syngo MR E11 Operator Manual Neuro Answers for life.

Transcription

1 syngo MR E11 Operator Manual Neuro Answers for life.

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3 syngo MR E11 Operator Manual Neuro

4 Legend Indicates a hint Is used to provide information on how to avoid operating errors or information emphasizing important details Indicates the solution of a problem Is used to provide troubleshooting information or answers to frequently asked questions Indicates a list item Indicates a prerequisite Is used for a condition that has to be fulfilled before starting a particular operation Indicates a one-step operation Indicates steps within operating sequences Italic Is used for references and for table or figure titles Is used to identify a link to related information as well as previous or next steps Bold Blue Courier Courier Menu > Menu Item <variable> Is used to identify window titles, menu items, function names, buttons, and keys, for example, the Save button Is used to emphasize particularly important sections of the text Is used for on-screen output of the system including code-related elements or commands Is used to identify inputs you need to provide Is used for the navigation to a certain submenu entry Is used to identify variables or parameters, for example, within a string CAUTION Used with the safety alert symbol, indicates a hazardous situation which, if not avoided, could result in minor or moderate injury or material damage. CAUTION consists of the following elements: Information about the nature of a hazardous situation Consequences of not avoiding a hazardous situation Methods of avoiding a hazardous situation 4 Neuro Operator Manual

5 Legend WARNING Indicates a hazardous situation which, if not avoided, could result in death or serious injury. WARNING consists of the following elements: Information about the nature of a hazardous situation Consequences of not avoiding a hazardous situation Methods of avoiding a hazardous situation syngo MR E11 5

6 Legend 6 Neuro Operator Manual

7 Table of contents 1 Introduction Layout of the operator manual The current operator manual Intended use Authorized operating personnel Definitions of different persons 15 2 Preparation Preparing and positioning the patient Reducing motion artifacts Preparing the contrast agent injection Preparing a BOLD examination 18 Instructing the patient 18 Positioning the patient Preparing ECG-triggered examinations 19 Positioning the electrodes and PERU 19 Attaching ECG electrodes 20 Procurement addresses 20 3 Measurement Application hints Head imaging with ipat Spine imaging with ipat Quiet MR sequences 25 Quiet SE and TSE 25 Quiet GRE 26 Quiet PETRA 26 syngo MR E11 7

8 Table of contents 3.2 Spine Dot Engine Planning the examination and measuring the localizer 30 Adapting the examination to the patient 30 Starting the measurement of the AASpine_Scout Measuring sagittal images Verifying vertebra labeling 34 Editing vertebra labeling 35 Adding / removing vertebra disk positions 36 Label transverse images 36 Saving images 36 Accepting vertebra position and labeling Measuring transverse images Brain Dot Engine Planning the examination and measuring the localizer 39 Adapting the examination to the patient 39 Starting the measurement of the AAHead_Scout Measuring transverse images Measuring post-contrast images (optional) Performing diffusion and perfusion examinations Measuring the diffusion 43 Selecting the diffusion mode 44 Setting specific parameters for RESOLVE 45 Setting the diffusion parameters 46 Result images Measuring the perfusion Diffusion Spectrum Imaging (DSI) Acquisition Planning the q-space measurement 49 8 Neuro Operator Manual

9 Table of contents 3.6 Measuring perfusion with Arterial Spin Labeling A brief description of the ASL technique 51 Explanation of the key acquisition parameters and limitations Setting parameters 52 The Quality check parameter (2D ASL only) Planning inversion slabs and determining evaluations 55 Dimensioning the labeling slab 56 Setting Inline evaluation Performing a BOLD examination Measuring the localizer, the 3D anatomy and the field map Establishing the GLM evaluation Defining the threshold value and paradigm Determining motion correction and the spatial filter Performing the measurement Measuring the flow in the internal carotid artery Measuring the localizers Determining the slice position Determining the flow sensitivity Performing the measurement H MR spectroscopy of the head Planning the examination 67 MRS with scan@center 68 CSI: transferring slice positioning 70 Positioning the CSI slice 71 CSI: suppressing interference signals Starting protocol adjustments (optional) Shimming interactively (optional) Improving shim results (optional) 75 Example Channel X Adjusting the frequency (optional) Measuring raw data 78 syngo MR E11 9

10 Table of contents 4 Post-processing Neuro perfusion evaluation Preparing the data 82 Loading images for evaluation 82 Optimizing the image display Evaluating the data 82 Selecting a post-processing protocol 83 Calculating the mean AIF (global AIF) 83 Setting the time range (global AIF) 84 Performing reconstructions Editing and saving the post-processing protocol BOLD 3D Evaluation Preparing the data 87 Loading the image series 87 Optimizing the display 88 Creating an MPR range 89 Setting the 3D view Evaluating the data 92 Evaluating a VOI 92 Displaying functional data as a film Saving and filming the images BOLD parameter map calculation Preparing the data 95 Loading the data Evaluating the data 96 Starting post-processing 96 Monitoring post-processing Editing and saving the post-processing protocol Evaluating ASL data D ASL-specific modules Interpretation of results Generating t-maps Creating alpha images with BOLD Preparing and evaluating the data 101 Loading the data 101 Scrolling through image stacks 101 Optimizing the image display Saving the images Neuro Operator Manual

11 Table of contents 4.6 DTI Evaluation Preparing the data 104 Loading the tensor series Evaluating the data 105 Visualizing the DTI maps Saving an image map DTI Tractography Preparing the data 108 Loading the volume data 108 Optimizing the display in Fusion mode 109 Showing the overview of diffusion tracts 110 Optimizing the diffusion display 110 Setting the view for tractography 111 Applying the Quicktrack function Evaluating the data 113 Creating seed points 113 Starting tractography 114 Managing seed points and tracts Saving seed points or tracts Flow analysis with Argus Preparing the data 116 Loading the image data 116 Optimizing the image display Defining the evaluation regions 118 Drawing the ROI for the ascending aorta 119 Drawing the ROI for the descending aorta 119 Analyzing low velocities (optional) 119 Propagating the vessel contours to other cardiac phases 120 Confirming the propagated vessel contours Evaluating the vessels 121 Calculating results with standard settings 122 Limiting the time range 122 Performing baseline correction 123 Correcting phase aliasing 123 syngo MR E11 11

12 Table of contents 4.9 Spectroscopy Evaluation Preparing the data 125 Loading the data 125 Adjusting the reference image Evaluating the data 126 Evaluating voxels of interest 126 Adjusting the spectrum display 126 Changing the CSI slice 127 Displaying spectral maps 128 Displaying metabolite images 129 Calculating the sum spectrum 129 Performing phase correction 130 Adding a peak Documenting the results 131 Generating and saving a result table 131 Saving and filming the results 133 Saving new post-processing protocol Appendix Diffusion cards Preset diffusion gradient directions Defining customized diffusion directions Creating the DVS 140 Required syntax 140 Valid DVS, example Importing the DVS Exporting the DVS 145 Index Neuro Operator Manual

13 Introduction 1 1 Introduction In order to operate the MR system accurately and safely, the operating personnel must have the necessary expertise as well as knowledge of the complete operator manual. The operator manual must be read carefully prior to using the MR system. 1.1 Layout of the operator manual Your complete operator manual is split up into several volumes to improve readability. Each of these individual operator manuals covers a specific topic: Hardware components (system, coils, etc.) Software (measurement, evaluation, etc.) Another element of the complete operator manual is the information provided for the system owner of the MR system. The extent of the respective operator manual depends on the system configuration used and may vary. All components of the complete operator manual may include safety information that needs to be adhered to. The operator manuals for hardware and software address the authorized user. Basic knowledge in operating PCs and software is a prerequisite. 1.2 The current operator manual This manual may include descriptions covering standard as well as optional hardware and software. Contact your Siemens Sales Organization with respect to the hardware and software available for your system. The description of an option does not infer a legal requirement to provide it. syngo MR E11 13

14 1 Introduction The graphics, figures, and medical images used in this operator manual are examples only. The actual display and design of these may be slightly different on your system. Male and female patients are referred to as the patient for the sake of simplicity. 1.3 Intended use Your MAGNETOM MR system is indicated for use as a magnetic resonance diagnostic device (MRDD) that produces transverse, sagittal, coronal and oblique cross sectional images, spectroscopic images and/or spectra, and that displays the internal structure and/or function of the head, body, or extremities. Other physical parameters derived from the images and/or spectra may also be produced. Depending on the region of interest, contrast agents 1 may be used. These images and/or spectra and the physical parameters derived from the images and/or spectra when interpreted by a trained physician yield information that may assist in diagnosis. 1 The drugs mentioned herein shall be used consistent with the approved labeling and/or indications for use of the drug. The treating physician bears the sole responsibility for the diagnosis and treatment of patients, including drugs and doses prescribed in connection with such use. Your MAGNETOM MR system may also be used for imaging during interventional procedures when performed with MR compatible devices such as in-room displays and MR Safe biopsy needles. The MAGNETOM MR system is not a device with measuring function as defined in the Medical Device Directive (MDD). Quantitative measured values obtained are for informational purposes 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. 14 Neuro Operator Manual

15 Introduction 1 Your MR system is a medical device for human use only! 1.4 Authorized operating personnel The MAGNETOM MR system must be operated according to the intended use and only by qualified persons with the necessary knowledge 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 as safe handling of MR systems. The user must be familiar with potential hazard and safety guidelines the same way the user is familiar with emergency and rescue scenarios. In addition, the user has to have read and understood the contents of the operator manual. Please contact Siemens Service for more information on available training options and suggested duration and frequency of such training Definitions of different persons Term used User/Operator/ Operating personnel System owner Explanation Person who operates the system or software, takes care of the patient or reads images Typically physicians, trained radiological technicians, or technologists Person who is responsible for the MR environment. This includes legal requirements, emergency plans, employee information and qualifications, as well as maintenance/repair. syngo MR E11 15

16 1 Introduction Term used MR worker Explanation Person who works within the controlled access area or MR environment User/Operator as well as further personnel (for example, cleaning staff, facility manager, service personnel) Siemens Service/service personnel Group of specially trained persons who are authorized by Siemens to perform certain maintenance activities References to Siemens Service include service personnel authorized by Siemens. 16 Neuro Operator Manual

17 Preparation 2 2 Preparation 2.1 Preparing and positioning the patient 18 syngo MR E11 17

18 2 Preparation Preparing and positioning the patient Reducing motion artifacts 1 Instruct the patient to hold completely still during the entire examination. 2 Instruct the patient to take shallow and gentle breaths during the measurements Preparing the contrast agent injection Prior to moving the patient table into the magnet, you route the tube for 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 from the outside when the patient is in the magnet bore. 3 Connect the tube to the contrast agent injector Preparing a BOLD examination A targeted search for active brain areas requires precisely defined stimulations. These are obtained through stimulation during the measurement. In what follows we explain BOLD imaging using finger tapping as our example. Optimal cooperation by the patient plays a decisive role in the success of the BOLD examination. Instructing the patient During the BOLD measurement, the patient first moves the fingers of his right hand for 10 measurements during finger tapping. The patient then switches over to his left hand and moves his fingers again for 10 measurements. 18 Neuro Operator Manual

19 Preparation 2 Explain in detail the tasks to be performed and practice them with the patient. Positioning the patient 1 Ensure that the patient is comfortable to avoid motion and consequent artifacts. 2 If required, use positioning aids Preparing ECG-triggered examinations Positioning the electrodes and PERU Electrodes: Positioning of the electrodes varies according to the position 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 the patient table even though the patient may be positioned feet first in the direction of the magnet bore. Position the PERU in the appropriate support or add absorbent material between the ECG cables, PERU and skin. The distance between PERU and patient should be at least 2 cm. Positioning the ECG electrodes (left) and the PERU (right). syngo MR E11 19

20 2 Preparation The transmitter unit of the PERU includes three LEDs for signaling the battery status and one LED as fault indicator (e.g. insufficient skin contact of the ECG electrodes). Battery status and electrode fault are also indicated on the Dot display above the magnet bore and the Physiological Display dialog window. If the red LED Electrode fault on the PERU flashes, the ECG electrodes are not attached correctly. Check to ensure that the electrodes are not falling off. Attaching ECG electrodes The electrodes must be positioned and attached with care to ensure a sufficient and consistent ECG signal. 1 Discuss the breathholds and respective commands with the patient. 2 Ensure satisfactory contact between the electrodes and the patient's skin. 3 Thoroughly clean the patient's skin with a dry cloth or NUPREP ECG & EEG Abrasive Skin Prepping Gel. ( Page 20 Procurement addresses) 4 If the patient is hirsute, shave the location where you want to attach 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 the location of the electrodes. Use new electrodes every single time. 8 If one of the leads does not provide a sufficient signal, change to a single ECG lead in the Physiological Display dialog window. Procurement addresses Disposable ECG electrodes may be ordered from: 20 Neuro Operator Manual

21 Preparation 2 Siemens Commercial goods (Catalog Med & More), CONMED 2700 Cleartrace Item no (600 pieces) or from: CONMED CORPORATION, 310 Broad Street, Utica, New York 13501, USA Cleaning gel: NUPREP ECG & EEG Abrasive Skin Prepping Gel Weaver and Company, 565 Nucla Way, Unit B, Aurora, Colorado 80011, USA syngo MR E11 21

22 2 Preparation 22 Neuro Operator Manual

23 Measurement 3 3 Measurement 3.1 Application hints Spine Dot Engine Brain Dot Engine Performing diffusion and perfusion examinations Diffusion Spectrum Imaging (DSI) Acquisition Measuring perfusion with Arterial Spin Labeling Performing a BOLD examination Measuring the flow in the internal carotid artery H MR spectroscopy of the head 66 syngo MR E11 23

24 3 Measurement Application hints Head imaging with ipat The Head/Neck 20 is ipat-compatible in all directions. Advantages: Shorter measurement times for standard protocols (e.g., T1 or T2 weighting). 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 ipat Phase-encoding direction/ipat factor: When you use the Spine 32 with phase-encoding direction H>>F or L>>R a maximum ipat factor of 4 is possible. Phase-encoding direction H>>F: The FoV (including phase oversampling) must be covered by a sufficient number of coil elements. For example, for an ipat factor of 3, the selected FoV must cover at least 3 coil elements. 24 Neuro Operator Manual

25 Measurement 3 Phase-encoding direction A>>P is not sensible because the coil acts like a single coil in this case Quiet MR sequences Quiet MR sequences offer increased patient comfort examinations by enabling noise-reduced studies. Siemens original noise-reduced protocols are provided in the Quiet program folders of the exam database, for example, Head>Library>Quiet. CAUTION Performing a noise reduced measurement without adequate hearing protection! Danger of temporary damaging the sense of hearing Always wear adequate hearing protection, even with noise reduced measurements. Quiet SE and TSE Both SE and FSE quiet TSE sequences are standard siemens sequences but provided with an additional Acoustic noise reduction parameter. Protocols based on Quiet SE/TSE sequences provide T1 weighted, T2 weighted, and Dark-Fluid contrast, and a consistent contrast behaviour like the regular protocols. syngo MR E11 25

26 3 Measurement Use: Protocols with a Quiet SE/TSE sequence are measured as normal protocols. You can toggle between quiet and regular imaging by enabling/disabling Acoustic noise reduction in the corresponding selection list of the Sequence/Part 2 parameter card. In case of the Quiet TSE sequence, raising the value of Echo Spacing in the Sequence/Part 1 parameter card increases the effect of noise reduction. Quiet GRE The Quiet GRE sequence is a standard siemens sequence but provided with an additional Acoustic noise reduction parameter. Protocols based on the Quiet GRE sequence provide T1 weighted and SWI contrast, and a consistent contrast behaviour like the regular protocols. Use: Protocols with a Quiet GRE sequence are measured as usual protocols. You can toggle between quiet and regular imaging by enabling/disabling Acoustic noise reduction in the corresponding selection list of the Sequence/Part 2 parameter card. Quiet PETRA Quiet PETRA is a 3D only method and acquires 3D isotropic data. Protocols based on the Quiet PETRA sequence provide T1 weighted contrast similar to the MPRAGE protocol. 3.2 Spine Dot Engine The Spine Dot Engine provides comprehensive c-, t-, and l-spine examination workflows to help simplify the complexity of these examinations with respect to planning, scanning, and reviewing measurements. 26 Neuro Operator Manual

27 Measurement 3 If desired the Dot Engine workflow can be customized. In order to enable all the functionality of the Dot Engine workflow the following 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 met For a detailed description, please refer to: Operator Manual - Dot Cockpit. The Dot Engine user interfaces shown in this operator manual are examples only. The actual guidance texts and the design may be slightly different on your system. Functions: The following are key features of the Spine Dot Engine: Detection of the spine geometry including vertebras and vertebra disks 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 spine anatomy as pure sagittal or coronal projections onto a virtual center plane, providing an X-ray/MIP-like overview of the spine geometry. Thin/normal CPR images are labeled "CPR" and thick CPR images are labeled "CPR*" in the image text. CPR and CPR* images must not be used for diagnostic purposes. Series containing CPR* images cannot be used as reference images for position display. syngo MR E11 27

28 3 Measurement Example of coronal (left) and sagittal (right) CPR images with vertebra numbering In addition to standard MPR images, CPR images serve as a basis for validation of the vertebrae labeling suggested by the system and may be used primarily for positioning of mainly sagittal or coronal slices. A warning symbol is displayed in CPR images with axial intersection lines indicating possible deviations between the displayed lines and the true intersected anatomy due to spinal curvature. Spine Planning Layout: A special GSP layout with three planning segments is provided to simplify the image management in spine examinations. (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 28 Neuro Operator Manual

29 Measurement 3 Using individual protocols: The following requirements have to be met when using individual protocols within the Spine Dot workflow: The AutoAlign parameter Spine > Cervical, Spine > Thoracic, or Spine > Lumbar must be selected The Spine Positioning AddIn must be linked to the protocol Specific advice: For scanning l-spine with a three-stage AA localiser feet to head, positioning the laser light marker at the l-spine is recommended. The three-stage AASpine_Scout is then measured from bottom to top starting at the l-spine. As an advantage, the localizer images of the l-spine are displayed first which allows to check the l-spine slice positioning while the remaining localizer images are being acquired. To reduce the noise level of the AASpine_Scout, TR can be slightly increased. This may involve a few additional seconds of measurement time. For patients with strong kyphosis the AASpine_Scout should be measured with a slight increase of the Slices per slab in the AutoAlign_Spine scout to avoid missing parts of the spine. Please be aware that additional slices may involve a few additional seconds of measurement time. syngo MR E11 29

30 3 Measurement For children, a two-stage scout may be sufficient to cover the whole spine during routine positioning. To ensure sufficient overlapping of the measured regions, table movement between the scout stages should not exceed 210 mm. MR scanning has not been established as safe for imaging fetuses and infants under two years of age. The responsible physician must evaluate the benefit of the MRI examination in comparison to other imaging procedures Planning the examination and measuring the localizer In 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 superior portion of the acetabulum Adapting the examination to the patient After registration, the Patient View opens automatically. The default examination parameters are loaded. 30 Neuro Operator Manual

31 Measurement 3 Selecting the examination strategy From the list: Select a suitable Exam Strategy for the patient. Standard Standard examination for clinical routine issues like back pain, osteoporosis, etc. Lesion Standard examination for c-spine and t- spine, with contrast agent and special lesion contrast by tirm (mainly for MS, but also for unspecific inflammation processes) Post Surgery High Bandwidth Routine post surgery examination with contrast agent (mandatory) Provides protocols using the WARP sequence technique with reduced sensitivity to susceptibility artifacts if the patient has MR Conditional implants. Please adhere to all safety instructions regarding implants. (Refer to Operator Manual MR System.) The pending protocols of the measurement queue are updated upon your selection. syngo MR E11 31

32 3 Measurement In the following example, the strategy Standard is selected. To change the examination strategy after beginning a study, you can access the Patient View at any time with this icon: For more information, please refer to the Scanning section of the Operator Manual Scanning and postprocessing. Starting the measurement of the AASpine_Scout The AASpine_Scout is a 3D localizer used to determine anatomical structures within the respective spine region, providing high contrast between vertebras and vertebra disks. 32 Neuro Operator Manual

33 Measurement 3 To start the Spine Dot Engine workflow, confirm the settings on the 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 the AutoAlign 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 the protocol before measurement. syngo MR E11 33

34 3 Measurement AutoCoverage can be used here to let the system auto-adapt the protocol to the detected width of the spine part within a predefined range of parameters (e.g. slices per slab, distance factor). A working-man symbol should be applied in the protocol setup if opening and confirming the sagittal protocol prior to measurement is desired in general Verifying vertebra labeling In this step the detected position and labeling of the vertebras and intervertebral disks are checked and confirmed. The position of the vertebral disks is used for the prescription of the slices and anterior saturation region. Within this step, the user also decides that all following transverse images are labeled with their corresponding location in the spine (For example: the image comment is set to L5/ S1 ). 34 Neuro Operator Manual

35 Measurement 3 AASpine_Scout has been measured The AutoAlign verification step has been opened 1 Carefully check for correct positioning and labeling of the vertebras in the reference images. 2 To check positioning, scroll through the image stacks with the Series +/ and the Image +/ keys. Editing vertebra labeling 1 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 be edited. 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. syngo MR E11 35

36 3 Measurement Missing label positions can be created by adding missing vertebra disk positions above/below the vertebra body first. Adding / removing vertebra disk positions 1 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 image first, 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 images You can specify whether the corresponding vertebra labels will be added 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, the transverse images of the subsequent measurements will not be labeled. Selecting either Confirm or Decline is necessary to unlock the Apply button to continue scanning. Saving images You can save the current slice positioning and vertebra labeling overview images. These images are appended to the patient data within an additional AutoAlign verification series. Save the images with this icon. 36 Neuro Operator Manual

37 Measurement 3 The image of the active GSP segment will be saved to the local database. To save the sagittal and coronal images, select the corresponding segment and save each independently. If the images are not saved, you may view the spine geometry later on by duplicating the concluded AutoAlign verification step with Append. Accepting vertebra position and labeling Conclude the verification step with this icon. The confirmed intervertrebral disc positions and vertebra labeling are applied. Further modifications are disabled. If the check box Label transverse images is selected the vertebra labeling is applied as image comment to the subsequent transverse measurements. 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 for final positioning of axial slices. syngo MR E11 37

38 3 Measurement 1 In the reference images, check the positioning of the slices or slabs and correct them, if necessary. Spine Positioning Assistant and AutoCoverage cannot be used in combination with Set-n-Go protocols in this software version. The slice / slab groups snap into the disk cartridges upon dragging if the number of slices within a slice group is less than 9. Thick slice groups (with 9 or more slices) can be smoothly moved up and down along the detected spine geometry. If the protocol contains a regular sat, it will be placed anterior to the spine. If a protocol initially has more than one regular sat, only the first sat will be auto-positioned and used as an anterior sat. The other sats remain unchanged. 38 Neuro Operator Manual

39 Measurement 3 To suppress snapping, keep the following keys pressed while dragging: Shift key for free translation of slice / slab groups Ctrl key for free rotation of slice / slab groups Slight corrections within proximity of the disk position are possible without pressing the Shift or Ctrl key. 2 Start the measurement. 3.3 Brain Dot Engine The Brain Dot Engine provides a simplified workflow to perform a standard head examination. You may also configure the Dot Engine workflow. For a detailed description, please refer to: Operator Manual System and data management. The Dot Engine user interfaces shown in this operator manual are examples only. The actual guidance texts and the design may be slightly different on your system Planning the examination and measuring the localizer Head coil has been selected Patient has been registered Brain Dot Engine has been selected Adapting the examination to the patient After registration, the Patient View opens automatically. The default examination parameters are loaded. syngo MR E11 39

40 3 Measurement In the Patient View you select a suitable examination strategy and decide if contrast agent is to be administered. The pending protocols of the measurement queue are updated upon your selection. Selecting the examination strategy From the list: Select a suitable Exam Strategy for the patient. Standard Standard examination with 2D protocols. Resolution focus Speed focus Motion-insensitive Examination with 3D protocols for detailed views. Examination with fast protocols. Examination with BLADE protocols for motion correction. In the following example, the strategy Standard is selected. To change the examination strategy after beginning a study, you can access the Patient View at any time with this icon: For more information, please refer to the Scanning section of the Operator Manual Scanning and postprocessing. 40 Neuro Operator Manual

41 Measurement 3 Using contrast agent Select without Contrast agent if no contrast agent is to be used. All contrast agent protocols will be removed from the measurement queue. Starting the measurement of the AAHead_Scout The AAHead_Scout is used to determine anatomical structures within the 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 protocol parameters for covering the head part of interest are determined (AutoCoverage) and taken into account. (For a detailed description of the AutoAlign feature, please refer to: Operator Manual System and data management.) Subsequently, the sagittal protocol is automatically measured and loaded to the GSP (protocol without working man symbol). The next protocol opens (protocol with working man symbol). syngo MR E11 41

42 3 Measurement Measuring transverse images Sagittal images have been measured 1 Check the positioning of the slices or slabs and reposition them if necessary. You can also modify several sequence parameters of the current protocol using the Parameter View. Here, you find the most important sequence parameters, e.g., the number of slices or the FoV. To display the complete sequence parameters of the Routine parameter card, click the icon. 2 Start the measurement 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. 42 Neuro Operator Manual

43 Measurement 3 2 In the Exam paused dialog window: Start the post-contrast measurement after a suitable time with Continue. 3.4 Performing diffusion and perfusion examinations If you want to obtain both structural and functional information regarding the pathophysiology of a brain disease, perform an MR examination by combining anatomical MR imaging with MR angiography as well as diffusion and perfusion imaging. Typically, prior to the diffusion measurement the following measurements have been performed: Control measurement for bleeding Angiography measurement (e.g., Time-of-flight protocol) T2 diagnosis Measuring the diffusion To evaluate diffusion in the brain, you measure transverse slices of the entire head. You set the diffusion-specific parameter on the Diff parameter card. syngo MR E11 43

44 3 Measurement Single-shot or multi-shot (RESOLVE) imaging: With the RESOLVE method, a multi-shot diffusion-weighted imaging sequence is used which provides an improved image quality compared to standard single-shot echo-planar imaging (ss-epi). RESOLVE supports all the standard acquisition and data processing features for diffusion imaging (DWI) and diffusion tensor imaging (DTI) that appear on the Diff parameter card with the ss-epi (ep2d_diff) sequence. Selecting the diffusion mode The diffusion mode describes the measurement procedure and the diffusion-sensitive orientation. In the following, we are focusing on diffusion modes 3-Scan Trace and MDDW. 3-Scan Trace diffusion mode: The measurements are performed in three random directions. 3 scans are required per image. Since the diffusion directions are not linked to anatomy, no diffusion-weighted images are stored. Original images cannot be saved. Trace-weighted images and ADC maps can be stored by activating the corresponding checkboxes. Diffusion mode MDDW: Measurements are performed in at least 6 directions, a maximum of 256 directions is possible. For b-value = 0, a diffusion-weighted image is generated for each slice position. When the b-value is > 0, an image is generated for the b-value and each diffusion orientation. These images can be saved as original images in the mosaic format. Trace-weighted images and ADC maps are stored 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 postprocessed with the Neuro 3D task card. Setting diffusion mode parameter 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). 44 Neuro Operator Manual

45 Measurement 3 Example: 3-Scan Trace mode selected. Setting specific parameters for RESOLVE The following additional parameters are specific for resolve sequences: Parameter card Resolution Common Resolution Common Sequence Part 2 Parameter Readout segments Readout partial Fourier Reacquisition mode Effect Increasing the number of Readout segments reduces the minimum echospacing (and the associated artefacts) for a given spatial resolution increases the available spatial resolution for a fixed echospacing Reduces the number of shots that are required to generate an image A reacquisition process is used to repeat scans that result in unusable data. On is recommended for all brain studies. syngo MR E11 45

46 3 Measurement Set the required parameters in the respective parameter cards. Setting the diffusion parameters Requested diffusion mode (3-Scan Trace or MDDW) has been selected. 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. The maximum value that can be set is 10,000. Higher b-values extend TE. In the 3-Scan Trace mode 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 the Inline technique. In the MDDW mode 1 Determine the number of Diffusion directions. 2 Select FA maps (Fractional Anisotropy) and the Tensor. The Tensor parameter determines whether the diffusion tensor data are stored in the database. It is therefore possible to evaluate diffusion in the Neuro 3D task card. Trace-weighted images and ADC maps can be stored by activating the corresponding checkboxes. Noise level 1 Use Noise level to establish the intensity at which pixels are included for the calculation of the ADC value. 2 Start the measurement. Computing tensor data offline It is also possible to retroactively (offline) compute tensor data from diffusion images. 1 In the Patient Browser: Select a series with diffusion images (MDDW). 2 Start the computation of the tensor data. 46 Neuro Operator Manual

47 Measurement 3 Result images 3-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 perfusion As a supplement to the diffusion imaging, you may want to determine the perfusion parameters in the region under examination. You perform a perfusion measurement with contrast agent administration and 50 measurement repetitions. Use the Inline technology to compute the GBP, PBP, relcbf, relcbv, relcbvcorr, and TTP 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. syngo MR E11 47

48 3 Measurement 3 Set the number of measurement repetitions (in this case: 50 measurements). 4 Select GBP, PBP, relcbf, relcbv, relcbvcorr, and TTP. 5 Start the measurement. 6 While the measurement is running, administer the contrast agent intravenously as a bolus. Original images are generated per slice position (one image per measurement) 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. 3.5 Diffusion Spectrum Imaging (DSI) Acquisition Advanced 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 diffusion directions and b-values in a single measurement. DSI is only available for MAGNETOM Prisma, Prima fit and Skyra fit. 48 Neuro Operator Manual

49 Measurement 3 A dedicated diffusion mode (q-space) enables the acquisition of corresponding data. This mode employs a Cartesian sampling pattern, permitting isotropic sampling of a spherical region in q-space with user defined step size. Concerning image processing: The DICOM images using the DSI acquired method can be used for further post-processing offline. Processing can also be performed using the same functionality provided with the MDDW diffusion mode. This utilizes the diffusion tensor imaging model, supporting up to 256 directions Planning the q-space measurement 1 Open the Diff Neuro parameter card. 2 Select the q-space diffusion mode. 3 Set the q-space specific measurement parameters. q-space weightings q-space max. b- value Number of q-space coordinates sampled along each positive coordinate axis (including the origin). b-value that corresponds to the diffusion weighting of the outermost q-space coordinates. syngo MR E11 49

50 3 Measurement q-space coverage Full Complete q-space coverage (sampling of a spherical q- space region). Half Partial q-space coverage (only one half of the sphere is sampled, thus reducing the acquisition time). 3.6 Measuring perfusion with Arterial Spin Labeling Perfusion measurements with Arterial Spin Labeling (ASL) require no contrast agent. In addition, if contrast agent has been administered, ASL imaging is not possible during the session. The sequence acquires an M0 scan (2D ASL only) followed by pairs of label/control images. The Inline Display shows the progress of the ASL measurement. No post-processing step is necessary and you are able to evaluate the image results as usual or you can use the extended functions 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. 50 Neuro Operator Manual

51 Measurement A brief description of the ASL technique ASL is a magnetization preparation technique that sensitizes the MR contrast to the inflowing blood signal. Using the blood water content as an endogenous tracer coupled with a long delay time, a labeled bolus of blood passes through the vascular tree into the capillary bed and eventually the parenchyma. When a label image and a suitable control image are subtracted, as in digital subtraction angiography, the resulting difference signal directly reflects tissue perfusion.the spin labeling magnetization preparation for syngo ASL uses a selective adiabatic inversion pulse to label inflowing spins with high efficiency. Explanation of the key acquisition parameters and limitations The bolus of blood delivered to the tissue of interest is controlled via periodic saturation pulses. The periodic saturation pulses terminate the bolus at a predefined time interval resulting in an accurate definition of the bolus. The resulting effect on the images is the removal of late arriving blood and the reduction of intravascular signal in the perfusion-weighted image. Coupling bolus termination with long inflow times allows the labeled bolus to reach the tissue phase of the vascular tree and improves the perfusion weighting. The length of the bolus is determined by the Bolus Duration parameter, and the inflow time is directly specified by the Inversion Time parameter. Shorter bolus duration times, i.e. lower than ms, typically result in reduced signal and hence poorer signal-to-noise ratio. Inflow time is the time between the labeling/inversion pulse and the readout/imaging module. PICORE, proximal inversion with a control for off-resonance effects (2D ASL), is the labelling strategy which labels blood below the imaging slab. syngo MR E11 51

52 3 Measurement FAIR, flow-sensitive alternating inversion recovery (3D ASL), is the imaging strategy which labels blood within the imaging slab Setting parameters Localizer has been measured Set the labeling/timing parameters in the Contrast ASL parameter card for the 2D sequence. 52 Neuro Operator Manual

53 Measurement 3 or Alternatively, set the labeling/timing parameters in the Contrast ASL parameter card for the 3D sequence. Perfusion mode Suppression Mode Bolus Duration Quality check Inversion Time Picore Q2T labels below the imaging slab (fixed 2D) while FAIR QII labels on the imaging slab (fixed 3D). Enables background suppression of multiple tissues. (3D only, fixed) Determines the duration of the bolus of labeled blood. Typical value is 700 ms. Enables outlier analysis to detect and reject images with excessive motion before calculating parameter maps (2D only). Array of independent inversion times giving the overall time between inversion pulse and excitation of the first slice. The ASL signal increases with shorter inversion times. However transit artifacts are created in the arterial voxels as well. syngo MR E11 53

54 3 Measurement Inversion time should be long enough to transport the bolus into the image slices, that is, it should be equal or larger than the arterial transit time. Typical values: ms. When adjusting the inversion time, consider the patient's age, the pathology, and the expected blood flow rates. Particularly for neonates, children, and elderly persons, the adequate values might differ substantially. Averaging mode Inversion Array Size Measurements can be weighted to acquire more images at later inversion times to optimize contrast-to-noise. (3D only, fixed to CONSTANT) Determines the number of inversion times to measure. (2D limited to 1) Collecting data at multiple inversion times allows quantification of bolus arrival times. Flow Limit Strength of the bipolar gradient between excitation and readout. The parameter is used to attenuate the signal from large arteries. TE is increased. At the maximum value 100 cm/s (standard setting), the gradient is switched off. (2D only) With shorter inversion times ( ms), lower flow limits of 1 10 cm/s are required. The Quality check parameter (2D ASL only) To further ensure the quality of a series of paired label/control images, an outlier detection procedure is used to discard image pairs in which motion is detected. The outlier detection algorithm examines the difference map of pairs of label and control images as they are acquired (inline processing). When a control/label pair is identified as an outlier it is discarded and does not participate in the construction of final ASL maps, e.g. perfusion-weighted maps. 54 Neuro Operator Manual

55 Measurement 3 The Quality check parameter has 3 modes: Off On On extended No outlier rejection takes place Outlier rejection automatically takes place and final/corrected results are displayed (default) In addition to the results displayed in the On case, additional information is also displayed, such as the difference image of the perfusion-weighted images in On and Off cases Planning inversion slabs and determining evaluations ASL measurements should be performed with a minimized TE and acquired in transverse planes. The sequences assume that blood is traveling perpendicular to the imaging slab. Parameters for labeling/timing have been set syngo MR E11 55

56 3 Measurement Dimensioning the labeling slab Picore Q2T labels below the imaging slab. The gap between the inversion slab and the imaging plane should be minimized. and is controlled by the Gap parameter. Set the Gap in the Geometry Saturation parameter card. FAIR QII requires no special planning. Setting Inline evaluation Evaluation and motion correction are set in the Perf parameter card. 1 Activate the Motion correction checkbox to enable motion compensation. 2 Activate the Spatial filter checkbox to apply spatial filtering to the data. 3 Specify the Filter Width in mm to precisely control the level of filtering. Typical range for ASL is 4 mm to 8 mm. 56 Neuro Operator Manual

57 Measurement Performing a BOLD examination In the following example we show functional localization during motor stimulation by finger tapping. The course as well as the selection of parameters have been established for evaluating the measurement data with the Neuro 3D task card. For other stimulations, specific stimulation devices are available from third-party companies. With the BOLD Add-In, synchronization of certain stimulation devices and data acquisition can be facilitated. BOLD imaging requires excellent planning and evaluations. Sufficient experience is required to obtain precise localization and reliable results. Paradigm files: BOLD AddIn allows the usage of (external) paradigm files. If a paradigm is selected, the calculation of the t-maps is controlled by the settings in the paradigm file. The corresponding parameters on the BOLD parameter card are hidden. Example of the BOLD parameter card when a paradigm is selected via BOLD AddIn. The BOLD AddIn also supports realtime exporting of image data to an external PC, if configured. syngo MR E11 57

58 3 Measurement Measuring the localizer, the 3D anatomy and the field map 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 subsequent overlays. 3 Measure the images as 3D anatomy (3D slab), e.g., with an MPRAGE 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 36 transverse slices (slice thickness = 3 mm) to cover the area of interest. If the number of slices corresponds to a square number (6 6, 7 7, 8 8, ), the total surface area of the mosaic images is optimally used. T-maps may be spatially distorted. As a result, superposed images may lead to spatial shifts. Check at all times by superposing anatomical EPI images or a field map Establishing the GLM evaluation 1 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. 58 Neuro Operator Manual

59 Measurement 3 The GLM Statistics checkbox is activated. The data are acquired with the GLM Method (General Linear Model). If the parameter is deactivated, the images are saved without evaluation. 4 Activate the Dynamic t-maps. 5 Confirm the changes with Apply. The t-maps generated during the measurement of each measurement volume are saved. During the measurement, they are displayed in the Neuro 3D task card. In addition, at the beginning of the measurement, a StartFMRI series is generated which can be deleted after ending the experiment. 6 Set Starting ignore meas to 0. Determines the number of measurements that are ignored at the beginning of the experiment to avoid interferences caused by the experimental response at the beginning of the measurement. 7 Set Ignore after transition to 0. Determines the number of measurements to be ignored when changing the stimulus to avoid interferences caused by the experimental response. syngo MR E11 59

60 3 Measurement When measurements are ignored after the transitions, it is no longer possible to account for the time offset between the data measured and the model in GLM. 8 Activate Model transition states. Determines that the hemodynamic response of the brain will be used for computation. The paradigm is convoluted with the hemodynamic response to obtain a reasonable model of the activity-time course. When Model transition states is active and the parameter Ignore after transition is at zero, the first derivation of the model of the hemodynamic response is added to the design matrix at the covariants of no Interest. This means that a timeoffset of the measured data to the model is modelled up to one second and therefore considered in the statistics. 9 Activate Temp. highpass filter. Determines whether amplitude fluctuations can be eliminated over time via a high-pass filter. The limit frequency is determined automatically. The basic functions of a modeled drift are shown in the last columns of the design matrix. They are part of the covariants of no 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 will be 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 hand and 10 measurements of the left hand). 60 Neuro Operator Manual

61 Measurement 3 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 the total number of Measurements. A duration of e.g., 60 or 100 is appropriate. It must correspond to at least the size of the paradigm. If the BOLD Add-In is attached to the protocol and a paradigm is selected in the BOLD Add-In, modification of the paradigm on the BOLD parameter card is not possible. If an appropriate paradigm is selected in the BOLD Add-In, also multi-contrast BOLD acquisitions 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 method under Interpolation. Prospective motion correction is performed automatically via the PACE protocol. 3 Activate spatial filtration. syngo MR E11 61

62 3 Measurement Motion-corrected and/or filtered images can no longer be converted into original images. For this reason, images that are not corrected are stored automatically as their own series when selecting motion correction and/or filtration. For example, the series can be processed at external evaluation consoles (for research purposes, etc.). Motion correction via PACE is performed during the measurement. This means that it is retained in the uncorrected series as well Performing the measurement Motion correction/filtration has been determined 1 Start the measurement. 2 Perform the entire measurement sequence of the periodic paradigm with the set number of measurements (sequential measurement series). Example: The paradigm includes 10 measurements each of the left and right hand. Provide the respective command after 10 measurements (after the end of the baseline or active). For this purpose, monitor the measurement counter in the status line. You can monitor the measurements on the optional Neuro 3D task card 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 62 Neuro Operator Manual

63 Measurement 3 t-maps (EvaSeries_GLM) Overlaid images (Mean-&-t-maps) An uncooperative patient (moves or does not follow the paradigm) leads to artifacts and incorrect results. For this reason, monitor the patient during the measurement. 3.8 Measuring the flow in the internal carotid artery To display flow and the encoding of the flow velocity, phase contrast images are used. (For a detailed description of the phase contrast technique, please refer to the MR Basic Manual Magnets, Flows, and Artifacts.) A number of stenotic changes in the cervical vessels take place 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 chin frequently 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 the center of the slab. syngo MR E11 63

64 3 Measurement 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 internal carotid artery. The resulting image should show the vessel of interest with a circular shape. Positioning the measurement slice (left, center) and the slice image with the 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 task card. 5 Accept the slice position of the image from the 3D series. 6 Select the correctly positioned slice and select Tools > Copy Image Position. 64 Neuro Operator Manual

65 Measurement Determining the flow sensitivity To obtain the correct velocity and venc to be applied to the sequence the user may use a venc_scout scan, applied with 4 different venc values. 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 the average cycle. 3 On the Angio Common parameter card: Set the velocity encoding to 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 v max Performing the measurement Flow sensitivity has been determined 1 Check the FoV. 2 On the Physio Signal1 parameter card: Accept the average heart cycle for the acquisition window. 3 On the Angio Common parameter card: Enter the computed venc into 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. 6 Start the measurement. syngo MR E11 65

66 3 Measurement Flow-compensated, flow-encoded, and phase-contrast image of the internal carotid artery (arrow). As an alternative, the measurement can be performed with retrospective gating. The average heart cycle is then accepted in the target RR window H MR spectroscopy of the head Two techniques are used for allocating the spectra signals with the anatomical volume given. 1H SVS measurement: The SVS (Single Voxel Spectroscopy) technique is used in 1H MRS of the brain to examine focal pathologies (e.g. tumors). In order to optimally distinguish between pathological and healthy structures, you have to acquire a reference spectrum from a healthy part of the brain in addition to the spectrum of the examination volume. The SVS method allows focusing of the shimming 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 3D slab). A spectra matrix is produced. 1H CSI MRS of the brain enables you to detect, for example changes in the concentration of specific metabolites caused by strokes or tumors. This includes metabolites such as N-acetyl-aspartate (NAA), creatine (Cr) and choline (Cho). The detection and spatial distribution of lactate also plays an important role. 66 Neuro Operator Manual

67 Measurement Planning the examination Appropriate coil has been selected Patient has been registered Compile a suitable spectroscopy measurement program. Example SVS. Example CSI: csi_se = 2D hybrid CSI with spin echo; _135 = echo time in ms. syngo MR E11 67

68 3 Measurement This is how you ensure correct spatial allocation of spectra to reference images: Ensure that the reference images and spectra are measured without temporary repositioning Instruct the patient not to move at all, if possible during the entire examination (including measurement pauses). MRS with To plan spectroscopy measurement and for the post-processing you need non-distortion corrected images (ND) in the three main orientations. Spectroscopy measurements must be performed at the same table position as the ND images used for planning. When performing spectroscopy after a routine imaging examination, the existing images are generally used to plan the measurement. If you already know at the beginning of the examination that a spectroscopy measurement will follow, you can deselect the Positioning mode ISO prior to measuring the reference images. Planning in non-isocentric reference images Centrally localized images (DIS3D) of the examination region from the same table position are available 1 Select a reference image with high contrast in the graphic slice positioning (GSP). 2 Open a spectroscopy protocol. All images of the selected series are reloaded as ND images into the GSP. Images of different orientations (DIS3D) are automatically unloaded from the GSP. 68 Neuro Operator Manual

69 Measurement 3 ND images: table position = 0. If ND images with different orientations are available from the current examination, you can load them directly from the program control. You can also generate a new series with ND images from suitable, distortion-corrected images (menu: Evaluation > Inverse 2D Distortion Correction). Planning in isocentric reference images 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 reference image, are automatically removed from the GSP. The selected reference image is converted into a ND image. DIS2D images: different table positions. syngo MR E11 69

70 3 Measurement 3 Measure additional localizers or reference images with additional orientations (ND images). Measuring scan@center reference images Use the scan@center localizers to measure ND images in the isocenter which are optimally suited for planning and post-processing in spectroscopy. 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 or localizer_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 ND images 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 and orientation of the reference images. 1 Look for the reference image including the anatomical region of interest. 2 Change the display of the reference image until it is optimal for planning the examination. 3 Select the reference image. 70 Neuro Operator Manual

71 Measurement 3 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 plane of the reference image. The orientation of the CSI slice corresponds now to the slice orientation of the reference image. For controlling the position of the measurement volume in adjacent reference images, menu: Scroll > Nearest. Positioning the CSI slice Both position and size of the CSI slice have to be adjusted to the anatomical characteristics of the patient. In the Geometry Common parameter card: Adjust the FoV and VOI. syngo MR E11 71

72 3 Measurement 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 predefined plane (in-plane). If the CSI protocol uses an interpolated matrix, you are able to adjust the screen display (menu: View > CSI Matrix > Interpolated Matrix). CSI: suppressing interference signals For CSI measurements with a spin echo sequence, it is recommended to suppress signal contributions outside the VOI (Outer Volume Suppression, OVS). 1 In the Geometry Common parameter card: Select Fully excited VOI. All metabolites of interest are uniformly excited in the VOI selected. Additionally, 4 saturation regions are positioned automatically (not displayed). 2 Suppress interfering signal contributions by arranging up to 8 freely positionable saturation regions around the VOI. Typical positioning in the head: 4 saturation regions for covering the skull cap, including 2 transverse saturation regions for suppressing venous and arterial flow. 72 Neuro Operator Manual

73 Measurement Starting protocol adjustments (optional) Semi-automatic adjustments are recommended for difficult anatomical regions (e.g., flow, vessels, jumps in susceptibility). You can check the shim status prior to the spectroscopy measurement and 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. syngo MR E11 73

74 3 Measurement All protocol adjustments are performed (as displayed in the information window) Shimming interactively (optional) The shim quality is particularly important for spectroscopy examinations. Use interactive shimming for checking and improving the examination. By changing the shim currents, you are able to optimize the results (FWHM, T2*). Protocol adjustment has ended 1 In the Manual Adjustments dialog window: Select the Interactive Shim subtask card. 74 Neuro Operator Manual

75 Measurement 3 2 Start the shim with Measure. An infinite measurement is performed with the currently set shim parameters. 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 Hz T2*: as large as possible. Depends on voxel size and the metabolites contained within. 4 End the measurement with Stop as soon as you are satisfied with the results. (Otherwise: ( Page 75 Improving shim results (optional)).) During visual inspection: If the water is less than twice the fat amplitude, the size and/or position of the voxel should be readjusted. 5 Apply the shim results to the following spectroscopy measurement with 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 improve the homogeneity of the magnetic field by changing the shim currents. Interactive Shim subtask card has been opened Shim results are not satisfactory Change the gradient offset for one shim channel. Example Channel X 1 Increase the value with the up arrow button. syngo MR E11 75

76 3 Measurement 2 Monitor FWHM and T2*. If the result worsens: 3 Use the best shim results of the current measurement with Load Best. 4 Change the gradient offset in the other direction (use the down arrow 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 measurement with 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 Frequency subtask card. 76 Neuro Operator Manual

77 Measurement 3 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 system with Close. You can now begin with the spectroscopy measurement. syngo MR E11 77

78 3 Measurement Measuring raw data You are starting to generate the spectroscopy raw data. During the measurement, you are able to monitor the raw signal in the Inline Display and control the measurement accordingly. 1 Start the measurement. All adjustments required are performed automatically prior to the measurement. For most applications, the default values of the adjustment configuration that have been currently determined are considered optimal. (Otherwise: ( Page 73 Starting protocol adjustments (optional)) 2 To open the Inline Display, select View > Inline Display from the main 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 the reference images are automatically stored in the patient database (as shown by the icons). 78 Neuro Operator Manual

79 Measurement 3 Icons for reference images and spectroscopy raw data in the Patient Browser. For a description of evaluating spectra, please refer to: ( Page 124 Spectroscopy Evaluation) syngo MR E11 Follow-up examinations: Use the Phoenix functionality of the syngo software to recall the same measurement protocol. This ensures that the same parameters are used for all measurements except the voxel size, which may be adjusted to the reduced size of the tumor. 79

80 3 Measurement 80 Neuro Operator Manual

81 Post-processing 4 4 Post-processing 4.1 Neuro perfusion evaluation BOLD 3D Evaluation BOLD parameter map calculation Evaluating ASL data Creating alpha images with BOLD DTI Evaluation DTI Tractography Flow analysis with Argus Spectroscopy Evaluation 124 syngo MR E11 81

82 4 Post-processing 4.1 Neuro perfusion evaluation The perfusion post-processing function allows you to display and evaluate perfusion-weighted images, for example, as a tool to help in tumor diagnosis. The reconstructed parameter images are based on a post-processing protocol, a calculated arterial input function (AIF), and a set time range. The following example describes how to perform analysis of neuro perfusion data Preparing the data Loading 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 display 1 Window the images to optimize their contrast and brightness. 2 Define the color display of the parameter images via the color palette in the control area Evaluating the data Local AIF method: The local AIF method determines the incoming flow of contrast agent for a reference volume around every voxel. 82 Neuro Operator Manual

83 Post-processing 4 This method reduces artifacts due to arterial flow differences between 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 method determines the incoming flow of contrast agent in one reference ROI for all voxels. To reduce sensitivity to vascular delays when calculating relcbf and relmtt, Delay Correction should be active in the global AIF post-processing protocol. ( Page 86 Editing and saving the post-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, and relmtt maps, you can also use the local AIF method to calculate relcbf, relcbv, relcvbcorr, and relmtt maps. This avoids the manual selection of the arterial input function The local AIF checkbox has been deactivated to calculate maps with the global AIF method. 1 Scroll through the series in the top left segment to find a suitable basic image for positioning the AIF ROI. 2 Draw an AIF ROI in the basic image with the icon in the control area. The AIF curves are displayed on the Step 1: Select AIF subtask card for all pixels within the AIF ROI. syngo MR E11 83

84 4 Post-processing 3 Click and drag the AIF ROI box over the selected artery. After you release the mouse button, the associated AIF curves are displayed 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 not explicitly recognizable as vessels in the basic image. 4 Select the AIF curve(s) with the flattest base line and the deepest curve (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. 84 Neuro Operator Manual

85 Post-processing 4 2 Define the time range used for perfusion analysis by moving the lines. Observe the GBP curve. The bolus arrives later in the tissue than in the vessel. Do not define the end of the first pass (right line) to the 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 postprocessing. When reconstruction is completed, the parameter images are shown in the lower two segments. syngo MR E11 85

86 4 Post-processing Editing and saving the post-processing protocol The post-processing protocol defines the sequence and properties of the individual post-processing steps. Only experienced users should edit post-processing protocols! 1 Select the required post-processing protocol from the selection list in 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. 86 Neuro Operator Manual

87 Post-processing 4 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. 4.2 BOLD 3D Evaluation syngo BOLD 3D Evaluation allows post-processing of fmri data including motion correction, spatial filtering, and statistical evaluation. The results of the evaluation of specific regions of the brain are displayed graphically. The movie function allows you to track the movement of the head during the examination. The following example describes how to visualize and evaluate BOLD fmri data Preparing the data Loading 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. syngo MR E11 87

88 4 Post-processing 3 Click the Study icon in the upper control area for an overview of the loaded volumes. Optimizing the display Click the icon to activate the Fusion mode. Adjusting the VRT display 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 the selected parameter set is displayed. Defining the image area 1 Open the Fieldmap Properties dialog window with Visual > Fieldmap Properties. 2 Use the slider to determine the pixel shift of the field map that marks the image area. Adjusting the functional data display 1 Open the Functional Properties dialog window with Visual > Functional Properties. 88 Neuro Operator Manual

89 Post-processing 4 2 Select the expanded view of the dialog window with More >>. 3 Activate the Activation Map Filter checkbox to make the display of activation data a function of cluster size. 4 Enter the desired cluster size. Creating an MPR range You can create a series of parallel MPR Thick images which are perpendicular 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. syngo MR E11 89

90 4 Post-processing The image planes of the planned result images are drawn into the reference segment. The MPR corresponding to the center line is displayed in the 3D segment. 3 To move the image planes, click and drag the center to the desired position. Saving the MPR range 4 To change the distance between images, activate the icon in the MPR Range Properties dialog window. 5 Move the first or last line of the MPR range in the 3D segment up or down. 6 Start reconstruction with the icon in the MPR Range Properties dialog window. When reconstruction is finished, the reference images are displayed 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 view In the Fusion mode, the 3D view is superposed on the fourth segment. 90 Neuro Operator Manual

91 Post-processing 4 Showing clip planes Clip planes are used to eliminate overlying tissue. In this way, areas with activation in the image volume are shown. The volume outside the 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 VRT volume image. 3 Double-click the fourth segment to enlarge the 3D view. Rotating the 3D view The orientation cube at the bottom right of the image shows the orientation 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. syngo MR E11 91

92 4 Post-processing A double-click anywhere in the orientation cube sets the volume image to front view and original size. Moving clip planes Drag the frame of the clip plane to the desired position. Rotating clip planes 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. Moving image planes Drag the reference line between the image center and the arrow to the desired position Evaluating the data Evaluating a VOI 1 Switch to Evaluation Mode with the icon in the control area. The VOI tool is activated. The graphic segment superposes the third image segment. 2 To evaluate specific regions of the brain, draw a circle over the region of interest in a 2D segment. The graphic segment displays the evaluated functional data of the drawn Volume of Interest (VOI). 92 Neuro Operator Manual

93 Post-processing 4 (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 film Using the movie properties in the Functional mode, you can track the movement 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 of the BOLD volume and the activation distribution (standard MPR) are displayed. 2 Start the movie with the icon in the control area. syngo MR E11 93

94 4 Post-processing The movie task bar opens. The individual BOLD volumes are displayed in sequence from first to last, then again from the beginning Saving and filming the images 1 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 segment displays 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. 4.3 BOLD parameter map calculation The following example describes how to calculate parameter maps retroactively with syngo BOLD. The pixels of the post-processed parameter images carry functional information. CAUTION BOLD post-processing with image data generated by Numaris 3 or 3.5! Incorrect diagnosis through erroneous superposition of anatomical and functional image Do not use syngo MR for BOLD processing with image data generated with Numaris 3 or Neuro Operator Manual

95 Post-processing Preparing the data Loading the data Functional image series (EPI measurements) is available for evaluation 1 Select the functional series in the Patient Browser. 2 Load the series into the BOLD task card with Applications > BOLD Evaluation. 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 meet all requirements. This means that the series (EPI measurements) does not originate from the same series block with identical table position, frame of reference, slice position, and number of images. Remove the series from the list with Delete Series. syngo MR E11 95

96 4 Post-processing Evaluating the data Starting post-processing 1 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 as mosaic 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 protocol The post-processing protocol defines the sequence and properties of the individual post-processing steps. Only experienced users should edit post-processing protocols! 1 Select the required post-processing protocol from the selection list in the Evaluation Controller Dialog. 2 Open the Edit Protocol dialog window with Edit. 96 Neuro Operator Manual

97 Post-processing 4 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 modules syngo ASL 3D incorporates a double inversion background suppression scheme that can simultaneously suppress two tissue types with differing T1 values. Background suppression reduces sensitivity to motion and improves the subtraction between the label and control images. The imaging module employed in syngo ASL 3D uses a modified fast spin echo approach that acquires several gradient recalled echoes during the interval between the refocusing pulses. The gradient recalled echoes are encoded using echo-planar imaging. Variants of this approach are often termed 3D GRASE or TGSE. The sequence acquires volumetric imaging with 3D encoding and short echo times with centric reordering tables. For large imaging matrices the echo train may become prohibitively long due to T2 relaxation of the signal. For these cases the sequence offers the flexibility to segment the acquisition in both phase encoding directions. Segmentation improves image quality and reduces blurring while also increasing the number of shots used and hence leads to improved signal-to-noise ratio. syngo MR E11 97

98 4 Post-processing 3D ASL acquisition output: (left) Original EPI image series; (right) Perfusionweighted image Interpretation of results For 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: 98 Neuro Operator Manual

99 Post-processing 4 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 (in that order). PWI and relcbf images are typically represented using a colour map where low signal values are depicted using black/dark blue colour and high signal values are shown in yellow/red. The windowing of the colourmap can be performed by selecting an image, pressing the mouse wheel and moving the mouse cursor Generating t-maps EPI-PASL measurement has been performed For further processing, the image results obtained are displayed in the Viewing task card. You can perform additional inline or offline processing on the original or motion corrected EPI series using the GLM Statistics of the BOLD task card. (1) Original EPI image series (2) Motion-corrected EPI image series syngo MR E11 99

100 4 Post-processing (3) Perfusion-weighted images (PWI) (4) relcbf images 1 Transfer the requested EPI series (original or motion-corrected) to the BOLD task card. ( Page 94 BOLD parameter map calculation) 2 In the Evaluation Controller Dialog: Select the requested postprocessing 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. Only experienced users should edit post-processing protocols! Starting ignore meas. Model transition states 1 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 with Execute. The dialog window closes and post-processing starts. The resulting t-map corresponds to the perfusion-weighted map. 4.5 Creating alpha images with BOLD The following example describes how to create alpha images with syngo BOLD. The Alpha image is created by overlaying an anatomical image with a parameter map. 100 Neuro Operator Manual

101 Post-processing Preparing and evaluating the data Loading the data MR anatomical images and corresponding MR parameter images are available 1 Select the anatomical series and the parameter image series in the Patient Browser. 2 Transfer the images to the BOLD task card with Applications > BOLD. Anatomical series are loaded to the first segment, parameter image series to the second segment. Automatically calculated alpha images are displayed in the third segment. Only the alpha image for the currently displayed image pair (anatomical image and parameter image) is calculated and displayed. If calculation of an alpha image is not possible, the third 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 is displayed. If the new series originate from the same study, they are sorted according to their series number. You can scroll between series. If the new series are from another study, you decide whether the currently loaded series should be replaced by the new series. Scrolling through image stacks Alpha images are automatically calculated for the images displayed during scrolling. 1 Use the dog ears to scroll image by image through a series. syngo MR E11 101

102 4 Post-processing If the slice position of the currently displayed parameter image matches the slice position of an image in the anatomical series, the anatomical image is displayed and the associated alpha image is calculated. 2 Select Scroll > Series Next / Series Previous to scroll from series to series. If at least one slice position of the selected anatomical series and the parameter image series matches, the first suitable image pair is displayed. The correponding alpha image is calculated and displayed. Optimizing the image display 1 Window the images to optimize their contrast and brightness. 2 Select the color palette for positive (Upper Palette) and negative values (Lower Palette). 3 Use the spin boxes or the lines in the color palettes to adjust the Upper Range and Lower Range of the functional values assigned to a color. 4 Define the minimum pixel intensity of the alpha image in this input field. Anatomical pixels whose intensity falls below the Anatomical Threshold are hidden. 5 Adjust the value in this input field to suppress randomly occuring pixels in the alpha image. Pixel clusters smaller than the Simple Clustering are hidden. 102 Neuro Operator Manual

103 Post-processing 4 6 Define the transparency of the functional data with this input field. The Alpha Value defines the degree to which the pixels of the activation map cover the anatomical image. If the value is 0, only the anatomy is visible. The maximum is Saving the images 1 Store the selected alpha or parameter image with Patient > Save As. or Store all alpha images of the loaded series with Patient > Save All Alpha As. The Save As dialog window opens. 2 Save image(s) in new series. or Append image(s) to an existing series. syngo MR E11 103

104 4 Post-processing 4.6 DTI Evaluation syngo DTI Evaluation allows for quantitative evaluation of the rate and direction of water motion within a voxel, calculation of different diffusion parameters, and graphic display of colored DTI maps Preparing the data Loading 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. 104 Neuro Operator Manual

105 Post-processing 4 (1) FA map (2) ADC map (3) Trace-weighted map (4) b0 map Evaluating the data Visualizing the DTI maps 1 Select the segment you want to change to a new diffusion map. 2 Display the tensor graphic using the icon on the Diffusion subtask card. syngo MR E11 105

106 4 Post-processing Enlarged tensor graphic 3 Display the diffusion texture with the icon on the Diffusion subtask card. 106 Neuro Operator Manual

107 Post-processing 4 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 map 1 Select the segment of the map. 2 Select Patient > Save Diffusion. You can load the saved map in the Viewing task card or send it via PACS. syngo MR E11 107

108 4 Post-processing 4.7 DTI Tractography syngo DTI (Diffusion Tensor Imaging) Tractography uses anisotropic diffusion to graphically display diffusion tracts. When evaluating the diffusion data, 3D visualization of specific white matter tracts is possible. The following example describes how to perform syngo DTI tractography using diffusion tensor data Preparing the data Loading 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 not absolutely necessary. Instead the b0-volume can be used for displaying the anatomy. The b0-volume is included in the tensor dataset 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 and functional data if you first measure the anatomy protocol followed by the BOLD protocol. 108 Neuro Operator Manual

109 Post-processing 4 3 Click the study icon in the upper control area for an overview of the loaded volumes. Optimizing the display in Fusion mode Click the icon to activate the Fusion mode. Adjusting the VRT display 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 the selected parameter set is displayed. Defining the display of the anatomical image 1 Open the Blend Factor Properties dialog window with Visual > Blend Factor Properties. 2 Use the sliders to determine to what level activation and diffusion data are superposed on the anatomical image. Optimizing the image display Window the images to optimize their contrast and brightness. syngo MR E11 109

110 4 Post-processing Showing the overview of diffusion tracts 1 Click the icon to activate the Diffusion mode. 2 To display the diffusion texture, click the icon on the Diffusion subtask 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 diffusion tracts. 5 Use the dog ear to scroll through the image stack. Optimizing the diffusion display 1 Change the display type of the selected image to tensor graphic with the icon on the Diffusion subtask card. 110 Neuro Operator Manual

111 Post-processing 4 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 and the diffusion orientation is shown by the orientation sphere. 4 Open the Diffusion Properties dialog window with the icon on the Diffusion 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 the context menu. Setting the view for tractography Click the icon to activate the Fusion mode. The 3D view is superposed in the fourth segment. syngo MR E11 111

112 4 Post-processing Showing clip planes Clip planes are used to eliminate overlying tissue. That way, areas with activation in the image volume are shown. The volume outside the 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 VRT volume image. 3 Double-click the fourth segment to enlarge the 3D view. Rotating 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 the corresponding side of the orientation cube. 112 Neuro Operator Manual

113 Post-processing 4 A double-click anywhere in the orientation cube sets the volume image to front view and original size. Moving clip planes 1 Select a frame of the clip plane. 2 Drag the frame to the desired position with the mouse. Applying the Quicktrack function The Quicktrack function provides a tractography preview. It is available 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 the image pixel acquired by the mouse pointer. The results are shown automatically in step with the movements of the mouse Evaluating the data Creating seed points Seed points are used as the starting areas for tractography. Seed points can consist of a single voxel only. It is also possible to combine several 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. syngo MR E11 113

114 4 Post-processing The acquired voxels are highlighted in color. They are assigned to the same seed point until you start with a new seed point. You can interrupt marking the voxels at any time to change the view, e.g., by moving the MPR image plane or a clip plane. 2 If desired, start another seed point with New Diffusion Seed-point in the context menu. Newly acquired voxels are immediately assigned to the new seed point and identified with another color. After having started tractography, a new seed point is created automatically. Starting tractography Tractography with a single seed point Select Start Tractography in the context menu for the seed point. All tracts connected to the seed point are acquired and displayed. Tractography between two seed points 1 Select Start Tractography to in the context menu for the seed point. 2 Select the other seed point in the sub-menu. 114 Neuro Operator Manual

115 Post-processing 4 All tracts connected between the two seed points are acquired and displayed. Managing seed points and tracts Changing seed point properties 1 Open the Seed-point Properties dialog window with Properties in the context menu for the seed point. 2 Change the properties of the seed point (name, color) as required. Deleting seed points Changing tract properties Remove all seed points with Tools > Delete All Diffusion Seedpoints. 1 Open the Diffusion Tractography Properties dialog window with Properties in the context menu for the tract group. 2 Select the Visualization subtask card to change the display properties of the tract group (e.g., color). or Select the Tractography subtask card to change the calculation properties (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 As button. 2 Select the File System option to export a seed point or tract to the file system. or Select the Database option to save a seed point or tract as a NonImage series to the database. syngo MR E11 115

116 4 Post-processing or Select Save Tract Volume in the context menu for the tract group to export a tract as a 3D series. 4.8 Flow analysis with Argus Flow analysis is used to determine the mean and maximum velocity of blood flow and the vessel cross-sections depending on the trigger time. The following example describes how to perform flow analysis of through-plane data for the ascending and descending aorta. As the analysis for in-plane data is largely the same, it is not described in what follows. Please note that it is not possible to simultaneously process through-plane and in-plane data within the Argus flow analysis Preparing the data Loading the image data Phase-contrast images and corresponding rephased images are available 1 Select the data series to be analyzed in the Patient Browser (use the Ctrl key for multi-selection). You may also select magnitude images for loading as additional data. 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. 116 Neuro Operator Manual

117 Post-processing 4 (1) Work segments (2) Rephased images (labeled M) (3) Magnitude images (labeled MAG) (4) Phase-contrast images (labeled P) Optimizing the image display 1 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 flow velocities. syngo MR E11 117

118 4 Post-processing If necessary, you can assign a linear color scale instead of the grayscale 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 regions You draw the contours of the vessel cross-sections to define the ROIs for 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 are copied automatically to the images belonging to the same phase. The rephased images show the edges of the vessels more clearly than the phase-contrast images. This makes them especially suitable for drawing. 118 Neuro Operator Manual

119 Post-processing 4 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-sections into a work segment. 2 Draw a circular ROI around the cross section of the ascending aorta. 3 Fit the ROI to the vessel contours of the ascending aorta by clicking the icon. Once the ROI is drawn, the result of the statistical evaluation is shown next to it. The value of the highest flow velocity in the ROI is marked by a point in the image. Drawing the ROI for the descending aorta 1 To start drawing the second ROI, click the R2 icon. 2 Draw a circular ROI around the cross section of the descending aorta. 3 Fit the ROI to the vessel contours of the descending aorta by clicking 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 near the vessel of interest (e.g., in the chest wall or the spine). syngo MR E11 119

120 4 Post-processing The flow parameters of the reference ROI are used for subsequent baseline correction. Please note that if the background signal in the reference region differs significantly from the vessel region, the correction by the reference ROI might not be valid! Propagating the vessel contours to other cardiac phases During propagation, the contours of the ROIs are fitted to the anatomy. 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 Checking the ROIs View the images in a work segment one by one by scrolling through them with the arrow keys of the keyboard. or Display the images using the movie display function of the View subtask card with Graphics On. Correcting the ROIs If ROIs are misaligned, you correct them with the drawing and editing tools. 1 Change the size and the position of the ROI with the Move tool. 120 Neuro Operator Manual

121 Post-processing 4 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, browse through the images with the arrow keys or click the icon on the Drawing subtask card. Confirming the ROIs If propagated ROIs are not explicitly confirmed, a warning will be displayed in the results of the flow analysis. Accept the contours by clicking the icon Evaluating the vessels All tools for evaluation are available on the Result subtask card. You can graph the following parameters as a function of time: Velocity Peak Velocity Flow Net Flow Area Mean velocity within the ROI Peak velocity within the ROI Product of mean velocity and surface area Difference between forward and return flow Cross-section of the vessel During the analysis of in-plane data, it is physically not useful to compute the (net) flow because the vessels are merely truncated. As a result, it is not possible to reliably determine the blood flow through the vessel. For this reason, only the velocity as well as the cross-sectional area of the ROI are determined with in-plane data. syngo MR E11 121

122 4 Post-processing Calculating results with standard settings If the patient data are incomplete, the Patient Information dialog 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, select Flow 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 range By default, the time between the first and last trigger time is used for evaluation. 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. 122 Neuro Operator Manual

123 Post-processing 4 Performing baseline correction Reference ROI has been defined Apply baseline correction with Flow Options > Use Baseline Correction. A baseline is calculated from the flow parameters of the reference ROI and subtracted from the result curve. Baseline correction is indicated in both the image text and the result tables. Correcting phase aliasing Flow velocities that exceed the defined flow sensitivity are shown with an incorrect grey value, resulting in phase aliasing. An exceedingly high positive velocity is shown as a high negative flow velocity (black) and vice versa ( phase reversals ). Phase aliasing can be corrected, as long as the maximum flow velocity does not exceed double the value set as flow sensitivity during the measurement. Examples: (1) Blood flowing too fast causes dark spots in the region of the ascending aorta and bright spots in the region of the descending aorta. (2) Phase reversals can be identified by the local minimum in the systolic phase. The highest velocities are much smaller than expected. syngo MR E11 123

124 4 Post-processing CAUTION Incorrect selection of the range of velocity for a specific organ (preset range of velocity is lower than physiological range of velocity)! Incorrect flow and volume values Correct the parameter range for the organ to be examined. Applying correction 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 this correction. It would require a new measurement. 4.9 Spectroscopy Evaluation Evaluation in MR spectroscopy of the head is typically based on 1 H MRS measurements applying the SVS or the CSI localization technique. The following example describes how to evaluate CSI data. The evaluation of CSI data results in spectra from the voxels of interest in the CSI slice. The spectra provide information regarding the existence, distribution, and ratio of diagnostically relevant metabolites in the examination region. Spectroscopy evaluation also allows creating spectral maps for an overview of spectra of interest as well as displaying the CSI data as colored metabolite images. 124 Neuro Operator Manual

125 Post-processing 4 CAUTION Selection of unsuitable evaluation parameters! Artifacts in the spectrum (additional or covered lines) Ensure that interactive evaluations are handled by experts Preparing the data Loading 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 the CSI slice are displayed. The raw data of a predefined voxel (blue) in the center of the CSI grid is automatically evaluated with the appropriate post-processing protocol. The resulting spectrum is shown together with the associated stamp reference images. syngo MR E11 125

126 4 Post-processing Adjusting the reference image The displayed reference image should show the anatomical region of interest. 1 Activate Image > Auto Selection Mode. When scrolling through reference images, the most suitable CSI slice is selected. 2 Use the dog ear to look for the reference image that shows the anatomical region of interest. 3 To hide interfering graphics, open the Display Parameters dialog window with the icon and deselect the graphic objects in the Images tab card. To only display the VOI and voxel for evaluation, hide Saturation regions, Slice intersections and CSI matrix grid Evaluating the data Evaluating voxels of interest 1 Set the Single Dataset Mode with the icon. 2 Use the protocol for all spectra segments with Protocols > Keep Common. 3 Click the voxel of interest in the CSI slice. The associated spectrum is displayed immediately. Adjusting the spectrum display Scaling the display To improve the interpretation of smaller peaks in the spectrum, you can 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 to enlarge the peaks. 126 Neuro Operator Manual

127 Post-processing 4 As an alternative to alpha-numeric changes, use the mouse to change the scaling of the axes. 4 Drag the mouse across the spectrum. (1) X-axis (range) (2) Y-axis (scale) Displaying peak information 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 slice Instead of the currently displayed CSI slice, you can select another diagnostically 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. The matching reference image is displayed if Auto selection mode is activated. 3 If required, change the Main orientation of the slice. Voxel selection in the reference image remains unchanged. syngo MR E11 127

128 4 Post-processing Displaying spectral maps Spectral maps can be generated only if the reference image lies roughly in parallel to the CSI plane and the projection view includes a complete plane of the CSI grid. 1 Select an empty segment. 2 Open the Spectral Map dialog window with the icon in the control area. 3 Activate the drawing mode with the icon. 4 Draw a polygon around the area of interest in the reference image with Ctrl and left mouse button pressed. 5 Generate the spectral map with OK. The spectral map is superposed on the reference image and displayed in the selected segment. 6 To reduce the computation range again, press the icon and draw a new polygon. 128 Neuro Operator Manual

129 Post-processing 4 7 To delete the computation range completely, press the icon. Displaying metabolite images You can display the voxel-dependent intensity ratio of different metabolites 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 the control 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 and displayed in the selected segment. Metabolite images should be checked against the spectral map to ensure that the fitting process created reasonable values. Calculating the sum spectrum You can display the calculated spectra of the anatomical region of interest 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 > Add spectra. syngo MR E11 129

130 4 Post-processing 3 Select User defined to add the region of interest to the computation range. 4 Generate the sum spectrum with OK. Performing phase correction You can improve the spectrum display with interactive postprocessing. To show the positive signals for the metabolites, correct the phase shift. 130 Neuro Operator Manual

131 Post-processing 4 1 Open the Interactive Post-processing Protocol dialog window with the icon. 2 Select the Phase correction post-processing step. 3 Adjust the constant phase and the frequency-dependent phase component. (1) Moving the mouse left/right keeping the center mouse button pressed changes the constant phase. (2) Moving the mouse up/down keeping the center mouse button pressed changes the frequency-dependent phase component. Adding a peak If the spectrum shows a peak that is not included in the theoretical spectrum (e.g. the lactate peak), you can add it and recalculate the curve 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 a double-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 computation of the curve fit with Automatic Documenting the results Generating and saving a result table The result table shows the integrals of metabolites and metabolite ratios with respect to a reference metabolite. 1 Select the segment for displaying the result table of the selected spectrum. syngo MR E11 131

132 4 Post-processing 2 Open the Result Table Of Current Spectrum dialog window with Signal > Result Table. 3 Select the reference metabolite for computation of metabolite ratios. 4 To combine metabolite results, click Combine. 5 Select the Store in text file checkbox to save the table as a text file. 6 Display the result table in the selected segment with OK. 132 Neuro Operator Manual

133 Post-processing 4 Saving and filming the results 1 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 Film Sheet. Saving new post-processing protocol You can save a changed post-processing protocol, e.g. changes due to 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. syngo MR E11 133

134 4 Post-processing 134 Neuro Operator Manual

135 Appendix 5 5 Appendix 5.1 Diffusion cards Preset diffusion gradient directions Defining customized diffusion directions 140 syngo MR E11 135

136 5 Appendix 5.1 Diffusion cards In what follows you will find the formulas for the diffusion cards. ADC map: Exp map: EXP Map = exp(-b D ) TraceW map: TW Map = S 0 exp(-b D ) FA map: The FA map shows the ratio of the anisotropic diffusion to the medium overall diffusion. RA map: Like the FA map, the RA map (Relative Anisotropy) displays the degree of anisotropy. It shows the ratio of the anisotropic diffusion to the 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 sphere having 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 the diffusion. 136 Neuro Operator Manual

137 Appendix 5 Linear map Shows diffusion taking place in (mostly) one direction only (the ellipsoid is a prolate spheroid) Planar map Shows diffusion taking place in (mostly) two directions (oblate ellipsoid) Spherical map Shows diffusion that is (almost) isotropic (spherical ellipsoid) Mode: The Mode map displays the form of the diffusion tensor. It connects information about the average diffusion coefficient (ADC), the degree of anisotropy (FA), and the orientation of anisotropy. GA map: The GA map (Geodesic Anisotropy) shows the differences in anisotropy by measuring anisotropy similar to Fractional Anisotropy. In this case, the geodesic distance between tensor and the closest isotropic diffusion tensor is measured. (In mathematics, the term geodesic is used for theoretically the shortest connection between two points on a curved surface.) syngo MR E11 137

138 5 Appendix 5.2 Preset diffusion gradient directions The following tables provide you with the diffusion gradient directions used for the 6, 12, and 20 diffusion directions that are used during a MDDW measurement. MDDW 6 directions Direction vectors in the magnet coordinate 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) MDDW 12 directions Direction vectors in the magnet coordinate system 1 ( , , ) 2 ( , , ) 3 ( , , ) 4 ( , , ) 5 ( , , ) 6 ( , , ) 7 ( , , ) 138 Neuro Operator Manual

139 Appendix 5 MDDW 12 directions Direction vectors in the magnet coordinate system 8 ( , , ) 9 ( , , ) 10 ( , , ) 11 ( , , ) 12 ( , , ) MDDW 20 directions Direction vectors in the magnet coordinate system 1 ( , , ) 2 ( , , ) 3 ( , , ) 4 ( , , ) 5 ( , , ) 6 ( , , ) 7 ( , , ) 8 ( , , ) 9 ( , , ) 10 ( , , ) 11 ( , , ) 12 ( , , ) 13 ( , , ) 14 ( , , ) 15 ( , , ) syngo MR E11 139

140 5 Appendix MDDW 20 directions Direction vectors in the magnet coordinate system 16 ( , , ) 17 ( , , ) 18 ( , , ) 19 ( , , ) 20 ( , , ) Direction vectors for additional sets of directions can be obtained through the Application Hotline. 5.3 Defining customized diffusion directions For Diffusion Tensor Imaging (DTI), you can define customized diffusion directions (= diffusion vector sets, DVS). Multiple direction sets (each containing at least 6 linearly independent directions) can be provided in a text file that has to comply with a specific syntax. Careful direction selection is required to ensure a reliable tensor estimation. In general, an isotropic distribution of the diffusion directions is recommended Creating the DVS Required syntax General: #: Lines starting with a hash symbol # are interpreted as comments and get ignored. Empty lines, tabulators and space characters get ignored (with one exception as explained below). There is no case sensitivity. 140 Neuro Operator Manual

141 Appendix 5 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 different numbers of vectors. Please note that this instruction must not contain any spaces or tabulators. Normalization: Each DVS might include a normalization directive: normalization = <norm> where <norm> is either maximum, unity or none. If this directive is missing, unity is used. unity: Each vector gets normalized to unity. This mode will ensure that every direction receives a weighting with the same b-value. maximum: First a unity normalization gets applied. Afterwards, the whole vector set is scaled such that the largest vector component of the whole set is 1.0. This mode you ensure best use of the gradient performance thus yielding the shortest echo times. However, it should only be used in the xyz coordinate system. none: No normalization is applied at all, the vectors are used as provided. For the internal diffusion gradient calculation, the vector with the largest magnitude is taken as the reference. Its amplitude will produce the b-value specified in the user interface (UI). The actual b-value corresponding to a user defined diffusion vector can be calculated by the following equation: b actual = b UI Magnitude actual 2 / Magnitude maximum 2 syngo MR E11 141

142 5 Appendix 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 coordinate system. Diffusion vector directions do not depend on the actual slice orientation. prs: The DVS is played out using the rotation matrix of the current slice, i.e. the phase-read-slice coordinate system is used. Therefore, diffusion vector directions are linked to the actual slice orientation. Comment: Each DVS might contain a comment: comment = <comment> where <comment> is a user defined text that appears as a tooltip in 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 component exceeds a value of 1.0. In prs coordinates, it is required that no vector length exceeds a value of 1.0. Valid DVS, example The following is an example for a valid DVS containing one direction set. # # Example # [directions=6] 142 Neuro Operator Manual

143 Appendix 5 Normalization = unity CoordinateSystem = xyz Comment = 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 vectors given in physical gradient coordinates. It includes a user comment and a unity normalization directive. The latter triggers internal vector re-scaling so their length equals 1.0: Vector[0] = ( , ) Vector[1] = ( , , ) Vector[2] = ( , , ) 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. syngo MR E11 143

144 5 Appendix 3 Start the import of the DVS file. (1) Import A dialogue window opens, displaying the available DVS files. 144 Neuro Operator Manual

145 Appendix 5 4 Select one DVS file and confirm with Open. If the syntax is correct, all contained diffusion vector sets are imported and can be selected, by choosing the corresponding number of diffusion directions in the Diff Neuro parameter card. When a user defined DVS file has been imported, the information becomes part of the measurement protocol. Therefore, it is possible to rerun the same protocol even if the original DVS file is no longer present (for example, when using the Phoenix feature to run the sequence on another scanner). Still, the DTI license will be 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. syngo MR E11 145

146 5 Appendix 3 Start the export of the DVS file. (1) Export A dialogue window opens, allowing you to specify a DVS file. The currently selected user defined DVS is exported using the same syntax as described above. 146 Neuro Operator Manual