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syngo MR E11Operator Manual – Neuro

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syngo MR E11Operator Manual – Neuro

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4 Neuro | Operator ManualPrint No. MR-05014.630.10.06.24

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◾ Consequences of not avoiding a hazardous situation

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syngo MR E11 5Print No. MR-05014.630.10.06.24

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1 Introduction 131.1 Layout of the operator manual 131.2 The current operator manual 131.3 Intended use 141.4 Authorized operating personnel 15

1.4.1 Definitions of different persons 15

2 Preparation 172.1 Preparing and positioning the patient 18

2.1.1 Reducing motion artifacts 182.1.2 Preparing the contrast agent injection 182.1.3 Preparing a BOLD examination 18

Instructing the patient 18Positioning the patient 19

2.1.4 Preparing ECG-triggered examinations 19Positioning the electrodes and PERU 19Attaching ECG electrodes 20Procurement addresses 20

3 Measurement 233.1 Application hints 24

3.1.1 Head imaging with iPat 243.1.2 Spine imaging with iPat 243.1.3 Quiet MR sequences 25

Quiet SE and TSE 25Quiet GRE 26Quiet PETRA 26

Table of contents


3.2 Spine Dot Engine 263.2.1 Planning the examination and measuring

the localizer 30Adapting the examination to thepatient 30Starting the measurement of theAASpine_Scout 32

3.2.2 Measuring sagittal images 333.2.3 Verifying vertebra labeling 34

Editing vertebra labeling 35Adding / removing vertebra diskpositions 36Label transverse images 36Saving images 36Accepting vertebra position andlabeling 37

3.2.4 Measuring transverse images 373.3 Brain Dot Engine 39

3.3.1 Planning the examination and measuringthe localizer 39

Adapting the examination to thepatient 39Starting the measurement of theAAHead_Scout 41

3.3.2 Measuring transverse images 423.3.3 Measuring post-contrast images

(optional) 423.4 Performing diffusion and perfusion examinations 43

3.4.1 Measuring the diffusion 43Selecting the diffusion mode 44Setting specific parameters forRESOLVE 45Setting the diffusion parameters 46Result images 47

3.4.2 Measuring the perfusion 473.5 Diffusion Spectrum Imaging (DSI) Acquisition 48

3.5.1 Planning the q-space measurement 49

Table of contents


3.6 Measuring perfusion with Arterial Spin Labeling 503.6.1 A brief description of the ASL technique 51

Explanation of the key acquisitionparameters and limitations 51

3.6.2 Setting parameters 52The Quality check parameter (2D ASLonly) 54

3.6.3 Planning inversion slabs and determiningevaluations 55

Dimensioning the labeling slab 56Setting Inline evaluation 56

3.7 Performing a BOLD examination 573.7.1 Measuring the localizer, the 3D anatomy

and the field map 583.7.2 Establishing the GLM evaluation 583.7.3 Defining the threshold value and

paradigm 603.7.4 Determining motion correction and the

spatial filter 613.7.5 Performing the measurement 62

3.8 Measuring the flow in the internal carotid artery 633.8.1 Measuring the localizers 633.8.2 Determining the slice position 643.8.3 Determining the flow sensitivity 653.8.4 Performing the measurement 65

3.9 1H MR spectroscopy of the head 663.9.1 Planning the examination 67

MRS with scan@center 68CSI: transferring slice positioning 70Positioning the CSI slice 71CSI: suppressing interference signals 72

3.9.2 Starting protocol adjustments (optional) 733.9.3 Shimming interactively (optional) 743.9.4 Improving shim results (optional) 75

Example Channel X 753.9.5 Adjusting the frequency (optional) 763.9.6 Measuring raw data 78

Table of contents


4 Post-processing 814.1 Neuro perfusion evaluation 82

4.1.1 Preparing the data 82Loading images for evaluation 82Optimizing the image display 82

4.1.2 Evaluating the data 82Selecting a post-processing protocol 83Calculating the mean AIF (global AIF) 83Setting the time range (global AIF) 84Performing reconstructions 85

4.1.3 Editing and saving the post-processingprotocol 86

4.2 BOLD 3D Evaluation 874.2.1 Preparing the data 87

Loading the image series 87Optimizing the display 88Creating an MPR range 89Setting the 3D view 90

4.2.2 Evaluating the data 92Evaluating a VOI 92Displaying functional data as a film 93

4.2.3 Saving and filming the images 944.3 BOLD parameter map calculation 94

4.3.1 Preparing the data 95Loading the data 95

4.3.2 Evaluating the data 96Starting post-processing 96Monitoring post-processing 96

4.3.3 Editing and saving the post-processingprotocol 96

4.4 Evaluating ASL data 974.4.1 3D ASL-specific modules 974.4.2 Interpretation of results 984.4.3 Generating t-maps 99

4.5 Creating alpha images with BOLD 1004.5.1 Preparing and evaluating the data 101

Loading the data 101Scrolling through image stacks 101Optimizing the image display 102

4.5.2 Saving the images 103

Table of contents


4.6 DTI Evaluation 1044.6.1 Preparing the data 104

Loading the tensor series 1044.6.2 Evaluating the data 105

Visualizing the DTI maps 1054.6.3 Saving an image map 107

4.7 DTI Tractography 1084.7.1 Preparing the data 108

Loading the volume data 108Optimizing the display in Fusion mode 109Showing the overview of diffusiontracts 110Optimizing the diffusion display 110Setting the view for tractography 111Applying the Quicktrack function 113

4.7.2 Evaluating the data 113Creating seed points 113Starting tractography 114Managing seed points and tracts 115

4.7.3 Saving seed points or tracts 1154.8 Flow analysis with Argus 116

4.8.1 Preparing the data 116Loading the image data 116Optimizing the image display 117

4.8.2 Defining the evaluation regions 118Drawing the ROI for the ascendingaorta 119Drawing the ROI for the descendingaorta 119Analyzing low velocities (optional) 119Propagating the vessel contours toother cardiac phases 120Confirming the propagated vesselcontours 120

4.8.3 Evaluating the vessels 121Calculating results with standardsettings 122Limiting the time range 122Performing baseline correction 123Correcting phase aliasing 123

Table of contents


4.9 Spectroscopy Evaluation 1244.9.1 Preparing the data 125

Loading the data 125Adjusting the reference image 126

4.9.2 Evaluating the data 126Evaluating voxels of interest 126Adjusting the spectrum display 126Changing the CSI slice 127Displaying spectral maps 128Displaying metabolite images 129Calculating the sum spectrum 129Performing phase correction 130Adding a peak 131

4.9.3 Documenting the results 131Generating and saving a result table 131Saving and filming the results 133Saving new post-processing protocol 133

5 Appendix 1355.1 Diffusion cards 1365.2 Preset diffusion gradient directions 1385.3 Defining customized diffusion directions 140

5.3.1 Creating the DVS 140Required syntax 140Valid DVS, example 142

5.3.2 Importing the DVS 1435.3.3 Exporting the DVS 145

Index 147

Table of contents


Introduction

In order to operate the MR system accurately and safely, theoperating personnel must have the necessary expertise as well asknowledge of the complete operator manual. The operator manualmust be read carefully prior to using the MR system.

Layout of the operator manualYour complete operator manual is split up into several volumes toimprove readability. Each of these individual operator manuals coversa specific topic:

◾ Hardware components (system, coils, etc.)◾ Software (measurement, evaluation, etc.)Another element of the complete operator manual is the informationprovided for the system owner of the MR system.The extent of the respective operator manual depends on the systemconfiguration used and may vary.

All components of the complete operator manual may includesafety information that needs to be adhered to.

The operator manuals for hardware and software address theauthorized user. Basic knowledge in operating PCs and software is aprerequisite.

The current operator manualThis manual may include descriptions covering standard as well asoptional hardware and software. Contact your Siemens SalesOrganization with respect to the hardware and software available foryour system. The description of an option does not infer a legalrequirement to provide it.

1

1.1

1.2

Introduction 1


The graphics, figures, and medical images used in this operatormanual are examples only. The actual display and design of thesemay be slightly different on your system.Male and female patients are referred to as “the patient” for the sakeof simplicity.

Intended useYour MAGNETOM MR system is indicated for use as a magneticresonance diagnostic device (MRDD) that produces transverse,sagittal, coronal and oblique cross sectional images, spectroscopicimages and/or spectra, and that displays the internal structure and/orfunction of the head, body, or extremities. Other physical parametersderived from the images and/or spectra may also be produced.Depending on the region of interest, contrast agents1 may be used.These images and/or spectra and the physical parameters derivedfrom the images and/or spectra when interpreted by a trainedphysician yield information that may assist in diagnosis.1 The drugs mentioned herein shall be used consistent with theapproved labeling and/or indications for use of the drug. The treatingphysician bears the sole responsibility for the diagnosis and treatmentof patients, including drugs and doses prescribed in connection withsuch use.Your MAGNETOM MR system may also be used for imaging duringinterventional procedures when performed with MR compatibledevices such as in-room displays and MR Safe biopsy needles.

The MAGNETOM MR system is not a device with measuringfunction as defined in the Medical Device Directive (MDD).Quantitative measured values obtained are for informationalpurposes and cannot be used as the only basis for diagnosis.

For the USA only: Federal law restricts this device to sale,distribution and use by or on the order of a physician.

1.3

1 Introduction


Your MR system is a medical device for human use only!

Authorized operating personnelThe MAGNETOM MR system must be operated according to theintended use and only by qualified persons with the necessaryknowledge in accordance with country-specific regulations, e.g.physicians, trained radiological technicians or technologists,subsequent to the necessary user training.This user training must include basics in MR technology as well assafe handling of MR systems. The user must be familiar with potentialhazard and safety guidelines the same way the user is familiar withemergency and rescue scenarios. In addition, the user has to haveread and understood the contents of the operator manual.Please contact Siemens Service for more information on availabletraining options and suggested duration and frequency of suchtraining.

Definitions of different persons

Term used Explanation

User/Operator/Operating per-sonnel

Person who operates the system or software,takes care of the patient or reads imagesTypically physicians, trained radiological techni-cians, or technologists

System owner Person who is responsible for the MR environ-ment. This includes legal requirements, emer-gency plans, employee information and qualifica-tions, as well as maintenance/repair.

1.4

1.4.1

Introduction 1


Term used Explanation

MR worker Person who works within the controlled accessarea or MR environmentUser/Operator as well as further personnel (forexample, cleaning staff, facility manager, servicepersonnel)

Siemens Serv-ice/service per-sonnel

Group of specially trained persons who areauthorized by Siemens to perform certain mainte-nance activitiesReferences to “Siemens Service” include servicepersonnel authorized by Siemens.

1 Introduction


Preparation

2.1 Preparing and positioning the patient 18

2

Preparation 2


Preparing and positioning the patient

Reducing motion artifacts1 Instruct the patient to hold completely still during the entire

examination.

2 Instruct the patient to take shallow and gentle breaths during themeasurements.

Preparing the contrast agent injectionPrior to moving the patient table into the magnet, you route the tubefor the infusion.1 Insert an intravenous port into the forearm vein of the patient.

2 Connect the port to the extension tube.

The tube should be long enough so that it can be accessed fromthe outside when the patient is in the magnet bore.

3 Connect the tube to the contrast agent injector.

Preparing a BOLD examinationA targeted search for active brain areas requires precisely definedstimulations. These are obtained through stimulation during themeasurement. In what follows we explain BOLD imaging using fingertapping as our example.

Optimal cooperation by the patient plays a decisive role in thesuccess of the BOLD examination.

Instructing the patientDuring the BOLD measurement, the patient first moves the fingers ofhis right hand for 10 measurements during finger tapping. Thepatient then switches over to his left hand and moves his fingersagain for 10 measurements.

2.1

2.1.1

2.1.2

2.1.3

2 Preparation


◆ Explain in detail the tasks to be performed and practice them withthe patient.

Positioning the patient1 Ensure that the patient is comfortable to avoid motion and

consequent artifacts.

2 If required, use positioning aids.

Preparing ECG-triggered examinationsPositioning the electrodes and PERUElectrodes: Positioning of the electrodes varies according to theposition of the heart. An example is provided in the figure below.

Use only disposable ECG electrodes as released by Siemens.( Page 20 Procurement addresses)

PERU: The ECG sensor in the PERU ensures transfer of the ECG signal.Typically, the PERU is aligned in the direction of the foot end of thepatient table even though the patient may be positioned feet first inthe direction of the magnet bore.◆ Position the PERU in the appropriate support or add absorbent

material between the ECG cables, PERU and skin. The distancebetween PERU and patient should be at least 2 cm.

Positioning the ECG electrodes (left) and the PERU (right).

2.1.4

Preparation 2


The transmitter unit of the PERU includes three LEDs for signalingthe battery status and one LED as fault indicator (e.g. insufficientskin contact of the ECG electrodes).Battery status and electrode fault are also indicated on the Dotdisplay above the magnet bore and the Physiological Displaydialog window.

If the red LED Electrode fault on the PERU flashes, the ECGelectrodes are not attached correctly. Check to ensure that theelectrodes are not falling off.

Attaching ECG electrodesThe electrodes must be positioned and attached with care to ensure asufficient and consistent ECG signal.1 Discuss the breathholds and respective commands with the

patient.

2 Ensure satisfactory contact between the electrodes and thepatient's skin.

3 Thoroughly clean the patient's skin with a dry cloth or NUPREP ECG& EEG Abrasive Skin Prepping Gel . ( Procurementaddresses)

4 If the patient is hirsute, shave the location where you want toattach the electrodes.

5 Dry the skin carefully.

6 Check the signal at the Dot display above the magnet bore.

7 If the signal received is not satisfactory and consistent, vary thelocation of the electrodes. Use new electrodes every single time.

8 If one of the leads does not provide a sufficient signal, change to asingle ECG lead in the Physiological Display dialog window.

Procurement addressesDisposable ECG electrodes may be ordered from:

2 Preparation


Siemens Commercial goods (Catalog Med & More), CONMED 2700Cleartrace

◾ Item no. 07437598 (600 pieces)or from:CONMED CORPORATION, 310 Broad Street, Utica, New York 13501,USACleaning gel: NUPREP ECG & EEG Abrasive Skin Prepping GelWeaver and Company, 565 Nucla Way, Unit B, Aurora, Colorado80011, USA

Preparation 2


2 Preparation


Measurement

3.1 Application hints 243.2 Spine Dot Engine 263.3 Brain Dot Engine 393.4 Performing diffusion and perfusion examinations 433.5 Diffusion Spectrum Imaging (DSI) Acquisition 483.6 Measuring perfusion with Arterial Spin Labeling 503.7 Performing a BOLD examination 573.8 Measuring the flow in the internal carotid artery 633.9 1H MR spectroscopy of the head 66

3

Measurement 3


Application hints

Head imaging with iPatThe Head/Neck 20 is iPAT-compatible in all directions.Advantages:

◾ Shorter measurement times for standard protocols (e.g., T1 or T2weighting).

◾ Noticeable reduction in susceptibility artifacts for EPI sequences(e.g., diffusion protocols).

Shorter measurement time and improved EPI image quality with iPAT.

(1) Dark Fluid TSE with iPAT factor 2 (1 min, 49 s)(2) Diffusion EPI with iPAT factor 2 (b = 1000)

Spine imaging with iPatPhase-encoding direction/iPAT factor: When you use the Spine 32with phase-encoding direction H>>F or L>>R a maximum iPAT factorof 4 is possible.

Phase-encoding direction H>>F: The FoV (including phaseoversampling) must be covered by a sufficient number of coilelements. For example, for an iPAT factor of 3, the selected FoVmust cover at least 3 coil elements.

3.1

3.1.1

3.1.2

3 Measurement


Phase-encoding direction A>>P is not sensible because the coil acts like asingle coil in this case.

Quiet MR sequencesQuiet MR sequences offer increased patient comfort examinations byenabling noise-reduced studies.Siemens original noise-reduced protocols are provided in the Quietprogram folders of the exam database, for example,Head>Library>Quiet.

CAUTION

Performing a noise reduced measurement without adequatehearing protection!Danger of temporary damaging the sense of hearing◆ Always wear adequate hearing protection, even with noise

reduced measurements.

Quiet SE and TSEBoth SE and FSE quiet TSE sequences are standard siemens sequencesbut provided with an additional Acoustic noise reduction parameter.Protocols based on Quiet SE/TSE sequences provide T1 weighted, T2weighted, and Dark-Fluid contrast, and a consistent contrastbehaviour like the regular protocols.

3.1.3

Measurement 3


Use: Protocols with a Quiet SE/TSE sequence are measured as normalprotocols. You can toggle between quiet and regular imaging byenabling/disabling Acoustic noise reduction in the correspondingselection list of the Sequence/Part 2 parameter card.

In case of the Quiet TSE sequence, raising the value of EchoSpacing in the Sequence/Part 1 parameter card increases theeffect of noise reduction.

Quiet GREThe Quiet GRE sequence is a standard siemens sequence but providedwith an additional Acoustic noise reduction parameter. Protocolsbased on the Quiet GRE sequence provide T1 weighted and SWIcontrast, and a consistent contrast behaviour like the regularprotocols.Use: Protocols with a Quiet GRE sequence are measured as usualprotocols. You can toggle between quiet and regular imaging byenabling/disabling Acoustic noise reduction in the correspondingselection list of the Sequence/Part 2 parameter card.Quiet PETRAQuiet PETRA is a 3D only method and acquires 3D isotropic data.Protocols based on the Quiet PETRA sequence provide T1 weightedcontrast similar to the MPRAGE protocol.

Spine Dot EngineThe Spine Dot Engine provides comprehensive c-, t-, and l-spineexamination workflows to help simplify the complexity of theseexaminations with respect to planning, scanning, and reviewingmeasurements.

3.2

3 Measurement


If desired the Dot Engine workflow can be customized. In order toenable all the functionality of the Dot Engine workflow thefollowing requirements are needed:

◾ First measurement must be an AASpine_Scout protocol◾ The AASpine_Scout AddIn should be linked to this protocol◾ Requirements for using individual protocols within the Spine

Dot workflow are metFor a detailed description, please refer to: Operator Manual - DotCockpit.

The Dot Engine user interfaces shown in this operator manual areexamples only. The actual guidance texts and the design may beslightly different on your system.

Functions: The following are key features of the Spine Dot Engine:

◾ Detection of the spine geometry including vertebras and vertebradisks

◾ Labeling of the vertebras◾ Positioning of double-oblique slices, slabs, sat regions, and

adjustment volumes (Spine Positioning Assistant)◾ Determination of the necessary number of slices and protocol

parameters to cover the spine region of interest (AutoCoverage).CPR images: CPR (Curved Planar Resampled) images show the spineanatomy as pure sagittal or coronal projections onto a virtual centerplane, providing an X-ray/MIP-like overview of the spine geometry.Thin/normal CPR images are labeled "CPR" and thick CPR images arelabeled "CPR*" in the image text.

CPR and CPR* images must not be used for diagnostic purposes.Series containing CPR* images cannot be used as referenceimages for position display.

Measurement 3


Example of coronal (left) and sagittal (right) CPR images with vertebranumbering

In addition to standard MPR images, CPR images serve as a basis forvalidation of the vertebrae labeling suggested by the system and maybe used primarily for positioning of mainly sagittal or coronal slices.A warning symbol is displayed in CPR images with axial intersectionlines indicating possible deviations between the displayed lines andthe true intersected anatomy due to spinal curvature.Spine Planning Layout: A special GSP layout with three planningsegments is provided to simplify the image management in spineexaminations.

(1) Transverse MPR images(2) Coronal CPR image, if available (else: coronal original images)(3) Sagittal CPR image, if available (else: sagittal MPR images)(4) Stamp segments

3 Measurement


Using individual protocols: The following requirements have to bemet when using individual protocols within the Spine Dot workflow:

◾ The AutoAlign parameter Spine > Cervical, Spine > Thoracic, orSpine > Lumbar must be selected

◾ The Spine Positioning AddIn must be linked to the protocolSpecific advice: For scanning l-spine with a three-stage AA localiserfeet to head, positioning the laser light marker at the l-spine isrecommended. The three-stage AASpine_Scout is then measuredfrom bottom to top starting at the l-spine. As an advantage, thelocalizer images of the l-spine are displayed first which allows tocheck the l-spine slice positioning while the remaining localizerimages are being acquired.To reduce the noise level of the AASpine_Scout, TR can be slightlyincreased. This may involve a few additional seconds of measurementtime.For patients with strong kyphosis the AASpine_Scout should bemeasured with a slight increase of the Slices per slab in theAutoAlign_Spine scout to avoid missing parts of the spine. Please beaware that additional slices may involve a few additional seconds ofmeasurement time.

Measurement 3


For children, a two-stage scout may be sufficient to cover the wholespine during routine positioning. To ensure sufficient overlapping ofthe measured regions, table movement between the scout stagesshould not exceed 210 mm.

MR scanning has not been established as safe for imaging fetusesand infants under two years of age. The responsible physicianmust evaluate the benefit of the MRI examination in comparisonto other imaging procedures.

Planning the examination and measuring thelocalizerIn the following example, the prerequisites and the workflow of an l-spine examination are described.

✓ Spine and additional neck and / or head coils have been placed

✓ L-Spine Dot Engine has been selected

✓ Patient has been registered

✓ Light marker has been positioned approximately at the superiorportion of the acetabulum

Adapting the examination to the patientAfter registration, the Patient View opens automatically. The defaultexamination parameters are loaded.

3.2.1

3 Measurement


◆ From the list: Select a suitable Exam Strategy for the patient.

Standard Standard examination for clinical routineissues like back pain, osteoporosis, etc.

Lesion Standard examination for c-spine and t-spine, with contrast agent and speciallesion contrast by tirm (mainly for MS, butalso for unspecific inflammation pro-cesses)

Post Surgery Routine post surgery examination withcontrast agent (mandatory)

High Bandwidth Provides protocols using the WARPsequence technique with reduced sensitiv-ity to susceptibility artifacts if the patienthas MR Conditional implants.

Please adhere to all safety instructions regarding implants. (Referto Operator Manual – MR System.)

The pending protocols of the measurement queue are updatedupon your selection.

Selecting the examinationstrategy

Measurement 3


In the following example, the strategy Standard is selected.

To change the examination strategy after beginning a study, youcan access the Patient View at any time with this icon:

For more information, please refer to the Scanning section ofthe Operator Manual – Scanning and postprocessing.

Starting the measurement of the AASpine_Scout

The AASpine_Scout is a 3D localizer used to determine anatomicalstructures within the respective spine region, providing high contrastbetween vertebras and vertebra disks.

3 Measurement


◆ To start the Spine Dot Engine workflow, confirm the settings onthe Patient View.

Results:

◾ The AASpine_Scout is measured.◾ The system calculates the following images and loads them in

the Spine Planning Layout:– Sagittal and transverse (MPR) plane– One sagittal and one coronal CPR image– Composed images in coronal and sagittal orientation

(threestage AASpine_Scout, only)

Measuring sagittal images✓ AASpine_Scout has been measured

The sagittal protocol becomes auto-aligned according to theAutoAlign parameter setting of the preselected spine region:

◾ Spine > Cervical focuses the region C2 to T2◾ Spine > Thoracic focuses the region T1 to T12◾ Spine > Lumbar focuses the region L1 to S1

◆ To change the suggested slice positioning, open and modify theprotocol before measurement.

3.2.2

Measurement 3


AutoCoverage can be used here to let the system auto-adapt theprotocol to the detected width of the spine part within apredefined range of parameters (e.g. slices per slab, distancefactor).

A working-man symbol should be applied in the protocol setup ifopening and confirming the sagittal protocol prior tomeasurement is desired in general.

Verifying vertebra labelingIn this step the detected position and labeling of the vertebras andintervertebral disks are checked and confirmed. The position of thevertebral disks is used for the prescription of the slices and anteriorsaturation region. Within this step, the user also decides that allfollowing transverse images are labeled with their correspondinglocation in the spine (For example: the image comment is set to “L5/S1”).

3.2.3

3 Measurement


✓ AASpine_Scout has been measured

✓ The AutoAlign verification step has been opened

1 Carefully check for correct positioning and labeling of the vertebrasin the reference images.

2 To check positioning, scroll through the image stacks with theSeries +/– and the Image +/– keys.

Editing vertebra labeling1 Select the desired spine region (i.e. C, T, or L spine) from the

Vertebra selector graphic of the Guidance card.

2 Next select the individual vertebra label from the "zoomed"Vetebra selector graphic of the Guidance card that needs to beedited.

On the Guidance card this icon is activated.

3 Click the wrong vertebra label in the reference image.

Automatic relabeling is performed on every correction.

Measurement 3


Missing label positions can be created by adding missing vertebradisk positions above/below the vertebra body first.

Adding / removing vertebra disk positions1 To add a disk position, click this icon first, then click the desired

position in the reference image.

2 To remove a disk position, click the disk in the reference imagefirst, then click this icon or use the Del key.

The corresponding vertebra disk position is added or removed.Automatic relabeling is performed on every correction.

Label transverse imagesYou can specify whether the corresponding vertebra labels will beadded to the image comment of the following transverse images.1 Select the Label transverse images check box.

2 Accept the current vertebra position and labeling with Confirm.

If you revoke the vertebra labeling and position with Decline, thetransverse images of the subsequent measurements will not belabeled.Selecting either Confirm or Decline is necessary to unlock theApply button to continue scanning.

Saving imagesYou can save the current slice positioning and vertebra labelingoverview images. These images are appended to the patient datawithin an additional “AutoAlign verification” series.◆ Save the images with this icon.

3 Measurement


The image of the active GSP segment will be saved to the localdatabase. To save the sagittal and coronal images, select thecorresponding segment and save each independently.If the images are not saved, you may view the spine geometrylater on by duplicating the concluded AutoAlign verification stepwith Append.

Accepting vertebra position and labeling◆ Conclude the verification step with this icon.

The confirmed intervertrebral disc positions and vertebra labelingare applied. Further modifications are disabled.

If the check box Label transverse images is selected the vertebralabeling is applied as image comment to the subsequent transversemeasurements.

Examples of image comments for subsequent axial images:

◾ L4: Transverse slice intersects inner third of vertebra L4◾ L4/L5: Transverse slice intersects vertebra disk L4/L5 or one of

the neighbouring outer thirds of vertebras L4 and L5◾ L3-L5: Transverse slice runs through both outer thirds of

vertebra L4 (e.g. slice intersects vertebra disks L3/L4 and L4/L5)

Measuring transverse images

The use of sagittal high resolution images is recommended forfinal positioning of axial slices.

3.2.4

Measurement 3


1 In the reference images, check the positioning of the slices or slabsand correct them, if necessary.

Spine Positioning Assistant and AutoCoverage cannot be usedin combination with Set-n-Go protocols in this software version.

The slice / slab groups “snap” into the disk cartridges upon draggingif the number of slices within a slice group is less than 9. Thick slicegroups (with 9 or more slices) can be smoothly moved up anddown along the detected spine geometry.

If the protocol contains a regular sat, it will be placed anterior tothe spine.

If a protocol initially has more than one regular sat, only the firstsat will be auto-positioned and used as an anterior sat. The othersats remain unchanged.

3 Measurement


To suppress “snapping”, keep the following keys pressed whiledragging:

◾ Shift key for free translation of slice / slab groups◾ Ctrl key for free rotation of slice / slab groupsSlight corrections within proximity of the disk position arepossible without pressing the Shift or Ctrl key.

2 Start the measurement.

Brain Dot EngineThe Brain Dot Engine provides a simplified workflow to perform astandard head examination.

You may also configure the Dot Engine workflow. For a detaileddescription, please refer to: Operator Manual – System and datamanagement.

The Dot Engine user interfaces shown in this operator manual areexamples only. The actual guidance texts and the design may beslightly different on your system.

Planning the examination and measuring thelocalizer✓ Head coil has been selected


✓ Brain Dot Engine has been selected

Adapting the examination to the patientAfter registration, the Patient View opens automatically. The defaultexamination parameters are loaded.

3.3

3.3.1

Measurement 3


In the Patient View you select a suitable examination strategy anddecide if contrast agent is to be administered. The pending protocolsof the measurement queue are updated upon your selection.

◆ From the list: Select a suitable Exam Strategy for the patient.

Standard Standard examination with 2D protocols.

Resolution focus Examination with 3D protocols for detailedviews.

Speed focus Examination with fast protocols.

Motion-insensitive Examination with BLADE protocols formotion correction.

In the following example, the strategy Standard is selected.

To change the examination strategy after beginning a study, youcan access the Patient View at any time with this icon:

For more information, please refer to the Scanning section ofthe Operator Manual – Scanning and postprocessing.

Selecting the examinationstrategy

3 Measurement


◆ Select without Contrast agent if no contrast agent is to be used.

All contrast agent protocols will be removed from themeasurement queue.

Starting the measurement of the AAHead_ScoutThe AAHead_Scout is used to determine anatomical structures withinthe head.◆ To start the Brain Dot Engine workflow, confirm the settings on

the Patient View.

Results:

◾ The AAHead_Scout is automatically measured.◾ The system automatically generates MPRs and loads them to the

GSP.◾ The slices for the following sagittal protocol are positioned by

AutoAlign Head. The necessary number of slices and protocolparameters for covering the head part of interest are determined(AutoCoverage) and taken into account. (For a detaileddescription of the AutoAlign feature, please refer to: OperatorManual – System and data management.)

◾ Subsequently, the sagittal protocol is automatically measuredand loaded to the GSP (protocol without working man symbol).

◾ The next protocol opens (protocol with working man symbol).

Using contrast agent

Measurement 3


Measuring transverse images✓ Sagittal images have been measured

1 Check the positioning of the slices or slabs and reposition them ifnecessary.

You can also modify several sequence parameters of the currentprotocol using the Parameter View. Here, you find the mostimportant sequence parameters, e.g., the number of slices or theFoV.To display the complete sequence parameters of the Routineparameter card, click the icon.


Measuring post-contrast images (optional)✓ Pre-contrast images have been measured

✓ Contrast medium has been selected in the Patient View

1 Start the injection of the contrast agent.

3.3.2

3.3.3

3 Measurement


2 In the Exam paused dialog window: Start the post-contrastmeasurement after a suitable time with Continue.

Performing diffusion and perfusionexaminationsIf you want to obtain both structural and functional informationregarding the pathophysiology of a brain disease, perform an MRexamination by combining anatomical MR imaging with MRangiography as well as diffusion and perfusion imaging.Typically, prior to the diffusion measurement the followingmeasurements have been performed:

◾ Control measurement for bleeding◾ Angiography measurement (e.g., Time-of-flight protocol)◾ T2 diagnosis

Measuring the diffusionTo evaluate diffusion in the brain, you measure transverse slices ofthe entire head. You set the diffusion-specific parameter on the Diffparameter card.

3.4

3.4.1

Measurement 3


Single-shot or multi-shot (RESOLVE) imaging: With the RESOLVEmethod, a multi-shot diffusion-weighted imaging sequence is usedwhich provides an improved image quality compared to standardsingle-shot echo-planar imaging (ss-EPI). RESOLVE supports all thestandard acquisition and data processing features for diffusionimaging (DWI) and diffusion tensor imaging (DTI) that appear on theDiff parameter card with the ss-EPI (ep2d_diff) sequence.Selecting the diffusion modeThe diffusion mode describes the measurement procedure and thediffusion-sensitive orientation.In the following, we are focusing on diffusion modes 3-Scan Traceand MDDW.3-Scan Trace diffusion mode: The measurements are performed inthree random directions. 3 scans are required per image. Since thediffusion directions are not linked to anatomy, no diffusion-weightedimages are stored.Original images cannot be saved. Trace-weighted images and ADCmaps can be stored by activating the corresponding checkboxes.Diffusion mode MDDW: Measurements are performed in at least 6directions, a maximum of 256 directions is possible. For b-value = 0, adiffusion-weighted image is generated for each slice position. Whenthe b-value is > 0, an image is generated for the b-value and eachdiffusion orientation. These images can be saved as original images inthe mosaic format. Trace-weighted images and ADC maps arestored by default. In addition, FA maps and the Tensor can be saved.

When data are acquired for DTI using the MDDW diffusion mode,RESOLVE generates diffusion tensor files that can be post-processed with the Neuro 3D task card.

✓ epi_diffusion protocol is open

✓ Slice position has been transferred

◆ On the Diff parameter card: Select the requested diffusion mode(3-Scan Trace or MDDW).

Setting diffusion modeparameter

3 Measurement


Example: 3-Scan Trace mode selected.

Setting specific parameters for RESOLVEThe following additional parameters are specific for resolvesequences:

Parametercard

Parameter Effect

Resolution –Common

Readout seg-ments

Increasing the number of “Read-out segments”

◾ reduces the minimum echo-spacing (and the associatedartefacts) for a given spatialresolution

◾ increases the available spatialresolution for a fixed echo-spacing

Resolution –Common

Readout par-tial Fourier

Reduces the number of shots thatare required to generate animage

Sequence –Part 2

Reacquisitionmode

A reacquisition process is used torepeat scans that result in unusa-ble data. “On” is recommendedfor all brain studies.

Measurement 3


◆ Set the required parameters in the respective parameter cards.

Setting the diffusion parameters

✓ Requested diffusion mode (3-Scan Trace or MDDW) has beenselected.

◆ On the Diff parameter card: Establish the b-value (e.g., 0, 500,1000) for each diffusion weighting.

You can measure a maximum of 16 different b-values. Themaximum value that can be set is 10,000. Higher b-values extendTE.

◆ Select Trace weighted images and ADC maps.

The number of Diffusion directions = 3 is set automatically.

Trace-weighted images and ADC maps are calculated using theInline technique.

1 Determine the number of Diffusion directions.

2 Select FA maps (Fractional Anisotropy) and the Tensor.

The Tensor parameter determines whether the diffusion tensordata are stored in the database. It is therefore possible to evaluatediffusion in the Neuro 3D task card.

Trace-weighted images and ADC maps can be stored byactivating the corresponding checkboxes.

1 Use Noise level to establish the intensity at which pixels areincluded for the calculation of the ADC value.


It is also possible to retroactively (offline) compute tensor data fromdiffusion images.1 In the Patient Browser: Select a series with diffusion images

(MDDW).

2 Start the computation of the tensor data.

In the 3-Scan Trace mode

In the MDDW mode

Noise level

Computing tensor data offline

3 Measurement


Result images3-Scan Trace mode:◾ Trace-weighted images: Per slice position and b-value > 0◾ ADC maps: Per slice position

3-Scan Trace: ADC maps can be calculated subsequently(Evaluation > Dynamic Analysis > ADC).

MDDW mode:◾ Original images in the mosaic format◾ Trace-weighted images (computed inline)◾ ADC maps (computed inline)◾ FA maps (computed inline)◾ Tensor

Measuring the perfusionAs a supplement to the diffusion imaging, you may want todetermine the perfusion parameters in the region under examination.You perform a perfusion measurement with contrast agentadministration and 50 measurement repetitions. Use the Inlinetechnology to compute the GBP, PBP, relCBF, relCBV, relCBVCorr, andTTP maps.

✓ Diffusion measurement has been completed

✓ Perfusion protocol is open

✓ Contrast injector is ready

1 Transfer the slice position from the T2 TSE protocol.

2 Open the Perf parameter card.

3.4.2

Measurement 3


3 Set the number of measurement repetitions (in this case: 50measurements).

4 Select GBP, PBP, relCBF, relCBV, relCBVCorr, and TTP.


6 While the measurement is running, administer the contrast agentintravenously as a bolus.

Original images are generated per slice position (one image permeasurement) and a GBP, a PBP, and a TTP map are computed.

For more precise perfusion evaluations: calculate relCBV, relCBF,and relMTT maps (in the Perf MR task card) additionally.

Diffusion Spectrum Imaging (DSI) AcquisitionAdvanced diffusion techniques, such as Diffusion Spectrum Imaging(DSI), make it possible to resolve fine anatomical details of the brain,such as crossing white-matter fibers by using multiple diffusiondirections and b-values in a single measurement.

DSI is only available for MAGNETOM Prisma, Primafit and Skyrafit.

3.5

3 Measurement


A dedicated diffusion mode (q-space) enables the acquisition ofcorresponding data. This mode employs a Cartesian sampling pattern,permitting isotropic sampling of a spherical region in q-space withuser defined step size.Concerning image processing: The DICOM images using the DSIacquired method can be used for further post-processing offline.Processing can also be performed using the same functionalityprovided with the MDDW diffusion mode. This utilizes the diffusiontensor imaging model, supporting up to 256 directions.

Planning the q-space measurement1 Open the Diff Neuro parameter card.

2 Select the q-Space diffusion mode.

3 Set the q-space specific measurement parameters.

q-Space weightings Number of q-space coordinates sampledalong each positive coordinate axis (includ-ing the origin).

q-Space max. b-value

b-value that corresponds to the diffusionweighting of the outermost q-space coordi-nates.

3.5.1

Measurement 3


q-Space coverage Full Complete q-spacecoverage (samplingof a spherical q-space region).

Half Partial q-space cov-erage (only one halfof the sphere is sam-pled, thus reducingthe acquisitiontime).

Measuring perfusion with Arterial SpinLabelingPerfusion measurements with Arterial Spin Labeling (ASL) require nocontrast agent. In addition, if contrast agent has been administered,ASL imaging is not possible during the session. The sequenceacquires an M0 scan (2D ASL only) followed by pairs of label/controlimages. The Inline Display shows the progress of the ASLmeasurement. No post-processing step is necessary and you are ableto evaluate the image results as usual or you can use the extendedfunctions of BOLD and Neuro3D. ( Page 97 Evaluating ASL data)ASL is possible with both a 2D (ep2d) and a 3D (tgse) sequence.

Please note that syngo ASL 3D provides qualitative results.

3.6

3 Measurement


A brief description of the ASL techniqueASL is a magnetization preparation technique that sensitizes the MRcontrast to the inflowing blood signal. Using the blood water contentas an endogenous tracer coupled with a long delay time, a labeledbolus of blood passes through the vascular tree into the capillary bedand eventually the parenchyma. When a label image and a suitablecontrol image are subtracted, as in digital subtraction angiography,the resulting difference signal directly reflects tissue perfusion.Thespin labeling magnetization preparation for syngo ASL uses aselective adiabatic inversion pulse to label inflowing spins with highefficiency.Explanation of the key acquisition parameters and limitationsThe bolus of blood delivered to the tissue of interest is controlled viaperiodic saturation pulses. The periodic saturation pulses terminatethe bolus at a predefined time interval resulting in an accuratedefinition of the bolus. The resulting effect on the images is theremoval of late arriving blood and the reduction of intravascularsignal in the perfusion-weighted image. Coupling bolus terminationwith long inflow times allows the labeled bolus to reach the tissuephase of the vascular tree and improves the perfusion weighting. Thelength of the bolus is determined by the Bolus Duration parameter,and the inflow time is directly specified by the Inversion Timeparameter.

Shorter bolus duration times, i.e. lower than 500–700 ms,typically result in reduced signal and hence poorer signal-to-noiseratio.

Inflow time is the time between the labeling/inversion pulse andthe readout/imaging module.

PICORE, proximal inversion with a control for off-resonanceeffects (2D ASL), is the labelling strategy which labels bloodbelow the imaging slab.

3.6.1

Measurement 3


FAIR, flow-sensitive alternating inversion recovery (3D ASL), isthe imaging strategy which labels blood within the imaging slab.

Setting parameters✓ Localizer has been measured

◆ Set the labeling/timing parameters in the Contrast ASL parametercard for the 2D sequence.

3.6.2

3 Measurement


– or –

Alternatively, set the labeling/timing parameters in the ContrastASL parameter card for the 3D sequence.

Perfusion mode Picore Q2T labels below the imaging slab(fixed 2D) while FAIR QII labels on theimaging slab (fixed 3D).

Suppression Mode Enables background suppression of multi-ple tissues. (3D only, fixed)

Bolus Duration Determines the duration of the bolus oflabeled blood. Typical value is 700 ms.

Quality check Enables outlier analysis to detect andreject images with excessive motionbefore calculating parameter maps (2Donly).

Inversion Time Array of independent inversion times giv-ing the overall time between inversionpulse and excitation of the first slice. TheASL signal increases with shorter inversiontimes. However transit artifacts are createdin the arterial voxels as well.

Measurement 3


Inversion time should be long enough to transport the bolus intothe image slices, that is, it should be equal or larger than thearterial transit time. Typical values: 1800–2000 ms.When adjusting the inversion time, consider the patient's age,the pathology, and the expected blood flow rates. Particularly forneonates, children, and elderly persons, the adequate valuesmight differ substantially.

Averaging mode Measurements can be weighted to acquiremore images at later inversion times tooptimize contrast-to-noise. (3D only, fixedto CONSTANT)

Inversion Array Size Determines the number of inversion timesto measure. (2D limited to 1)Collecting data at multiple inversion timesallows quantification of bolus arrival times.

Flow Limit Strength of the bipolar gradient betweenexcitation and readout. The parameter isused to attenuate the signal from largearteries. TE is increased. At the maximumvalue 100 cm/s (standard setting), the gra-dient is switched off. (2D only)

With shorter inversion times (1200–1500 ms), lower flow limitsof 1–10 cm/s are required.

The Quality check parameter (2D ASL only)To further ensure the quality of a series of paired label/controlimages, an outlier detection procedure is used to discard image pairsin which motion is detected. The outlier detection algorithmexamines the difference map of pairs of label and control images asthey are acquired (inline processing). When a control/label pair isidentified as an outlier it is discarded and does not participate in theconstruction of final ASL maps, e.g. perfusion-weighted maps.

3 Measurement


The Quality check parameter has 3 modes:

Off No outlier rejection takes place

On Outlier rejection automatically takes placeand final/corrected results are displayed(default)

On – extended In addition to the results displayed in theOn case, additional information is also dis-played, such as the difference image ofthe perfusion-weighted images in On andOff cases

Planning inversion slabs and determining evaluationsASL measurements should be performed with a minimized TE andacquired in transverse planes. The sequences assume that blood istraveling perpendicular to the imaging slab.

✓ Parameters for labeling/timing have been set

3.6.3

Measurement 3


Dimensioning the labeling slabPicore Q2T labels below the imaging slab. The gap between theinversion slab and the imaging plane should be minimized. and iscontrolled by the Gap parameter.◆ Set the Gap in the Geometry Saturation parameter card.

FAIR QII requires no special planning.

Setting Inline evaluationEvaluation and motion correction are set in the Perf parameter card.

1 Activate the Motion correction checkbox to enable motioncompensation.

2 Activate the Spatial filter checkbox to apply spatial filtering to thedata.

3 Specify the Filter Width in mm to precisely control the level offiltering. Typical range for ASL is 4 mm to 8 mm.

3 Measurement


Performing a BOLD examinationIn the following example we show functional localization duringmotor stimulation by finger tapping. The course as well as theselection of parameters have been established for evaluating themeasurement data with the Neuro 3D task card.

For other stimulations, specific stimulation devices are availablefrom third-party companies. With the BOLD Add-In,synchronization of certain stimulation devices and dataacquisition can be facilitated.

BOLD imaging requires excellent planning and evaluations.Sufficient experience is required to obtain precise localizationand reliable results.

Paradigm files: BOLD AddIn allows the usage of (external) paradigmfiles. If a paradigm is selected, the calculation of the t-maps iscontrolled by the settings in the paradigm file. The correspondingparameters on the BOLD parameter card are hidden.

Example of the BOLD parameter card when a paradigm is selected via BOLDAddIn.

The BOLD AddIn also supports realtime exporting of image datato an external PC, if configured.

3.7

Measurement 3


Measuring the localizer, the 3D anatomy and the fieldmap✓ Patient has been instructed

✓ Paradigm "Manual" has been selected in case BOLD AddIn is used

1 Measure the survey images with the localizer.

2 Use the localizer to define anatomical images for subsequentoverlays.

3 Measure the images as 3D anatomy (3D slab), e.g., with anMPRAGE sequence or with a noise-reduced PETRA sequence.

4 Open the field map protocol.

5 To generate the field map, use the localizers to position 36transverse slices (slice thickness = 3 mm) to cover the area ofinterest.

If the number of slices corresponds to a square number (6 × 6, 7× 7, 8 × 8, …), the total surface area of the mosaic images isoptimally used.

T-maps may be spatially distorted. As a result, superposed imagesmay lead to spatial shifts. Check at all times by superposinganatomical EPI images or a field map.

Establishing the GLM evaluation1 Open the BOLD protocol (ep2D protocol).

2 Copy the slice positioning from the field map to the BOLD protocol(Center of slice/Slab groups & sat regions).

3 Open the BOLD parameter card.

3.7.1

3.7.2

3 Measurement


The GLM Statistics checkbox is activated.

The data are acquired with the GLM Method (General LinearModel). If the parameter is deactivated, the images are savedwithout evaluation.

4 Activate the Dynamic t-maps.

5 Confirm the changes with Apply.

The t-maps generated during the measurement of eachmeasurement volume are saved. During the measurement, theyare displayed in the Neuro 3D task card.

In addition, at the beginning of the measurement, a StartFMRIseries is generated which can be deleted after ending theexperiment.

6 Set Starting ignore meas to 0.

Determines the number of measurements that are ignored at thebeginning of the experiment to avoid interferences caused by theexperimental response at the beginning of the measurement.

7 Set Ignore after transition to 0.

Determines the number of measurements to be ignored whenchanging the stimulus to avoid interferences caused by theexperimental response.

Measurement 3


When measurements are ignored after the transitions, it is nolonger possible to account for the time offset between the datameasured and the model in GLM.

8 Activate Model transition states.

Determines that the hemodynamic response of the brain will beused for computation. The paradigm is convoluted with thehemodynamic response to obtain a reasonable model of theactivity-time course.

When Model transition states is active and the parameterIgnore after transition is at zero, the first derivation of themodel of the hemodynamic response is added to the designmatrix at the covariants of no Interest. This means that a time-offset of the measured data to the model is modelled up to onesecond and therefore considered in the statistics.

9 Activate Temp. highpass filter.

Determines whether amplitude fluctuations can be eliminated overtime via a high-pass filter. The limit frequency is determinedautomatically.

The basic functions of a modeled drift are shown in the lastcolumns of the design matrix. They are part of the covariants ofno Interest.

Defining the threshold value and paradigm✓ BOLD parameter card has been opened

✓ Parameters for GLM evaluation have been selected

First, you determine at what intensity the pixels from the t-maps willbe used for calculating the overlay images.1 Check the threshold value.

2 Select the size of the paradigm.

Example: 20 Measurements (10 measurements of the right handand 10 measurements of the left hand).

3.7.3

3 Measurement


3 Define the course of the paradigm.

Example:

◾ Measurement [1]–[10]: Baseline (Finger tapping right hand)◾ Measurement [11]–[20]: Active (Finger tapping left hand)

4 Determine the duration of the periodic paradigm by setting thetotal number of Measurements.

A duration of e.g., 60 or 100 is appropriate. It must correspond toat least the size of the paradigm.

If the BOLD Add-In is attached to the protocol and a paradigm isselected in the BOLD Add-In, modification of the paradigm on theBOLD parameter card is not possible. If an appropriate paradigmis selected in the BOLD Add-In, also multi-contrast BOLDacquisitions and evaluations are possible.

Determining motion correction and the spatial filter✓ BOLD parameter card has been opened

✓ Paradigm has been defined

1 Define, as required, the retrospective motion correction.

2 Activate the Motion correction checkbox and select the methodunder Interpolation.

Prospective motion correction is performed automatically via thePACE protocol.

3 Activate spatial filtration.

3.7.4

Measurement 3


Motion-corrected and/or filtered images can no longer beconverted into original images.For this reason, images that are not corrected are storedautomatically as their own series when selecting motioncorrection and/or filtration. For example, the series can beprocessed at external evaluation consoles (for research purposes,etc.).

Motion correction via PACE is performed during themeasurement. This means that it is retained in the uncorrectedseries as well.

Performing the measurement✓ Motion correction/filtration has been determined


2 Perform the entire measurement sequence of the periodicparadigm with the set number of measurements (sequentialmeasurement series).

Example: The paradigm includes 10 measurements each of the leftand right hand. Provide the respective command after 10measurements (after the end of the baseline or active). For thispurpose, monitor the measurement counter in the status line.

You can monitor the measurements on the optional Neuro 3D taskcard if enabled on the system.

The following series are generated:

◾ StartFMRI (empty)◾ Original EPI series (not motion corrected or filtered, however,

PACE motion correction was used)◾ Motion-corrected data◾ Series for intermediate t-maps◾ Design matrix

3.7.5

3 Measurement


◾ t-maps (EvaSeries_GLM)◾ Overlaid images (Mean-&-t-maps)

An uncooperative patient (moves or does not follow theparadigm) leads to artifacts and incorrect results. For this reason,monitor the patient during the measurement.

Measuring the flow in the internal carotidarteryTo display flow and the encoding of the flow velocity, phase contrastimages are used. (For a detailed description of the phase contrasttechnique, please refer to the MR Basic Manual Magnets, Flows, andArtifacts.) A number of stenotic changes in the cervical vessels takeplace at the height of the carotid bifurcation.

Measuring the localizers✓ ECG electrodes have been attached to the patient

✓ Flow measurement program has been selected

1 Measure a sagittal as well as transverse localizer.

2 Position the localizer slices for a vessel scout.

Positioning with respect to the center of the tip of the chinfrequently corresponds to the position of the carotid bifurcation.

3 Start the measurement of the vessel scout.

Optional

4 Perform a 3D Time-of-Flight angiography.

Position the 3D slab such that the carotid bifurcation is in thecenter of the slab.

3.8

3.8.1

Measurement 3


Positioning the vessel scout (left) and the 3D ToF slab (center, right).

Determining the slice position✓ Localizers have been measured

1 Load the localizer images into the 3D task card.

2 Position the slice to be measured on the orthogonal slices.

Ensure that the measurement slice is orthogonal to the internalcarotid artery. The resulting image should show the vessel ofinterest with a circular shape.

Positioning the measurement slice (left, center) and the slice image withthe round cross-section of the internal carotid artery (left).

3 Store the images.

4 Load an image of the stored 3D series to the Examination taskcard.

5 Accept the slice position of the image from the 3D series.

6 Select the correctly positioned slice and select Tools > Copy ImagePosition.

3.8.2

3 Measurement


Determining the flow sensitivityTo obtain the correct velocity and venc to be applied to the sequencethe user may use a venc_scout scan, applied with 4 different vencvalues.

✓ Measurement slice has been determined

1 Adjust the FoV to the requested image section.

2 On the Physio Signal1 parameter card: Adjust the target RR to theaverage cycle.

3 On the Angio Common parameter card: Set the velocity encodingto a sufficiently high value, e.g. 150 cm/s.

4 Start the measurement of the velocity localizer.

5 Load the image series into Argus and read the maximum velocity.

6 Calculate a suitable value for velocity encoding.

venc ≈ vmax × 1.2

Performing the measurement✓ Flow sensitivity has been determined

1 Check the FoV.

2 On the Physio Signal1 parameter card: Accept the average heartcycle for the acquisition window.

3 On the Angio Common parameter card: Enter the computed vencinto the velocity encoding window.

4 Ensure that Through Plane is entered in the direction window.

5 Activate the checkbox of the image series you would like to save.


3.8.3

3.8.4

Measurement 3


Flow-compensated, flow-encoded, and phase-contrast image of the internalcarotid artery (arrow).

As an alternative, the measurement can be performed withretrospective gating. The average heart cycle is then accepted inthe target RR window.

1H MR spectroscopy of the headTwo techniques are used for allocating the spectra signals with theanatomical volume given.1H SVS measurement: The SVS (Single Voxel Spectroscopy)technique is used in 1H MRS of the brain to examine focalpathologies (e.g. tumors). In order to optimally distinguish betweenpathological and healthy structures, you have to acquire a referencespectrum from a healthy part of the brain in addition to the spectrumof the examination volume. The SVS method allows focusing of theshimming on the volume of the single spectrum to be measured.1H CSI measurement: The CSI (Chemical Shift Imaging)measurement volume comprises several voxels (2D slice or CSI 3Dslab). A spectra matrix is produced. 1H CSI MRS of the brain enablesyou to detect, for example changes in the concentration of specificmetabolites caused by strokes or tumors. This includes metabolitessuch as N-acetyl-aspartate (NAA), creatine (Cr) and choline (Cho). Thedetection and spatial distribution of lactate also plays an importantrole.

3.9

3 Measurement


Planning the examination✓ Appropriate coil has been selected


◆ Compile a suitable spectroscopy measurement program.

Example SVS.

Example CSI: csi_se… = 2D hybrid CSI with spin echo; …_135 = echo time in ms.

3.9.1

Measurement 3


This is how you ensure correct spatial allocation of spectra toreference images:

◾ Ensure that the reference images and spectra are measuredwithout temporary repositioning

◾ Instruct the patient not to move at all, if possible during theentire examination (including measurement pauses).

MRS with scan@centerTo plan spectroscopy measurement and for the post-processing youneed non-distortion corrected images (ND) in the three mainorientations. Spectroscopy measurements must be performed at thesame table position as the ND images used for planning.

When performing spectroscopy after a routine imagingexamination, the existing images are generally used to plan themeasurement.If you already know at the beginning of the examination that aspectroscopy measurement will follow, you can deselect thePositioning mode ISO prior to measuring the reference images.

✓ Centrally localized images (DIS3D) of the examination region fromthe same table position are available

1 Select a reference image with high contrast in the graphic slicepositioning (GSP).

2 Open a spectroscopy protocol.

All images of the selected series are reloaded as ND images intothe GSP. Images of different orientations (DIS3D) are automaticallyunloaded from the GSP.

Planning in non-isocentricreference images

3 Measurement


ND images: table position = 0.

If ND images with different orientations are available from thecurrent examination, you can load them directly from theprogram control.

You can also generate a new series with ND images fromsuitable, distortion-corrected images (menu: Evaluation >Inverse 2D Distortion Correction).

✓ All images (DIS2D/DIS3D) come from different table positions

1 Select a reference image with high contrast in the GSP.

2 Open a spectroscopy protocol.

Images that have a table position other than the selected referenceimage, are automatically removed from the GSP. The selectedreference image is converted into a ND image.

DIS2D images: different table positions.

Planning in isocentricreference images

Measurement 3


3 Measure additional localizers or reference images with additionalorientations (ND images).

Use the scan@center localizers to measure ND images in the isocenterwhich are optimally suited for planning and post-processing inspectroscopy.

✓ Centrally localized images of the examination region do not exist

1 Select a reference image with high contrast in the GSP.

2 Open a spectroscopy localizer (localizer@center orlocalizer_5@center).

3 Position the slices in the reference image.

4 Start the measurement of the localizer.

The patient table automatically moves into the isocenter. The NDimages are measured.

5 Load the measured reference images into the segments of the GSP.

The measurement object (VOI/CSI slice) is shown.

Example SVS.

CSI: transferring slice positioning

✓ Reference images with a CSI slice are displayed

The CSI slice to be planned must match the slice position andorientation of the reference images.

1 Look for the reference image including the anatomical region ofinterest.

2 Change the display of the reference image until it is optimal forplanning the examination.

3 Select the reference image.

Measuring scan@centerreference images

3 Measurement


4 Transfer the slice positioning of the reference image to the CSI slice(menu: Tools > Copy Image Position).

The center of the CSI slice is shifted perpendicularly into the planeof the reference image. The orientation of the CSI slice correspondsnow to the slice orientation of the reference image.

For controlling the position of the measurement volume inadjacent reference images, menu: Scroll > Nearest.

Positioning the CSI sliceBoth position and size of the CSI slice have to be adjusted to theanatomical characteristics of the patient.◆ In the Geometry Common parameter card: Adjust the FoV and

VOI.

Measurement 3


◾ FoV: large enough to avoid overfolding.◾ VOI: coverage of the entire area of interest.

You can still change the position of the CSI slice in the predefinedplane (in-plane).

If the CSI protocol uses an interpolated matrix, you are able toadjust the screen display (menu: View > CSI Matrix >Interpolated Matrix).

CSI: suppressing interference signalsFor CSI measurements with a spin echo sequence, it is recommendedto suppress signal contributions outside the VOI (Outer VolumeSuppression, OVS).1 In the Geometry Common parameter card: Select Fully excited

VOI.All metabolites of interest are uniformly excited in the VOIselected. Additionally, 4 saturation regions are positionedautomatically (not displayed).

2 Suppress interfering signal contributions by arranging up to 8freely positionable saturation regions around the VOI.

Typical positioning in the head: 4 saturation regions for covering the skullcap, including 2 transverse saturation regions for suppressing venous andarterial flow.

3 Measurement


Starting protocol adjustments (optional)Semi-automatic adjustments are recommended for difficultanatomical regions (e.g., flow, vessels, jumps in susceptibility). Youcan check the shim status prior to the spectroscopy measurementand improve it, if necessary.

✓ Automatic adjustment is not satisfactory

1 Select Options > Adjustments from the main menu.

The Manual Adjustments dialog window is opened.

2 Select the Show subtask card.

3 Start the adjustments with Adjust All.

3.9.2

Measurement 3


All protocol adjustments are performed (as displayed in theinformation window).

Shimming interactively (optional)The shim quality is particularly important for spectroscopyexaminations. Use interactive shimming for checking and improvingthe examination. By changing the shim currents, you are able tooptimize the results (FWHM, T2*).

✓ Protocol adjustment has ended

1 In the Manual Adjustments dialog window: Select the InteractiveShim subtask card.

3.9.3

3 Measurement


2 Start the shim with Measure.

An infinite measurement is performed with the currently set shimparameters.

3 Monitor the results for FWHM and T2*.

FWHM [Hz]: as small as possible◾ 1.5 T: SVS < 13 Hz, CSI < 15 Hz◾ 3 T: SVS < 20 Hz, CSI < 25 HzT2*: as large as possible. Depends on voxel size and themetabolites contained within.

4 End the measurement with Stop as soon as you are satisfied withthe results. (Otherwise: ( Improving shim results(optional)) .)

During visual inspection: If the water is less than twice the fatamplitude, the size and/or position of the voxel should bereadjusted.

5 Apply the shim results to the following spectroscopy measurementwith Apply.

6 Close the dialog window.

7 Start the spectroscopy measurement.

Improving shim results (optional)If the results for FWHM and T2* are not satisfactory, you can improvethe homogeneity of the magnetic field by changing the shimcurrents.

✓ Interactive Shim subtask card has been opened

✓ Shim results are not satisfactory

◆ Change the gradient offset for one shim channel.

Example Channel X1 Increase the value with the up arrow button.

3.9.4

Measurement 3


2 Monitor FWHM and T2*.

If the result worsens:

3 Use the best shim results of the current measurement with LoadBest.

4 Change the gradient offset in the other direction (use the downarrow button).

If the results for FWHM and T2 * continue to be unsatisfactory:

5 Repeat the steps for the other channels (Y, Z).

As soon as you are satisfied with the results:

6 End the measurement with Stop.

7 Apply the shim results to the following spectroscopy measurementwith Apply.

Adjusting the frequency (optional)Whenever you change shim currents, a “?” appears in the Frequency(syst) field. This means that the frequency still needs to be adjusted(if not performed manually, the system handles it automatically).

✓ Shim currents have been changed

1 In the Manual Adjustments dialog window: Select the Frequencysubtask card.

3.9.5

3 Measurement


2 Start the frequency adjustment with Go.

3 Monitor the tolerance parameter “Diff [Hz]”.

Optimal frequency: Diff [Hz] = 0 +/– 2 Hz

4 Repeat the adjustment until you obtain a satisfactory value for “Diff[Hz]” and the “Y” appears in the A. column.

5 Transfer the determined frequency to the measurement systemwith Close.

You can now begin with the spectroscopy measurement.

Measurement 3


Measuring raw dataYou are starting to generate the spectroscopy raw data. During themeasurement, you are able to monitor the raw signal in the InlineDisplay and control the measurement accordingly.1 Start the measurement.

All adjustments required are performed automatically prior to themeasurement. For most applications, the default values of theadjustment configuration that have been currently determined areconsidered optimal. (Otherwise: ( Page 73 Starting protocoladjustments (optional))

2 To open the Inline Display, select View > Inline Display from themain menu.

(1) Accumulated magnitude spectrum(2) Magnitude time signal of the current acquisition(3) Magnitude spectrum of the current acquisition

After the measurement, the spectroscopy raw data and thereference images are automatically stored in the patient database(as shown by the icons).

3.9.6

3 Measurement


Icons for reference images and spectroscopy raw data in thePatient Browser.

For a description of evaluating spectra, please refer to:( Page 124 Spectroscopy Evaluation)

Follow-up examinations: Use the Phoenix functionality of thesyngo software to recall the same measurement protocol. Thisensures that the same parameters are used for all measurementsexcept the voxel size, which may be adjusted to the reduced sizeof the tumor.

Measurement 3


3 Measurement


Post-processing

4.1 Neuro perfusion evaluation 824.2 BOLD 3D Evaluation 874.3 BOLD parameter map calculation 944.4 Evaluating ASL data 974.5 Creating alpha images with BOLD 1004.6 DTI Evaluation 1044.7 DTI Tractography 1084.8 Flow analysis with Argus 1164.9 Spectroscopy Evaluation 124

4

Post-processing 4


Neuro perfusion evaluationThe perfusion post-processing function allows you to display andevaluate perfusion-weighted images, for example, as a tool to help intumor diagnosis.The reconstructed parameter images are based on a post-processingprotocol, a calculated arterial input function (AIF), and a set timerange.The following example describes how to perform analysis of neuroperfusion data.

Preparing the dataLoading images for evaluation

✓ Suitable T2*- or T2-weighted single-shot EPI images are available

1 Select one or more series in the Patient Browser.

2 Transfer the images to the Perf MR task card with Applications >Perfusion (MR).

Optimizing the image display1 Window the images to optimize their contrast and brightness.

2 Define the color display of the parameter images via the colorpalette in the control area.

Evaluating the dataLocal AIF method: The local AIF method determines the incomingflow of contrast agent for a reference volume around every voxel.

4.1

4.1.1

4.1.2

4 Post-processing


This method reduces artifacts due to arterial flow differencesbetween different regions.It avoids the manual selection of the arterial input function.It supports the calculation of relCBF, relCBV, and relMTT maps.Additional relCBVCorr maps, which are T1 corrected, are provided.Global AIF method: In contrast to this, the global AIF methoddetermines the incoming flow of contrast agent in one reference ROIfor all voxels.

To reduce sensitivity to vascular delays when calculating relCBFand relMTT, Delay Correction should be active in the global AIFpost-processing protocol. ( Page 86 Editing and saving thepost-processing protocol)

Selecting a post-processing protocol◆ Select a protocol for calculating the parameter images from the

selection list in the lower control area.

Calculating the mean AIF (global AIF)

Instead of using the global AIF method for relCBF, relCBV, andrelMTT maps, you can also use the local AIF method to calculaterelCBF, relCBV, relCVBCorr, and relMTT maps.This avoids the manual selection of the arterial input function

✓ The local AIF checkbox has been deactivated to calculate mapswith the global AIF method.

1 Scroll through the series in the top left segment to find a suitablebasic image for positioning the AIF ROI.

2 Draw an AIF ROI in the basic image with the icon in the controlarea.

The AIF curves are displayed on the Step 1: Select AIF subtask cardfor all pixels within the AIF ROI.

Post-processing 4


3 Click and drag the AIF ROI box over the selected artery.

After you release the mouse button, the associated AIF curves aredisplayed on the Step 1: Select AIF subtask card.

Position the AIF ROI with great care!◾ Locate the AIF ROI close to the perfusion anomaly.◾ Position the AIF ROI over healthy arteries, such as the A.

cerebri media, but also over smaller arteries that are notexplicitly recognizable as vessels in the basic image.

4 Select the AIF curve(s) with the flattest base line and the deepestcurve (for multiple selections, use Ctrl and/or Shift).The mean AIF curve is calculated and displayed in the control area.It indicates the arithmetic mean of the selected AIF curves.

Setting the time range (global AIF)1 Select the Step 2: Set time ranges subtask card.

4 Post-processing


2 Define the time range used for perfusion analysis by moving thelines.

Observe the GBP curve. The bolus arrives later in the tissue thanin the vessel. Do not define the end of the first pass (right line) tothe far left. The bolus in the tissue could be cut off.

3 Confirm the time range with the checkbox.

Performing reconstructions

✓ Required post-processing protocol has been selected

1 Start reconstruction with the icon.

2 Click the icon in the status bar to monitor the status of image post-processing.

When reconstruction is completed, the parameter images areshown in the lower two segments.

Post-processing 4


Editing and saving the post-processing protocolThe post-processing protocol defines the sequence and properties ofthe individual post-processing steps.

Only experienced users should edit post-processing protocols!

1 Select the required post-processing protocol from the selection listin the lower control area of the Perf MR task card.

2 Open the Edit Protocol dialog window with Protocol > Edit.3 Adapt the parameters for perfusion post-processing to your

requirements.

4.1.3

4 Post-processing


4 Save the changed protocol with Save.

The old version is overwritten.

With Save As you can create a protocol with a different name.The old protocol remains unchanged.

BOLD 3D Evaluationsyngo BOLD 3D Evaluation allows post-processing of fMRI dataincluding motion correction, spatial filtering, and statisticalevaluation.The results of the evaluation of specific regions of the brain aredisplayed graphically. The movie function allows you to track themovement of the head during the examination.The following example describes how to visualize and evaluate BOLDfMRI data.

Preparing the dataLoading the image series

✓ BOLD fMRI data is available for evaluation

1 Select the BOLD tensor series in the Patient Browser.

2 Transfer the data to the Neuro 3D task card with the icon.

4.2

4.2.1

Post-processing 4


3 Click the Study icon in the upper control area for an overview ofthe loaded volumes.

Optimizing the display◆ Click the icon to activate the Fusion mode.

1 Open the VRT gallery with Visual > Anatomy Gallery.

2 Select a suitable VRT parameter set.

The VRT volume image including the tissue class parameters of theselected parameter set is displayed.

1 Open the Fieldmap Properties dialog window with Visual >Fieldmap Properties.

2 Use the slider to determine the pixel shift of the field map thatmarks the image area.

1 Open the Functional Properties dialog window with Visual >Functional Properties.

Adjusting the VRT display

Defining the image area

Adjusting the functional datadisplay

4 Post-processing


2 Select the expanded view of the dialog window with More >>.

3 Activate the Activation Map Filter checkbox to make the display ofactivation data a function of cluster size.

4 Enter the desired cluster size.

Creating an MPR rangeYou can create a series of parallel MPR Thick images which areperpendicular to a selected 2D view in the reference segment.1 Select the 2D reference segment.

2 Open the MPR Range Properties dialog window with the icon.

Post-processing 4


The image planes of the planned result images are drawn into thereference segment. The MPR corresponding to the center line isdisplayed in the 3D segment.

3 To move the image planes, click and drag the center to the desiredposition.

4 To change the distance between images, activate the icon in theMPR Range Properties dialog window.

5 Move the first or last line of the MPR range in the 3D segment up ordown.

6 Start reconstruction with the icon in the MPR Range Propertiesdialog window.

When reconstruction is finished, the reference images aredisplayed as an image stack in the fourth segment.

1 Open the Save MPR Range dialog window with the icon.

2 Select the series type, e.g. Fused (Secondary Capture).3 Enter the series name.

4 Click OK.

Setting the 3D viewIn the Fusion mode, the 3D view is superposed on the fourthsegment.

Saving the MPR range

4 Post-processing


Clip planes are used to eliminate overlying tissue. In this way, areaswith activation in the image volume are shown. The volume outsidethe clip planes is hidden. The interior, however, is visible.1 Right-click the icon on the Display subtask card to open the Clip

Plane Properties dialog window.

(1) Selected clip planes(2) Unselected clip planes

2 Click the clip planes you want to activate/deactivate.

The boundaries of the clip planes are marked in blue in the VRTvolume image.

3 Double-click the fourth segment to enlarge the 3D view.

The orientation cube at the bottom right of the image shows theorientation with respect to the patient coordinate system.1 Rotate the volume with the orientation cube.

2 To set the volume image to one of the standard view directions,click the corresponding side of the orientation cube.

Showing clip planes

Rotating the 3D view

Post-processing 4


A double-click anywhere in the orientation cube sets the volumeimage to front view and original size.

◆ Drag the frame of the clip plane to the desired position.

1 Select the frame of the clip plane.

Rotation points are displayed at the center of each frame side.

2 Use the points to rotate the clip plane in the desired direction.

◆ Drag the reference line between the image center and the arrow tothe desired position.

Evaluating the dataEvaluating a VOI1 Switch to Evaluation Mode with the icon in the control area.

The VOI tool is activated. The graphic segment superposes thethird image segment.

2 To evaluate specific regions of the brain, draw a circle over theregion of interest in a 2D segment.

The graphic segment displays the evaluated functional data of thedrawn Volume of Interest (VOI).

Moving clip planes

Rotating clip planes

Moving image planes

4.2.2

4 Post-processing


(1) BOLD: Signal intensity over time curves(2) Motion parameter: Translation over time curves(3) Motion parameter: Rotation over time curves

Displaying functional data as a filmUsing the movie properties in the Functional mode, you can track themovement of the head during the experiment.1 Switch to Functional Mode with the icon in the control area.

In the first to third image segment, the 2D superimposed images ofthe BOLD volume and the activation distribution (standard MPR)are displayed.

2 Start the movie with the icon in the control area.

Post-processing 4


The movie task bar opens. The individual BOLD volumes aredisplayed in sequence from first to last, then again from thebeginning.

Saving and filming the images1 Activate the Fusion Mode with the icon.

2 Switch off Evaluation Mode with the icon in the control area.

The graphic segment disappears. Instead, the third segmentdisplays images.

3 Select the respective segment for saving or filming.

4 Save the images as a new series with the icon.

5 Film the selected images with the icon.

BOLD parameter map calculationThe following example describes how to calculate parameter mapsretroactively with syngo BOLD. The pixels of the post-processedparameter images carry functional information.

CAUTION

BOLD post-processing with image data generated by Numaris 3or 3.5!Incorrect diagnosis through erroneous superposition ofanatomical and functional image◆ Do not use syngo MR for BOLD processing with image data

generated with Numaris 3 or 3.5.

4.2.3

4.3

4 Post-processing


Preparing the dataLoading the data

✓ Functional image series (EPI measurements) is available forevaluation

1 Select the functional series in the Patient Browser.

2 Load the series into the BOLD task card with Applications > BOLDEvaluation.

The Evaluation Controller Dialog opens.

(1) Selected series(2) Post-processing protocol last used

The MR system informs you about a series that does not meetall requirements.This means that the series (EPI measurements) does not originatefrom the same series block with identical table position, frame ofreference, slice position, and number of images.◆ Remove the series from the list with Delete Series.

4.3.1

Post-processing 4


Evaluating the dataStarting post-processing1 Select the required post-processing protocol from the selection list

in the Evaluation Controller Dialog.

2 Start the calculation with Execute.

After successful calculation, the parameter images are displayed asmosaic images in the second segment of the BOLD task card.Additionally, the alpha image is calculated and displayed.

Monitoring post-processing◆ Display the Postprocessing Queue dialog window with this icon in

the status bar to monitor the status of image post-processing.

Editing and saving the post-processing protocolThe post-processing protocol defines the sequence and properties ofthe individual post-processing steps.


1 Select the required post-processing protocol from the selection listin the Evaluation Controller Dialog.

2 Open the Edit Protocol dialog window with Edit.

4.3.2

4.3.3

4 Post-processing


3 Adapt the parameters to your requirements.

4 Save the changed protocol with Save.

The old version is overwritten.

With Save As you can create a protocol with a different name.The old protocol remains unchanged.

Evaluating ASL data

3D ASL-specific modulessyngo ASL 3D incorporates a double inversion backgroundsuppression scheme that can simultaneously suppress two tissuetypes with differing T1 values. Background suppression reducessensitivity to motion and improves the subtraction between the labeland control images. The imaging module employed in syngo ASL 3Duses a modified fast spin echo approach that acquires severalgradient recalled echoes during the interval between the refocusingpulses. The gradient recalled echoes are encoded using echo-planarimaging. Variants of this approach are often termed 3D GRASE orTGSE. The sequence acquires volumetric imaging with 3D encodingand short echo times with centric reordering tables. For large imagingmatrices the echo train may become prohibitively long due to T2relaxation of the signal. For these cases the sequence offers theflexibility to segment the acquisition in both phase encodingdirections. Segmentation improves image quality and reducesblurring while also increasing the number of shots used and henceleads to improved signal-to-noise ratio.

4.4

4.4.1

Post-processing 4


3D ASL acquisition output: (left) Original EPI image series; (right) Perfusion-weighted image.

Interpretation of resultsFor the results of a 2D ASL acquisition, please also refer to( Page 99 Generating t-maps) .They include:◾ Original EPI image series (alternating label and control

acquisitions)◾ Motion-corrected EPI image series◾ Perfusion-weighted image (PWI)◾ relCBF image◾ Depending on the Quality check parameter, additional output is

possible ( Page 52 Setting parameters)For the results of a 3D ASL acquisition, please also refer to( Page 97 3D ASL-specific modules) .They include:

4.4.2

4 Post-processing


◾ Original TGSE image series (label and control acquisition)◾ Perfusion-weighted image (PWI). If number of inversion times is

greater than 1, only original label/control images are produced (inthat order).

PWI and relCBF images are typically represented using a colour mapwhere low signal values are depicted using black/dark blue colour andhigh signal values are shown in yellow/red. The windowing of thecolourmap can be performed by selecting an image, pressing themouse wheel and moving the mouse cursor.

Generating t-maps✓ EPI-PASL measurement has been performed

For further processing, the image results obtained are displayed inthe Viewing task card. You can perform additional inline or offlineprocessing on the original or motion corrected EPI series using theGLM Statistics of the BOLD task card.

(1) Original EPI image series(2) Motion-corrected EPI image series

4.4.3

Post-processing 4


(3) Perfusion-weighted images (PWI)(4) relCBF images

1 Transfer the requested EPI series (original or motion-corrected) tothe BOLD task card. ( Page 94 BOLD parameter map calculation)

2 In the Evaluation Controller Dialog: Select the requested post-processing protocol from the selection list.

3 Open the Edit Protocol dialog window with Edit.4 To compute a perfusion-weighted map as a t-map, activate the

GLM Statistics checkbox and set the following parameters.


Starting ignoremeas.

1

Model transitionstates

OFF

Paradigm size 4

Paradigm Baseline, Active, Baseline, Active

5 Save the changed protocol with Save or Save As.

6 In the Evaluation Controller Dialog: Start post-processing withExecute.

The dialog window closes and post-processing starts.

The resulting t-map corresponds to the perfusion-weighted map.

Creating alpha images with BOLDThe following example describes how to create alpha images withsyngo BOLD. The Alpha image is created by overlaying an anatomicalimage with a parameter map.

4.5

4 Post-processing


Preparing and evaluating the dataLoading the data

✓ MR anatomical images and corresponding MR parameter imagesare available

1 Select the anatomical series and the parameter image series in thePatient Browser.

2 Transfer the images to the BOLD task card with Applications >BOLD.

Anatomical series are loaded to the first segment, parameter imageseries to the second segment. Automatically calculated alphaimages are displayed in the third segment.

Only the alpha image for the currently displayed image pair(anatomical image and parameter image) is calculated anddisplayed. If calculation of an alpha image is not possible, thethird segment remains blank.

It is possible to load additional series to those already loaded.The following rules apply when loading additional series:

◾ The first image of the first additionally loaded series isdisplayed.

◾ If the new series originate from the same study, they aresorted according to their series number. You can scrollbetween series.

◾ If the new series are from another study, you decide whetherthe currently loaded series should be replaced by the newseries.

Scrolling through image stacksAlpha images are automatically calculated for the images displayedduring scrolling.1 Use the dog ears to scroll image by image through a series.

4.5.1

Post-processing 4


If the slice position of the currently displayed parameter imagematches the slice position of an image in the anatomical series, theanatomical image is displayed and the associated alpha image iscalculated.

2 Select Scroll > Series Next / Series Previous to scroll from series toseries.

If at least one slice position of the selected anatomical series andthe parameter image series matches, the first suitable image pair isdisplayed. The correponding alpha image is calculated anddisplayed.

Optimizing the image display1 Window the images to optimize their contrast and brightness.

2 Select the color palette for positive (Upper Palette) and negativevalues (Lower Palette).

3 Use the spin boxes or the lines in the color palettes to adjust theUpper Range and Lower Range of the functional values assignedto a color.

4 Define the minimum pixel intensity of the alpha image in this inputfield.

Anatomical pixels whose intensity falls below the AnatomicalThreshold are hidden.

5 Adjust the value in this input field to suppress randomly occuringpixels in the alpha image.

Pixel clusters smaller than the Simple Clustering are hidden.

4 Post-processing


6 Define the transparency of the functional data with this input field.

The Alpha Value defines the degree to which the pixels of theactivation map cover the anatomical image. If the value is 0, onlythe anatomy is visible. The maximum is 1.

Saving the images1 Store the selected alpha or parameter image with Patient > Save

As….

– or –

Store all alpha images of the loaded series with Patient > Save AllAlpha As….

The Save As… dialog window opens.

2 Save image(s) in new series.

– or –

Append image(s) to an existing series.

4.5.2

Post-processing 4


DTI Evaluationsyngo DTI Evaluation allows for quantitative evaluation of the rateand direction of water motion within a voxel, calculation of differentdiffusion parameters, and graphic display of colored DTI maps.

Preparing the dataLoading the tensor series

✓ Tensor data is available for evaluation

1 Select the tensor series in the Patient Browser.

2 Load the data into the Neuro 3D task card with Applications >Neuro 3D (MR).The data automatically loads in Diffusion mode.

4.6

4.6.1

4 Post-processing


(1) FA map(2) ADC map(3) Trace-weighted map(4) b0 map

Evaluating the dataVisualizing the DTI maps1 Select the segment you want to change to a new diffusion map.

2 Display the tensor graphic using the icon on the Diffusion subtaskcard.

4.6.2

Post-processing 4


Enlarged tensor graphic

3 Display the diffusion texture with the icon on the Diffusion subtaskcard.

4 Post-processing


Image in selected segment with diffusion texture

4 Use the dog ear to scroll through the images.

5 Open the Diffusion menu to select additional maps.

Saving an image map1 Select the segment of the map.

2 Select Patient > Save Diffusion.

You can load the saved map in the Viewing task card or send itvia PACS.

4.6.3

Post-processing 4


DTI Tractographysyngo DTI (Diffusion Tensor Imaging) Tractography uses anisotropicdiffusion to graphically display diffusion tracts. When evaluating thediffusion data, 3D visualization of specific white matter tracts ispossible.The following example describes how to perform syngo DTItractography using diffusion tensor data.

Preparing the dataLoading the volume data

✓ Diffusion data is available as a tensor dataset (no images)

✓ All series are from the same study

✓ Field map and 3D anatomy images (recommended) are available

High-resolution anatomy facilitates orientation. However, it is notabsolutely necessary. Instead the b0-volume can be used fordisplaying the anatomy. The b0-volume is included in the tensordataset and is available when loading the diffusion tensor data.

1 Select the data series to be analyzed in the Patient Browser.

2 Transfer the data to the Neuro 3D task card with the icon.

The field map is automatically loaded with anatomy andfunctional data if you first measure the anatomy protocolfollowed by the BOLD protocol.

4.7

4.7.1

4 Post-processing


3 Click the study icon in the upper control area for an overview of theloaded volumes.

Optimizing the display in Fusion mode◆ Click the icon to activate the Fusion mode.

1 Open the VRT gallery with Visual > Anatomy Gallery.

2 Select a suitable VRT parameter set.

The VRT volume image including the tissue class parameters of theselected parameter set is displayed.

1 Open the Blend Factor Properties dialog window with Visual >Blend Factor Properties.

2 Use the sliders to determine to what level activation and diffusiondata are superposed on the anatomical image.

◆ Window the images to optimize their contrast and brightness.

Adjusting the VRT display

Defining the display of theanatomical image

Optimizing the image display

Post-processing 4


Showing the overview of diffusion tracts1 Click the icon to activate the Diffusion mode.

2 To display the diffusion texture, click the icon on the Diffusionsubtask card.

Image in selected segment with diffusion texture

3 Double-click the segment to display the image in full-screen view.

4 Provide yourself with an overview of the placement of the diffusiontracts.

5 Use the dog ear to scroll through the image stack.

Optimizing the diffusion display1 Change the display type of the selected image to tensor graphic

with the icon on the Diffusion subtask card.

4 Post-processing


You can display different diffusion properties of the loaded data,e. g. ADC, diffusion contrast, and spatial diffusion characteristics.

2 Click the icon to activate the Zooming/Panning mode.

3 Zoom into the desired image section.

The connection between the color flows in the color displays andthe diffusion orientation is shown by the orientation sphere.

4 Open the Diffusion Properties dialog window with the icon on theDiffusion subtask card.

5 Click the icon to display the direction-encoded sphere.

The Direction Encoded Color dialog window opens.

6 Rotate the sphere to the desired position using the mouse.

7 Double-click the segment to return to normal view.

8 Right-click the segment and select Home Zoom/Pan from thecontext menu.

Setting the view for tractography◆ Click the icon to activate the Fusion mode.

The 3D view is superposed in the fourth segment.

Post-processing 4


Clip planes are used to eliminate overlying tissue. That way, areaswith activation in the image volume are shown. The volume outsidethe clip planes is hidden. The interior, however, is visible.1 Right-click the icon on the Display subtask card to open the Clip

Plane Properties dialog window.

(1) Selected clip planes(2) Unselected clip planes

2 Click the clip planes you want to activate/deactivate.

The boundaries of the clip planes are marked in blue in the VRTvolume image.

3 Double-click the fourth segment to enlarge the 3D view.

1 Rotate the volume image with the orientation cube.

2 To set the image to one of the standard view directions, click thecorresponding side of the orientation cube.

Showing clip planes

Rotating the 3D view

4 Post-processing


A double-click anywhere in the orientation cube sets the volumeimage to front view and original size.

1 Select a frame of the clip plane.

2 Drag the frame to the desired position with the mouse.

Applying the Quicktrack functionThe Quicktrack function provides a tractography preview. It isavailable for tensor graphics in the area of the loaded diffusion data.

✓ Diffusion data has been loaded

1 Press and hold the Shift key.

2 Move the mouse pointer across the view.

A tract computation with predefined settings is started with theimage pixel acquired by the mouse pointer. The results are shownautomatically in step with the movements of the mouse.

Evaluating the dataCreating seed pointsSeed points are used as the starting areas for tractography. Seedpoints can consist of a single voxel only. It is also possible to combineseveral voxels into one seed point.1 Keep the Ctrl key pressed and move the mouse pointer across the

requested area with the mouse button pressed.

Moving clip planes

4.7.2

Post-processing 4


The acquired voxels are highlighted in color. They are assigned tothe same seed point until you start with a new seed point.

You can interrupt marking the voxels at any time to change theview, e.g., by moving the MPR image plane or a clip plane.

2 If desired, start another seed point with New Diffusion Seed-pointin the context menu.

Newly acquired voxels are immediately assigned to the new seedpoint and identified with another color.

After having started tractography, a new seed point is createdautomatically.

Starting tractography

◆ Select Start Tractography in the context menu for the seed point.

All tracts connected to the seed point are acquired and displayed.

1 Select Start Tractography to in the context menu for the seedpoint.

2 Select the other seed point in the sub-menu.

Tractography with a singleseed point

Tractography between twoseed points

4 Post-processing


All tracts connected between the two seed points are acquired anddisplayed.

Managing seed points and tracts

1 Open the Seed-point Properties dialog window with Properties inthe context menu for the seed point.

2 Change the properties of the seed point (name, color) as required.

◆ Remove all seed points with Tools > Delete All Diffusion Seed-points.

1 Open the Diffusion Tractography Properties dialog window withProperties in the context menu for the tract group.

2 Select the Visualization subtask card to change the displayproperties of the tract group (e.g., color).

– or –

Select the Tractography subtask card to change the calculationproperties (e.g., Samples per voxel length).

Saving seed points or tracts✓ The Diffusion Seed points Properties or Diffusion Tracts

Properties dialog window has been opened.

1 Open the Save Tractography dialog window with the Save Asbutton.

2 Select the File System option to export a seed point or tract to thefile system.

– or –

Select the Database option to save a seed point or tract as aNonImage series to the database.

Changing seed point properties

Deleting seed points

Changing tract properties

4.7.3

Post-processing 4


– or –

Select Save Tract Volume in the context menu for the tract groupto export a tract as a 3D series.

Flow analysis with ArgusFlow analysis is used to determine the mean and maximum velocityof blood flow and the vessel cross-sections depending on the triggertime.The following example describes how to perform flow analysis ofthrough-plane data for the ascending and descending aorta. As theanalysis for in-plane data is largely the same, it is not described inwhat follows.

Please note that it is not possible to simultaneously processthrough-plane and in-plane data within the Argus flow analysis.

Preparing the dataLoading the image data

✓ Phase-contrast images and corresponding rephased images areavailable

1 Select the data series to be analyzed in the Patient Browser (usethe Ctrl key for multi-selection).

You may also select magnitude images for loading as additionaldata.

2 Transfer the data to the Argus task card by clicking the Argus icon.

The Argus task card opens in the Argus Viewer mode.

3 Start flow analysis by clicking the icon.

The image matrix is rearranged:

◾ Images in a row are from the same image reconstruction type.◾ Images in a column are from the same cardiac phase.

4.8

4.8.1

4 Post-processing


(1) Work segments(2) Rephased images (labeled M)(3) Magnitude images (labeled MAG)(4) Phase-contrast images (labeled P)

Optimizing the image display1 Enlarge the image area showing the ascending and descending

aorta.

2 Window the images to optimize their contrast and brightness.

The grayscale values of the phase-contrast images represent flowvelocities.

Post-processing 4


If necessary, you can assign a linear color scale instead of thegrayscale in the Color selection list of the View subtask card.

Example: Assignment of the Red to Blue color scale.

You cannot window phase-contrast images in color. However,you can continue to use zooming and panning.

Defining the evaluation regionsYou draw the contours of the vessel cross-sections to define the ROIsfor flow analysis.All tools for ROI definition are available on the Drawing subtask card.You can draw ROIs into any image. Later during propagation, they arecopied automatically to the images belonging to the same phase.

The rephased images show the edges of the vessels more clearlythan the phase-contrast images. This makes them especiallysuitable for drawing.

4.8.2

4 Post-processing


Drawing the ROI for the ascending aorta

✓ R1 icon for drawing the 1st ROI is active

1 Load an image containing easily recognizable vessel cross-sectionsinto a work segment.

2 Draw a circular ROI around the cross section of the ascendingaorta.

3 Fit the ROI to the vessel contours of the ascending aorta by clickingthe icon.

Once the ROI is drawn, the result of the statistical evaluation isshown next to it.

The value of the highest flow velocity in the ROI is marked by apoint in the image.

Drawing the ROI for the descending aorta1 To start drawing the second ROI, click the R2 icon.

2 Draw a circular ROI around the cross section of the descendingaorta.

3 Fit the ROI to the vessel contours of the descending aorta byclicking the icon.

Analyzing low velocities (optional)When analyzing low velocities you have to define a reference ROI.1 Start drawing the reference ROI by clicking the Ref. icon.

2 Draw a small reference ROI in an area with stationary tissue nearthe vessel of interest (e.g., in the chest wall or the spine).

Post-processing 4


The flow parameters of the reference ROI are used for subsequentbaseline correction.

Please note that if the background signal in the reference regiondiffers significantly from the vessel region, the correction by thereference ROI might not be valid!

Propagating the vessel contours to other cardiac phasesDuring propagation, the contours of the ROIs are fitted to theanatomy. The contour of the reference ROI is copied without fitting.1 Select all vessel cross-section ROIs that were drawn by clicking the

icon.

2 Start the propagation by clicking the icon.

3 Select the reference ROI with the Ref. icon.

4 Copy the reference ROI by clicking the icon.

The ROIs are drawn into the remaining images of the matrix row.

Confirming the propagated vessel contours

◆ View the images in a work segment one by one by scrollingthrough them with the arrow keys of the keyboard.

– or –

Display the images using the movie display function of the Viewsubtask card with Graphics On.

If ROIs are misaligned, you correct them with the drawing and editingtools.1 Change the size and the position of the ROI with the Move tool.

Checking the ROIs

Correcting the ROIs

4 Post-processing


2 Correct the shape of the ROI with the Nudge tool.

3 Redraw a segment of the ROI with the Splice tool.

4 To apply the correction to the other series of this phase, browsethrough the images with the arrow keys or click the icon on theDrawing subtask card.

If propagated ROIs are not explicitly confirmed, a warning will bedisplayed in the results of the flow analysis.◆ Accept the contours by clicking the icon.

Evaluating the vesselsAll tools for evaluation are available on the Result subtask card.You can graph the following parameters as a function of time:

Velocity Mean velocity within the ROI

Peak Velocity Peak velocity within the ROI

Flow Product of mean velocity andsurface area

Net Flow Difference between forward andreturn flow

Area Cross-section of the vessel

During the analysis of in-plane data, it is physically not useful tocompute the (net) flow because the vessels are merely truncated.As a result, it is not possible to reliably determine the blood flowthrough the vessel. For this reason, only the velocity as well asthe cross-sectional area of the ROI are determined with in-planedata.

Confirming the ROIs

4.8.3

Post-processing 4


Calculating results with standard settings

If the patient data are incomplete, the Patient Informationdialog window is displayed when starting the calculation.

1 Select the vessels with the R1, R2, and Ref. icons.

2 Start the calculation by clicking the respective parameter icon.

The results for each ROI are displayed in graphic format.

3 To smooth the curve characteristic using a spline function, selectFlow Options > Fit Curve as Cubic Spline.

The spline curve is displayed in the graph as a dotted line.

4 Display the result tables by clicking Summary.

Limiting the time rangeBy default, the time between the first and last trigger time is used forevaluation.1 Change the time range by overwriting the start and end values in

the Result subtask card.

2 Start the recalculation with the Enter key.

4 Post-processing


Performing baseline correction

✓ Reference ROI has been defined

◆ Apply baseline correction with Flow Options > Use BaselineCorrection.

A baseline is calculated from the flow parameters of the referenceROI and subtracted from the result curve.

Baseline correction is indicated in both the image text and theresult tables.

Correcting phase aliasingFlow velocities that exceed the defined flow sensitivity are shownwith an incorrect grey value, resulting in phase aliasing. Anexceedingly high positive velocity is shown as a high negative flowvelocity (black) and vice versa (“phase reversals”).

Phase aliasing can be corrected, as long as the maximum flowvelocity does not exceed double the value set as flow sensitivityduring the measurement.

Examples:

(1) Blood flowing too fast causes dark spots in the region of theascending aorta and bright spots in the region of the descendingaorta.

(2) Phase reversals can be identified by the local minimum in thesystolic phase. The highest velocities are much smaller thanexpected.

Post-processing 4


CAUTION

Incorrect selection of the range of velocity for a specific organ(preset range of velocity is lower than physiological range ofvelocity)!Incorrect flow and volume values◆ Correct the parameter range for the organ to be examined.

You adjust the curves by retroactively changing the velocity range(flow sensitivity) which is set to symmetrical by default.1 Open the Venc Adjustment dialog window with the corresponding

button.

2 Change the velocity range numerically or with the scroll bar.

3 Confirm the new velocity encoding with Update Results.

The actual flow velocity cannot be determined with thiscorrection. It would require a new measurement.

Spectroscopy EvaluationEvaluation in MR spectroscopy of the head is typically based on 1HMRS measurements applying the SVS or the CSI localizationtechnique. The following example describes how to evaluate CSIdata.The evaluation of CSI data results in spectra from the voxels ofinterest in the CSI slice. The spectra provide information regardingthe existence, distribution, and ratio of diagnostically relevantmetabolites in the examination region. Spectroscopy evaluation alsoallows creating spectral maps for an overview of spectra of interest aswell as displaying the CSI data as colored metabolite images.

Applying correction

4.9

4 Post-processing


CAUTION

Selection of unsuitable evaluation parameters!Artifacts in the spectrum (additional or covered lines)◆ Ensure that interactive evaluations are handled by experts.

Preparing the dataLoading the data

✓ CSI data is available for evaluation

◆ Load the raw data into the Spectroscopy task card with the icon(double-click).

The reference images from the graphic slice positioning and theCSI slice are displayed. The raw data of a predefined voxel (blue) inthe center of the CSI grid is automatically evaluated with theappropriate post-processing protocol. The resulting spectrum isshown together with the associated stamp reference images.

4.9.1

Post-processing 4


Adjusting the reference imageThe displayed reference image should show the anatomical region ofinterest.1 Activate Image > Auto Selection Mode.

When scrolling through reference images, the most suitable CSIslice is selected.

2 Use the dog ear to look for the reference image that shows theanatomical region of interest.

3 To hide interfering graphics, open the Display Parameters dialogwindow with the icon and deselect the graphic objects in theImages tab card.

To only display the VOI and voxel for evaluation, hide Saturationregions, Slice intersections and CSI matrix grid.

Evaluating the dataEvaluating voxels of interest1 Set the Single Dataset Mode with the icon.

2 Use the protocol for all spectra segments with Protocols > KeepCommon.

3 Click the voxel of interest in the CSI slice.

The associated spectrum is displayed immediately.

Adjusting the spectrum display

To improve the interpretation of smaller peaks in the spectrum, youcan enlarge the scale of the display area.1 Select the segment displaying the spectrum.

2 Open the Display Parameters dialog window with the icon.

3 Limit the Scale (display area for the Y-axis) on the Signal tab toenlarge the peaks.

4.9.2

Scaling the display

4 Post-processing


As an alternative to alpha-numeric changes, use the mouse tochange the scaling of the axes.

4 Drag the mouse across the spectrum.

(1) X-axis (range)(2) Y-axis (scale)

After a curve fit, the curve of the theoretical spectrum (red fit line)and the default peak information are superimposed.1 Select the Peak info tab of the Display Parameters dialog

window.

2 Select the desired peak information.

The selected information is displayed above each peak.

Changing the CSI sliceInstead of the currently displayed CSI slice, you can select anotherdiagnostically relevant slice for evaluation within the CSI 3D slab.1 Open the 3D CSI Selection dialog window with Postprocessing >

3D CSI Selection.

2 Set the Plane number of the desired CSI slice.

The spectrum in the active segment is newly calculated. Thematching reference image is displayed if Auto selection mode isactivated.

3 If required, change the Main orientation of the slice.

Voxel selection in the reference image remains unchanged.

Displaying peak information

Post-processing 4


Displaying spectral mapsSpectral maps can be generated only if the reference image liesroughly in parallel to the CSI plane and the projection view includes acomplete plane of the CSI grid.1 Select an empty segment.

2 Open the Spectral Map dialog window with the icon in the controlarea.

3 Activate the drawing mode with the icon.

4 Draw a polygon around the area of interest in the reference imagewith Ctrl and left mouse button pressed.

5 Generate the spectral map with OK.

The spectral map is superposed on the reference image anddisplayed in the selected segment.

6 To reduce the computation range again, press the icon and draw anew polygon.

4 Post-processing


7 To delete the computation range completely, press the icon.

Displaying metabolite imagesYou can display the voxel-dependent intensity ratio of differentmetabolites within the area of interest in a metabolite image.1 Select the last empty segment.

2 Open the Metabolite Image dialog window with the icon in thecontrol area.

3 Select the Ratio of metabolites checkbox to create ratio maps.

4 Select the desired metabolites.

5 Generate the metabolite image with OK.

The metabolite image is superposed on the reference image anddisplayed in the selected segment.

Metabolite images should be checked against the spectral map toensure that the fitting process created reasonable values.

Calculating the sum spectrumYou can display the calculated spectra of the anatomical region ofinterest which covers several voxels as a sum spectrum.1 Select the segment for displaying the sum spectrum.

2 Open the Add Spectra dialog window with Postprocessing > Addspectra.

Post-processing 4


3 Select User defined to add the region of interest to thecomputation range.

4 Generate the sum spectrum with OK.

Performing phase correctionYou can improve the spectrum display with interactive post-processing. To show the positive signals for the metabolites, correctthe phase shift.

4 Post-processing


1 Open the Interactive Post-processing – Protocol dialog windowwith the icon.

2 Select the Phase correction post-processing step.

3 Adjust the constant phase and the frequency-dependent phasecomponent.

(1) Moving the mouse left/right keeping the center mouse buttonpressed changes the constant phase.

(2) Moving the mouse up/down keeping the center mouse buttonpressed changes the frequency-dependent phase component.

Adding a peakIf the spectrum shows a peak that is not included in the theoreticalspectrum (e.g. the lactate peak), you can add it and recalculate thecurve fit.1 Open the Interactive Post-processing – Protocol dialog window

with the icon.

2 Select the Curve fitting post-processing step.

3 Click the Add… button to open the Peak Editor.

4 Select the desired peak from the list of Peak templates with adouble-click.

The peak parameters are shown in the Editor.

5 Accept the desired peak template for the curve fit with OK.

The parameters are transferred to the Curve fitting window.

6 In the Interactive Postprocessing dialog window: Start computationof the curve fit with Automatic.

Documenting the resultsGenerating and saving a result tableThe result table shows the integrals of metabolites and metaboliteratios with respect to a reference metabolite.1 Select the segment for displaying the result table of the selected

spectrum.

4.9.3

Post-processing 4


2 Open the Result Table Of Current Spectrum dialog window withSignal > Result Table.

3 Select the reference metabolite for computation of metaboliteratios.

4 To combine metabolite results, click Combine.

5 Select the Store in text file checkbox to save the table as a textfile.

6 Display the result table in the selected segment with OK.

4 Post-processing


Saving and filming the results1 Select the respective segment for saving or filming.

2 Save the results with the icon.

3 Transfer the result to the film sheet with Patient > Copy to FilmSheet.

Saving new post-processing protocolYou can save a changed post-processing protocol, e.g. changes dueto phase correction, as a new protocol.1 Open the Save Protocol dialog window with Protocols > Save As.

2 Select the directory of the new protocol and enter a suitable name.

Post-processing 4


4 Post-processing


Appendix

5.1 Diffusion cards 1365.2 Preset diffusion gradient directions 1385.3 Defining customized diffusion directions 140

5

Appendix 5


Diffusion cardsIn what follows you will find the formulas for the diffusion cards.ADC map:

Exp map:EXP Map = exp(-b⟨D⟩)TraceW map:TW Map = S0exp(-b⟨D⟩)

FA map:The FA map shows the ratio of the anisotropic diffusion to themedium overall diffusion.

RA map:Like the FA map, the RA map (Relative Anisotropy) displays thedegree of anisotropy. It shows the ratio of the anisotropic diffusion tothe isotropic diffusion.

VR map:The VR map (Volume Ratio) displays the degree of anisotropy as well.It shows the ratio of the ellipsoid volume to the volume of a spherehaving a radius of the mean eigen value of the ellipsoid.

Linear, planar and spherical map:Linear, planar and spherical maps show the spatial distribution of thediffusion.

5.1

5 Appendix


◾ Linear mapShows diffusion taking place in (mostly) one direction only (theellipsoid is a prolate spheroid)

◾ Planar mapShows diffusion taking place in (mostly) two directions (oblateellipsoid)

◾ Spherical mapShows diffusion that is (almost) isotropic (spherical ellipsoid)

Mode:The Mode map displays the form of the diffusion tensor. It connectsinformation about the average diffusion coefficient (ADC), the degreeof anisotropy (FA), and the orientation of anisotropy.

GA map:The GA map (Geodesic Anisotropy) shows the differences inanisotropy by measuring anisotropy similar to “Fractional Anisotropy”.In this case, the “geodesic” distance between tensor and the closestisotropic diffusion tensor is measured. (In mathematics, the term“geodesic” is used for theoretically the shortest connection betweentwo points on a curved surface.)

Appendix 5


Preset diffusion gradient directionsThe following tables provide you with the diffusion gradientdirections used for the 6, 12, and 20 diffusion directions that are usedduring a MDDW measurement.

MDDW 6 directions Direction vectors in the magnet coordi-nate system

1 (1.0, 0.0, 1.0)

2 (–1.0, 0.0, 1.0)

3 (0.0, 1.0, 1.0)

4 (0.0, 1.0, –1.0)

5 (1.0, 1.0, 0.0)

6 (–1.0, 1.0, 0.0)


1 (1.000000, 0.414250, –0.414250)

2 (1.000000, –0.414250, –0.414250)

3 (1.000000, –0.414250, 0.414250)

4 (1.000000, 0.414250, 0.414250)

5 (0.414250, 0.414250, 1.000000)

6 (0.414250, 1.000000, 0.414250)

7 (0.414250, 1.000000, –0.414250)

5.2

5 Appendix



8 (0.414250, 0.414250, –1.000000)

9 (0.414250, –0.414250, –1.000000)

10 (0.414250, –1.000000, –0.414250)

11 (0.414250, –1.000000, 0.414250)

12 (0.414250, –0.414250, 1.000000)


1 (1.000000, 0.000000, 0.000000)

2 (0.000000, 1.000000, 0.000000)

3 (–0.031984, 0.799591, 0.599693)

4 (0.856706, 0.493831, –0.148949)

5 (0.834429, 0.309159, 0.456234)

6 (0.834429, –0.309159, 0.456234)

7 (0.856706, –0.493831, –0.148949)

8 (0.822228, 0.000000, –0.569158)

9 (0.550834, 0.425872, –0.717784)

10 (0.468173, 0.834308, –0.291108)

11 (0.515933, 0.808894, 0.281963)

12 (0.391890, 0.515855, 0.761785)

13 (0.478151, 0.000000, 0.878278)

14 (0.391890, –0.515855, 0.761785)

15 (0.515933, –0.808894, 0.281963)

Appendix 5



16 (0.468173, –0.834308, –0.291108)

17 (0.550834, –0.425872, –0.717784)

18 (0.111012, –0.264029, –0.958105)

19 (0.111012, 0.264029, –0.958105)

20 (0.031984, 0.799591, –0.599693)

Direction vectors for additional sets of directions can be obtainedthrough the Application Hotline.

Defining customized diffusion directionsFor Diffusion Tensor Imaging (DTI), you can define customizeddiffusion directions (= diffusion vector sets, DVS). Multiple directionsets (each containing at least 6 linearly independent directions) canbe provided in a text file that has to comply with a specific syntax.

Careful direction selection is required to ensure a reliable tensorestimation. In general, an isotropic distribution of the diffusiondirections is recommended.

Creating the DVSRequired syntaxGeneral:

◾ #: Lines starting with a hash symbol # are interpreted as commentsand get ignored.

◾ Empty lines, tabulators and space characters get ignored (with oneexception as explained below).

◾ There is no case sensitivity.

5.3

5.3.1

5 Appendix


Number of diffusion directions:

◾ Each section containing a DVS is introduced with the instruction:[directions = <number>]where <number> indicates the actual number of diffusion vectors.A single file might contain multiple sections with differentnumbers of vectors. Please note that this instruction must notcontain any spaces or tabulators.

Normalization:

◾ Each DVS might include a normalization directive:normalization = <norm>where <norm> is either maximum, unity or none. If this directiveis missing, unity is used.

– unity: Each vector gets normalized to unity. This mode willensure that every direction receives a weighting with the sameb-value.

– maximum: First a unity normalization gets applied. Afterwards,the whole vector set is scaled such that the largest vectorcomponent of the whole set is 1.0. This mode you ensure bestuse of the gradient performance thus yielding the shortest echotimes. However, it should only be used in the xyz coordinatesystem.

– none: No normalization is applied at all, the vectors are used asprovided. For the internal diffusion gradient calculation, thevector with the largest magnitude is taken as the reference. Itsamplitude will produce the b-value specified in the user interface(UI).The actual b-value corresponding to a user defined diffusionvector can be calculated by the following equation:

bactual = bUI × Magnitudeactual 2 / Magnitudemaximum 2

Appendix 5


Coordinate system:

◾ Each DVS might include a coordinate system definition:coordinatesystem = <system>where <system> is either prs or xyz. If this definition is missing,xyz is used.

– xyz: The DVS is played out in the physical gradient coordinatesystem. Diffusion vector directions do not depend on the actualslice orientation.

– prs: The DVS is played out using the rotation matrix of thecurrent slice, i.e. the phase-read-slice coordinate system is used.Therefore, diffusion vector directions are linked to the actualslice orientation.

Comment:

◾ Each DVS might contain a comment:comment = <comment>where <comment> is a user defined text that appears as a tooltipin the user interface.

Number of diffusion vectors:

◾ Each DVS must include the specified number of diffusion vectors:vector[<index>] = ( <value1>, <value2>,<value3> )where <index> specifies the vector index (counting starts at 0)and <value1> ... <value3> define the three spatial coordinates.In xyz coordinates, it is required that no vector componentexceeds a value of 1.0. In prs coordinates, it is required that novector length exceeds a value of 1.0.

Valid DVS, exampleThe following is an example for a valid DVS containing one directionset.# -----------------------------------# Example# -----------------------------------[directions=6]

5 Appendix


Normalization = unityCoordinateSystem = xyzComment = This is an example!vector[0] = ( 1.0, 0.0, 1.0 )vector[1] = ( -1.0, 0.0, 1.0 )vector[2] = ( 0.0, 1.0, 1.0 )vector[3] = ( 0.0, 1.0, -1.0 )vector[4] = ( 1.0, 1.0, 0.0 )vector[5] = ( -1.0, 1.0, 0.0 )This file defines a single DVS consisting of six non-colinear vectorsgiven in physical gradient coordinates. It includes a user commentand a unity normalization directive. The latter triggers internal vectorre-scaling so their length equals 1.0:Vector[0] = ( 0.707107, 0.000000 0.707107 )Vector[1] = ( -0.707107, 0.000000, 0.707107 )Vector[2] = ( 0.000000, 0.707107, 0.707107 ) etc.

Importing the DVS✓ DTI license is available

✓ DVS file (extension .dvs) is available on the file system of the host,directory: %CustomerSeq%/DiffusionVectorSets

✓ EPI diffusion sequence has been selected

1 Open the Diff Neuro parameter card.

2 Select the Free diffusion mode.

5.3.2

Appendix 5


3 Start the import of the DVS file.

(1) Import

A dialogue window opens, displaying the available DVS files.

5 Appendix


4 Select one DVS file and confirm with Open.

If the syntax is correct, all contained diffusion vector sets areimported and can be selected, by choosing the correspondingnumber of diffusion directions in the Diff Neuro parameter card.

When a user defined DVS file has been imported, the informationbecomes part of the measurement protocol. Therefore, it ispossible to rerun the same protocol even if the original DVS file isno longer present (for example, when using the “Phoenix” featureto run the sequence on another scanner). Still, the DTI license willbe required.

Exporting the DVS✓ DTI license is available

✓ EPI diffusion sequence has been selected

1 Open the Diff Neuro parameter card.

2 Select the Free diffusion mode.

5.3.3

Appendix 5


3 Start the export of the DVS file.

(1) Export

A dialogue window opens, allowing you to specify a DVS file. Thecurrently selected user defined DVS is exported using the samesyntax as described above.

5 Appendix


1,2,3 …1H MR spectroscopy

Refer to spectroscopy 66

AAlpha images 100

Loading data 101Optimizing image display 102Saving images 103Scrolling 101

Argus flow analysis 116Analyzing low velocities 119Ascending aorta 119Calculating results 122Confirming contours 120Correcting phase aliasing 123Correcting ROIs 120Defining evaluation regions 118Descending aorta 119Drawing ROIs 119, 119, 119Evaluating vessels 121Limiting the time range 122Loading images 116Optimizing image display 117Performing baselinecorrection 123Propagating vessel contours 120

Arterial Spin LabelingRefer to ASL 50

ASLInline evaluation 55Inversion slabs 55Quality check parameter 54Setting parameters 52

ASL data evaluation 97Generating t-maps 99

BBOLD 3D evaluation 87

Clip planes 90Creating MPR ranges 89Displaying functional data 93Evaluating VOIs 92Loading BOLD tensor series 87Optimizing image display 88Saving results 94

Setting 3D view 90BOLD examination 57

3D anatomy 58BOLD AddIn 57Field map 58GLM evaluation 58Measuring the localizer 58Motion correction 61Paradigm 60Performing the measurement 62Preparing 18Spatial filter 61Threshold value 60

BOLD parameter map calculation 94Editing protocols 96Loading data 95Monitoring post-processing 96Saving protocols 96Starting post-processing 96

Brain Dot Engine 39Examination strategy 39Measuring the scout 41Post-contrast images 42Transverse images 42

CCA

Preparing the injection 18Carotid artery

Flow measurements 63Contrast agent

Refer to CA 18Creating alpha images with BOLD

Refer to Alpha images 100

DDiffusion

Cards 136Gradient directions 138Measuring 43Mode 44Parameters 46Result images 47

Dot EngineBrain Dot Engine 39Spine Dot Engine 26

DSI Acquisition 48DTI Evaluation 104

Loading tensor series 104Saving image maps 107Visualizing DTI maps 105

DTI Tractography 108Applying quicktrackfunction 113Creating seed points 113Loading data 108Managing seed points 115Managing tracts 115Optimizing diffusion display 110Optimizing image display 109Saving seed points 115Saving tracts 115Setting the view fortractography 111Showing the overview ofdiffusion tracts 110Starting tractography 114

EElectrodes

Attaching 20Positioning 19Procurement addresses 20

Evaluating ASL dataRefer to ASL data evaluation 97

Examination strategyBrain Dot Engine 39Spine Dot Engine 30

FFlow analysis with argus

Refer to Argus flow analysis 116Flow measurements 63

Flow sensitivity 65Localizer 63Performing the measurement 65Slice position 64

HHead imaging 24

Index


IiPat

Head imaging 24Spine imaging 24

MMotion artifacts

Reducing 18

NNeuro diffusion examination

Refer to Diffusion 43Neuro perfusion evaluation

Refer to Perfusion 82Neuro perfusion examination

Refer to Perfusion 43

PPatient

Preparing 18Perfusion

Calculating the mean AIF 83Editing protocols 86Loading data 82Measuring 47Optimizing image display 82Performing reconstructions 85Saving protocols 86Selecting a post-processingprotocol 83Setting the time range 84

PERUPositioning 19

PositioningElectrodes 19PERU 19

Post-contrast imagesBrain Dot Engine 42

Preparing the patient 18Procurement addresses

Electrodes 20

RResolve sequence 45

SSagittal images

Spine Dot Engine 33Scan@center 68Scout

Brain Dot Engine 41Spine Dot Engine 32

SequenceQuiet 25

SpectroscopyCSI: slice positioning 70, 71CSI: suppressing interferencesignals 72Frequency adjustment 76Measuring raw data 78Planning the examination 67Protocol adjustment 73Scan@center 68Shim results 75Shimming interactively 74

Spectroscopy evaluationAdding peaks 131Adjusting the referenceimage 126Adjusting the spectrumdisplay 126Calculatint the sumspectrum 129Changing the CSI slice 127Displaying metaboliteimages 129Displaying spectral maps 128Evaluating voxels of interest 126Loading CSI data 125Performing phasecorrection 130Saving protocols 133Saving result tables 131

Spectroscopy Evaluation 124Spine Dot Engine 26

Examination strategy 30Measuring the scout 32Sagittal images 33Transverse images 37Vertebra labeling 34

Spine imaging 24

StrategyBrain Dot Engine 39Spine Dot Engine 30

TTransverse images

Brain Dot Engine 42Spine Dot Engine 37

VVertebra labeling 34


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The CE marking applies only to medico-technical products/medical products introduced in connection with the above-mentioned comprehensive EC regulation.

Global Business UnitSiemens AGMedical SolutionsMagnetic ResonanceHenkestr. 127DE-91052 ErlangenGermanyPhone: +49913184-0www.siemens.com/healthcare

Global Siemens HeadquartersSiemens AGWittelsbacherplatz 280333 MuenchenGermany

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Legal ManufacturerSiemens AGWittelsbacherplatz 2DE-80333 MuenchenGermany

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