Development and application of multi-atlas attenuation correction for brain imaging with simultaneous PET-MR

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(1)Development and application of multi-atlas attenuation correction for brain imaging with simultaneous PET-MR Inès Merida. To cite this version: Inès Merida. Development and application of multi-atlas attenuation correction for brain imaging with simultaneous PET-MR. Neurons and Cognition [q-bio.NC]. Université de Lyon, 2017. English. �NNT : 2017LYSE1116�. �tel-01579485�. HAL Id: tel-01579485 https://tel.archives-ouvertes.fr/tel-01579485 Submitted on 31 Aug 2017. HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés..

(2) N°d’ordre NNT : 2017LYSE1116. THESE de DOCTORAT DE L’UNIVERSITE DE LYON opérée au sein de. l’Université Claude Bernard Lyon 1 Ecole Doctorale N° 476 Neurosciences et cognition Spécialité de doctorat : Neurosciences Soutenue publiquement le 23/06/2017, par:. Inés Mérida Development and application of multi-atlas attenuation correction for brain imaging with simultaneous PET-MR Devant le jury composé de: Irène Buvat Stefaan Vandenberghe. Directeur de recherche (CNRS) Professeur (University of Gent). Rapporteur Rapporteur. Carole Lartizien Marine Soret Luc Zimmer. Chargée de recherche (CNRS) Physicienne médicale (AP-HP) Professeur (Université Lyon1, HCL). Examinateur Examinateur Examinateur. Olivier Bertrand Nicolas Costes Alexander Hammers. Directeur de recherche (INSERM) Ingénieur de recherche (CNRS) Professeur (King's College London). Directeur de thèse Co-directeur Co-directeur. Matthieu Lepetit-Coiffé. Ingénieur (Siemens Healthineers). Invité.

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(58) -533FZ -5 #,:?&< xZ ?,& ' ! 4&?,6% -= ::3-&% ?6 "63@=c-5*@=-65 :<6?6#63 @=-5+ huui<#36:<-%&],&=&5=-?-C-?F6* ' !?6%-=?-5+@-=,%-**&<&5#&=-5?<#&<@:?2&"&?D&&5+<6@:= -= -5C&=?-+?&% D-?, =-4@3?&% 5% <&3 %?] &=@3?= <& #64:<&% ?6 ?,6=& 6"?-5&% D-?, ?,& C&5%6<c:<6C-%&%?&#,5-;@&] ,&?,&=-=-=#65#3@%&%"F=,6<?#,:?&<=F5?,&=-=-5+?,&4-5-5=-+,?=+-5&%%@<-5+?,-=D6<2Z5% =@++&=?-65=*6<*@?@<&D6<2] . . . vu.

(59) . . . vv.

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(61) ?,&4+5&?-#*-&3%=?<&5+?,]-5#&=3-+,?&E#&==6*=:-5=<&-5?,&t6<-&5??-65Zt,=:6=-?-C& 365+-?@%-53#64:65&5?ZD,&<&=-?,=5@33?<5=C&<=&#64:65&5?"&#@=&?,&=:-5=%656?<6??& -5:,=&Z=6?,&4#<6=#6:-#?<5=C&<=&#64:65&5?-=#5#&33&%6@?f-+@<&ug] 5 ?,6=& #65%-?-65=Z <%-6c*<&;@&5#F fg :@3=& ?@5&% ?6 ?,& <46< *<&;@&5#F #5 "& ::3-&% ?6 &E#-?&?,&=F=?&45%%-=?@<"?,&&;@-3-"<-@4=??&]5&E#,5+&6*&5&<+F6##@<="&?D&&5?,& 5%?,&5@#3&-ZD,-#,<&=@3?=-5?-:%6D56*?,&5&?4+5&?-G?-65C&#?6<f-+@<&ug]@<-5+?,& &E#-??-65Z?,&365+-?@%-534+5&?-G?-65%&#<&=&=Z5%?<5=C&<=&4+5&?-G?-65::&<=f&E#&:? *6<u|tp*3-:5+3&g],&*3-:5+3&fQg%&:&5%=65?,&-5?&5=-?FZDC&*6<45%%@<?-656*?,& :@3=&]&3E?-65-=?,&%F54-#:,F=-#3:<6#&==-5D,-#,?,&=F=?&46*=:-5=<&?@<5=?6&;@-3-"<-@4] &3E?-65#5"&"<62&5%6D5-5?6?D6:,=&=\ug?,&365+-?@%-534+5&?-G?-65Z3-+5&%D-?,tZ D,-#, -= <&#6C&<&% *6336D-5+ 5 &E:65&5?-3 #@<C& #,<#?&<-G&% "F ?-4& #65=?5? uZ 5% vg ?,& ?<5=C&<=& 4+5&?-G?-65Z %@& ?6 =:-5= +&??-5+ 6@? 6* :,=&Z D,-#, %&#F= ##6<%-5+ ?6 5 &E:65&5?-3*@5#?-65D-?,?-4&#65=?5?vf-+@<&ug],&?-4&#65=?5?=u5%v<&=:&#-*-# ?6 ?,& =@<<6@5%-5+ "-636+-#3 ?-==@&=Z ?F:-#33F -5*3@&5#&% "F ?,&-< #,&4-#3 #64:6=-?-65Z "@? 3=6 %&:&5%65?,&=?<&5+?,6*t] 5#& ?,& ?<5=4-??&< -= ?@<5&% 6**Z ?,& &3&#?<64+5&?-# =-+53 :<6%@#&% "F ?,& t <&3E?-65 -= <&#6<%&% D-?, =:&#-*-# #6-3= f-+@<& u g] 5 :<#?-#&Z vlZ 5 &**&#?-C& C3@& 6* &E:&#?&% vZ -= 4&=@<&%] vl <&=@3?= :<-5#-:33F *<64 -5,646+&5&-?-&= -5 t] ,&=& -5,646+&5&-?-&= 4F "& ?,& <&=@3? 6* -5?<-5=-# %&*&#?= -5 ?,& 4+5&? -?=&3* 6< *<64 =@=#&:?-"-3-?Fc-5%@#&% *-&3% %-=?6<?-65= :<6%@#&% "F ?,& ?-==@& 6< 6?,&< 4?&<-3= :3#&% D-?,-5 ?,& *-&3%] 5 =&;@&5#& -= "=&% 65 <&:&?-?-65 6* :@3=&= 5% ?,& =-+53 <&#6<%&% -= =4:3&% ? =&C&<3 ?-4& -5?&<C3=] ,& &#,6 ?-4& fg-=%&*-5&%=?,&?-4&"&?D&&5?,&:@3=&5%?,&=-+53=4:3-5+Z5%?,&<&:&?-?-65?-4& fg-=?,&?-4&"&?D&&5?D6&E#-??-65:@3=&=]&:&5%-5+65?,&=&;@&5#&:<4&?&<=Z&]+]?,& #,6=&5bC3@&=Z?,&?-==@&=-+53D-33&E,-"-?C<-6@=#65?<=?=65?,&-4+&f-+@<&vg] ,& ?D6 4-5 *4-3-&= 6* =&;@&5#&= <& =:-5c&#,6 5% +<%-&5?c&#,6 =&;@&5#&=] 5F ?&#,5-;@&= "=&% 65 ?,&=& ?D6 *4-3-&= 6* =&;@&5#&=Z -5#3@%-5+ ,F"<-% =&;@&5#&=Z ,C& "&&5 %&C&36:&% ?6 #;@-<& %-**&<&5? #65?<=? -4+&= f56? %&?-3&% -5 ?,-= D6<2g f-?< &? 3]Z vttz[ -""FZvtty[ 6&?3]Zvtt|g]. . vx.

(62) B. A B0. =. Macroscopic magnetization. RF. Mz. M0. . z. z. α. . RF excitation. x. y. y. Mxy. x. z. C. Mz(t). Mz. Mxy(t) M0e-t/T2. y Mxy. M0(1-e-t/T1) 0. t. t. 0. Spin relaxation. x. D. z. RF coil. Mz y. T2* decay t. Mxy. x. Measure of the MR signal. . &$30 PA%71&)1&1,#2% 1&$+)B0,1,.&*$+ 2&82&,+2 /3&)&0&3*&+)3&+$.0 11&,+HI? &,E#0 /3 +7 ..)& 2, &1230 2% /3&)&0&3* HI? .&+ 0 )62&,+A 0 ,4 0 ,# ),+$&23&+) ,*.,3+ + 7,#20+14 01 ,*.,3+HI? 130 ,#2% 1&$+)HIB. . PBPBQ ,+20121&+&*$&+$ 65=-%&<-5+?,&D-%&C<-&?F6* =&;@&5#&=?,?:<6C-%&%-**&<&5??-==@&#65?<=?=Z-5?,-==&#?-65 D&*6#@=655%"<-&*3F%&=#<-"&*6@<=&;@&5#&=6*?&5@=&%-5?,&#65?&E?6*c\u5%vc D&-+,?&%-4+&=Z?,&?D6c:6-5?-E65c?&<c?=&;@&5#&Z5%?,&@3?<c=,6<?&#,6?-4&=&;@&5#&] u 5% vcD&-+,?&% =&;@&5#&= <& ?D6 =?5%<% -4+& #65?<=?= D-%&3F &4:36F&% -5 #3-5-#3 #65?&E?]ucD&-+,?&%-4+&=f-+@<&vg<&6"?-5&%"F@=-5+=,6<?5%=,6<?]-?,?,-= -4+&#65?<=?Z%@&?6=,6<?u?-4&#65=?5?Z*?::&<=D-?,,F:&<=-+53-5D,-?&ZD,-3&=6*? ?-==@&=<&-5+<&F]?&<Z-<5%"65&33::&<%<2+<&F5%"3#2%@&?6?,&,F:6c=-+53?,&F :<6%@#&Z=6?,&F#556?"&#6<<&#?3F%-=?-5+@-=,&%-5?,&-4+&]6<vcD&-+,?&%-4+&=f-+@<&vgZ. . vy.

(63) 365+5%365+<&&4:36F&%] 5?,-=D&-+,?-5+ZD?&<-=D,-?&Z*?::&<=+<&FZ=6*??-==@&%<2 +<&FZ5%"6?,-<5%"65&::&<"3#2]+-5Z-<5%"65&#556?"&%-**&<&5?-?&%] 2-5+%C5?+&6*?,&%-**&<&5#&=-5<&=655#&:<6:&<?-&=6*D?&<5%3-:-%=Z?,&?D6c:6-5?-E65c ?&<c? =&;@&5#& f-E65g =&:<?&= D?&< 5% *? =-+53= "F &E:36-?-5+ ?,& %-**&<&5? <&=655#& *<&;@&5#-&= 6* ?,& ?D6 f664"= &? 3]Z u}}{g] F %%-5+ 5% =@"?<#?-5+ :,=&c#6<<&#?&% -4+&= 6"?-5&%*<64?D6&E#-??-65=f-E65-5c:,=&5%-E656@?c6*c:,=&gZ`D?&<-4+&a5%`*? -4+&a<&+&5&<?&%B-+@<&vHEI=,6D=5-33@=?<?-656*?,&-E65=&;@&5#&] ,&3=?=&;@&5#&%&=#<-"&%,&<&-=?,&@3?<c=,6<?&#,6?-4&fg=&;@&5#&fF3&<&?3]Zvtt{g] ?-= @=&%?6%&?&#?=-+53=*<64?-==@&=D-?,C&<F=,6<?vl<&3E?-65?-4&fvl-5?,&<5+&6*t]tydv 4=gZ=@#,=#6<?-#3"65&]=&;@&5#&=#65=-=?-5?,&#;@-=-?-656*?D6#65=&#@?-C&-4+&=fu 5%vg??D6%-**&<&5?&#,6?-4&=Z?F:-#33Fuzt=5%vv]vx4=],&=-+53*<64?,& "65&-=:<&=&5?-5?,&u"@?56?-5?,&vZD,&<&=?,&=-+53=*<646?,&<?-==@&#3==&=f-]&]Z =6*??-==@&5%-<g<&=-4-3<-5"6?,#=&=]f&*6336D?,&&=?"3-=,&%?&<4-5636+F5%<&*&<?6?,& 4?&<-3=-5"6%F=`?-==@&a#3==&=Z&C&5?,6@+,-<-=56?#?@33F?-==@&g] &5#&Z"65&=-+53#5 "&,-+,3-+,?&%"F=@"?<#?-5+u5%v-4+&=]5&E4:3&6*?,&=&;@&5#&-==,6D5-5 -+@<&vH+ I] . A. C. E. G. B. D. F. H. &$30 QA ,+20121APE5 &$%2 HI?QE5 &$%2 HI?&6,+E2 0HI?&6,+E2HI?&6,+&+E.%1 HI +&6,+,32E,#E.%1 HI?PHI?QH IB. . . vz.