripheral gating Peripheral gating: a fiber optic connection for the peripheral gating

leadlead Patient call to signal assistancePatient call to signal assistance Pulse meterPulse meter

• MRI Devices 8 channel high resolution brain coil (HRBRAIN)MRI Devices 8 channel high resolution brain coil (HRBRAIN)• 1 channel birdcage volume head coil1 channel birdcage volume head coil• Two actively shielded gradient coils:Two actively shielded gradient coils:

Zoom: Optimizes slew rate and amplitude for small FOV applications. Max. Zoom: Optimizes slew rate and amplitude for small FOV applications. Max. FOV: 35 cm (S/I), 44 cm (A/P), 44 cm (R/L) FOV: 35 cm (S/I), 44 cm (A/P), 44 cm (R/L)

Whole Body: Intended for large FOV applicationsWhole Body: Intended for large FOV applications

Status Display Panel: located on Status Display Panel: located on the magnet coverthe magnet cover

Pressing Pressing Emergency Stop Emergency Stop on the operators console:on the operators console:•The scan abortsThe scan aborts•The power disables the patient handling and scan The power disables the patient handling and scan related equipmentrelated equipment

Control Panel ButtonControl Panel Button

Alignment light on the magnet control panel button

Move to Scan: the table moves to patient isocenter

Control Panel Button in the magnet room

1.1. Desktop control Desktop control panelpanel

2.2. System status System status displaydisplay

3.3. Area titleArea title4.4. Text boxText box5.5. Pull down menuPull down menu6.6. Autoview Autoview

windowwindow7.7. Image sliderImage slider8.8. System activity System activity

statusstatus9.9. Window toggle Window toggle

buttonbutton10.10. Pop-up window Pop-up window

buttonbutton11.11. List/Select menuList/Select menu12.12. Scroll arrowsScroll arrows13.13. Control panelsControl panels14.14. Scan operation Scan operation

areaarea

Desktop OverviewDesktop Overview

Patient Information/Position PanelPatient Information/Position Panel

Accession Number: Typically prescribed by hospital Patient ID: Any combination of numbers, letters and dashes. Limited to Patient ID: Any combination of numbers, letters and dashes. Limited to

64 characters. System will notify if identical ID is found.64 characters. System will notify if identical ID is found. Patient Name: Limited to 64 characters and should not be preceded by Patient Name: Limited to 64 characters and should not be preceded by

numbers. numbers. Rad: Name of radiologist – can be used to specify PI.Rad: Name of radiologist – can be used to specify PI. Refer: Name of referring physician – also available for PI specification. Refer: Name of referring physician – also available for PI specification. Operator: Any combination of 3 characters.Operator: Any combination of 3 characters. Patient Position: Typical setting: Supine, Head First, HRBRAINPatient Position: Typical setting: Supine, Head First, HRBRAIN

Abbreviated Patient Information

Full Info

KeyboardKeyboard1.1. Emergency stopEmergency stop2.2. Operator microphoneOperator microphone3.3. Patient speakerPatient speaker4.4. Microphone volume adjustMicrophone volume adjust5.5. Press to talkPress to talk6.6. Start ScanStart Scan7.7. Pause ScanPause Scan8.8. Stop ScanStop Scan9.9. Move to ScanMove to Scan10.10. Stop Move ScanStop Move Scan11.11. Host Computer ControlHost Computer Control12.12. Functional KeysFunctional Keys13.13. KeyboardKeyboard

Selecting a ProtocolSelecting a Protocol

Other: Protocols belonging to each group is placed

Site: Standard Protocols placed by the Center. Including:•BIRN•fMRI•fRMI-All

Protocols selected from any of the protocol libraries (Site, GE) can be modified and saved in the Site (other) Library.Also available is the Protocol Lockout that restricts site protocols by requiring password.

The Rx ManagerThe Rx Manager The Rx manager is used to create, view, The Rx manager is used to create, view,

edit, and prepare series for scanning.edit, and prepare series for scanning. The Rx manager list shows the The Rx manager list shows the

prescribed series state and series prescribed series state and series description:description:• NewNew:: series is not prescribed or series is not prescribed or

saved and cannot be scannedsaved and cannot be scanned• INRXINRX:: (in prescription) series is (in prescription) series is

opened, not yet saved, and cannot opened, not yet saved, and cannot be scanned.be scanned.

• RXDRXD: (prescribed) series is saved : (prescribed) series is saved and can be scannedand can be scanned

• ACTACT: (active) series is ready for scan : (active) series is ready for scan and can no longer be editedand can no longer be edited

• SCNDSCND: (scanned) series has been : (scanned) series has been scanned and can no longer be scanned and can no longer be edited but can be re-scanned. edited but can be re-scanned.

• PSCDPSCD: (pre-scanned) series is pre-: (pre-scanned) series is pre-scanned and ready for scan. scanned and ready for scan.

Graphical PrescriptionGraphical Prescription

3D graphic object

3 plane graphic prescription

2D graphic object

fMRI StudyfMRI Study

3-Plane localizer3-Plane localizer Functional scan (s)Functional scan (s) High resolution structural scanHigh resolution structural scan

Added scans could includeAdded scans could include High-order ShimHigh-order Shim 3D Arterial TOF3D Arterial TOF Phase mapPhase map 2D Venous TOF2D Venous TOF

PrescanningPrescanning

Automatic Prescan: Automatic Prescan: Automatically adjusts Automatically adjusts the center frequency the center frequency and the transmit and and the transmit and receiver gain.receiver gain.

Manual Prescan: Manual Prescan: Allows manual Allows manual adjustment of prescan adjustment of prescan parameters.parameters.• CautionCaution: You are : You are

delivering RF to the delivering RF to the patient during prescan.patient during prescan.

Manual Prescan window

Select AutoPrescan or Manual Prescan

Shimming Autoshim: Improves image quality by optimizing the X, Y, Z gradient Autoshim: Improves image quality by optimizing the X, Y, Z gradient

settings. It is the system’s default and is included in the prescan.settings. It is the system’s default and is included in the prescan. High Order Shims: Allow shimming over a ROI, and likely to improve local High Order Shims: Allow shimming over a ROI, and likely to improve local

field inhomogeneity.field inhomogeneity. If you enable the [Autoshim] option after running a High Order Shim seris, If you enable the [Autoshim] option after running a High Order Shim seris,

you will receive a message informing you that scanning with this series you will receive a message informing you that scanning with this series resets resets ALLALL the shim coils, i.e. all shim channels will be reset to zero. the shim coils, i.e. all shim channels will be reset to zero.

ROI Selection Window

1. Select a ROI to run shim value

2. Calculations with current ROI

3. Compare calculated and predicted RMS4. If difference is significant, press Done, otherwise Quit.

Caution: After High Order Phase Correction, make sure the Phase CorrectionOption is ON, and only the AutoShim option is turned OFF.

3-Plane Localizer3-Plane Localizer The 3-Plane localizer acquires three planes in a single acquisition,

eliminating the need for three separate scans. It then displays the 3-planes in graphic Rx to prescribe off of.

fMRI Imaging OptionsfMRI Imaging Options Imaging Options: A list of Imaging Options: A list of

imaging options from the imaging options from the Imaging Parameter area.Imaging Parameter area.

Availability depends on Availability depends on pulse sequence and pulse sequence and system configuration.system configuration.

GRE EPI Imaging Options GRE EPI Imaging Options Include: Include: • ASSET, Cardiac ASSET, Cardiac

Gating/Triggering, fMRI, IR Gating/Triggering, fMRI, IR prepared, sequential, multi-prepared, sequential, multi-phase, etc.phase, etc.

fMRI with BrainWave RTfMRI with BrainWave RT

BrainWave Real-Time software BrainWave Real-Time software features:features:

• Overlay of segmented image with Overlay of segmented image with functional image set.functional image set.

1.1. Acquire a high resolution structural scanAcquire a high resolution structural scan

2.2. Acquire fMRI data with BrainWave RTAcquire fMRI data with BrainWave RT

3.3. Perform segmentationPerform segmentation

4.4. Visualize fMRI data with BrainWave PAVisualize fMRI data with BrainWave PA

User Control VariableUser Control Variable

Default setting: Ramp Sampling = 1, Spin-Echo Reference Scan = 0To change the receiver bandwidth (rBW), set at 250 kHZ, the ramp sampling first be must be turned off. This will allow the user to make changes to rBW.

Acquisition of echoes during the rise and fall times of the gradient slope.

Use Spin Echo EPI to generate phase correction coefficients.

fMRI Control WindowfMRI Control Window•The fMRI Control Window is the default window that launches after [Prep Scan] button is clicked.

•It is used to prepare, start, stop the fMRI acquisition.

•

Statistical Threshold SliderAllows selection of matched structural scan

Starts the fMRI acquisition

Takes an image capture of allor one the images in the RT.

Caution: You must Close the fMRI Control window before proceeding. Failure to do so will prevent you from scanning the next Rx.

Paradigm ManagerParadigm Manager

Total reps

0 means initial state is rest,1 means initial stat is stimulus

rest reps and stimulus reps per cycle

Can add and delete an entry but cannot modify anexisting paradigm.

Specify a paradigm name

Paradigm DevelopmentParadigm Development

Clicking the fMRI Screen icon opens the fMRI additional parameter window which has available a number of standard fMRI paradigms (including the ones you have previously created) and sequence parameters.

Research mode: When the research agreements have been signed, this step will no longer be required. One can generate fMRI paradigms during the series prescription.

Interleaved/Sequential

Select Paradigm

Internal/External

Image ManagementImage Management

Scan reconstruction status

Feature Status Area (located below the Desktop Control Panel):

Filming status

Archive status Network status

Managing Disk Space:

Center Recommendations: It is recommended for the disk occupancy not to exceed 50%. We hope that each group removes their data within a one week period of the scanning session. If you have started an exam and notice that the disk occupancy is high, you may remove data starting from the least recent, and not to exceed a one week window.

Caution: There is no protection for data belonging to other group.

% disk is full

Networking-Image TransferNetworking-Image Transfer

Transfer’s data by exam.

Transfer’s data by series.

Data can be transferred to a number of locations such as the Advantage Window.

See the instructions for data transfer to the fmriserver for transfering data to the server.

TPS Reset / System ShutdownTPS Reset / System Shutdown The TPS is a subsystem that overseas all raw data The TPS is a subsystem that overseas all raw data

processing.processing. Resetting the TPS is one way to safely recover from Resetting the TPS is one way to safely recover from

many errors and conditions.many errors and conditions. Is performed 2-3 times/weekIs performed 2-3 times/week Might be necessary during a scanMight be necessary during a scan

• Caution: Caution: Performing a TPS reset in the middle of a Performing a TPS reset in the middle of a scan or reconstruction stops the reconstruction, scan or reconstruction stops the reconstruction, eliminates the landmark, and deletes the image data. eliminates the landmark, and deletes the image data.

Click on the Service Desktop iconClick on the Service Desktop icon Click Click [TPS Reset][TPS Reset] Wait for a Wait for a TPS reset is completedTPS reset is completed message. message. Re-landmark and resume scanningRe-landmark and resume scanning System Shutdown: terminates power to the system System Shutdown: terminates power to the system

electronics in an orderly fashion so that image files electronics in an orderly fashion so that image files are saved, but does not turn off power to the MRI are saved, but does not turn off power to the MRI magnet.magnet.

Additional NotesAdditional Notes

A data transfer and conversion to A data transfer and conversion to AFNI program has been constructed AFNI program has been constructed by Eman Ghobrial.by Eman Ghobrial.

In addition to the general training, In addition to the general training, we plan to have additional training we plan to have additional training designed to the individual needs of designed to the individual needs of each group so please let us know if each group so please let us know if you have particular needs.you have particular needs.