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Related Manuals for Siemens fMRI
Summary of Contents for Siemens fMRI
- Page 1 User Guide Version 1.03 www.usa.siemens.com/healthcare...
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Page 2: Table Of Contents
Prerequisites for Running fMRI Studies ........ -
Page 3: Prerequisites For Running Fmri Studies
User Guide 1 Prerequisites for Running fMRI Studies 1.1 Licenses 1.1.1 VB13A, VB15A, VB15B, VB17A Application Package • Licenses – Features Inline BOLD Imaging • Inline BOLD Imaging – Single Shot EPI for BOLD Imaging (ep2d_bold) – Inline BOLD Processing: Paradigm, GLM (General Linear Model), Spatial Filter, ART (Advanced Retrospective Technique) –... -
Page 4: Revisiting The Bold Effect
User Guide 2 Revisiting the Bold Effect fMRI uses the BOLD effect to detect neuronal activation. Let’s review the basic facts: • Oxygen is delivered to the cells attached to hemoglobin • Oxygenated hemoglobin is diamagnetic – very small magnetic moment •... -
Page 5: Sequences
User Guide 3 Sequences 3.1 EPI sequences for BOLD Imaging The following sequences are available as options for acquiring BOLD sensitive images: ep2d_fid • Basic single-shot EPI sequence ep2d_bold • Single-shot EPI sequence with the BOLD imaging card • paradigm, GLM, t-test, spatial filter, etc. -
Page 6: Fmri Acquisition
An optical to TTL “fMRI Trigger Converter” may be purchased from Siemens for this purpose. The output from this box is via a BNC or serial port. There are two different modes of TTL output on this box – impulse mode or toggle mode. Refer to the converter box manual for details. Please contact your local Inside sales representative to purchase this equipment. -
Page 7: Motion Correction
User Guide 3.2.4 Motion Correction MoCo checkbox controls motion correction in general. In the ep2d_pace sequence, if MoCo is not checked, no motion correction is performed. Only the original EPI images are generated. If MoCo is selected, the following functions are performed in MotionCorrDecorator (ICE): •... -
Page 8: Accessing Motion Detection Parameters
User Guide 3.2.7 Accessing Motion Detection Parameters From the above explanation, it is obvious that there is only one set of motion parameters. The difference lies in whether they are used for prospective or retrospective motion correction. The motion parameters can be found under: VB15: C:\Medcom\MCIR\Med\SimMeasData\MotionDetectionParameter.txt... -
Page 9: Slice Timing
User Guide If the number of measurements or averages is greater than one, dummy scans are used. The numbers of dummy scans (used for stabilizing the signal) depend on the TR selected. The sequence takes the TR that is selected by the user, and then calculates how many repeats (so-called “dummy scans”... -
Page 10: Spatial Filter Specifications (Conversion To Mm)
There is no co-registration done in the Neuro3D taskcard. The recommendation is to use AutoAlign during data measurement. This will automatically place all the data sets in the same reference frame. 3.3 fMRI Data analysis For details on how to analyze the BOLD data, please refer to the BOLD Imaging Application brochure. -
Page 11: Peripherals
Following are some of the typical peripheral devices that are used for fMRI studies, and can be interfaced with the Siemens scanners: 1. -
Page 12: Lcd Screen
Scanner Room Control Room Figure 4. An example of an fMRI peripheral equipment setup. GSR: galvanic skin resistance. The cables carrying power and the video signals from the stimulus computer must connect to the screen by means of two filter panels, one between the scanner and control rooms, and the other on the Faraday enclosure around... -
Page 13: Auditory
Both DC and AC power can be easily supplied via a filter in the penetration panel. An extra AC power filter is available in the Siemens panel, but a custom penetration panel can be installed for other filtering needs. -
Page 14: Synchronization
OFF for the next “x” measurements, and ON again for the next set of “x” measurements, and so on. fMRI data analysis then tracks signal change in a voxel over time and correlates signal change to the stimulus presented, as a function of time. -
Page 15: Installing Peripheral Devices
User Guide There are two ways in which one can synchronize activities: manual or automatic. Manual synchronization is not accurate and is therefore not recommended. However, if it is absolutely necessary to manually synchronize your stimulus presentation with the EPI sequence, one first needs to calculate how many dummy scans the EPI sequence will be running (see Section 3.2.8). -
Page 16: Identifying Rf Interference
User Guide 4.8 Identifying RF interference 4.8.1 RF Noise tests Please ask your local service engineer for details on how to run RF noise tests. Noise tests must be performed with the head coil and the table in either the home position or with the table positioned at its farthest end (head coil outside the bore). -
Page 17: Typical Epi Artifacts
User Guide 5 Typical EPI Artifacts The most typical image artifacts in an fMRI exam may be: • N/2 ghosting • Distortion • Spatial shifts • Chemical shift 5.1 N/2 Ghosting Figure 7. Example of N/2 ghosting in an EPI sequence. -
Page 18: Distortion
User Guide 5.2 Distortion Figure 8. Distortion in an EPI sequence. Image (a) (reference) was acquired after shimming and frequency adjustments were performed. The shim was intentionally disturbed in the y-direction to demonstrate global image distortion (stretching) in (b). Despite shimming, there are large susceptibility induced gradients near the sinuses due to air-tissue interfaces that cause local distortions in the frontal lobe (c). -
Page 19: Chemical Shift Artifact
6.1 Study design Let’s run a basic experiment to get started on fMRI. We will run a block design experiment, i.e. ON and OFF design, with a simple motor task such as finger tapping. In this task, the subject touches his/her thumb consecutively with the index, middle, ring, and little fingers of one hand at a time. -
Page 20: Running The Study
6.2 Running the study 1. Set up patient in the head coil. 2. Run a localizer scan from Exam Explorer->Siemens->Head->clinical libraries->general->localizer 3. Then run the MPRAGE scan (t1_mpr_ns_sag_p2_iso) to get an anatomical reference scan. This sequence can be found under Exam Explorer->Siemens->Head->advanced applications->bold-imaging. Use sagittal orientation for the scan volume, and position the volume such that the whole brain is covered. - Page 21 User Guide Figure 14. Positioning scan for the EPI BOLD scan using finger tapping as the paradigm. 5. Ask subject to start finger tapping with his/her right hand, and then start the sequence. 6. The sequence will first run the prep scans. At the bottom left on the screen is a display that indicates what part of the paradigm is running, baseline (“B”) or active (“A”), and the current measurement number (see...
- Page 22 User Guide Figure 15. Counter that indicates time when to switch hands for finger tapping. The sequence starts with displaying “B”, and will show the numbers of measurements counting up from 1 to 60 (total number of measurements). Image (a) shows the counter switching to “A” when the measurement number goes to 11 (since paradigm size is 10).
- Page 23 Also seen in these plots are the motion parameters (translation and rotations in x, y, and z) that were used for prospective motion correction (PACE), as a function of the numbers of measurements. Figure 16. fMRI data processing in the Neuro3D taskcard. Location of the “StartEvaluationMode” button is also indicated.
- Page 24 Wittelsbacherplatz 2 80333 Muenchen Healthcare Sector DE-80333 Muenchen Germany Henkestrasse 127 Germany 91052 Erlangen Germany Phone: +49 9131 84-0 www.siemens.com/healthcare www.siemens.com/healthcare Order No. A9119-91183-C1-4A00 | Printed in USA 07-2009 | All rights reserved | © 2009 Siemens Medical Solutions USA, Inc.