Appendix I MR System User Manual -...

© MRI-Tech 12/12/2012

Appendix I

MR System User Manual

The User Manual presented in this section is supplemented with information presented in the main FDA 510(k) submission document entitled “Traditional 510(k) Submission: CIRRUS OPEN” under section: Proposed Labeling, User Manual. Ultimately, where appropriate, both sets of information will be amalgamated into one self-contained reference material.

© MRI-Tech 12/12/2012

Cirrus Open 0.2 T Clinical Imaging System User Manual

Operating procedures for low-field imaging data acquisition

© MRI-Tech iii Cirrus Open User Manual

Table of Contents

Introduction ...................................................................................................................... 6 MRI System ............................................................................................................................................... 7 Magnet (Scanner) Room ........................................................................................................................... 8

Magnet ................................................................................................................................................... 8 Gradient Coils ........................................................................................................................................ 8 Patient Bed ............................................................................................................................................ 8 RF Coil ................................................................................................................................................. 10 Head Coil ............................................................................................................................................. 10

Equipment Room ..................................................................................................................................... 12 RF and Gradient Amplifier Rack .......................................................................................................... 12 MR Console Rack ................................................................................................................................ 13

Control Room .......................................................................................................................................... 14 MR Operator Station ............................................................................................................................ 14

Software Concepts ........................................................................................................ 15 Data Storage Concepts ........................................................................................................................... 16

Patient .................................................................................................................................................. 16 Exam .................................................................................................................................................... 16 Scan ..................................................................................................................................................... 16

Working Scan and Active Scan ............................................................................................................... 18 Scan Index Numbers ........................................................................................................................... 18 Setting the Working Scan .................................................................................................................... 18 Setting the Active Scan ........................................................................................................................ 18 Summary Information........................................................................................................................... 18

The Pulse Sequence Protocol Library ..................................................................................................... 19 Definition of a Protocol ......................................................................................................................... 19 Parameter File Format ......................................................................................................................... 19

System Startup and Shutdown ...................................................................................... 20 Startup Procedure ................................................................................................................................... 21

Starting the Sync, Async and GUI computers ..................................................................................... 21 Powering-up the console rack.............................................................................................................. 21 Powering-up the RF amplifier .............................................................................................................. 21 Powering-up the gradient amplifiers .................................................................................................... 21

Shutdown Procedure ............................................................................................................................... 23 Shutting Down the Sync, Async and GUI Computers .......................................................................... 23 Shutting-down the console rack ........................................................................................................... 24 Shutting-down the RF amplifier ........................................................................................................... 24 Shutting-down the gradient amplifiers ................................................................................................. 24

Software Operation ........................................................................................................ 26 More on the “Select Task Menu” .......................................................................................................... 27

“Select Working” (Select Working Scan) ................................................................................................. 28 Working Patient Selection (1

st Tab) ......................................................................................................... 29

To Register (Create) a new Patient: .................................................................................................... 29 To modify Entries for an existing patient .............................................................................................. 29

Working Exam Selection (2nd

Tab) .......................................................................................................... 31 Operation ............................................................................................................................................. 31 To Create a New Exam ........................................................................................................................ 31 To Modify Previous Exam Information ................................................................................................. 31

Working Scan Selection (3rd

Tab) ............................................................................................................ 32 Operation ............................................................................................................................................. 32 Left-hand-side Menu Buttons ............................................................................................................... 33 Protocol File Sub-Panel ....................................................................................................................... 33 Scan-note Sub-Panel ........................................................................................................................... 33

Edit Mode (Parameter Editor) .................................................................................................................. 34 Operation ............................................................................................................................................. 34 Parameter Datatypes ........................................................................................................................... 34 Out-of-Range Parameter Values ......................................................................................................... 35

© MRI-Tech iv Cirrus Open User Manual

Sequence Compilation ......................................................................................................................... 35 Commonly used Parameters ............................................................................................................... 35

Navigation Mode ...................................................................................................................................... 36 Operation ............................................................................................................................................. 36 Using the Active Scan dataset as Scout Images: ................................................................................ 36 Using an Alternative dataset as Scout Images: ................................................................................... 36 Perform Navigation Functions: ............................................................................................................ 36

Setup and Run Modes - Panels ............................................................................................................... 38 Panels .................................................................................................................................................. 38 Active Scan Panel ................................................................................................................................ 38 Advanced Controls Panel .................................................................................................................... 39

Setup Mode - Operation .......................................................................................................................... 40 Interactive Adjustments of any Sequence Parameters ........................................................................ 40

Run (Data Acquisition) Mode - Operation ............................................................................................... 42 Undoing a Scan ....................................................................................................................................... 43 View Images Mode .................................................................................................................................. 44

View Active Image (Top Panel - Left Section) ..................................................................................... 44 View Other Images (Top Panel - Right Section) .................................................................................. 44

Help/Shutdown Mode .............................................................................................................................. 45 Clinical Safety ................................................................................................................ 46

Compile-time SAR Safety Check............................................................................................................. 47 Compile-time dB/dt Safety Check ........................................................................................................... 48 Compile-time Gradient Duty Cycle Check ............................................................................................... 50

Quality Assurance Procedures ...................................................................................... 51 Measurement Conditions......................................................................................................................... 52

Frequency of Testing ........................................................................................................................... 52 QA Phantom and RF Coil .................................................................................................................... 52 Temperature ........................................................................................................................................ 52 Scan Parameters ................................................................................................................................. 52

Measurement Procedures ....................................................................................................................... 54 Acquisition of images ........................................................................................................................... 54 Signal Measurements .......................................................................................................................... 54

Documentation of Results ....................................................................................................................... 55 Procedures in Magnet Room for Imaging ...................................................................... 56

Routine Cleaning ..................................................................................................................................... 57 Steps to Insert Patient to Magnet Iso-centre ........................................................................................... 58 Extracting Patient After Scanning ............................................................................................................ 63

Pre-scan Adjustments ................................................................................................... 64 Working Frequency Adjustment .............................................................................................................. 65

Select ‘SF_cal’ pulse sequence ........................................................................................................... 65 Activate ‘SF_cal’ pulse sequence ........................................................................................................ 65 Acquire signal in “Setup” mode ............................................................................................................ 65 Search for the working frequency ........................................................................................................ 65

Shimming ................................................................................................................................................. 66 RF Flip Angle Adjustment ........................................................................................................................ 67

Select Pulse Sequence ........................................................................................................................ 67 Activate scan of Spin Echo pulse sequence ........................................................................................ 67 Acquire spin echo signal in Setup mode .............................................................................................. 67 Adjust RF transmission power ............................................................................................................. 67

Receiver Gain Adjustment ....................................................................................................................... 69 Create a scan with your chosen pulse sequence ................................................................................ 69 Activate the scan .................................................................................................................................. 69 Acquire signal without phase-encoding ............................................................................................... 69 Adjust receiver gain ............................................................................................................................. 69 Finish the adjustment and do image acquisition .................................................................................. 69

Notes on Image Orientation ........................................................................................... 70 Coordinate Systems and the Cirrus Open 0.2 T MR Console ................................................................. 71

Logical Gradient Coordinate System ................................................................................................... 71

© MRI-Tech v Cirrus Open User Manual

Patient Coordinate System .................................................................................................................. 72 Marevisi requirement of coordinate system ............................................................................................. 73 Standard Slice Orientation Rotations ...................................................................................................... 74 Physical Gradient Cable Connections ..................................................................................................... 75 Image Reconstruction and Image Layout in Marevisi ............................................................................. 76

Troubleshooting ............................................................................................................. 77 Solving Common Problems ..................................................................................................................... 78 Async-DAQ Mode .................................................................................................................................... 81 Operating the Console in Loopback Mode .............................................................................................. 82

Operating Procedures .......................................................................................................................... 82 Examples: ............................................................................................................................................ 82 Timing .................................................................................................................................................. 82

Digital Receiver Function Verification Using test_rxdev.exe ................................................................... 83 Digital Receiver Function Verification Using test_rxdev.exe ................................................................... 84

Method ................................................................................................................................................. 84 Diagnosis ............................................................................................................................................. 84

RF Pulse Shapes ........................................................................................................... 86 Types of RF Pulse Shapes ...................................................................................................................... 87

Table of Supplied RF Waveforms – Integrated Pulses ......................................................................... 87 Table of Supplied RF Waveforms – ‘On-the-fly’ Pulses........................................................................ 87

Gradient Preemphasis ................................................................................................... 91 Using the Autopreemphasis Sequences ................................................................................................. 92

Introduction

© MRI-Tech 6 Cirrus Open User Manual

Introduction

This manual is intended for first-time users of the MRI system. It assumes no specialist knowledge of the hardware.

Introduction


MRI System

An illustration of the major system components of the MRI system is shown below in Figure 1. More detail is given in the remainder of this section.

Figure 1: Major System Components of the MRI System

Introduction


Magnet (Scanner) Room

The magnet room contains the magnet and the patient interfacing components such as the patient bed and the radio frequency (RF) coil. This is the room in which a patient undergoes the scanning (magnetic resonance imaging, MRI) procedure.

Magnet The magnet provides a homogeneous magnetic field in the patient space to enable the imaging process. The magnet comprises of two permanent magnetic pole assemblies, an upper and a lower, that are separated by four corner posts to create space or volume in which a patient is placed for imaging. Magnetic flux flows from one pole to the other resulting in a vertical magnetic field in the imaging volume. The field strength is 0.2 Tesla (T). It is important to note that the region of interest, (ROI), which is the anatomy of the patient to be imaged must be placed in the center of the magnet, called the iso-center as this is the region where the field is most homogeneous. The magnet is enclosed with a multitude of panels that protect the magnet from liquid spills. The enclosure can be wiped down and cleaned with mild cleaning agents and disinfectants. The enclosure panels also separate the patient and MR personnel from the internal components of the magnet including the electrically energized gradient coils.

Gradient Coils The gradient coils are integral with the magnet and work in pairs, with one attached to the upper magnet pole and the other to the lower pole. The gradient coils generate linear gradient magnetic fields in the imaging volume for slice selection, frequency encoding and phase encoding during MRI scans. They are electrically energized by the powerful gradient amplifiers.

Patient Bed The patient bed assembly is shown on the following two figures that illustrate the movement of the patient bed and its connection to the magnet (in cut-away view). As shown in Figure 2, the patient bed is a two-part assembly comprising of a stationary platform that straddles and secures to the lower pole assembly of the magnet and a bed top that rolls on the platform to translate the patient into the magnet. The patient bed system supports a patient (with padding placed beneath the patient for comfort) and has features to help properly position the RF coil and patient’s ROI at magnet iso-center for imaging.

Introduction


Figure 2: Patient Bed in Loading Position The bed top is manually moved into the magnet into one of six (numbered) detent (discreet snap-in) positions. On the bed top, there are six sets of receptacles, in the form of pairs of shallow holes that accept matching features, a pair of short stubs, on the bottom of the RF coil. The receptacle locations are number-matched to the detents of the bed platform so that when the bed top is inserted so the end of the bed top aligns with the marker line on the platform with the same number as that at which the RF coil is placed, the RF coil and patient’s ROI are at magnet iso-center, ready for imaging. This situation, for Detent Position 4, is shown in Figure 3. The bed top system also has a detent at the fully extracted position (shown in Figure 2) to prevent the bed top from rolling during patient loading / unloading.

Introduction


Figure 3: Patient Bed Inserted into Magnet to Place RF Coil at Magnet Iso-centre The patient bed assembly is comprised of all non-ferromagnetic materials such as wood, plastic and brass. It is important to note that even small amounts of ferromagnetic material in the patient space can adversely affect magnetic field homogeneity and hence the quality of the imaging results.

RF Coil The RF coil is the “antenna” of the MRI system that broadcasts, transmits, the RF signal into the patient and receives the return signal. The RF Coil is used directly around a patient’s ROI. The coil rests on the patient bed top and is inserted with the patient into the imaging volume of the magnet. The coil is connected to a cable that is electrically energized (pulsed) by the RF amplifier.

Head Coil The head coil is used to exchange pulsed RF energy with the patient’s head. The head coil is shown below in Figure 4 that shows its main components.

Introduction


Figure 4: RF Head Coil The head coil is a solenoid volume coil, a hollow cylindrical structure, that envelopes the patient’s head. To facilitate patient loading, the head coil translates between a loading position, with the coil moved away from the patient’s head that allows the patient to lie down and get comforted with proper padding (not shown), and an imaging position that properly envelopes the head so that the head is within the region of the uniform field within the coil.

Electrically, the head coil both transmits and receives RF signals. It does this with electronic hardware that actively switches between the two directions of RF energy flow. The head coil assembly is made of non-ferromagnetic materials such as plastics and copper. It is important to note that even small amounts of ferromagnetic material in the patient space can adversely affect magnetic field homogeneity and hence the quality of the imaging results.

Introduction


Equipment Room

The equipment room contains the electronic hardware components that drive the MR system. The main components include the RF and gradient amplifiers and the MR console equipment all of which are contained in equipment racks.

RF and Gradient Amplifier Rack The physical layout of the components of this rack is shown below in Figure 5. The RF and gradient amplifiers drive the RF and gradient coils, respectively, in the magnet room. Also shown are the power amplifier (PA) switches that turn on and off the amplifiers.

Figure 5: RF and Gradient Power Amplifier Rack

Introduction


MR Console Rack The physical layout of the components of this rack is shown below in Figure 6. This rack contains the equipment (power supplies, computers, interface electronics and RF components) that generate the MR waveforms needed to correctly stimulate the RF and gradient amplifiers, and to acquire and process the received RF signals. Also shown is the power supply switch.

Figure 6: MR Console Rack

Introduction


Control Room

The control or console room contains the scanner control station that is used by the MR system operator.

MR Operator Station The MR operator station is shown in the illustration, Figure 1 under the foregoing section “MRI System”. This system component is the graphical user interface, GUI, consists of a Windows-based XP computer that is used by the MR system operator to interface with the computers in the MR Console Rack and MR clinic’s computer network via a local area network (LAN) connection. This station also allows the MR system operator to display, store and/or print the images produced by the system. Visual and audible contact (monitoring) between the patient in the magnet room and the MR operator is also accomplished via this operator’s station.

Software Concepts


Software Concepts

Before describing the detailed operation of the software, we first introduce a few underlying concepts.

Software Concepts


Data Storage Concepts

MR data are stored on disk in the Store, which is organized as a hierarchy of folders: Patient / Exam / Scan

Patient

A folder is created for each patient. This contains a text file containing patient information, such as patient name, date-of-birth and so on. In the patient folder (Z:\Store\P0001, in the example presented in the figure below) are sub-folders for each exam (EX00001) of that patient.

Exam

A new exam should be created each and every time the patient is repositioned, or each time a coil is repositioned or changed. The console software assumes that all scans within one exam are collected with the same coil, same patient and identical positioning. Exam information (e.g. patient positioning, RF coil used, etc.) is stored in a text file. An exam will consist of one or more scans, which are represented as sub-folders.

Scan

A scan is the name given to the execution of a single pulse sequence. It also refers to a specific sub-folder of the Exam folder. Within each Scan folder there are several files. These include:

Four files describing the acquisition protocol

The image raw data (*.mar) (image data is always stored in Marevisi raw binary data format)

A sub-folder (Aves) which contains separate raw data files for each acquired average.

Protocol and data storage hierarchy.

Software Concepts


Software Concepts


Working Scan and Active Scan

It is essential to clearly understand the difference between the Working Scan and the Active Scan:

The main purpose of the Working Scan is preparation for the next or a future scan.

The main purpose of the Active Scan is data acquisition.

It is possible to create/modify/edit etc. the Working Scan while the Active Scan is running.

Parameters of the Active Scan (e.g. TE) cannot be changed while data acquisition is active.

The working or active scans can be the same or different.

Scan Index Numbers

Every scan in an exam has a number

The working scan has a number

The active scan has a number

The working or active scans can be the same – or different

Setting the Working Scan The current Working Scan (if any) is always displayed in the toolbar. A new Working Scan can be selected by these methods:

Use the ‘Select Working’ module to create a new scan, which becomes the Working Scan

Use the ‘Select Working’ module to select some previous scan as the Working Scan

Setting the Active Scan

The current Active Scan (if any) is always displayed in the toolbar. The only way to set the Active Scan is to click on the large downward pointing arrow that copies the Active Scan from the Working Scan.

Summary Information

The patient, exam and scan information entered upon creation of the Working Scan can be displayed by moving the cursor over the note icons.

Scan information obtained by placing the mouse cursor over the note icon in either

Working or Active Scan.

Software Concepts


The Pulse Sequence Protocol Library

The pulse sequence library consists of standard protocols and user-defined protocols.

When Scans are created, a set of files describing the protocol is copied from the library to the scan folder. Subsequent user changes to protocol parameters (e.g. changes in TR, TE etc.) are made on the copy within the scan folder, thus user actions do not affect the content of the library.

Definition of a Protocol

Protocol = Pulse Sequence + Parameters

A pulse sequence protocol consists of four text files:

Protocol file – this is a short Python (.py) file that contains the locations of each of the other three files below.

Parameter file - this is a file with information on sequence variables, such as TR, TE, etc., The file name is always paramfile.txt. The format is described below.

Sequence file - this is the pulse program itself – the ordering of the RF and gradient pulses and the loop-structure are defined here. The compiled version of this program is executed on the sequencer at run-time.

Sequence code file – this Python (.py) file is the longest and most complex of the four files. It contains all the sequence-specific parameter calculations and is executed at compile-time. Compilation takes the parameter file and sequence file as inputs and produces files that can be run on the sequencer.

Parameter File Format

Parameter files are normally edited using the Parameter Editor (described later). The parameter files are text files, so can be viewed and edited by text editors (NOT by word processors). Each parameter is described by four text lines:

['TimeGp', 'READOUT_FOV_MM'] ['FOV (Readout)', 'mm', 'DBL', 1] [10.0, 5.0, 5000.0] [100.000000]

The meaning of these 4 rows is as follows:

Row 1: [ParameterGroup, Internal Parameter Name]

Row 2: [Label, Units, DataType, #Values]

Row 3: [minimum value, increment, maximum] or [RING labels]

Row 4: [value(s)]

Warning: HARDWARE DAMAGE CAN RESULT FROM CHANGES TO THE PARAMETER FILE.

A user-defined protocol can be created by copying the standard protocol Python and parameter files to a new directory location (C:\MR\Protocols\protocol_name\, for instance). The protocol Python file must be edited in order that the proper locations of the protocol and parameter files is pointed to. Parameters for the new protocol can be set by editing the parameter file. Only advanced users should attempt this, as hardware damage may result.

System Startup and Shutdown



Procedure for starting up the Cirrus 0.2 T MR console hardware and software and for shutting the system down.



Startup Procedure

Starting the Sync, Async and GUI computers Assuming all the computers are turned off:

1. Turn on the GUI computer by pushing on the power button.

2. Turn on the Sync computer by pushing the power button. The light on the power button should be green; otherwise something is wrong.

3. Turn on the Async computer by pushing the power button. The async computer’s:

a. Power button should be lit green;

b. Windows should start to load;

c. You should see two programs running; and

If there are any errors, for example Windows error message, then there is something wrong with the Async computer.

Powering-up the console rack To apply electrical power to the Console rack, do the following:

1. Ensure that the rocker switch on the Power Supply Access Restriction panel located at the front top of the Console rack is in the off (O) position.

2. Connect the plug on the AC power cord exiting the Console rack at its back to equipment room AC power.

3. Apply power to the Sync and Async computers located on the Computer Shelf Assembly by pushing the power switch to the ON (recessed) position. The light in the ON switch should be continuously green.

4. Apply power to the Power Supply Assembly by pressing the rocker switch on the Power Supply Access Restriction panel to the on (1) position.

5. Ensure that the LEDs on the Power Supply Access Restriction panel are all green.

Powering-up the RF amplifier

To apply electrical power to the RF amplifier in the Power Amplifier rack, do the following:

1. Ensure that the circuit breaker on the rear of the unit is in the on (1) position.

2. Ensure that the AC power switch on the panel immediately below the RF amp is in the OFF position.

3. Connect the 3 bladed, non-twist lock plug on the small diameter AC power cord exiting the Power Amplifier rack to equipment room AC power.

4. Apply power to the RF amplifier by setting the AC power switch on the panel immediately below the RF amp to the ON position.

5. The RF amplifier will turn on and the POWER LED on the front panel of the unit will turn green. After approximately 2 seconds the STANDBY LED will turn green, and shortly thereafter the DIAG LED will flash yellow. After approximately a further 3 seconds the READY LED will turn green. The amplifier is then ready for use.

Powering-up the gradient amplifiers

To apply electrical power to the three axis gradient amplifiers in the Power Amplifier rack, do the following:

1. Ensure that the circuit breaker on the front panel of the unit is in the on (1) position.



2. Ensure that the AC power switch on the panel immediately below the RF amp is in the OFF position.

3. Connect the 4-bladed, twist lock plug on the large diameter AC power cord exiting the Power Amplifier rack to equipment room AC power.

4. Apply power to the three axis gradient amplifiers by setting the AC power switch on the panel immediately below the amp to the ON position.

5. The gradient amplifier will turn on and the STANDBY LED on the front panel of the unit will light. To set the amplifier into the READY state, the pushbutton switch beside the LEDs must be pressed and held for at least 8 seconds and then released, and then it must be pressed again for 2 seconds or less and released. The READY LED will then light.

6. To return the amplifier to the STANDBY state, the pushbutton switch should again be pressed for 2 seconds or less and then released.

NOTE: Immediately after the amplifier is powered on, it enters REMOTE mode whereby control of the amplifier’s state is only possible via a computer connected to the amp’s serial interface. Pressing and holding the pushbutton switch for 5 or more seconds puts the amplifier into LOCAL mode, whereby control of the amplifier state is possible via the pushbutton. To return the amplifier to REMOTE mode, the pushbutton must again be pressed and held for 5 seconds.



Shutdown Procedure

Shutting Down the Sync, Async and GUI Computers Close the MR Console GUI software. On the GUI computer click on Start Programs TightVNC TightVNC Viewer. Either Fast or Best compression will do. Close the DAQ software by clicking on the Exit DAQ switch (see figure below).

Close the Async software by clicking on the Close button. When the DAQ and Async programs has closed click on Start Turn Off Computer…

DAQ software on the Async computer.

Async software on the Async computer.



The following window will pop up:

Click on Turn Off.

TightVNC viewer will automatically close and inform the user with the message “Connection has been closed”. On the GUI computer click on Start Turn Off Computer… A window will pop up, just like the one above. Click on Turn Off. The GUI computer will automatically turn itself off. Manually power off both the Async and Sync computers by depressing the power button.

Shutting-down the console rack

To remove electrical power from the Console rack, do the following: 1. Shutdown the Sync and Async computers as described above. The light in the ON switch for each

should go out.

2. Remove power from the Power Supply Assembly by pressing the rocker switch on the Power Supply Access Restriction panel to the off (0) position.

3. If required, remove the plug on the AC power cord exiting the Console rack from the room AC power.

Shutting-down the RF amplifier

To remove power from the RF amplifier, do the following:

1. Set the AC power switch on the panel immediately below the RF amp to the OFF position.

2. If required, remove the 3 bladed, non-twist lock plug on the small diameter AC power cord exiting the Power Amplifier rack from equipment room AC power.

NOTE: In normal operation, the circuit breaker at the rear of the unit is left in the on (1) position.

Shutting-down the gradient amplifiers

To remove power from the three axis gradient amplifiers, do the following:

1. Set each amplifier to the STANDBY state using the method described above.

2. Set the AC power switch on the panel immediately below the amp to the OFF position.

Windows XP shutdown menu.



3. If required, remove the 4-bladed, twist lock plug on the large diameter AC power cord exiting the Power Amplifier rack from equipment room AC power.

Software Operation


Software Operation

The console software is designed to control the MRI hardware such as the RF amplifier, gradient amplifiers, frequency synthesizer, receiver…etc. It is also the interface for the users to input patient information, exam information and scan information. By using the console software, the users can prepare scans, perform scans and view the resultant images.

The software is started by clicking on the ‘MR Console’ icon on the desktop, which brings up the main control panel. The software has eight different selections available arranged in three groups (Working; Active; Misc.) as indicated:

Select Working (Working Scan)

Edit (Working Scan)

Navigate (Working Scan)

Setup (Active Scan)

Run (Active Scan)

View Images (Active Scan)

Async-DAQ (used for trouble-shooting only)

Help/Shutdown

The user can select the mode by clicking on the Select Task menu. When an item in the menu is selected, it will be highlighted (white text on black background). When items are grayed-out they are not available.

There are also two areas for selecting the Working Scan and the Active Scan. The current Working Scan can be made the Active Scan by clicking on the arrow located between the two. Two checkboxes at the bottom of the

Main MR Console GUI Interface.

Software Operation


toolbar allow the user to view any error messages in the compilation process and to start Internet Explorer to view online help files.

More on the “Select Task Menu”

The main control in this window is the Select Task menu. The mode selected in this menu controls which other windows are visible. The main action of this menu selector is to hide or show various windows. For most windows (except the editor window) the software runs continuously, but the window is just made visible or invisible depending upon the selected mode. The editor is an exception: when the window is not shown, the editor is closed.

The normal sequence of operations is from top to bottom, but any mode can be selected at any time, provided that it is not grayed-out. Note that the modes are always changed by the user, never by the system – so you are in control.

Software Operation


“Select Working” (Select Working Scan)

Fundamentally all this module does is to manipulate files and folders in the MR Store. The Store functions as a database for the acquired data. Thus this mode can be regarded as the system database manager. Users can input, edit and remove data to and from the database (‘the Store’).

Clicking on ‘Select Working’ will bring up a new window to the right of the toolbar. The three sub-modes of the module are described in the next three sections of this document:

Working Patient information

Working Exam information

Working Scan information

Software Operation


Working Patient Selection (1st Tab)

The first tab under the “Select Working” menu item is the Patient Entry screen. All patient information should be entered here. The Patient selected in the Patient List becomes the patient for the working scan. In addition, by making a patient the “Working Patient” the records for that patient can be viewed on this screen, so this screen also acts as a browser of patient information.

To Register (Create) a new Patient:

To register a new patient into the database:

Click the ‘New’ button.

An entry is added into the ‘Patient List’ area indicating a new patient folder has been created in the store

The color of the data entry areas will change to orange, indicating that the system is ready to accept the information.

Enter necessary information for the patient

Once all data is entered, clicking the ‘Save’ button saves the patient information to system database and this patient becomes the Working Patient.

To modify Entries for an existing patient

Select the patient entry in the ‘Patient List’ area

Click on ‘Edit’ button. The color of the text editors will all be turned to orange and the system is ready for the operator to modify the information of the selected patient.

Enter necessary information for the patient

Software Operation


Click on the ‘Save’ button. The modified information of patient will be saved to system database.

Patient data interface in the ‘Select Working’ mode.

Software Operation


Working Exam Selection (2nd

Tab)

The basic function of this tab is to create an exam folder in the database hierarchy and to populate it with the appropriate files. More generally - this mode is used to manage exam folders.

Operation

Clicking on the ‘Exam’ tab will cause the ‘Exam Entry’ page to be displayed. This page is for exam related information. The operator can input the following: Anatomical part, Patient positioning, RF coil, Exam label, MR operator and Notes.

The Exam Id, Patient Id and Entry Date fields are created by the system and are read only.

To Create a New Exam

Click on the ‘New’ button.

The colors of the text editors on the right side of the page are turned to orange. The system is ready to accept the input from the operator.

Input necessary information for the exam

Click ‘Save’ button to save the information to the system database.

To Modify Previous Exam Information

As in the ‘Pat’ tab, you can modify information of previously entered and saved exams.

Click on ‘Edit’ button, the color of the text editors will be turned to orange.

Make the modifications

Click ‘Save’ button to save your modified information.

Exam data entry interface.

Software Operation


Working Scan Selection (3rd

Tab)

The basic function of this tab is to create a scan folder in the database hierarchy and to populate it with the appropriate files. More generally - this mode is used to manage the scan folders.

Operation

Click on the ‘Scan’ tab, to display the Scan page. This page is for scan configuration:

Scan folders can be created (‘New’), edited and deleted

A protocol can be loaded into a scan folder from the library

A protocol can be deleted from the scan folder

A protocol can be saved to a new location in the library

Protocol Loading:

A protocol can only be loaded into an existing scan folder that does not already contain a protocol. To change the protocol within a scan already containing a protocol the current protocol must be deleted using the ‘Delete’ button.

Click on the ‘Load from Library’ button.

Browse in the file selector dialog window to select a protocol folder, open it, select the protocol file and click OK.

There will be some file names shown in the windows marked ‘Parameter Files’ and ‘Other Files’. All these files are related to the protocol you selected for the current scan. The ‘Sequence File’ window will display the current pulse program Python code file. A comment line may be entered in the ‘Scan

Scan data entry interface.

Software Operation


Note’ window by clicking the ‘Update Note’ button.

Left-hand-side Menu Buttons

New: Create a new scan folder

Clone: Creates a new scan folder, then copy the current scan protocol files to the new folder. This is used quite frequently.

Delete: Delete scan folder – only enabled if folder is empty.

Refresh: refresh all file lists – may be necessary if scan folder contents have been modified by other parts of the system.

Protocol File Sub-Panel

Delete: Deletes the protocol from the current scan. This does not delete from Pulse Sequence Library.

Load from Library: Loads a new protocol from the library.

Save to ...: Saves the entire protocol to a user-specified library location. This allows users to save their own versions of sequences with specific parameters.

Scan-note Sub-Panel

This is a text field for any notes. You must click “Update Note” after entry of text. Otherwise, text entry will be lost as soon as you leave the Scan Tab.

Software Operation


Edit Mode (Parameter Editor)

The function of this mode is to edit the pulse sequence parameters. Thus this module is an editor for pulse sequence parameter files. There is one additional function invoked – compilation. Each time a parameter is modified the compiler is called. (The compiler is not regarded as part of the editor itself.)

Operation

Once the Working Scan has been selected, parameters for the pulse sequence can be viewed and changed by pressing ‘Edit’. The ‘Select Working’ window will disappear and the Parameter Editor panel will appear.

Most sequences have several pages of parameters arranged in tabs. To change tabs, simply left-click on the tab or, if the page is outside the viewing region, use the arrows to the right of the tabs. Alternatively, the mouse can be used to select a tab in the Parameter Groups window.

A parameter value is changed by typing in a new value or by clicking the up/down arrows beside the parameter entry. Some parameters are choices and are selected by left-clicking on the data entry, such as the ‘Shape’ parameter in the figure above. When the value of a parameter is changed, the Parameter Changed indicator will flash in the same time.

WARNING: Every time a parameter is changed the entire sequence is recalculated (‘compiled’). This can take about a second, so rapid clicking of the parameter increment/decrement arrows can cause errors. Avoid this problem by not clicking the up/down arrows too rapidly and repeatedly or by directly entering the parameter value.

Parameter Datatypes

Eight parameter data types are supported:

INT32 – 32-bit integer (range approx. -32,000 … +32,000)

INT32 Array

DBL – Floating point, double precision

DBL Array

RING – a drop-down menu of predefined items

RING Array

STR – String (i.e., a text field)

STR Array

Note: The editor is implemented in LabVIEW, so further technical details of the behavior of these datatypes can be found in LabVIEW documentation.

A page from the Parameter Editor displaying pulse sequence parameters

and their values. Note the parameter groupings under tabs.

Software Operation


Out-of-Range Parameter Values

In the parameter file a range is defined for each parameter. The editor will not allow the entry of values that are out of this range. If an out of range parameter is entered then editor coerces the value to the minimum or maximum allowed, as appropriate. This does not generate an error or warning. These limit values can be modified by editing the parameter file with a text editor. You might need to do this for instance when created you own protocols in the user protocol library. It is good policy to limit the range of parameters as much as possible to help the user avoid selecting unrealistic values.

Note: these limits are individual hard limits for each parameter; they are not affected by values of other parameters. Interactions between parameters can only be dealt with in the sequence code file.

Sequence Compilation

Each time the editor detects that you changed a parameter value the pulse sequence is recompiled. During compilation many calculations are performed and checks for consistency are made. It is common that the set of parameters that you have selected cannot be logically compiled. For instance in a multi-slice sequence you may have selected more slices than can be achieved for the selected TR.

Such inconsistencies will result in a compiler error. This is indicated by an error message in the small text box in the editor window and in a red cross replacing the green tick mark. A full error message is also displayed in the Status Window. When this occurs you must change one or more parameter values until you achieve a valid compilation.

The estimate of total scan time for the current parameters setting will be display upon compilation in the Status Window. The scan time changes with different TR, number of averages and number of phase encode steps.

Commonly used Parameters

Usually the following parameters need to be changed in order to get images with proper contrast, good S/N ratio and correct slice locations:

TR

TE

Number of Slices

Number of Averages

FOV Read

FOV Phase

Offset in Slice Position

Offset in Read Direction

Offset in Phase Direction

Slice Orientation

X angle

Y angle

Z angle

Often geometric parameters, such as the angles, will be set using the Navigate Module, as described elsewhere in this document.

Software Operation


Navigation Mode

The purpose of the Navigate module is to permit the graphical definition of geometric scan parameters such as slice position, FOV, slice thickness, slice gap, read-out offset, phase-offset etc. For this purpose it is necessary to specify:

Scout images.

A Working Scan whose geometry parameters are to be modified.

Operation

For the Navigate selection in the MR Toolbar to be enabled, the Working Scan must be different from the Active Scan. Generally, this will occur after an image has been taken and a new Working Scan created prior to obtaining a new set of images with the desired orientation.

The Navigate selection is enabled by going back to the Select Working Scan window and selecting the scan containing the image to be used as the scout image.

Scout Images (reference images) may be selected here, or the current scan may be used if the “Use as Scout?” box is checked.

Click Navigate in Select Task menu to enter Navigation mode. Two windows will appear: the upper window is Navigation control panel (shown below), and the lower window is the interface of Marevisi. Slice definition operation is performed in Marevisi.

Using the Active Scan dataset as Scout Images:

Ensure the “Use as Scout” check-box is checked

Click “Load Scout”

Using an Alternative dataset as Scout Images:

Uncheck the “Use as Scout” check-box

Browse using the “Alternative Image” control

Click “Load Scout”

Perform Navigation Functions:

Click “Start” to load geometry data to Marevisi (LED goes Red)

Perform Marevisi manipulations to define slices. SEE MAREVISI MANUAL.

Click the ‘Accept’ button on the right-low corner of the Navigate panel to accept the definition of slices.

The geometry parameters have now been updated. Go to Setup or Run mode to acquire images.

Selecting imaging geometry parameters interactively by selecting a scout image

using Navigation.

Software Operation


Software Operation


Using Marevisi for navigation. The scout image is used to define the slices for the next scan. Geometry parameters are set in the menu immediately to the left of the image.

Setup and Run Modes - Panels

The Setup and Run modes are very similar, so they are discussed together. The Setup mode is for making interactive adjustments to acquisition parameters. The Run mode is intended for data acquisition. The distinction between the two is somewhat blurred as the common window (Active Scan) of the two modes has both Setup Acquisition and Run Acquisition functionality. These two modes are available for selection from the Toolbar once an Active Scan has been created.

Panels

There are three panels: Editor, Active Scan, and Advanced Controls. The Parameter Editor window (operation discussed previously) is only shown in setup mode.

1. Parameter Editor – for editing of the Active Scan (SETUP Mode only)

2. Active Scan Panel – for control of data acquisition

3. Advanced Control Panel – (System Parameter Editor) – Optionally displayed with the Advanced Control ‘ON’ toggle in the Active Scan Panel.

Active Scan Panel

The Active Scan panel contains the following sections:

A prominent Active Scan index indicator

Graphical display region with controls for viewing NMR signal

Software Operation


Scan Progress Indicators (# averages completed, etc.)

Button cluster (Show Waveform / Setup / {Run | Overwrite} / Stop)

Advanced Control toggle switch – displays Advanced Controls window.

Advanced Controls Panel

This window contains a number of panels selected by the buttons in the lower right of the Advanced Controls panel:

1. Shim

2. RF Gains

3. Transmitter Loopback

4. Transmit offset

In addition to these, the lower subpanel can be selected for one of two other functions by selecting the appropriate button:

1. DAQ (Receiver configuration – e.g., receiver channel selection)

2. Frequency (for setting of transmitter frequency)

Software Operation


Setup Mode - Operation

Setup mode is invoked by Setup button on the Toolbar. This mode is usually used for system setting adjustment (e.g., receiver gain, transmitter amplifier gain and scaling, shims). It has the following features:

Phase Encoding: often it is desirable to disable phase encoding during Setup. The user needs to explicitly disable Phase Encoding in the Parameter Editor;

The pulse sequence will run until user clicks "STOP" to stop the sequence. The sequence will immediately terminate (including acquisition), even if it is in the middle of the execution. The sequence will only recompile once it has gone through all data acquisition loops (i.e., number of slices, averages, phase encodes, etc.);

The NMR signal will be shown in the display area (even in RUN mode);

The sequence file will be loaded up again and again after the previous runs are finished. User can edit parameters during setup if desired, and the change will take effect after the current run is finished;

Data is not recorded to the hard disk (signals are only displayed, not stored).

The pulse sequence is recompiled every time a sequence parameter is changed. (In effect the acquisition is run once, stopped, recompiled if necessary, reloaded and run again. The penalty is that this can take around a second, however this does allow any parameter in the editor window to be changed interactively.).

From the Setup mode advanced adjustments can be made by switching the ‘Advanced Control’ toggle to ‘On’ described previously. This will bring up a new window below the Active Scan window to allow adjustments to shim values, receiver gain, transmitter amplifier gain and scaling and DAQ adjustment.

Interactive Adjustments of any Sequence Parameters

In Setup Mode any parameter in the Parameter Editor may be changed, the changes taking effect after the next compilation. The effects of these changes may be observed using the ‘Show Waveform’ button (best done with the ‘Preview sequence’

Setup Mode windows.

Software Operation


parameter set to ‘On’). Parameters in the Advance Control window (transmitter scaling/amp gain, receiver gain, frequency), however, do not require sequence compilation and take effect on the next scan.

Software Operation


Run (Data Acquisition) Mode - Operation

Users can use Data acquisition Mode to acquire NMR signal or images by clicking ‘New’ or ‘Overwrite’ button. If the scan has no data, the button will be labeled as ‘New’, otherwise it’ll be labeled as ‘Overwrite’. This acquisition mode will go through every phase-encoding step and every average of sequence. Phase-encoding gradient will be applied in order to obtain images. The acquisition stops when the pulse sequence when the data acquisition loops (number of averages, phase encode steps, slices, etc...) are completed and a raw data file is created on the hard disk. At this point users can go to View Images mode to view images obtained.

The Run Mode consists of simply the ‘Active Scan Window’. It is thus a simplified version of the Setup Mode.

Software Operation


Undoing a Scan

Once data has been acquired in the current active scan, the user cannot (even if the scan is stopped prematurely):

Acquire data with this scan;

Edit the parameter file;

Perform setup using the scan;

Delete the scan from the database; and

Remove the sequence protocol.

Some entries in the toolbar will become disabled and grayed-out, and the parameter editor will be read-only.

To remove these restrictions in order to rerun the scan to acquire new data with new parameters

Click on the “Select Working” menu item in the console GUI interface (if the scan is not already the current active scan);

Select the patient and exam containing the obsolete scan;

Select the obsolete scan;

Change the working into active scan;

Click on the “Undo Scan” button.

The parameters in the parameter editor will no longer be read-only and data can be acquired with new parameters, or the scan can be deleted entirely.

Software Operation


View Images Mode

The View Images mode is for users to view the images from a completed scan. Click View Images in the Toolbar menu to enter this mode. Two windows will appear on the right side of the screen. The upper window is the View Images panel in which the users choose a scan to be displayed. The lower window is the interface of Marevisi software used to display the acquired images. Marevisi is a standalone program that has been integrated with the console software. For detailed information on Marevisi, refer to the Marevisi manual.

View Active Image (Top Panel - Left Section) The indicator shows the full path for the active scan raw image data file. If the raw data exists, the Exists indicator beside the path box will be light green in color; otherwise it will be dark green (‘unlit’). To view the images from the active scan:

Click the ‘View Image’ button The raw data file will be loaded by Marevisi The images will be reconstructed by Marevisi The images will be displayed by Marevisi.

View Other Images (Top Panel - Right Section) To view any other dataset that exists in the Store, from left to right:

Select a Patient

Select an Exam Select a Scan If the scan raw data exists, the corresponding Exists indicator will be lit. Click the View Image button. Images will appear in a different Marevisi sub-window from the one used for the active image display. This is therefore a way to display two datasets in Marevisi for side-by-side comparison.

View Images Mode windows.

Software Operation


Help/Shutdown Mode

This mode is used for shutting down the console software. Enter this mode by clicking on ‘Help/Shutdown’ item in the main GUI panel. All other panels except main GUI interface will be closed in this mode. There will be a ‘Shutdown’ button appearing in the bottom of the panel. Clicking on this button will close down the whole console GUI software.

Clinical Safety


Clinical Safety

Prior to using the system with a human in the magnet, there are a number of software and hardware checks to ensure safe operation of the console. These include:

1. Software checks to ensure pulse sequence parameters provide safe levels of specific absorption rate (SAR);

2. Software checks to ensure pulse sequence parameters provide safe levels of dB/dt to prevent neurostimulation;

3. Hardware monitoring of RF output to ensure safe SAR levels;

4. Software checks to maintain a safe gradient amplifier duty cycle during pulse sequence execution to prevent hardware damage

Clinical Safety


Compile-time SAR Safety Check

For use as a clinical imaging system, the Cirrus 0.2 T MR console must adhere to FDA specific absorption rate (SAR) safety limits: 4.0 W/kg averaged over the whole body for any 15-minute period; 3.0 W/kg averaged over the head for any 10-minute period; 8.0 W/kg in any gram of tissue in the extremities for any period of 5 minutes.

Each time a pulse sequence is compiled, pulse sequence parameters from various sources used to predict RF energy deposited on tissue, including:

Patient data file: patient weight

Parameter file: pulse shape(s)

flip angle(s)

number of slices

TR

number of acquisitions

Async: Coil code (for calibrated SAR of each pulse/coil

combination)

The calculation assumes that proper adjustment of the transmitter gain and amplitude to produce the desired flip angles contained in the parameter file. There is no way round this assumption, since the calculation at compilation time will involve calibrated peak RF power deposited on the sample.

Calibration of RF power deposited by a coil is done as part of the system setup for coils delivered with the system and subsequent addtion of coils to the Cirrus system. The setup requires a coupler and oscilloscope in-line with the transmitter output to measure forward and reflected power. The first step is the determination of the power dissipated on an unloaded coil and with a suitably sized phantom (coil-dependent). To determine the power dissipated on the coil, the transmitter gain and amplitude are adjusted to generate pulses yielding accurate flip angles. The forward and reflected power of the pulse producing a known flip angle is measured. The difference is the power dissipated on the coil:

Next, this procedure is repeated with a loaded coil (i.e., with a phantom approximating tissue characteristics and sample mass in the coil volume). The power deposited on the sample is then:

To determine the amount of energy deposited on the sample, it is easiest to determine what the equivalent rectangular pulse duration would be using:

The power per pulse is simply:

Knowing the number and type of pulses as well as TR allows the calculation total SAR:

The calibration need only be done for one pulse type. The average SAR for any other pulse type can be predicted from the RF waveform. But the calibration must be carried out on each coil.

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Clinical Safety


Compile-time dB/dt Safety Check

The FDA limits on dB/dt used are those outlined in IEC 60601-2-33, which involves determining experimentally the magnitude of the fields produced in each of the three orthogonal directions for each gradient channel. The calculation assumes that for each gradient channel the conversion of V to mT/m is properly calibrated during installation of the console. The calculation requires several parameters from a number of sources in the software:

Parameter file: gradient ramp time slice orientation parameters Compiled sequence code: gradient amplitudes System configuration file: conversion of gradient amplitude to dB for each

gradient channel Since the calculation of dB/dt requires that the change in field by a gradient pulse be determined in laboratory coordinates, the gradient amplitudes for the ramp frames must first be converted from Gslice, Gphase and Gread to individual gradient channel amplitudes Gx, Gy and Gz. These conversion factors (dB/G)i are determined for each of gradient channel by calculating the ratio of the experimentally-determined maximum magnitude of dB/dt produced to the amplitude of the test gradient lobe (which must be set to the maximum amplitude with the shortest ramp time the system allows):

The search coil is designed to directly measure the magnitude of dB/dt, so that the numerator in the above equations is calculated by the hardware used in its measurement. These conversion factors are system-dependent and are stored in the Python module ClinicalSafetyConfig.py for use in calculating dB/dt with different ramp times and gradient amplitudes.

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Clinical Safety


dB/dt is calculated for each channel after correction for slice orientation by:

and the resultant is given by:

The maximum dB/dt allowed is determined from:

where tramp is the ramp time which (for trapezoidal waveforms to which pulse sequences on this system are limited to) is the same as the effective stimulus duration described in IEC 60601-2-33. When (dB/dt)calc for a gradient ramp in the pulse sequence is greater than this value, a Python exception is raised and compilation of the pulse sequence is terminated. The result of this is that since there is no compiled pulse sequence code, execution by the sequencer is not possible. The operator is informed as to which gradient ramp produced the exception during compilation and is able to adjust relevant parameters (e.g., increase the ramp time) to correct the problem.

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Clinical Safety


Compile-time Gradient Duty Cycle Check

Parameters from various sources are required for the duty cycle calculation:

Parameter file: gradient duration for each channel for each frame gradient amplitude for each channel for each frame number of slices TR Sequence code: shape of gradient waveform

Typically, the gradient duty cycle should not exceed 25% as calculated from:

The calculation assumes that proper adjustment of the conversion of the input voltage to the gradient amplifiers to produce the desired gradient. Gmax is set in the console configuration file. Since all gradients used in the clinical console system are trapezoidal, calculating the integral in the above equation is simple: For ramps, the integral is the ½ ramp time × amplitude; For flat waveforms, the integral is simply ramp time × amplitude. The duty cycle is calculated over TR and thus all gradient waveforms for all slices must be included. This is accomplished simply by multiplying the duty cycle for a single slice by the number of slices, keeping TR the same. When the maximum duty cycle is exceeded, a Python exception is raised on compilation and the operator notified of the error with a message sent to the console GUI.

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Quality Assurance Procedures



Monitoring quality assurance helps ensure that the Cirrus Open MR imaging system continually meets image quality specifications and diagnose potentially serious problems at a more manageable point. The tests are designed to measure:

1. Resonance frequency drift.

2. Signal-to-noise ratio.

3. Image uniformity.

4. Ghost intensity.



Measurement Conditions

Frequency of Testing

It is recommended that Quality Assurance (QA) tests be conducted daily before patient imaging is started. Once MR operators become familiar with the system and find minimal or no change in the measurements the frequency of some or all of the QA tests may be altered, at the discretion of the MR operator, to longer time periods. QA testing should be performed whenever deficient performance of the system is suspected, if images reveal abnormalities or if room temperature has altered significantly out of specification.

QA Phantom and RF Coil

For the Quality Assurance scans use a spherical phantom of the diameter of 20 mm and fill it with the mixture of 0.25% (m/v) NaCl and 0.125% (m/v) CuSO4 solution. Position the phantom in the centre of the imaging coil and place the coil assembly in the centre of the magnet.

The RF head coil is to be used.

Temperature

Room temperature during the QA scans should be 20 20C.

Scan Parameters

All protocols for acquisition of images for determination of measurements are found in the appropriate folders in the pulse sequence protocol library. These protocols are:

SF_cal for adjusting the resonance frequency and global shimming

Localizer for pilot scans

GE for acquiring the Gradient Echo image

SE for acquiring the Spin Echo image

The GE protocol is a gradient echo pulse sequence with the following acquisition parameters:

Matrix dimensions: 128 x128

TE 10 ms

TR 100 ms

Receiver bandwidth 10000 Hz

FOV 250 mm x 250 mm

NEX 1

No. of slices 1

Slice thickness 3.0 mm

Slice orientation Transverse

Slice position at isocenter

Pulse shape 5-lobe sinc

The SE protocol is a spin echo (single echo) pulse sequence with the following acquisition parameters:

Matrix dimensions: 128 x128

TE 30 ms

TR 2500 ms

Receiver bandwidth 10000 Hz



FOV 250 mm x 250 mm

No. of averages 1

No. of slices 1

Slice thickness 3.0 mm

Slice orientation Transverse

Slice position at isocenter

Pulse shape 5-lobe sinc



Measurement Procedures

Acquisition of images

Perform the normal experiment registration. Carry out the standard pre-scan procedure using SF_cal and Localizer protocols. Record the properly adjusted resonance frequency. Select the SE protocol with the listed standard parameters and complete typical adjustments of the RF pulse attenuations (record these as well) and receiver gain. Acquire a spin echo image at isocentre (image 1 below) and at +5mm offset (image 1a). Repeat the above steps using the GE protocols with standard parameters listed above.

Signal Measurements

Select a region-of-interest (ROI) enclosing ~75% of the area of the image 1 (see Fig.1) and determine the following:

Mean intensity of pixels in the ROI – Mean SI.

Minimum intensity of pixels in the ROI – Min SI.

Maximum intensity of pixels in the ROI – Max SI.

Select the ROI of the background, free of any artifacts (top left ROIs in Fig.1) and determine its mean intensity of pixels – Mean SB.

Select the region in the background containing ghosts (top middle ROIs in Fig.1) and determine its mean intensity of pixels – Mean SG.

Signal-To-Noise Ratio (SNR). Calculate the SNR using the following definition:

SNR = Mean SI / Mean SB

Image Uniformity (IU). Calculate the IU using:

IU = (Max SI – Min SI) / (Max SI + Min SI) x 100 %

Ghost Intensity (GI). Calculate the GI according to:

GI = Mean SG /Mean SI x 100 %

Repeat the above SNR, IU, and GI calculations for images obtained using the STANDARD GE protocol.



Documentation of Results

After finishing the QA tests, the following results and particulars are to be recorded in the Quality Assurance Logbook (see the example below):

Date of the test

Name of the operator

Experiment name

Resonance frequency

900 pulse attenuation (both Transmit. scaling and Transmit amp gain) for a 5-lobe sinc pulse

1800 pulse attenuation (both Transmit. scaling and Transmit amp gain) for a 5-lobe sinc pulse

Raw data values for SNR, IU, GI determination

Signal-To-Noise Ratio (SNR)

Image Uniformity (IU)

Ghost Intensity (GI)

Any important remarks

Any following deviations should be reported to MRI-Tech immediately:

Signal-To-Noise Ratio (SNR) 10 %

Image Uniformity (IU) 10 %

Ghost Intensity (GI) 20 %

Example of the Quality Assurance Logbook page:

Procedures in the Magnet Room for Imaging


Procedures in Magnet Room for Imaging

An EXAM begins when the patient is placed in the magnet with an RF coil. If the patient or coil is moved relative to the tabletop then this is considered a NEW EXAM. The reason for this is that if the patient or coil is moved then all previous positional information and adjustments become invalid. Note: Sliding the patient table does NOT necessarily constitute a new exam.



Routine Cleaning

Before accepting a patient into the magnet room all necessary items and surfaces that have come into contact with the previous patient and that may come into contact with the next patient must be cleaned and disinfected according to protocol. Items requiring this routine cleaning procedure include but are not limited to the following:

Patient Bed

Comfort Pads

RF Head Coil

Magnet Enclosure

Door handles, chairs, floor, etc. The cleaning solutions listed below have been tested and can be used for cleaning of the patient bed

and magnet enclosure (the following solutions have not been tested on any other surfaces):

Quatricide

Isopropyl alcohol

Bleach Solution (1:20 dilution)

CLINICIDE Note: If other cleaning agents are to be used, or if the solutions listed above are to be used on items other than the patient bed or the magnet enclosure, they should be trial tested on an inconspicuous location of that item first.

If towels, sheets, pillow cases, patient gowns are used for patient protection ensure that soiled articles are cleaned before their next use and that an adequate supply of clean and ready-to-use articles are on hand. Also, ensure that surfaces covered by these means of patient protection are clean regardless. If disposable paper is used for patient protection, ensure that a new covering is laid down before each patient. Also, ensure the cleanliness of surfaces covered by this means of patient protection.



Steps to Insert Patient to Magnet Iso-centre

1. If necessary perform quality assurance procedures. See section on Quality Assurance Procedures.

2. Start with a clean and disinfected environment for the new patient. See section on Routine Cleaning. Apply clean coverings (sheets, pillow cases, paper) as required.

3. Plan out where and how to position the patient on the bed top according to the imaging requirements for the NEW EXAM.

4. Start with the bed top in the fully extracted position, as shown below in Figure 1, (pull it out of the magnet if necessary) with the detent (snap-in) engaged to lock the bed top into this position to facilitate safe loading of the patient onto the bed top.

Figure 1: Patient Bed in Loading Position

5. According to the plan made previously, place the RF head coil at one of the six numbered

positions (receptacles or socket pairs) on the bed top. The pair of stubs that protrude from the bottom of the coil base engage into the chosen pair of sockets in the bed top. The numbered line that extends from the sockets into which the stubs engage determine the position number of the coil. A coil placement at Position 4 is shown below in Figure 2. Note that the head coil is shown in the patient loading position and will be translated to the imaging position that will place the coil itself at Position 4. For reference, the RF head coil is shown below in Figure 3.



Figure 2: Patient Bed with RF Head Coil (in Patient Loading Position) at Position 4

Figure 3: RF Head Coil and its Main Parts



6. Plug the RF head coil connector into its receptacle that is located on the side panel of the bed

platform. Figure 4 shows the location of the receptacle.

Figure 4: Location of the RF Coil Receptacle on the side of the Patient Bed Platform

7. Ensure the head coil is in the patient loading position, the state with the coil translated closest to

the magnet. This situation is shown above in Figure 2. This enables the patient to lie down and place their head on the head rest without the head coil in the way. If it is not, referring the illustration of the head coil in Figure 3, pull out the locking pin that passes through the head rest of the head coil base and then slide the head coil to the patient loading position and engage the locking pin to secure the coil in the loading position.

8. Place the appropriate comfort / positioning cushions on the bed top and the head rest of the coil base ready to accept the patient. CAUTION: When assisting the patient onto the Bed Top, have the patient avoid sitting on the

edge of the bed top as this may cause the bed top to tip. The weight of the patient should be contained within the confines of the fluid trough, i.e. within the confines of the colored edging in order ensure bed top stability.

9. Accompany, and assist if necessary, the patient into the magnet room (if necessary, patient

should already be gowned according to protocol). Explain the procedure as necessary to the patient.

10. Position the patient on the bed top with their shoulders properly resting against the head coil base and their head properly resting on the head rest.



11. Equip the patient with hearing protection according to protocol or with the patient communication system that includes placing the (sound attenuating) head set about the patient’s ears and the squeeze ball in the patient’s hand of preference.

12. Describe the communication system to the patient and go through a practice run, if necessary, to ensure proper system operation and the patient’s understanding of how to communicate with the MR operator if the need arises.

13. Readjust the positioning cushions and add more as necessary to accomplish all three of the following conditions:

a. Ensure the patient’s head will be centrally located within the RF coil. b. Ensure adequate and comfortable support of the patient’s head and body (e.g. lumbar

and legs). c. Ensure that the patient’s head is supported to remain motionless during the imaging

procedure. Explain to the patient the importance of remaining motionless. 14. Pull out the locking pin that passes through the head rest of the head coil base and translate the

RF head coil over the patient’s head to the imaging position and engage the locking pin to secure the coil in the imaging position. This imaging position is shown below in Figure 5.

Figure 5: RF Head Coil in the Imaging Postion on the Bed

15. If necessary, readjust the positioning cushions and add more as necessary to confirm all three of

the following conditions: a. Ensure the patient’s head is centrally located within the RF coil. b. Ensure adequate and comfortable support of the patient’s head and body (e.g. lumbar

and legs). c. Ensure that the patient’s head is supported to remain motionless during the imaging

procedure.



16. Ensure all cables, hoses, and tubes are positioned accordingly to accommodate the insertion (and extraction) of the bed top.

17. Properly position the patient’s hands, arms, feet and the RF cables according to protocol (for example, to avoid patient injury due to RF heating from a loop in the RF coil cable).

Inserting the Bed Top into the magnet

The process of pushing the bed top into the magnet from the patient loading position will involve simultaneously disengaging the bed top out of the loading position detent lock and overcoming the inertia of the stationary patient. This will require a push force that will decrease once out of this lock position and the patient / bed top is in motion. If detent Position 1 is the final insertion position then bed top insertion will terminate upon engagement of the first detent (snap-in). If further insertion of the bed top is required, to Position 2 or greater, then as bed top insertion continues the operator will hear and feel the clicking of the engagement / disengagement action of the detent as the bed top passes through these discreet locations.

18. Push the bed top into the magnet up to the point at which the (foot) end of the bed top, with the push/pull handle, aligns with the numbered marker line on the bed platform that matches the position number of the RF Coil (on the bed top). Figure 6 shows the bed top inserted to Detent Position 4.

Figure 6: Patient Bed Inserted into Magnet to Place RF Coil at Magnet Iso-centre

19. The RF head coil and the patient’s head should now be at iso-centre of the magnet. 20. Ensure patient’s comfort. 21. Close the magnet room door. 22. The patient is in position ready for pre-scan adjustments as necessary. See section on Pre-scan

Adjustments. Afterward, real imaging can be carried out.



Extracting Patient After Scanning

1. Once the imaging process has been completed, confirm that the patient can be extracted from the magnet.

2. Ensure all cables, hoses, and tubes are positioned accordingly to accommodate the extraction of the bed top.

3. While watching both the patient and all cables, hoses and tubes, pull on the handle of the bed top to disengage the imaging position detent and begin moving the patient out of the magnet to the fully extracted position, the patient loading position, so that it engages the detent at this end of travel position.

4. At the head coil, pull out the locking pin that passes through the head rest of the head coil base and then slide the head coil to the patient loading position, away from the patient, and ensure the locking pin engages to secure the coil in the loading position.

5. Remove the components of the patient communication system from the patient.

CAUTION: When assisting the patient off the Bed Top, have the patient avoid sitting on the edge of the bed top as this may cause the bed top to tip. The weight of the patient should be contained within the confines of the fluid trough, i.e. within the confines of the colored edging in order ensure bed top stability.

6. Assist the patient off the bed top. 7. Assist the patient out of the magnet room. 8. If it is necessary to remove the RF head coil from the bed top, first remove or rearrange the

comfort pads as necessary, then unplug the connector of the head coil from its socket, coil up the cable and place on or near the head coil, lift coil off the bed top and place it elsewhere.

9. Clean and disinfect the environment for the next patient. See section on Routine Cleaning.

Pre-scan Adjustments



After turning on all hardware needed and inserting the patient bed into the magnet so that the patient’s ROI is at magnet iso-centre, ready for imaging, the MR system operator needs to do some system tuning and adjustment works using console software before commencing the real scans on the patient. The steps are:

1. Search for the current working frequency of the magnet (the spin resonant frequency).

2. Adjust the shimming (magnetic field homogeneity) to improve image quality (Optional).

3. Adjust the flip angle (transmitter scaling/gain) of RF system.

4. Adjust the receiver gain.



Working Frequency Adjustment

Working frequency searching is very important for permanent magnet MRI systems. When the temperature of the room in which the permanent magnet resides changes, the magnetic field changes with the temperature. Therefore the working frequency changes with the room temperature. A MRI system relies on the working frequency to do many calculations, such as navigation. If the on-resonance frequency of the magnet is not the same as that in the software, images will not be obtained from the expected location and the image quality will degrade.

The user can change the value of the edit box ‘Offset (Hz)’ on the ‘Adjust’ tab of ‘Active Scan’ panel to change working frequency of the system.

When the user shuts down the console software in ‘Shut Down’ mode, console software will automatically save the current working frequency offset (the value in ‘Offset (Hz) edit box) to hard disk before it exits. The next time the user starts console software, the software will restore the saved frequency offset as a beginning point for frequency searching.

The procedure of searching working frequency is:

Select ‘SF_cal’ pulse sequence

Select “Select Working” mode from the Selector Menu;

Create a new scan in ‘Scan’ tab page;

Click ‘Load from library’ button to load the SF_cal pulse sequence from “C:\MR\Protocols\STANDARD\Adjust\SF_cal”;

Activate ‘SF_cal’ pulse sequence

Select ‘Edit’ mode if you want to change parameters for the SF_cal pulse sequence. Usually you don’t need to change anything.

Select ‘Select Active’ mode. Activate the scan with SF_cal pulse sequence by click the ‘work -> active’ arrow either on the main GUI panel or on the ‘Select Active’ front panel.

Acquire signal in “Setup” mode

Select ‘Setup’ mode.

Click ‘setup’ button on the ‘Active Scan’ panel to start the signal acquisition. The signal will be displayed in the display area on ‘Active Scan’ panel.

Search for the working frequency

Check the ‘FFT’ checkbox in the display area.

Select the ‘Advanced Control’ toggle on the ‘Active Scan’ panel and select the ‘Frequency’ button on the DAQ subpanel.

Change the value in the ‘offset (Hz)’ edit box to make the peak of FID signal after FFT transform appear at the center of the display window.

The value in the ‘Actual Freq (Hz)’ edit box is the current working frequency.

Click the STOP button on the “Active Scan” panel to stop acquisition of FID signal.



Shimming

The aim of shimming is to make the magnetic field over the imaging area more homogeneous in order to get good quality images. By shimming, the magnetic field in the actual imaging area can be more homogeneous.

The user can change the values of three edit boxes ‘Gx’, ‘Gy’ and ‘Gz’ on ‘Shim’ tab of the ‘Active Scan’ panel to do the shimming.

When the user shuts down the console software the shimming values (the values in ‘Gx’, ‘Gy’ and ‘Gz’ edit boxes) are automatically saved before exiting. The next time the console GUI is restarted the shim values are restored and can be used as a new starting point for shimming.

The SF_cal pulse sequence is used to perform shimming. The MRI operator can use the same scan as used to adjust the frequency to shim.

Ensure that the ‘FFT’ checkbox in the display area is unchecked and check the ‘Magnitude?’ box. Acquire an FID signal in Setup mode. (Click ‘setup’ button on “Active Scan” panel to start acquisition of FID signal.) It may be desirable to change the frequency to more easily see the effects of changing shim value.

Shim using the sliders or buttons marked ‘+’ or ‘-‘, each of which controls one of the three primary shim coils (Gx, Gy or Gz). The size of the increment per button click and the slider ranges may be altered using the appropriate controls. The waveform in the display area will change with the Gx, Gy, Gz values. Find the best values to make the FID as large in area as possible.

Click the ‘STOP’ button on the “Active Scan” panel to stop the acquisition of FID signal.

Note: If frequency was set prior to shimming, it will in all likelihood need to be readjusted following shimming as well.



RF Flip Angle Adjustment

Prerequisite: Frequency adjustment and shimming should have been done.

The aim of RF flip angle adjustment is to find out what RF power level needed to achieve 90° and 180° RF pulse of the type that will be used in the imaging sequence. If the RF power lever is not adjusted properly, the S/N ratio of images could be degraded. Also the contrast of the images may not be as you expect.

There are two different transmitter scaling parameters which must be adjusted to optimize the pulse flip angles. The first is ‘Transmit Scaling’, which adjusts the amplitude of the waveform output to the RF amplifier. The second, ‘Transmit amp gain’, controls the gain of the signal output by the RF amplifier. The first can be considered to control software waveform gain and the second to control hardware gain. There is a limit to the amount of software gain which will depend on the peak amplitude of the RF waveform. Typically, the higher the bandwidth of the RF pulse the lower this maximal ‘Transmit Scaling’ value will be. If the waveform amplitude is too high an error message will be generated. If this occurs and the optimal RF pulse amplitude is not yet reached it is then necessary to increase the ‘Transmit amp gain’ and then readjust the ‘Transmit Scaling’.

Different coils need different RF power level in order to achieve 90-degree flip angle. So the adjustment ranges of ‘Transmit Scaling’ and ‘Transmit amp gain’ will differ from coil to coil. If coil detection is implemented the console software can automatically set the range and default value of the preceding controls according to the coil used in the current exam. When the user activates a scan of another exam and the coil is different from the previous exam, the adjustment ranges of two RF power edit boxes will be set to the new ones for the new coil. And the values of the two boxes will also be set to their default values. For example, if you choose ’10 cm head solenoid’ coil when you create a new exam. The ‘transmit Attn.’ will be set to 16. The user can only adjust ‘transmit scaling’ within 0.5 – 1.5. Any input beyond this range will be changed to 0.5 or 1.5 (depends on which side the input value exceeds).

The engineers of the Cirrus console configure the ranges and default values. When necessary, these values can be modified.

While it is best to use the pulse sequence used for acquiring the data for the purpose of adjusting the RF gains, this is not always convenient (such as in the case of EPI) and using the Pulse_gains sequence with the appropriate pulse types is best. Using the sequence acquiring the data (with the phase encode turned off in the Parameter Editor) ensures that all RF waveforms in the sequence are within the nominal amplitude range. The following steps describe how to do the adjustment using Pulse_gains:

Select Pulse Sequence

Select “Select Working“ mode from Advance Selector;

New a scan in ‘Scan’ tab page;

Click ‘Load from library’ button to load the pulse sequence from, e.g., “C:\SharpSCC\ClinicalProtocols_v2\Adjust\Pulse_gains”.

Activate scan of Spin Echo pulse sequence

Select “Edit” mode if you want to the parameters of the pulse sequence. Usually you don’t need to change anything.

Select “Select Active” mode. Activate the scan by clicking the ‘work ->active’ arrow either on the main GUI panel or on the ‘Select Active’ front panel.

Acquire spin echo signal in Setup mode

Select ‘Setup’ mode. Click Setup button on the “Active Scan” panel to start the acquisition of spin echo signal. The signal will be displayed in the display area on “Active Scan” panel.

Adjust RF transmission power

Ensure that the ‘FFT?’ checkbox in the display area is unchecked and check the ‘Magnitude?’ check box.



Select ‘RF gains’ tab page on “Active Scan” panel.

Change the values in the ‘Transmit Scaling’ edit box and ‘Transmit amp gain.’ The waveform in the display area will change with the transmitter scaling values. Find the combination of values which maximizes the magnitude of the peak of the spin echo signal. If the ‘Transmit Scaling’ is set too high and an error dialog box is generated increase ‘Transmit amp gain’ and readjust ‘Transmit Scaling’. Once the values maximizing the signal observed in the acquisition window are determined the RF transmission level adjustment is finished. The default value of ‘Transmit amp gain’ is 16 db. This value can be used for most coils. Large coils may required that ‘Transmit amp gain’ be set to higher db values as they require greater power to generate the same flip angle. High Transmit amp gains (≥ 39 dB) should be avoided, as oscillations may be produced in the transmitter causing significant noise to be introduced.

Click the ‘STOP’ button on the “Active Scan” panel to stop the acquisition of spin echo signal.



Receiver Gain Adjustment

All previous adjustment procedures should have been done. The aim of this adjustment is to set the receive gain to a proper value get good the S/N ratio of images and less digitalization errors in analog-digital transfer stage. The procedure of adjusting the receiver is given below.

Create a scan with your chosen pulse sequence

Select “Select Working“ mode from the main menu.

Click ‘New’ to create a scan in ‘Scan’ tab page.

Click ‘Load from library’ button to load a pulse sequence you want from of “C:\MR\Protocols\... \protocolname”

Activate the scan

Select “Edit” mode if you want to change the parameters of the pulse sequence.

Select “Select Active” mode. Activate the scan you created in step a by click the ‘work ->active’ arrow either on the main GUI panel or on the ‘Select Active’ front panel.

Acquire signal without phase-encoding

Select Setup mode.

Click ‘Setup’ button on the “Active Scan” panel to start the acquisition of the signal. The signal will be displayed in the display area on “Active Scan” panel. The echo signal will have no phase-encoding.

Adjust receiver gain

Uncheck the ‘FFT’ checkbox in the display area and check the ‘Magnitude?’ check box.

Click on the ‘Advanced Control’ toggle page on “Active Scan” panel.

Change the values in the ‘Rx Gain Step’ edit box. The waveform in the display area will change with the Rx Gain Step value. Select one value to make the magnitude of the peak of the echo signal to be in the range of 10,000-20,000. The maximum signal amplitude before signal clipping occurs is ±32,767. Clipping of the signal is to be avoided, as this will introduce large artifacts in the resulting images. High receiver gains (≥ 39 dB) should also be avoided, regardless of whether signal clipping is occurring. At high gain oscillations may be produced in the receiver causing significant noise to be introduced.

Finish the adjustment and do image acquisition

Click the ‘STOP’ button on the “Active Scan” panel to stop the acquisition of echo signal.

After the ‘Setup’ button is re-enables the system is ready to acquire images using the scan you just adjusted.

Remember to enable phase encoding prior to data acquisition.

Note: Usually you need to readjust the receiver gain if you change the active scan to another one with different sequence type or same sequence type but different slice orientation. Generally speaking, when something has been changed in the software that will affect signal level, the receiver gain should be re-adjusted.

Notes on Image Orientation



This document describes the logical gradient coordinate system definitions used by Marevisi. It can be used for gradient coil design, console gradient output cable connections and software configuration.



Coordinate Systems and the Cirrus Open 0.2 T MR Console

Logical Gradient Coordinate System

The Logical Gradient Coordinate System is used by the Cirrus Open console to make sure that navigation software can be used on any MRI system as long as the gradient hardware supports this definition. As shown below, the coordinate system used is a right-handed coordinate system with the origin at the iso-center:

X axis: horizontal axis from the right of the magnet to the left;

Y axis: vertical axis from low to high;

Z axis: patient insertion direction from near edge to far.

The cables between gradient amplifier and gradient coils and those between gradient amplifier and console should be connected correctly to make sure the polarities of three gradient channels are the same as the definitions above.



Patient Coordinate System

The patient coordinate system is also right-handed system. The positive directions for each of the three axes on the patient are defined as:

X: From the patient’s left hand to the right hand;

Y: From the patient’s back to the front;

Z: From the patient’s feet to the head.

Note that while (in this case) the patient coordinate system differs from that of the Logical Gradient Coordinate System, the system user must typically select the patient orientation in the Select Working mode.

Marevisi patient coordinate

system.



Marevisi requirement of coordinate system

Marevisi is the module in charge of MRI data processing, navigating, image displaying in this MR Console. Marevisi can work with both right-handed and left-handed systems. Gradient and Patient coordinate systems defined above are compactable with Marevisi’s right-handed system. It’s very important to make sure the right-handed system is used when the operator uses Marevisi to navigate slices to be scanned. Otherwise, slices to be scanned might go to the opposite direction and the wrong section of patient might be scanned. For more information of Marevisi coordinate system please refer to Marevisi documentation ‘Navigation 10.doc --- 4. Mathematical background’.

Marevisi uses Euler angles (α, β, γ) in its navigation calculation. The Euler angles given by Marevisi after the navigation operation convert the Laboratory (Logical Gradient) to the Patient Coordinate System. The rotation matrix used to calculate the coordinates in the new coordinate system from the Euler angles is:

cossinsinsincos

sinsincoscossincossincossinsincoscos

cossinsincoscoscossinsinsincoscoscos

)()()( RRR

.....(1)

If we want to find out the gradient values in Laboratory Coordinate for slices of a specific orientation, we need to find out the Euler angles from the Experimental (Imaging) Coordinate System and use (1) for the calculation of gradient values. Let the Euler angles given by Marevisi after navigation be (A, B, G). The Euler rotation from Experimental to Laboratory Coordinate System is a reversed operation of that from Laboratory to Experimental Coordinate System. So,

),,(),,( ABG .....(2)

If we substitute (2) into (1), we can find the rotation matrix from Experimental Coordinate System to Laboratory Coordinate System with A, B and G as variables.

BGBGB

BAGAGBAGAGBA

BAGAGBAGAGBA

BBGBG

ABAGABGAGABG

ABAGABGAGABG

BBGBG

ABAGABGAGABG

ABAGABGAGABG

GBAR

cossinsincossin

sinsincoscossincossinsincoscoscossin

sincoscossinsincoscossinsincoscoscos

cossinsinsincos


cossinsin)coscoscossinsinsincoscoscos

)cos()sin()sin()sin()cos(

)sin()sin()cos()cos()sin()cos()sin()cos()sin()sin()cos()cos(

)cos()sin()sin()cos()cos()cos()sin()sin()sin()cos()cos()cos(

cossinsinsincos


cossinsincoscoscossinsinsincoscoscos

),,(

.....(3)



Standard Slice Orientation Rotations

There are three standard slice orientations most commonly used for imaging: Transverse, Sagittal and Coronal. In order to achieve a specific standard slice orientation, the proper coordinate rotation operations must be done. The following are Euler angles for each of the three standard slice orientations (P = phase encode, R = frequency encode, and S = slice selection gradient directions):

Transverse: (0, 0, 0)

Sagittal : (0, 90, 90)

Coronal : (-90, 90, 90)



Physical Gradient Cable Connections

When making gradient coils, designers may define Gx, Gy and Gz different from logical gradient coordinate system. During installation it is important to make sure that the X, Y and Z gradient waveform outputs from the Cirrus Open console are sent to gradient amplifiers that can output currents to X, Y and Z channel in logical gradient coordinate.

Console gradient signal outputs should be tested on an oscilloscope before being connected to the corresponding gradient power amplifier. After verifying that the gradient signal outputs from the Cirrus Open console are correct, the cable connection of each channel should be checked to ensure that the X, Y and Z gradient signals are really creating X, Y and Z gradient magnetic fields in the Logical Gradient Coordinate Frame.



Image Reconstruction and Image Layout in Marevisi

When Marevisi is used to reconstruct images acquired using the Cirrus Open console, the ‘conjugate’ option should be checked in order to layout the images correctly following reconstruction. Marevisi will always place the positive direction of the patient to the left side or the top side of the image. Marevisi relies on this rule to judge the sign of the slice offsets.

For the three standard slice orientations, the images will be laid out as shown below (patient is lying down on his/her back and head first):

Transverse: Sagittal: Coronal:

If the images do not turn out as expected, check the reconstruction and pulse sequence programs for corrections.

Patient’s right

Patient’s left

Patient’s front

Patient’s back

Patient’s front

Patient’s back

Patient’s top (head)

Patient’s bottom (feet)

Patient’s top (head)

Patient’s bottom (Feet)

Patient’s right

Patient’s left

Troubleshooting


Troubleshooting

Troubleshooting


Solving Common Problems

Problem Possible reasons Actions

No signal RF amplifier not on RF coil not connected Frequency far off resonance No sample in coil Data acquisition computer error Pre-amp power off Large frequency drift

Turn on RF amplifier Connect coil to proper connector at magnet Adjust RF frequency to on-resonance in setup mode Put a sample in coil Contact MRI-Tech Contact MRI-Tech Check gradient temperature

Shimming not effective Gradient amplifier not on Gradient output inhibited

Turn on gradient amplifier Release inhibited button of gradient amplifier

Images turn out to be bright lines or spots in the centers of images

Gradient amplifier not on Gradient output inhibited Phase encoding disabled

Turn on gradient amplifier Release inhibited button of gradient amplifier Enable phase encoding in parameter editor

Poor image quality: Regions outside of sample contain significant signal

Low SNR

Low SNR, blurred and distorted image Folded image

Receiver gain too high (produces large signal in regions outside of sample) RF coil not matched and/or tuned RF and/or receiver gain not optimized RF pulse flip angles not optimized Poor magnetic field homogeneity B1 field produced by RF coil not orthogonal to main B0 field FOV too small and/or not centered; RF frequency off-resonance

Adjust receiver gain in setup mode with phase encoding disabled to eliminate artifact (best done with FFT box checked) Tune and match coil Perform pre-scan adjustments Adjust flip angles to optimize signal intensity in setup mode with phase encoding disabled Adjust shims using SF_cal sequence Adjust coil position to make the RF B1 field orthogonal to main field B0 Increase field of view and/or center in order to encompass all of sample; ensure RF frequency

Troubleshooting


Regions of distortion and signal loss in image Noisy image

Metal or other debris RF interference

is on-resonance Check for metal objects in magnet Check for failed filter or metal wires going through shielded room directly without going through any filter

Incorrect image annotation Software bug Contact MRI-Tech

Console GUI hangs GUI instability Loss of communication to Sync and Async computers DAQ problems Sequencer problems

Exit GUI (may require the use of Windows Task Manager), ensuring ALL related processes are stopped; restart GUI Ensure Sync and Async computers turned on Use ‘Async-DAQ’ menu item to communicate with the Async computer, exit and restart DAQ software Exit console gui and power cycle Sync computer

Console GUI does not start No recognized receive/transmit coil connected

Connect a valid coil to the T/R switch

Sequence does not acquire data Preview enabled Sequence did not compile Sequence is not supported by DAQ Async or DAQ not running

Disable preview in parameter editor Observe any error messages produced in the Status Window and correct Contact MRI-Tech Connect to Async-DAQ computer using “Async-DAQ” under the Select Task menu item and double click on the Async/DAQ icon located on the Async computer’s desktop

Async and DAQ software doesn’t start after reboot.

Communication problem between the GUI and the Async computers

Check if the contents of drive used for data storage are visible using “My Computer”. If the contents are not visible then check: network cable connections; all the lights on the hub are on; any firewalls on GUI computer are disabled.

DAQ returns error message “<path> daq_data_processing.txt is not found”

Network drive not connected Log on to the Async computer using VNC, go to My Computer, double click on Q:

Troubleshooting


Acquisition aborts and no data is stored

Sequence or hardware problem Contact MRI-Tech

GUI repeatedly issues error dialog box with the message "Open Application Reference in Run Proto D.vi -> TopRunProto.vi"

AS.exe and DAQ TopLevel.exe, may not be running on the Async-DAQ computer.

Connect to Async-DAQ computer screen using “Async-DAQ” under the Select Task part of the GUI, then reboot Async-DAQ computer

Connection to Async-DAQ screen using the “Async-DAQ” selection fails; GUI issues errors such as "rdr.IOException: java.net.SocketException: Connection reset."

Async-DAQ is not responsive. Manually reboot Async-DAQ, leave GUI computer and console software running. Allow sufficient time for boot-up of Async-DAQ computer

Overload light on gradient amplifier is lit

Gradient amplitude too high; internal damage to amplifier

Check imaging parameters and ensure gradient strengths are within operating limits; Use Reset button- if Overload persists notify MRI-Tech immediately

Non-zero value in “DAQ Backlog” (Active Scan window)

Increasing values indicate a software/hardware problem

Contact MRI-Tech

Troubleshooting


Async-DAQ Mode

This mode allows visual access to the Async / DAQ computer. Selection of the ‘Async-DAQ‘ menu item will connect to the Async computer using Internet Explorer. Here it is possible to observe whether the DAQ software is performing correctly and, if it is not, restart the DAQ software remotely.

Troubleshooting


Operating the Console in Loopback Mode

The console GUI has the ability to ‘loopback’ the transmit RF signal to one of the input channels to acquire and display the RF signal on the computer screen for system troubleshooting purposes.

Operating Procedures

In the Active Scan window of the console software, click “Advanced Control” button to ON. This is to bring up the hardware control window to the user.

In the “Loopback States” selector of the hardware control window, choose Tx-> Rx 1 (A) or B, depending on “rx channel config”, which is also located in the same window. This is to route the transmit RF back into one of the input channels.

Set the “combined Tx len us” to an appropriate value. This tells the system the length of each TX_ON window. TX_ON is a pulsed hardware signal that is used to gate the data acquisition in loopback mode. The software needs to know the TX_ON length so that it can properly prune or pad zeros to the acquired data (ie transmit RF signal) to fit into acquisition buffers that have a length determined by RX_ON window.

Go back to Active Scan window, and select the number of traces to monitor. Data traces represent segments of time continuous signal acquired by the system. One trace usually holds one MR echo, or one transmit pulse if in loopback mode. It is best to use a number smaller than 32, with a maximum of 256 traces.

Examples:

Gradient Echo Sequence.

Type into “combined Tx len us” the length of the transmit RF pulse, set “Loopback States” properly based on “rx channel config”, use 1 trace.

Spin Echo Sequence

Type into “combined Tx len us” total length of 90 and 180 degree transmit pulse, set “Loopback States” properly based on “rx channel config”, use 1 trace.

Fast Spin-Echo sequence

Type into “combined Tx len us” the length of the transmit RF pulse (assume 90 and 180° pulses are of equal duration), set “Loopback States” properly based on “rx channel config”, use 10 traces for an echo train length of 8. The number of traces used allows for simultaneous display of all 90 and 180° pulses. The accompanying figure shows the captured transmit RF signal (baseband).

Timing

Loopback transmit RF monitoring makes use of existing data acquisition software. As there is difference in the width between TX_ON and RX_ON gating signals, it is necessary to prune or pad TX_ON data so that it can fit into an RX_ON sized buffer. In case TX_ON is longer, only a fraction of the transmit signal can be displayed on the computer screen (see figure on next page).

The difference in the total number of TX_ON windows can also affect data acquisition. If there are fewer TX_ON windows than RX_ON, the acquisition can wait indefinitely until there is a time-out error (30 seconds is the default acquisition time-out). This however will not affect the display of acquired transmit pulses.

Troubleshooting


Fast spin echo sequence (8 echoes) in Loopback Mode.

MR signal if not

loopbacked

180° Tx pulse90°Tx pulse

TX_ON_180TX_ON_90 RX_ON

data buffer – RX_ON sized

screen display

Set TX_ON length

= TX_ON_90 + TX_ON_180

To acquire both 90 and 180°

Tx pulses for each

acquisition the data buffer is

sized using RX_ON length.

If not enough data is

contained in TX_ON, the

data is padded with zeros.

If the data buffer is too short

to hold TX_ON, the data is

clipped at either end to fit the

buffer

MR signal if not

loopbacked

180° Tx pulse90°Tx pulse

TX_ON_180TX_ON_90 RX_ON

data buffer – RX_ON sized

screen display

Set TX_ON length

= TX_ON_90 + TX_ON_180

To acquire both 90 and 180°

Tx pulses for each

acquisition the data buffer is

sized using RX_ON length.

If not enough data is

contained in TX_ON, the

data is padded with zeros.

If the data buffer is too short

to hold TX_ON, the data is

clipped at either end to fit the

buffer

Timing for spin echo sequence.

Troubleshooting


Digital Receiver Function Verification Using test_rxdev.exe

Test_rxdev.exe is a standalone software program used for the diagnosis and troubleshooting of digital receiver related issues (both hardware and software). The executable file is located in the K:\DAQ

directory

It verifies the operations of the following hardware modules:

NI 7831 FPGA on DAQ computer

Digital receiver

PTS and its 10 MHz output to DAQ PXI computer.

PXS 70 MHz source

Console DC power supply and its 5 V output

Digital receiver related cabling

The program also verifies the installation and operation of the following software modules:

National Instruments LabVIEW driver

NI DAQ 7.x

Digital receiver driver (Rx11Dev.dll by default)

Method

1) Connect DAQ PXI computer 10 MHz output directly to digital receiver channel B;

2) Logon to Async-DAQ computer using VNC;

3) Locate test_rxdev.exe in the K:\DAQ directory;

4) Double click on test_rxdev.exe;

5) Stops the program if it is running. Make sure the settings are correct:

Set “channel config” to channel B;

Set “Rx freq” to 10.0001 MHz;

Leave all other settings at their default values;

6) Re-run the program.

Diagnosis

If a sine wave with 0.1 kHz frequency is seen in the chart, then the above hardware and software items are functioning correctly. The dwell time of the waveform shown in the chart is calculated as

10-6

/rate (s). The default value for the rate is 50,000 samples/s, with a maximum value of 400,000 samples/s.

Other possible outcomes:

Time-out error occurs: This is read from the ‘source’ field of the ‘error out’ indicator. A likely source of this problem is the console DC PS is switched off;

Zero level signal is displayed: Digital receiver module is not connected or damaged;

A wave is displayed but the frequency is not equal to the specified offset: The frequency from the PTS unit is incorrect or its 10 MHz clock is not functioning properly;

Software stops immediately after it is set to run: Missing or damaged Rx11Dev.dll (the digital receiver driver).

Troubleshooting


If any of these conditions occur contact MRI-Tech immediately.

Interface for the digital receiver test program test_rxdev.vi.

RF Pulse Shapes


RF Pulse Shapes

Table of RF pulse shapes available on the Cirrus console.

RF Pulse Shapes


Types of RF Pulse Shapes

There are several ways to select RF pulse shapes in the Parameter Editor: Integrated pulses Part of the console GUI, these are typically selected from the pull-down menus

in Parameter Editor. These include Gaussian and several sinc pulse waveforms.

On-the-fly pulses To use pulses not integrated with the console, the ‘User pulse’ pull-down menu item for pulse shape choice is selected and a string defining the RF pulse shape is entered in the appropriate text box.

User-defined on-the-fly pulses

Similar to the ‘on-the-fly pulses’ supplied with the console software, the user has the ability to write on-the-fly calculated pulse shapes. These waveforms are selected in the same manner as the supplied on-the-fly calculated pulses.

Table of Supplied RF Waveforms – Integrated Pulses

Time-bandwidth

product

3-Lobed SINC 4.0

5-Lobed SINC 6.0

9-Lobed SINC 10.0

Hanning-filtered SINC 10.0

Gaussian 2.8

Table of Supplied RF Waveforms – ‘On-the-fly’ Pulses

Pulse Shape Syntax Parameters

Sinc sinc(nlobes;window)

sinc(nlobes)

assumes no windowing

nlobes number of lobes in waveform (determines TB; float)

window ‘han’ Hanning window

‘ham’ Hamming window

Shinnar-La Roux slr(filter; type; TB; order; 1; 2)

slr(filter; type; TB; 1; 2)

assumes order = 128

slr(filter; type; TB; order)

assumes 1 = 2 = 1%

slr(filter; type; TB)

assumes order = 128; 1 = 2 = 1%

filter ‘lin’ linear phase

‘min’ minimum phase

‘max’ maximum phase

type ‘small’ small tip excitation

‘exc’ excitation (90°)

‘ref’ refocusing

RF Pulse Shapes


‘cref’ crushed refocusing

‘inv’ inversion

‘sat’ saturation

TB time-bandwidth product (float)

order filter order (int)

1 filter pass-band ripple (%; float)

2 filter stop-band ripple (%; float)

Hyperbolic secant hsec(sech(amp) bandwidth (kHz; float)

sech( fraction of peak amplitude at extrema (float)

amp peak amplitude (G; float)

Adiabatic half passage pulses

ahp( amp;; tan()) bandwidth (kHz; float)


dimensionless parameter (float)

tan() dimensionless parameter (float)

B1-Insensitive rotation pulses

bir4(TB; amp; ; tan()) TB time-bandwidth product (float)


dimensionless parameter (float)

tan() dimensionless parameter (float)

Tilted optimized nonsaturation excitation (sinc)

sinctone(nlobes; window; _final)

sinctone(nlobes; window)

assumes a 2:1 _final/_init ratio

sinctone(nlobes)

assumes a 2:1 _final/_init ratio and no windowing

nlobes number of lobes in waveform (determines TB; float)

window ‘han’ Hanning window

‘ham’ Hamming window

RF Pulse Shapes


_final flip angle at the slice edge (degrees; float)

The initial flip angle is taken from value in ParamEdit in the appropriate box.

Tilted optimized nonsaturating excitation (SLR)

slrtone(filter; TB; order; 1; 2; _final)

slrtone(filter; TB; order; 1; 2)

assumes a 2:1 _final/_init ratio

slrtone(filter; TB; _final)

assumes order = 128; 1 = 2 = 1%

slrtone(filter; TB)

assumes order = 128; 1 = 2 =

1% and a 2:1 _final/_init ratio

filter ‘lin’ linear phase

‘min’ minimum phase

‘max’ maximum phase

TB time-bandwidth product (float)

order filter order (int)

1 filter pass-band ripple (%; float)

2 filter stop-band ripple (%; float)

_final flip angle at the slice edge (degrees; float)

The initial flip angle is taken from value in ParamEdit in the appropriate box.

Band-selective uniform response pure-phase pulses

burp(type) type ‘e-burp-1’ excitation pulse

‘e-burp-2’ excitation pulse

‘i-burp-1’ inversion pulse

‘i-burp-2’ inversion pulse

‘u-burp’ general excitation pulse

‘re-burp’ refocusing pulse

Optimized sinc pulses

opt_sinc(type; TB) type ‘exc’ excitation pulse

‘ref’ refocusing pulse

TB time-bandwidth product (integer from 2 to 10 inclusive)

Composite pulses composite(flip1:phase1;…;flipn:phasen) flip flip angle produced by the ith

pulse element (°; float)

phase phase of of the ith

pulse element (°; float)

RF Pulse Shapes


Hermite pulses hermite(b) b polynomial coefficient (0 ≤ b ≤ 1; float)

Gradient Preemphasis



Performing gradient preemphasis on the Cirrus Open 0.2 T System console gradient management unit.



Using the Autopreemphasis Sequences

This procedure for gradient preemphasis and is taken from Schmithorst VJ and Dardzinski BJ, Magn Reson Med 47:208-12 (2002). It provides a method for automated correction of preemphasis and B0 compensation and is extremely effective. The Cirrus Open 0.2 T MR console does not have the ability to perform B0 compensation.

The Autopreemphasis sequence consists of a test gradient lobe followed by a gradient echo sequence using a non-selective RF excitation pulse (refer to the Pulse Sequence Library Manual, v.

1). The delay separating the test gradient lobe from the gradient echo sequence () is steadily increased to measure the eddy currents as a function of time. After taking the FT of each gradient

echo, the eddy current (EC, in T/m) is given by:

mr) is the slope of the phase (rads/m) across the projection, TE is the echo time and is the magnetogyric ratio.

To run the Autopreemphasis sequence, load the Autopreemphasis protocol and adjust the parameters to the desired values. Ensure that the test lobe gradient and the readout direction are the same when performing preemphasis.

A typical set of parameters for the Autopreemphasis protocol is as follows:

RF:

pulse length: 500 s

flip angle: 50°

Test gradient:

strength: 30 mT/m

duration: 1000 ms

ramp: 300 s

Readout:

number of points: 32

bandwidth: 20 kHz

Timing:

TR: 4 s

number of acquisitions: 48

minimum : 4 ms

maximum : 400 ms

The minimum should be as small as possible, while the maximum value should be long enough that the eddy currents have essentially decayed but not so long that most of the data collected has little or

no eddy current measurable. The delays are calculated by the sequence based on the minimum

and maximum values of and the number of acquisitions.

The true number of acquisitions is one more than that specified in the parameter file. This last acquisition is taken in the absence of a test gradient lobe and its phase subtracted from the phase of the previous acquisitions. This accounts for any phase introduced by the gradient echo sequence itself.

Eddy Current Measurement with Uncorrected Gradient

The primary gradient preemphasis is performed by starting the script C:\MR\Utilities\PreemphasisGUI\PreemphasisGUI.py bringing up a GUI window (see figure on next page). The dataset where the preemphasis amplitudes for the gradient currently being adjusted is located (A) and loaded. The time constants to be adjusted are selected or deselected using the checkboxes and calculated from the uncorrected autopreemphasis data (B). The time constants calculated using a multiexponential fit to the data will be displayed (C) and can be copied to the preemphasis file. This multiexponential fit is plotted in the display window (F).

TE

mtEC

r

2)(

)(



If the time constants and amplitudes make no sense (e.g., if there are two time constants with nearly identical values, or if the longest time constant is absurdly long), try manually adjusting the time constants and initial amplitude guesses. Systems with the console preemphasis unit can use up to six exponentials. It is recommended that preemphasis correction be performed twice: once with three exponentials to remove the large eddy currents, and a second with the remaining constants to remove residual eddy currents. For the second correction, expect both positive and negative amplitudes.

Eddy Current Correction Basis Set

The next step is to obtain the response of the eddy current to each time constant. This forms a basis set on which a preemphasis correction to the eddy currents can be calculated. Create a new scan folder for each basis function by cloning the scan containing the eddy current data in the absence of preemphasis. Starting with the shortest time constant, set the amplitude for that constant to 1% and obtain a new time series dataset. Once this is done, reset its amplitude to 0. This procedure is performed for all time constants in order of shortest to longest.

Enter the locations of the 1% amplitude basis datasets corresponding to each time constant being adjusted and once all data has been collected load the data sets (D). When loaded, the display window shows plots of each of the elements of the basis datasets.

A

B

C

D

E

F

G

GUI for primary gradient preemphasis.



When the ‘Amplitude Calculation’ button is pressed, the best-fit amplitude the time constants in order to correct for eddy currents are shown in the ‘Parameter Estimation’ section (C) and the fit compared to the uncorrected dataset (as well as the predicted residual eddy current) a plotted. Set the amplitudes for the preemphasis time constants using the ‘Copy Amplitudes’ button in (C).

Measuring the Eddy Currents After Correction

Once the best-fit amplitudes have been entered into the preemphasis, a final dataset can be obtained to ensure that the quality of the correction is satisfactory, and/or to obtain a new ‘uncorrected dataset’ to further improve correction by repeating the process. The best-fit amplitudes can be copied to the preemphasis file using the ‘Copy Amplitudes’ button. The location of the dataset is entered and loaded (E). The eddy current plots for the corrected and uncorrected datasets are displayed.

The current correction can be tweaked by pressing the ‘Tweak Correction’ button. This makes the corrected dataset the new uncorrected dataset and a further correction applied using the same time

constants and basis datasets. To monitor the tweaking process, a 2 statistic is displayed in the

statusbar. It is up to the user to determine whether 2 statistic is improving enough to continue the

tweaking process. When tweaking the preemphasis, be sure to use the ‘Add Amplitudes’ button when transferring the amplitudes rather than the ‘Copy Amplitudes’ button. The former adds the tweaked value to the file while the latter substitutes the value in the file.

Cross-term Eddy Current Correction

In a similar fashion to correcting primary eddy currents induced by gradients (that is, X eddy currents from X gradient impulse, etc.), cross-term eddy currents can be corrected. These are eddy currents induced in one of the other two orthogonal directions. This must be done after the primary eddy current correction, since the multiplier calculated in this procedure acts directly on the preemphasis function produced by the previous procedure . To begin, start the Python program C:\MR\Utilities\Crossterms\PreemphasisGUI.py and collect a dataset with the cross-term amplitudes set to 0% with full preemphasis. For cross-term correction, the read gradient direction is different from the test gradient direction (an error will be displayed if they are the same). The current preemphasis amplitudes and time constants for the test gradient are displayed, as is the cross-term eddy current generated by the test gradient in the display window (F). The location of this dataset is input in (A). The location of the preemphasis uncorrected dataset for the primary gradient for which the cross-term amplitude is being determined is input in (C) along with the 1% amplitude basis dataset locations for all non-zero amplitude time constants displayed in (B). From these data a cross-term amplitude is calculated and displayed (D) when the ‘Calculate multiplier’ button is left-clicked. This value can be copied directly to the preemphasis file with the ‘Copy to file’ button or added to the existing value with the ‘Add and copy to file’ button. As before, a final dataset is obtained as a check on the quality of the correction and its location entered (E). This dataset can then be used as the cross-term uncorrected dataset in order to tweak

the correction (using the 2 statistic displayed in the statusbar (G)), remembering to use the ‘Add and

copy to file’ rather than the ‘Copy to file’ button to transfer the calculated amplitude.



A

B

C

D

E

F

G

GUI for cross-term gradient preemphasis.

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Appendix I MR System User Manual -...

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