MRI Proton Spectroscopy Principles and Acquisition Techniques

MRI Proton Spectroscopy - Principles and Acquisition Techniques By the end of this course, you will be able to: Summarize the various applications used for MRI Proton Neuro Spectroscopy  Identify the 1H Proton MR Spectroscopy metabolites  Define Spectroscopy Peak Characteristics Review Long and Short echo 1H Proton Brain metabolites Define Single Voxel (SVS) and Multi Voxel (CSI) Proton Spectroscopy techniques Discuss Protocols, Pulse Sequences and Parameters for Single Voxel (SVS) and Multi Voxel (CSI) Proton Spectroscopy  Discuss the examination and voxel positioning workflow for Single Voxel (SVS) and Multi Voxel (CSI) Proton Spectroscopy  Review the semiLASER sequence available on 3 Tesla systems Identify variations of 1H Proton Brain metabolites in selected diseases Spectroscopy – clinical diagnostic tool used to collect biochemical information from localized areas of interest Non-invasive information about metabolic status of tissues Acquired as an additional sequence Clarifies ambiguous finding in clinical images Spectra contain information from tissue metabolites, so they: reflect metabolic states of various tissues show metabolic changes resulting from disease allows monitoring the effect of therapy allows following metabolic pathways in biochemial research   Applications Siemens Acquisition & Post Processing Protocols Tumor Grading 1H Brain, Short TE Tumor Therapy Monitoring & Surgery Planning 1H Brain  Pediatric diseases, inborn metabolic disorders 1H Brain Pediatric Lateralization in Epilepsy 1H Brain  Hepatic Encephalopathy 1H Brain  Complementary findings in Neuro-degenerative disorders 1H Brain  An array of the frequency components of the MR signal according to frequency   Nuclei with different resonant frequencies show up as values at different corresponding frequencies in the Spectrum   Resonances relatively isolated will appear as peaks in the spectrum   A graphic representation of the range over which a spectrum quantity extends Nuclei of different molecular groups "feel" different local magnetic fields N-acetylaspartate or NAA Neuronal and axonal marker – Mainly present in Neurons◦ Singlet Located – 2.02 ppm (CH3) Reduced concentration in tumors, stroke and MS (Multiple Sclerosis) Creatine (Cr) and Phosphocreatine (PCr) Energy marker – Energy metabolism phosphocreatine used in resynthesis of ATP and ADP Singlet Located – 3.02 ppm and 3.9 ppm At times, children show a severe lack of Creatine Phosphocreatine is also observed in muscles (31P MRS) Choline (Cho) Membrane turnover marker – Associated with membrane synthesis and breakdown Present in cell membranes, and reflects membrane synthesis and degradation Singlet Located – 3.2 ppm (CH3) Choline increases in tumors, MS, and ischemia Myo-Inositol (mI) Astrocyte marker Marks glial cells in brain tissue Observed with short echo times (e.g., TE = 20, 30, 40) Doublet Located – 3.56 ppm (CH) Myo-Inositol is elevated in Alzheimer’s Lactate (Lac) End product of anaerobic glycolytic cycle Normal concentration of 1 mM => usually not seen Doublet Located – 1.3 ppm (CH3) when present Lactate increases in tumors, necrosis, abscess, observed in tissues deprived of oxygen Overlaps with strong lipid signals of tumors Lipid Singlet 0.9 ppm and 1.30 ppm when present Lipids appear as a result of Pathology Lipids may appear as a result of contamination from outside VoI if close to lipid containing structures e.g., orbital areas and skull Pediatric Disclaimer: MR scanning has not been established as safe for imaging fetuses and infants less than two years of age. The responsible physician must evaluate the benefits of the MR examination compared to those of other imaging procedures. Name Choline Creatine NAA LactateTe135 Reference: www.radiopaedia.org Creatine Phosphocreatine Reference: www.radiopaedia.org; www.biology-online.org Reference: www.radiopaedia.org; www.biology-online.org Reference: www.radiopaedia.org; www.biology-online.org Reference: www.radiopaedia.org; www.biology-online.org Peak Position Peak position like a fingerprint FWHM (Full Width at Half Maximum height) Indication of Shim Quality Narrower the peak the better the shim Peak Amplitude Depends on amount of metabolite contributing to peak and system field strength Integral value Directly proportional to concentration of metabolite Peak integrals are preferred rather than peak amplitudes since integrated areas take variations of peak line widths into account Peak Amplitute Peak Area / Peak Interval FWHM Water Fat Metabolites Peak Position (ppm) N-Acetylaspartate (NAA) 2.02 ppm Creatine and Phosphocreaine (Cr/PCr) 3.01 ppm 3.90 ppm Choline (Cho) 3.2 ppm Lipids 0.9 ppm and 1.3 ppm Lactate* - when present *Lactate is not seen in normal Brain Spectra 1.3 ppm Additional Peaks Peak Position (ppm) Glutamine and Glutamate (Glx) 2 - 2.45 ppm 3.6 - 3.8 ppm Creatine, Choline, myo-Inositol(Cr/PCrml) 3.56 ppm Glucose 3.43 ppm 3.80 ppm SVS (Single Voxel Spectroscopy) – Techniques PRESS – Point RESolved Spectroscopy Spin-Echo – svs_se STEAM – STimulated Echo Acquisition Mode STEAM – svs_st PRESS or SE (Spin Echo) Benefits Increased Signal to Noise Shorter measurement time Less sensitivity to spin motion (diffusion) STEAM Benefits Less demands on RF Less sensitivity to B1-misadjustment Shortest TE TE = 20 ms Single Voxel Spectroscopy (SVS) Spin Echo sequence (PRESS) TE = 30 - 300 ms TR = 1500 - 5000 ms STEAM sequence TE = 20 - 300 ms TR = 1500 - 5000 ms Voxel Dimensions Spin Echo = 4 - 40 mm (minimum volume 0.5 cc) STEAM = 10 - 40 mm Chemical Shift Imaging Spectroscopy (CSI) Hybrid 2D/3D CSI Spin Echo sequence (PRESS) TE = 30 - 300 ms TR = 1500 - 5000 ms STEAM sequence TE = 20 - 300 ms TR = 1500 - 5000 ms sLASER sequence TE = 40 - 300 ms Voxel Size > 2.5 x 2.5 x 5mm3 Spin Echo FOV > 160 mm STEAM FOV > 160 mm   Exam Explorer – SVS Protocols Head 1H Protocols SVS matrix SVS TxRx Pediatric SVS_matrix Exam Explorer – CSI Protocols Head 1H Protocols CSI matrix CSI TxRx Pediatric CSI_matrix Pediatric Disclaimer: MR scanning has not been established as safe for imaging fetuses and infants less than two years of age. The responsible physician must evaluate the benefits of the MR examination compared to those of other imaging procedures. SVS – Dot Cockpit – Programs Head 1H Protocols SVS matrix SVS TxRx Pediatric SVS_matrix Pediatric Disclaimer: MR scanning has not been established as safe for imaging fetuses and infants less than two years of age. The responsible physician must evaluate the benefits of the MR examination compared to those of other imaging procedures. CSI – Dot Cockpit – Programs Head 1H Protocols CSI matrix CSI TxRx Pediatric CSI_matrix Pediatric Disclaimer: MR scanning has not been established as safe for imaging fetuses and infants less than two years of age. The responsible physician must evaluate the benefits of the MR examination compared to those of other imaging procedures. Applications 1H MRS – Brain Examination of focal pathologies e.g., tumor Helps differentiate between healthy and pathological structures Acquire a reference spectrum from a healthy part of the brain (contralateral); and affected side of the brain (pathology) Advantages Simplicity Flexibility in voxel size and position Accurate Volume of Interest (VOI) Excellent shim and spectral resolution Disclaimer: WIP – Multi nuclear spectroscopy is not currently under development; is not for sale in the U.S. Its future availability cannot be guaranteed. SVS Parameters TR 1.5T = 1500 ms (minimum) 3T = 1700 ms (minimum) TE PRESS or SE = 30, 135, 270 ms STEAM = 20, 135, 270 ms Voxel size = 20x20x20 = 8 cm3 Number of Averages Standardize Procedure Parameters Typical Values SNR Temporal Resolution Spatial Resolution TE ↑ 20 - 300 ms ↓   --- --- TR ↑ 1,500 - 5,000 ms ↑ ↓ --- Averages ↑ SVS = 96 - 256 CSI = 1 - 8 ↑ ↓ --- Voxel Size ↑ 1 - 16 mm3 ↑ --- ↓ TR = 1500 ms TR = 5000 ms 8 Averages 64 Averages 256 Averages Age Dependence – Pediatric versus Adult brain Normal Pediatric Brain Choline – dominant peak Long TE spectra Myo-Inositol – dominant peak Short TE spectra Normal Adult Brain NAA – dominant peak Long and Short TE spectra   Regions of the brain (Regional variations) White versus Gray matter, cerebellum, temporal lobe   Pathology Abscess, tumors, hepatic encephalopathy, epilepsy and degenerative brain disorders 3T Spectroscopy Benefits Increased SNR Increased Spectral Resolution 3T Spectroscopy Challenges Increased chemical shift displacement artifact Increased susceptibility effects Increased RF power Shorter T2 / T2* Increased SAR Decreased RF penetration Routine Parameter Card VoI 20x20x20 = 8 cm3 (Default) 75-80% of pathology should fill VoI of interest   TR 1.5T = 1500 ms (minimum) 3T = 1700 ms (minimum)   TE PRESS or SE = 30, 135, 270 ms STEAM = 20, 135, 270 ms Averages 80 – 1024 Standardize Sectroscopy Procedure Contrast Parameter Card   Water suppression None No Water suppression is applied during measurement Shorter TR available   Water Saturation – normal mode Water suppression pulse is transmitted to fully suppress water signal Contrast Parameter Card Water suppression Weak water suppression – residual water signal Water signal is reduced, not fully suppressed Ability to include water signal in various post-processing functions   Only RF off – reference scan Used to measure a reference raw data set if you want to perform eddy current compensation during a spectroscopy evaluation   Contrast Parameter Card   Water suppr. BW – Bandwidth of high frequency RF pulses for water suppression 1.5T – 35 Hz (Default) 3T – 50 Hz (Default)   Spectral suppr. – Mode for spectral signal suppression (e.g., SE sequences only) Lipid suppr. – Suppression of lipid signal Water suppr. – Suppression of water signals Lipid+ Water suppr. – Suppression of fat and water signal None – No spectral suppression Resolution Parameter Card   Prescan Normalize Filter is switched on – surface and matrix coils (e.g., filter is selected/deselected as a default in the protocol)   Vector size – Number of data points (resolution) 1024 – Brain Spectroscopy (Default) Geometry > Common Parameter Card  Sat. region SE Spectroscopy sequences only Maximum – 8 saturation pulses Freely position and angle sat pulses Sat delta freq. Range = -3.4 ppm – set sat delta frequency to lipid System > Adjustments Parameter Card Adj water suppr – correction factor to rectangular pulses to obtain best suppression On – (Default) Confirm freq adjustment Check box – dialog box appears prior to every measurement, confirm or modify resonance frequency calculated by adjustment On – (Default) Only after freq change – Confirmation dialog box only appears if the resonant frequency was changed during adjustments On – (Default) Sequence Parameter Card Preparation scans – preliminary measurements Sets the number of preparation measurements Results in magnetization equilibrium Delta frequency – indicates frequency shift based on system frequency System sets delta frequency to NAA (Range = -2.3 to -2.7 ppm) Sequence Parameter Card Ref. scan mode – reference scan for eddy current correction Off – No reference scan Inline correction – Reference scan is performed Spectra are corrected, based on reference scan and only corrected spectra are saved No inline correction –  Reference scan is performed Spectra saved – reference scan and uncorrected spectra e.g., Default Save all – Reference scan is performed Spectra are corrected based on reference scan Spectra saved – reference scan, uncorrected and corrected spectra Sequence Parameter Card No. of ref scans – number of averages acquired during the reference scan Phase cycling – phase cycle that eliminates signal interference Auto – Selects phase cycle of the longest cycle that fits into the number of acquisitions e.g., Default 2 Steps – Single phase cycle 8 Steps – eliminates all signal interference of the slice-selective pulses EXOR cycle – 4 steps 16 EXOR cycle – 16 steps, eliminates spurious signals due to RF pulse imperfections Sequence Parameter Card Bandwidth – determines current ADC on-time during data acquisition Acquisition duration – Readout duration Calculated from Bandwidth and Vector size Remove oversampling – oversampling data is removed during automatic evaluation of spectroscopy raw data ON (Default) Freq. corr. Accumulation – internal frequency correction to minimize motion artifacts caused by respiration Off (Default) Open Patient Registration Register a Patient for a Brain with Spectroscopy sequences Run Localizers Open Spectroscopy sequence Select View > Reference Lines On Right mouse > Copy Image Position Copies position & orientation of reference image into spectroscopy sequence Aligns voxel / VoI to reference image Position Voxel over area of interest Scroll > Nearest VOI Solid box Displayed voxel / VoI has true intersection in all 3 planes Dotted box Displayed voxel / VOI in front of or behind selected image plane Select Apply Spectroscopy sequence runs Single Spectrum Result Table Routine Parameter Card FoV – use Default FoV 2D CSI – R>>L and A>>P 3D CSI – R>>L, A>>P, and F>>H e.g., reducing FoV reduces SNR Thickness  15 mm (Default) Range – 5-40 mm Routine Parameter Card VoI – resize VoI 80 mm x 80 mm x 15 mm (Default) 2D CSI – R>>L and A>>P 3D CSI – R>>L, A>>P, and F>>H 75-80% of pathology should fill VoI of interest Routine Parameter Card TR 1.5T = 1500 ms (minimum) 3T = 1700 ms (minimum) TE PRESS or SE – 30 ms, 135 ms, 270 ms STEAM –  20 ms, 135 ms, 270 ms sLASER – 40 ms, 135, ms, 270 ms Averages 2D CSI – 3 or 4 (Default) 3D CSI – 3 or 4 (Default) Range – 1 – 64 Contrast Parameter Card Averaging mode Short Term – measure all averages for a point in the data matrix consecutively Goes to the next point in the data matrix   Long Term – measures all points of the data matrix prior to the data acquisition of the next average Leads to a better suppression of motion artifacts e.g., Default Note – CSI measurements can be terminated in Long Term mode without a complete loss of data if 1 complete average is acquired Contrast Parameter Card Water suppr. None No Water suppression is applied during measurement Shorter TR available   Water Saturation – normal mode Water suppression pulse is transmitted to fully suppress water signal Contrast Parameter Card Water suppr. Weak water suppression – residual water signal Water signal is reduced, not fully suppressed Ability to include water signal in various post-processing functions   Only RF off – reference scan Used to measure a reference raw data set if you want to perform eddy current compensation during a spectroscopy evaluation Contrast Parameter Card Water suppr. BW – Bandwidth of high frequency RF pulses for water suppression 1.5T – 35 Hz (Default) 3T – 50 Hz (Default)   Spectral suppr. – Mode for spectral signal suppression (e.g., SE sequences only) Lipid suppr. – Suppression of lipid signal Water suppr. – Suppression of water signals Lipid+ Water suppr. – Suppression of fats and water signal None – No spectral suppression Resolution Parameter Card Scan res – Define the number of phase-encoding steps in the two spatial directions of a CSI slice or in the three spatial directions of a CSI slab R>>L& A>>P – 16 (Default) Range – 8-32   Interpol res – Define the number of reconstructed spectra in two spatial directions of a CSI slice or in the three spatial directions of a CSI slab R>>L & A>>P – 16 (Default) Options – 16 or 32 Resolution Parameter Card Hamming – A raw data processing filter that prevents voxel bleeding for CSI measurements Prescan Normalize Filter is switched on – surface and matrix coils (e.g., filter is selected/deselected as a default in the protocol) Vector size – Number of data points (resolution) 1024 – Brain Spectroscopy (Default) Geometry > Common Parameter Card Fully excited VoI – Complete excitation of all metabolites within the VoI e.g., only available on CSI sequences Excitation, display and intersection of enlarged VoI   Saturation of unwanted signals Automatic and invisible regional saturation bands outside intersection display VoI Chemical shift artifacts may be problematic with CSI Solution – Fully excited VOI (Volume of Interest) Without Fully Excited VoI   With Fully Excited VoI   Geometry > Common Parameter Card Sat. region SE Spectroscopy sequences only Maximum – 8 saturation pulses Freely position and angle sat pulses   Sat delta freq. Range = -3.4 ppm – sets sat delta frequency to lipid System > Adjustments Parameter Card Adj water suppr – special RF pulse trains are used that suppress the water signal On – (Default)   Confirm freq adjustment Check box – dialog box appears prior to every measurement, confirm or modify resonance frequency calculated by adjustment On – (Default)   Only after freq change – Confirmation dialog box only appears if the resonant frequency was changed during adjustments On – (Default) Sequence Parameter Card Preparation scans  – preliminary measurements Sets the number of preparation measurements Results in equilibrium magnetization   Dimension – Select 2D or 3D CSI measurement   Delta frequency – indicates frequency shift based on system frequency System sets delta frequency to NAA (Range = -2.3 to -2.7 ppm) Sequence Parameter Card Phase encoding – Selection of a phase encoding type Full – entire k-space defined by number of phase-encoding steps is measured   Elliptical – Points within the k-space ellipse acquired with a different number of averages.  Center points acquired with full number of averages and with fewer averages for points near edge of ellipse    Weighted – identical to Elliptical with one average Hamming filter used during measurement increases SNR (e.g., Default) Sequence Parameter Card Bandwidth  – determines current ADC bandwidth during data acquisition   Acquisition duration – Readout duration Calculated from Bandwidth and Vector size   Remove oversampling – oversampling data is removed during automatic evaluation of spectroscopy raw data ON (Default) Open Patient Registration Register a Patient for a Brain with Spectroscopy sequences   Run Localizers   Open Spectroscopy sequence Select View > Reference Lines On Right mouse > Copy Image Position Copies position & orientation of reference image into spectroscopy sequence Aligns voxel / VoI to reference image prior to using scroll nearest Position Voxel over area of interest Scroll > Nearest VOI Solid box Displayed voxel / VoI has true intersection in all 3 planes Dotted box Displayed voxel / VOI in front of or behind selected image plane Select Apply Spectroscopy sequence runs CSI Spectrum CSI Spectral Map Result Table CSI Metabolite image Delta Frequency – 1.7 ppm for Cr Signal at 3.0 ppm; Excitation pulse in RL; Refocusing Pulses in A>>P and F>>H csi_se without fully excited VOI; No Sat bands  → chemical shift artifact for water   (shifted anterior) semiLASER, No Sat bands → reduced chemical shift artifact → in both cases the outer rows and columns have   a reduced intensity and altered metabolite ratios csi_se with fully excited VOI + 4 Sat bands => lipid contamination in edge voxels   semiLASER + 4 Sat bands ≥ no lipid contamination   Stroke NAA ↓ Cr ↓ Ins ↓ Lac ↑↑   Glial Tumors NAA ↓ Cho ↑ Cr ↓   Lac ↑ Lipids ↑ (not always) Meningiomas NAA ↓ Cho ↑ Cr ↓↓ Alanine ↑ Aspartate ↑ Necrosis NAA ↓↓↓ Cho ↓↓↓ Cr ↓↓↓       HIV and Related diseases NAA ↓ Cho ↑ Cr ↓? Lac ↑   MS NAA ↓ Cho ↑     Lac ↑ (Active Plaques) Lipids ↑ Alzheimer's NAA ↓ Cho ↑ Ins ↑   Epilepsy NAA ↓ Cho ↑         Hepatic Encephalopathy Cho↓ Ins ↓ Glx ↑   Hypoxia NAA ↓, Cho ↑, and Cr ↓ = Chronic Hypoxia ↓ Glx ↑, lac ↑, Ins ↑ = Recovered Hypoxia Anoxia NAA ↓ Lac ↑   Brain Abscess Absence NAA Absence Cho Absence Cr   Lac ↑   Diabetes Mellitus NAA ↓ Cho ↑ Ins ↑ Glx ↑   Reference: N. Salibi, M. Brown – Clinical MR Spectroscopy (Wiley-Liss)  You should now be able to: Identify the 1H Proton MR Spectroscopy metabolites    Define Spectroscopy Peak Characteristics   Review Long and Short echo 1H Proton Brain metabolites   Define Single Voxel (SVS) and Multi Voxel (CSI) Proton Spectroscopy techniques   Discuss Protocols, Pulse Sequences and Parameters for Single Voxel (SVS) and Multi Voxel (CSI) Proton Spectroscopy    Summarize the various applications used for MRI Proton Neuro Spectroscopy    Discuss the examination and voxel positioning workflow for Single Voxel (SVS) and Multi Voxel (CSI) Proton Spectroscopy    Review the semiLASER sequence available on 3 Tesla systems   Identify variations of 1H Proton Brain metabolites in selected diseases Chemical Shift in ppm (parts per million) ppm is expressed independent of the external magnetic field Absolute chemical shift in Hertz increases with increasing B0 Relative to reference TMS Tetramethylsilane = 0 ppm Water = 4.7 ppm Δ (fat in Hz) 150 Hz @ 1T 225 Hz @ 1.5T Δ (fat in ppm) 150 Hz      @ 1T 42 x 106 Hz 225 Hz     @  1.5T 63 x 106 Hz Δ (fat in ppm) 3.5 ppm 3.5 ppm Water Metabolites ppm scale - displayed right to left Water - left Peak Metabolites - to the right of Water 1H Spectrum     1 cm3 2 cm3 4 cm3 8 cm3