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Measuring T1 using MP2RAGE in Human Brain at 7T – Effect of B1+ and Inversion Pulse Efficiency

Kadhim, Mustafa LU (2021) MSFT01 20202
Medical Physics Programme
Abstract
Introduction: The MP2RAGE technique has become popular for structural MRI at ultra-high fields. The core idea behind MP2RAGE is to reduce the influence of flip angle inhomogeneity (B +), proton density and T2* by calculating the regularized signed ratio of two complex MP-RAGE images acquired at different inversion times (TI) within the cycle. From this MP2RAGE signal, the underlying T1 relaxation time can be determined by means of a look-up table obtained by forward signal modelling. Nonetheless, persistent B + influence on MP2RAGE may be observed which can reduce the accuracy of the calculated T1 maps. An additional factor that might influence the estimated T1 is the efficiency of the adiabatic inversion pulse. To study (and potentially... (More)
Introduction: The MP2RAGE technique has become popular for structural MRI at ultra-high fields. The core idea behind MP2RAGE is to reduce the influence of flip angle inhomogeneity (B +), proton density and T2* by calculating the regularized signed ratio of two complex MP-RAGE images acquired at different inversion times (TI) within the cycle. From this MP2RAGE signal, the underlying T1 relaxation time can be determined by means of a look-up table obtained by forward signal modelling. Nonetheless, persistent B + influence on MP2RAGE may be observed which can reduce the accuracy of the calculated T1 maps. An additional factor that might influence the estimated T1 is the efficiency of the adiabatic inversion pulse. To study (and potentially mitigate) the influence of these variables, the dynamics of longitudinal magnetization during the cycle is simulated. The sensitivity of a given (and later modified) MP2RAGE protocol to B + is studied. The efficiency of the inversion pulse is estimated for different adiabatic pulses through both experiments and simulations.

Methods: Healthy adult subjects were examined on a 7T MR system using a dual-transmit head coil with a 32-channel receive array. The standard MP2RAGE protocol featured flip angles of α1/α2 = 5o/3o, TR= 6.8 ms, TI1/TI2 = 900/2750 ms, turbo factor TF=256, and a 5000 ms cycle duration. A DREAM sequence protocol with preparation flip angles of 25°,40°,60°,90° was used for B + mapping. To study changes in inversion efficiency, finv, due to a spatially varying B + field, the maximum amplitude of the inversion pulse (B1-max) was varied between 3 µT and 20 µT while keeping the pulse duration constant. To explore potential improvements in finv and residual B + bias respectively, the standard “Full adiabatic” inversion pulse was replaced by a FOCI pulse and the flip angles were changed to α1/α2 = 4o/5o. Simulations were performed in Python and T1-mapping in MATLAB using a script provided by the authors of MP2RAGE.

Results: Simulation of the standard protocol showed optimal T1 accuracy when utilizing a separate B+ map and an inversion factor of 0.94 for the “adiabatic full” inversion pulse at B1-max =18 µT. At B1-max = 6 µT, finv was as low as 0.8. The inversion efficiency increased across the brain with increasing B +. The inversion efficiency also seems to increase with B -max. An empirical dependence of finv on B + was derived, by which the accuracy of the T1-maps can be improved. Additionally, the FOCI pulse yielded higher inversion efficiency at low B + regions in cerebellum and temporal lobes. Lastly, a higher second flip angle seems to result in T1-maps/MP2RAGE images that are less susceptible to B + inhomogeneity.

Discussion: The influence of B + inhomogeneity on a high-resolution MP2RAGE protocol at 7T was studied by simulation and experiment. Separately acquired B +-maps improved the accuracy of T1. In particular, the efficiency of the standard “Full adiabatic” inversion pulse depended on B + and the chosen B1-max. A similar investigation has been performed by Hagberg et al. at 9.4T. Notwithstanding better performance of the FOCI pulse in low- B + regions of the brain, B -max of the “Full adiabatic” pulse should be chosen as high as possible. The results prepare for further optimization of the MP2RAGE protocol and T1-mapping at UHF. (Less)
Popular Abstract (Swedish)
Den mänskliga hjärnan är ett anmärkningsvärt organ som formar våra mest komplexa tankar och medvetande. Ändå består den huvudsakligen av två typer av vävnader och en vätska, d.v.s. vit vävnad, (WM), grå vävnad (GM) och cerebrospinalvätska (CSF). Vit substans finns framför allt i de segment i centrala nervsystemet (CNS) som består av myeliniserade axoner och möjliggör långväga kommunikation mellan flera områden av grå vävnad samt överföring av nervimpulser mellan axoner i hjärnan. Grå vävnad å andra sidan kännetecknar de områden av hjärnan där neurala cellkroppar (soma) är belägna. När det gäller CSF sker dess produktion i kammarna där den absorberas av blodomloppet, vilket möjliggör transport av näring till olika delar av hjärnan och... (More)
Den mänskliga hjärnan är ett anmärkningsvärt organ som formar våra mest komplexa tankar och medvetande. Ändå består den huvudsakligen av två typer av vävnader och en vätska, d.v.s. vit vävnad, (WM), grå vävnad (GM) och cerebrospinalvätska (CSF). Vit substans finns framför allt i de segment i centrala nervsystemet (CNS) som består av myeliniserade axoner och möjliggör långväga kommunikation mellan flera områden av grå vävnad samt överföring av nervimpulser mellan axoner i hjärnan. Grå vävnad å andra sidan kännetecknar de områden av hjärnan där neurala cellkroppar (soma) är belägna. När det gäller CSF sker dess produktion i kammarna där den absorberas av blodomloppet, vilket möjliggör transport av näring till olika delar av hjärnan och ryggmärgen.

Dessa olika vävnader har olika biofysiska egenskaper vilket inom MR-avbildning (MRI) kan utnyttjas för att skilja mellan dem. Sådana egenskaper är till exempel den longitudinella relaxationstiden (T1), den transversella relaxationstiden (T2), den effektiva transversella relaxationstiden (T2*) och protondensiteten (PD). T1 är relaterad till koncentrationen av myeliniserade axoner, järn och makromolekyler i hjärnan, vilket gör den värdefull för strukturell MRI. Speciellt för undersökningar av atrofi vid neurodegenerativa sjukdomar (Alzheimers, Parkinsons etc.) i hjärnan. I detta arbete fokuserar vi på att bestämma T1- relaxationstiden i WM, GM och CSF genom att utnyttja ett ultrahögt magnetiskt fält (UHF) på 7 T. Den höga magnetfältsstyrkan underlättar avbildning av anatomiska strukturer samt undersökning av patologiska förändringar i hjärnan. Dock så lider UHF av ökad inhomogenitet hos både de mottagande
B - och sändande B + -fälten vilket inducerar spatiala variationer i bildintensiteten.

För att mildra denna variation har en viss teknik fått uppmärksamhet inom strukturell MR på ultrahöga fält (≥ 7T). Denna teknik är Magnetization Prepared 2 Rapid Acquisition Gradient Echoes (MP2RAGE), vilket är en mer sofistikerad utveckling av MPRAGE-sekvensen. Tanken bakom MP2RAGE är att minska påverkan av flippvinkelinhomogeniteter på grund av den ökade inhomogeniteten hos B + samt signalvariationer p.ga. B -. Dessutom kan signalvariationer p.g.a. skillnader i protondensitet och T2* elimineras. Detta görs genom att beräkna det regelbundna signalförhållandet mellan två komplexa MPRAGE-bilder som erhållits vid olika inversionstider (TI) inom en cykel. Av denna anledning är MP2RAGE sekvensen av intresse i detta arbete. Dock, trots användning av MP2RAGE-sekvensen, så kan kvarvarande effekter av variationer i B + fortfarande observeras. Detta kan resultera i minskad noggrannhet i de beräknade T1-värdena. En annan faktor som kan påverka noggrannheten i uppskattad T1 är inversionspulsens effektivitet.

Således, vårt mål med detta arbete var att bestämma inversionseffektivitetsfaktorn på en 7T Philips MR- kamera samt undersöka möjligheten att förbättra noggrannheten i de uppskattade T1-värdena genom att använda en lokal flippvinkelkarta. Dessutom har vi skapat ett simuleringsverktyg för att underlätta utvärderingen och förståelsen av utvecklingen av den longitudinella magnetiseringen under en MPRAGE eller MP2RAGE sekvens. Verktyget kan även användas till att simulera fler än två utläsningståg med arbiträra flippvinklar. Även hur signalen och den longitudinella magnetiseringen påverkas på grund av ovan nämnda faktorer undersöktes. Slutligen genomfördes en jämförelse mellan två inversionspulser för att studera deras inverkan på MP2RAGE-bilderna och T1-uppskattningen. (Less)
Please use this url to cite or link to this publication:
author
Kadhim, Mustafa LU
supervisor
organization
course
MSFT01 20202
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
9043213
date added to LUP
2021-04-20 15:42:43
date last changed
2021-04-20 15:42:43
@misc{9043213,
  abstract     = {{Introduction: The MP2RAGE technique has become popular for structural MRI at ultra-high fields. The core idea behind MP2RAGE is to reduce the influence of flip angle inhomogeneity (B +), proton density and T2* by calculating the regularized signed ratio of two complex MP-RAGE images acquired at different inversion times (TI) within the cycle. From this MP2RAGE signal, the underlying T1 relaxation time can be determined by means of a look-up table obtained by forward signal modelling. Nonetheless, persistent B + influence on MP2RAGE may be observed which can reduce the accuracy of the calculated T1 maps. An additional factor that might influence the estimated T1 is the efficiency of the adiabatic inversion pulse. To study (and potentially mitigate) the influence of these variables, the dynamics of longitudinal magnetization during the cycle is simulated. The sensitivity of a given (and later modified) MP2RAGE protocol to B + is studied. The efficiency of the inversion pulse is estimated for different adiabatic pulses through both experiments and simulations.

Methods: Healthy adult subjects were examined on a 7T MR system using a dual-transmit head coil with a 32-channel receive array. The standard MP2RAGE protocol featured flip angles of α1/α2 = 5o/3o, TR= 6.8 ms, TI1/TI2 = 900/2750 ms, turbo factor TF=256, and a 5000 ms cycle duration. A DREAM sequence protocol with preparation flip angles of 25°,40°,60°,90° was used for B + mapping. To study changes in inversion efficiency, finv, due to a spatially varying B + field, the maximum amplitude of the inversion pulse (B1-max) was varied between 3 µT and 20 µT while keeping the pulse duration constant. To explore potential improvements in finv and residual B + bias respectively, the standard “Full adiabatic” inversion pulse was replaced by a FOCI pulse and the flip angles were changed to α1/α2 = 4o/5o. Simulations were performed in Python and T1-mapping in MATLAB using a script provided by the authors of MP2RAGE.

Results: Simulation of the standard protocol showed optimal T1 accuracy when utilizing a separate B+ map and an inversion factor of 0.94 for the “adiabatic full” inversion pulse at B1-max =18 µT. At B1-max = 6 µT, finv was as low as 0.8. The inversion efficiency increased across the brain with increasing B +. The inversion efficiency also seems to increase with B -max. An empirical dependence of finv on B + was derived, by which the accuracy of the T1-maps can be improved. Additionally, the FOCI pulse yielded higher inversion efficiency at low B + regions in cerebellum and temporal lobes. Lastly, a higher second flip angle seems to result in T1-maps/MP2RAGE images that are less susceptible to B + inhomogeneity.

Discussion: The influence of B + inhomogeneity on a high-resolution MP2RAGE protocol at 7T was studied by simulation and experiment. Separately acquired B +-maps improved the accuracy of T1. In particular, the efficiency of the standard “Full adiabatic” inversion pulse depended on B + and the chosen B1-max. A similar investigation has been performed by Hagberg et al. at 9.4T. Notwithstanding better performance of the FOCI pulse in low- B + regions of the brain, B -max of the “Full adiabatic” pulse should be chosen as high as possible. The results prepare for further optimization of the MP2RAGE protocol and T1-mapping at UHF.}},
  author       = {{Kadhim, Mustafa}},
  language     = {{eng}},
  note         = {{Student Paper}},
  title        = {{Measuring T1 using MP2RAGE in Human Brain at 7T – Effect of B1+ and Inversion Pulse Efficiency}},
  year         = {{2021}},
}