title: Visualization of intra-thalamic nuclei with optimized white-matter-nulled MPRAGE at 7T.
abstract: Novel MR image acquisition strategies have been investigated to elicit contrast within the thalamus, but direct visualization of individual thalamic nuclei remains a challenge because of their small size and the low intrinsic contrast between adjacent nuclei. We present a step-by-step specific optimization of the 3D MPRAGE pulse sequence at 7T to visualize the intra-thalamic nuclei. We first measured T1 values within different sub-regions of the thalamus at 7T in 5 individuals. We used these to perform simulations and sequential experimental measurements (n=17) to tune the parameters of the MPRAGE sequence. The optimal set of parameters was used to collect high-quality data in 6 additional volunteers. Delineation of thalamic nuclei was performed twice by one rater and MR-defined nuclei were compared to the classic Morel histological atlas. T1 values within the thalamus ranged from 1400ms to 1800ms for adjacent nuclei. Using these values for theoretical evaluations combined with in vivo measurements, we showed that a short inversion time (TI) close to the white matter null regime (TI=670ms) enhanced the contrast between the thalamus and the surrounding tissues, and best revealed intra-thalamic contrast. At this particular nulling regime, lengthening the time between successive inversion pulses (TS=6000ms) increased the thalamic signal and contrast and lengthening the α pulse train time (N*TR) further increased the thalamic signal. Finally, a low flip angle during the gradient echo acquisition (α=4°) was observed to mitigate the blur induced by the evolution of the magnetization along the α pulse train. This optimized set of parameters enabled the 3D delineation of 15 substructures in all 6 individuals; these substructures corresponded well with the known anatomical structures of the thalamus based on the classic Morel atlas. The mean Euclidean distance between the centers of mass of MR- and Morel atlas-defined nuclei was 2.67mm (±1.02mm). The reproducibility of the MR-defined nuclei was excellent with intraclass correlation coefficient measured at 0.997 and a mean Euclidean distance between corresponding centers of mass found at first versus second readings of 0.69mm (±0.38mm). This 7T strategy paves the way to better identification of thalamic nuclei for neurosurgical planning and investigation of regional changes in neurological disorders.
authors.affiliation: Richard M. Lucas Center for Imaging, Radiology Department, Stanford University, 1201 Welch Road, Stanford, CA 94305-5488, USA. Electronic address: tourdias@stanford.edu.
authors.forename: Thomas
authors.initials: T
authors.lastname: Tourdias
authors.forename: Manojkumar
authors.initials: M
authors.lastname: Saranathan
authors.forename: Ives R
authors.initials: IR
authors.lastname: Levesque
authors.forename: Jason
authors.initials: J
authors.lastname: Su
authors.forename: Brian K
authors.initials: BK
authors.lastname: Rutt
mesh_terms: D000328:Adult; D000465:Algorithms; D005260:Female; D006801:Humans; D007089:Image Enhancement / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging; D008297:Male; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013382:Subtraction Technique; D013787:Thalamic Nuclei / Q000166:cytology*; D066127:White Matter / Q000166:cytology*
keywords: 7T; AV; Anterior ventral nucleus; CM; CNR; COM; CSF; Center median nucleus; Center of mass; Cerebro-spinal fluid; Contrast-to-noise ratio; Delay time; GM; Gray matter; Habenular nucleus; Hb; ICC; Intraclass correlation coefficient; Inversion time; LD; LGN; Lateral dorsal nucleus; Lateral geniculate nucleus; MD; MGN; MPRAGE sequence; MTT; Magnetization-prepared rapidly-acquired gradient echo sequence; Mammillothalamic tract; Medial geniculate nucleus; Mediodorsal nucleus; Pul; Pulvinar; RN; ROI; Red nucleus; Region-of-interest; SNR; Shot interval time; Signal-to-noise ratio; Sth; Subthalamic nucleus; TD; TI; TS; Thalamic nuclei; Thalamus; Ultra high field; VA; VLa; VLp; VPL; Ventral anterior nucleus; Ventral lateral anterior nucleus; Ventral lateral posterior nucleus; Ventral posterior lateral nucleus; WM; White matter; White matter nulled MPRAGE
references.citation: Hum Brain Mapp. 2009 Nov;30(11):3574-95
references.pmid: 19387981
references.citation: J Magn Reson Imaging. 2012 May;35(5):1063-70
references.pmid: 22170818
references.citation: NMR Biomed. 2001 Apr;14(2):57-64
references.pmid: 11320533
references.citation: J Magn Reson Imaging. 2008 Apr;27(4):685-91
references.pmid: 18302232
references.citation: Neuroimage. 2010 Feb 1;49(3):2053-62
references.pmid: 19853042
references.citation: Magn Reson Med. 2010 May;63(5):1315-22
references.pmid: 20432302
references.citation: J Comp Neurol. 1997 Nov 3;387(4):588-630
references.pmid: 9373015
references.citation: Neuroimage. 2007;37 Suppl 1:S109-15
references.pmid: 17644002
references.citation: Neurology. 2013 Jan 8;80(2):210-9
references.pmid: 23296131
references.citation: Neuroimage. 2011 Jun 1;56(3):1154-63
references.pmid: 21376814
references.citation: Neuroimage. 2009 Aug;47 Suppl 2:T44-52
references.pmid: 19362595
references.citation: AJNR Am J Neuroradiol. 2011 Dec;32(11):2110-5
references.pmid: 21979493
references.citation: Neuroimage. 2011 Jun 1;56(3):939-50
references.pmid: 21310246
references.citation: Neuroimage. 2003 Jun;19(2 Pt 1):391-401
references.pmid: 12814588
references.citation: Neuroimage. 2013 Jan 1;64:640-9
references.pmid: 22940589
references.citation: Neuroimage. 2006 Jul 1;31(3):1156-68
references.pmid: 16650780
references.citation: Nat Rev Neurol. 2010 Aug;6(8):438-44
references.pmid: 20625376
references.citation: Neurosurgery. 2010 Dec;67(6):1745-56; discussion 1756
references.pmid: 21107206
references.citation: Prog Brain Res. 2005;149:107-26
references.pmid: 16226580
references.citation: J Neurosci Methods. 2009 Dec 15;185(1):15-22
references.pmid: 19737577
references.citation: J Magn Reson Imaging. 2009 Jun;29(6):1285-92
references.pmid: 19472385
references.citation: Nat Neurosci. 2003 Jul;6(7):750-7
references.pmid: 12808459
references.citation: Neuroimage. 2010 Jan 15;49(2):1271-81
references.pmid: 19819338
references.citation: Neuroimage. 2009 Jan 15;44(2):373-84
references.pmid: 18845262
references.citation: Oper Neurosurg (Hagerstown). 2010 Mar;66(suppl_1):ons-E121-ons-E123
references.pmid: 20173580
references.citation: Magn Reson Med. 2010 Oct;64(4):1057-67
references.pmid: 20564597
references.citation: Magn Reson Med. 2007 Feb;57(2):308-18
references.pmid: 17260370
references.citation: Magn Reson Imaging. 2006 May;24(4):515-25
references.pmid: 16677958
references.citation: Neuroimage. 2000 Apr;11(4):341-6
references.pmid: 10725190
references.citation: Magn Reson Imaging. 2006 Feb;24(2):103-12
references.pmid: 16455399
references.citation: Magn Reson Med. 2012 Jan;67(1):118-26
references.pmid: 21656553
references.citation: BMC Neurol. 2008 Apr 16;8:8
references.pmid: 18412976
references.citation: Magn Reson Med. 1990 Jul;15(1):152-7
references.pmid: 2374495
references.citation: Neuroimage. 2013 Jan 15;65:299-314
references.pmid: 23036448
references.citation: Magn Reson Med. 2008 Sep;60(3):555-63
references.pmid: 18759367
references.citation: Nat Rev Neurosci. 2004 Nov;5(11):863-73
references.pmid: 15496864
references.citation: Brain Stimul. 2012 Oct;5(4):625-33
references.pmid: 22405744
references.citation: Neuroimage. 2013 Jan 15;65:1-12
references.pmid: 23036446
references.citation: Neuroimage. 2012 Oct 15;63(1):540-52
references.pmid: 22796988
references.citation: Neuroimage. 2000 Jul;12(1):112-27
references.pmid: 10875908
references.citation: Neuroimage. 2010 Jan 1;49(1):1-8
references.pmid: 19744568
references.citation: Hum Brain Mapp. 2009 Apr;30(4):1236-45
references.pmid: 18570200
references.citation: Magn Reson Med. 2014 Jan;71(1):375-87
references.pmid: 23468414
references.citation: Hum Brain Mapp. 2005 Jul;25(3):353-9
references.pmid: 15852386
references.citation: Neuroimage. 2007 Jan 1;34(1):117-26
references.pmid: 17070073
references.citation: Magn Reson Med. 2004 Nov;52(5):953-64
references.pmid: 15508167
references.citation: Neuroimage. 2004 Feb;21(2):757-67
references.pmid: 14980579
references.citation: Lancet Neurol. 2013 May;12(5):462-8
references.pmid: 23523144