Multi-site harmonization of 7 tesla MRI neuroimaging protocols

Clarke, William T.; Mougin, Olivier; Driver, Ian D.; Rua, Catarina; Morgan, Andrew; Asghar, Michael; Clare, Stuart; Francis, Susan T.; Wise, Richard G.; Rodgers, Christopher T.; Carpenter, Adrian; Muir, Keith W.; Bowtell, Richard

doi:10.1016/j.neuroimage.2019.116335

Cited by 42 publications

(46 citation statements)

References 37 publications

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“…B 1 + -calibration was performed initially using the vendor's default adjustment scans. A 3D DREAM sequence ( Nehrke and Bornert, 2012 ; Ehses et al., 2019 ) was subsequently acquired and the transmit voltage (or power attenuation) was then adjusted for all subsequent imaging based on the mean flip-angle from the brain in an anatomically-specified axial slice of the 3D DREAM flip angle map as described in Clarke et al. (2019) .…”

Section: Methodsmentioning

confidence: 99%

“…Multi-echo 1.4mm isotropic resolution T 2 *-weighted GE data were acquired with: TE 1 /TR=4/43ms; 8 echoes with monopolar gradient readouts; echo-spacing=5ms; FA=15°; bandwidth=260Hz/px; acceleration-factor=4 (Sites-1/2/4/5) or 2 × 1.5 (Site-3); FOV=269 × 218 × 157mm 3 ; scan-time ~6min (Sites-1/2/4/5) and ~4 min (Site-3). For Siemens data, coil combination was performed using a custom implementation of Roemer's algorithm, as previously described ( Clarke et al., 2019 ). Subject 6’s single-echo scan failed to reconstruct using Roemer's method on data from the first visit at Site-5 so a sum-of-squares (SoS) algorithm was used for coil combination for that scan instead.…”

Section: Methodsmentioning

confidence: 99%

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Multi-centre, multi-vendor reproducibility of 7T QSM and R2* in the human brain: Results from the UK7T study

et al. 2020

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Introduction We present the reliability of ultra-high field T 2 * MRI at 7T, as part of the UK7T Network's “Travelling Heads” study. T 2 *-weighted MRI images can be processed to produce quantitative susceptibility maps (QSM) and R 2 * maps. These reflect iron and myelin concentrations, which are altered in many pathophysiological processes. The relaxation parameters of human brain tissue are such that R 2 * mapping and QSM show particularly strong gains in contrast-to-noise ratio at ultra-high field (7T) vs clinical field strengths (1.5–3T). We aimed to determine the inter-subject and inter-site reproducibility of QSM and R 2 * mapping at 7T, in readiness for future multi-site clinical studies. Methods Ten healthy volunteers were scanned with harmonised single- and multi-echo T 2 *-weighted gradient echo pulse sequences. Participants were scanned five times at each “home” site and once at each of four other sites. The five sites had 1× Philips, 2× Siemens Magnetom, and 2× Siemens Terra scanners. QSM and R 2 * maps were computed with the Multi-Scale Dipole Inversion (MSDI) algorithm ( https://github.com/fil-physics/Publication-Code ). Results were assessed in relevant subcortical and cortical regions of interest (ROIs) defined manually or by the MNI152 standard space. Results and Discussion Mean susceptibility (χ) and R 2 * values agreed broadly with literature values in all ROIs. The inter-site within-subject standard deviation was 0.001–0.005 ppm (χ) and 0.0005–0.001 ms −1 (R 2 *). For χ this is 2.1–4.8 fold better than 3T reports, and 1.1–3.4 fold better for R 2 *. The median ICC from within- and cross-site R 2 * data was 0.98 and 0.91, respectively. Multi-echo QSM had greater variability vs single-echo QSM especially in areas with large B 0 inhomogeneity such as the inferior frontal cortex. Across sites, R 2 * values were more consistent than QSM in subcortical structures due to differences in B 0 -shimming. On a between-subject level, our measured χ and R 2 * cross-site variance is comparable to within-site variance in the literature, suggesting that it is reasonable to pool data across sites using our harmonised protocol. Conclusion The harmonized UK7T protocol and pipeline delivers on average a 3-fold improvement in the coefficient of reproducibility for QSM and R 2 * at 7T compared to previous reports of multi-site reproducibility at 3T. These protocols are ready for use i...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Multi-centre, multi-vendor reproducibility of 7T QSM and R2* in the human brain: Results from the UK7T study

et al. 2020

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“…A high resolution isotropic T1-w MP2RAGE image was also acquired sagittally for anatomical coregistration using the UK7T Network harmonised protocol (Clarke et al, 2019): TR = 3500 ms, TE = 2.58 ms, BW = 300 Hz/px, voxel size = 0.7 x 0.7 x 0.7 mm, FoV = 224 x 224 x 157 mm, acceleration factor (A>>P) = 3, flip angles = 5/2° and inversion times (TI) = 725/2150 ms for the first/second images. The total acquisition time of the MP2RAGE was 7 minutes and 51 seconds.…”

Section: Methodsmentioning

confidence: 99%

Anin vivoProbabilistic Atlas of the Human Locus Coeruleus at Ultra-high Field

Rua

O’Callaghan

et al. 2020

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Early and profound pathological changes are evident in the locus coeruleus (LC) in dementia and Parkinson’s disease, with effects on arousal, attention, cognitive and motor control. The LC can be identified in vivo using non-invasive magnetic resonance imaging techniques which have potential as biomarkers for detecting and monitoring disease progression. Technical limitations of existing imaging protocols have impaired the sensitivity to regional contrast variance or the spatial variability on the rostrocaudal extent of the LC, with spatial mapping consistent with post mortem findings. The current study employs a sensitive magnetisation transfer sequence using ultrahigh field 7T MRI to investigate the LC structure in vivo at high-resolution (resolution 0.4×0.4×0.5 mm, duration seven minutes). Magnetisation transfer images from 53 healthy older volunteers (52-84 years) revealed the spatial features of the LC and were used to create a probabilistic LC atlas for older adults, appropriate for clinical research. Consistent rostrocaudal gradients of slice-wise volume, contrast and variance differences of the LC were observed, mirroring distinctive ex vivo spatial distributions of LC cells in its subregions. The contrast-to-noise ratios were calculated for the peak voxels, and for the averaged signals within the atlas, to accommodate the volumetric differences in estimated contrast. The probabilistic atlas is freely available, and the MRI dataset is available for researchers, for replication or to facilitate accurate LC localisation and unbiased contrast extraction in future studies.

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“…Quality assessment, standardization and harmonization of 7T MRI protocols are increasingly becoming appreciated by the neuroimaging field to allow utilization and generalization of protocols across studies, imaging sites and scanner vendors (Poldrack et al, 2017). Several nationwide (Clarke et al, 2019;Voelker et al, 2016) and international (Düzel et al, 2019) initiatives have embarked on such establishments indicating the importance of this issue. These consortia aim to set up standardized sequences across the main 7T MRI vendors to limit the long-known effects of hard-(e.g.…”

Section: Introductionmentioning

confidence: 99%

Effects of MP2RAGE B₁⁺sensitivity on inter-site T₁reproducibility and morphometry at 7T

Haast¹,

Lau

Ivanov

et al. 2020

Preprint

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Most neuroanatomical studies are based on MR images, whose intensity profiles are not solely determined by the tissue's longitudinal relaxation times (T 1 ) but also affected by varying non-T 1 contributions, hampering data reproducibility. In contrast, quantitative imaging using the MP2RAGE sequence, for example, allows direct characterization of the brain based on the tissue property of interest. Combined with 7 Tesla (7T) MRI, this offers unique opportunities to obtain robust high-resolution brain data characterized by a high reproducibility, sensitivity and specificity. However, specific MP2RAGE parameters choicese.g., to emphasize intracortical myelin-dependent contrast variations -can substantially impact image quality and cortical analyses through remnants of B 1 + -related intensity variations, as illustrated in our previous work. To follow up on this: we (1) validate this protocol effect using a dataset acquired with a particularly B 1 + insensitive set of MP2RAGE parameters combined with parallel transmission excitation; and (2) extend our analyses to evaluate the effects on hippocampal and subcortical morphometry. The latter remained unexplored initially but will provide important insights related to generalizability and reproducibility of neurodegenerative research using 7T MRI. We confirm that B 1 + inhomogeneities have a considerably variable effect on cortical T 1 and thickness estimates, as well as on hippocampal and subcortical morphometry depending on MP2RAGE setup. While T 1 differed substantially across datasets initially, we show inter-site T 1 comparability improves after correcting for the spatially varying B 1 + field using a separately acquired Sa2RAGE B 1 + map. Finally, as for cortical thickness, removal of B 1 + residuals affects hippocampal and subcortical volumetry and boundary definitions, particularly near structures characterized by strong intensity changes (e.g. cerebral spinal fluid and arteries). Taken together, we show that the choice of MP2RAGE parameters can impact T 1 comparability across sites and present evidence that hippocampal and subcortical segmentation results are modulated by B 1 + inhomogeneities. This calls for careful (1) consideration of sequence parameters when setting acquisition protocols; as well as (2) interpretation of results focused on neuroanatomical changes due to disease. Keywords7 Tesla MRI; MP2RAGE; quantitative T 1 ; brain morphometry; transmit bias field. Highlights• Previously observed effects of B 1 + inhomogeneities on cortical T 1 and thickness depend strongly on MP2RAGE parameters • Inter-site comparability of cortical T 1 and thickness greatly improves after removal of B 1 + residuals • Post-hoc MP2RAGE B 1 + correction affects hippocampal (and subcortical) size and shape analyses • Neuroradiological research would benefit from careful examination of imaging protocols and their impact on results, especially when B 1 + maps are not acquired

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Multi-site harmonization of 7 tesla MRI neuroimaging protocols

Cited by 42 publications

References 37 publications

Multi-centre, multi-vendor reproducibility of 7T QSM and R2* in the human brain: Results from the UK7T study

Multi-centre, multi-vendor reproducibility of 7T QSM and R2* in the human brain: Results from the UK7T study

Anin vivoProbabilistic Atlas of the Human Locus Coeruleus at Ultra-high Field

Effects of MP2RAGE B₁⁺sensitivity on inter-site T₁reproducibility and morphometry at 7T

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Multi-site harmonization of 7 tesla MRI neuroimaging protocols

Cited by 42 publications

References 37 publications

Multi-centre, multi-vendor reproducibility of 7T QSM and R2* in the human brain: Results from the UK7T study

Multi-centre, multi-vendor reproducibility of 7T QSM and R2* in the human brain: Results from the UK7T study

Anin vivoProbabilistic Atlas of the Human Locus Coeruleus at Ultra-high Field

Effects of MP2RAGE B1+sensitivity on inter-site T1reproducibility and morphometry at 7T

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Effects of MP2RAGE B₁⁺sensitivity on inter-site T₁reproducibility and morphometry at 7T