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Image-based gradient non-linearity characterization to determine higher-order spherical harmonic coefficients for improved spatial position accuracy in magnetic resonance imaging.

ABSTRACT: PURPOSE:Spatial position accuracy in magnetic resonance imaging (MRI) is an important concern for a variety of applications, including radiation therapy planning, surgical planning, and longitudinal studies of morphologic changes to study neurodegenerative diseases. Spatial accuracy is strongly influenced by gradient linearity. This work presents a method for characterizing the gradient non-linearity fields on a per-system basis, and using this information to provide improved and higher-order (9th vs. 5th) spherical harmonic coefficients for better spatial accuracy in MRI. METHODS:A large fiducial phantom containing 5229 water-filled spheres in a grid pattern is scanned with the MR system, and the positions all the fiducials are measured and compared to the corresponding ground truth fiducial positions as reported from a computed tomography (CT) scan of the object. Systematic errors from off-resonance (i.e., B0) effects are minimized with the use of increased receiver bandwidth (±125kHz) and two acquisitions with reversed readout gradient polarity. The spherical harmonic coefficients are estimated using an iterative process, and can be subsequently used to correct for gradient non-linearity. Test-retest stability was assessed with five repeated measurements on a single scanner, and cross-scanner variation on four different, identically-configured 3T wide-bore systems. RESULTS:A decrease in the root-mean-square error (RMSE) over a 50cm diameter spherical volume from 1.80mm to 0.77mm is reported here in the case of replacing the vendor's standard 5th order spherical harmonic coefficients with custom fitted 9th order coefficients, and from 1.5mm to 1mm by extending custom fitted 5th order correction to the 9th order. Minimum RMSE varied between scanners, but was stable with repeated measurements in the same scanner. CONCLUSIONS:The results suggest that the proposed methods may be used on a per-system basis to more accurately calibrate MR gradient non-linearity coefficients when compared to vendor standard corrections.

SUBMITTER: Weavers PT

PROVIDER: S-EPMC5360473 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Image-based gradient non-linearity characterization to determine higher-order spherical harmonic coefficients for improved spatial position accuracy in magnetic resonance imaging.

Weavers Paul T PT Tao Shengzhen S Trzasko Joshua D JD Shu Yunhong Y Tryggestad Erik J EJ Gunter Jeffrey L JL McGee Kiaran P KP Litwiller Daniel V DV Hwang Ken-Pin KP Bernstein Matt A MA

Magnetic resonance imaging 20161227

<h4>Purpose</h4>Spatial position accuracy in magnetic resonance imaging (MRI) is an important concern for a variety of applications, including radiation therapy planning, surgical planning, and longitudinal studies of morphologic changes to study neurodegenerative diseases. Spatial accuracy is strongly influenced by gradient linearity. This work presents a method for characterizing the gradient non-linearity fields on a per-system basis, and using this information to provide improved and higher- ...[more]

PMID: 28034637

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Project description:It is increasingly being recognized that physical interactions between distant chromosomal loci influence the expressivity of the genome. Thus, multiple enhancers may converge on a single gene promoter 1,2 and a single enhancer can stochastically loop to multiple promoters 3. Regulatory elements from neighboring domains or from other chromosomes may interact to generate chromatin structures poised for transcription4-8 or repression 9-11. However, a broader perspective on the formation and function of such networks remains largely unexplored. Using the high-resolution 4C (Circular Chromosome Conformation Capture) analysis, we identify here a genome-wide physical network between genomically imprinted domains impinging H19 imprinting control region (ICR). Sequences interacting with the H19 ICR constitutively map at or within most of known imprinted domains both in mouse embryonic stem cells and in vitro-derived embryoid bodies, despite distinct differences in chromatin environments. Moreover, all-to-all 3D DNA FISH analyses revealed that imprinted domains from 7 different chromosomes co-localize with each other in pair-wise patterns, highlighting the dynamic nature of these interactions. The observed interaction network is dependent on CTCF binding sites within the maternally inherited H19 ICR allele and delays reprogramming of epigenetic features at imprinted domains during male germline development. As other imprinted regions can interact with each other in an H19 ICR-dependent manner, the H19 ICR emerges as an organizer of chromosomal networks by specifically recognizing and reconfiguring imprinted domains. We propose that an ancient key regulatory region, such as the H19 ICR, gradually impacted epigenetic modifications via long-range interactions in the germline to facilitate the recruitment of imprinted genes and their formation in clusters during mammalian radiation. Furthermore, the perspective of epigenetic lesions de-stabilizing such chromosomal networks may advance our understanding of how quantitative traits influence human diseases, such as cancer.

Dataset Information

Image-based gradient non-linearity characterization to determine higher-order spherical harmonic coefficients for improved spatial position accuracy in magnetic resonance imaging.

Publications

Image-based gradient non-linearity characterization to determine higher-order spherical harmonic coefficients for improved spatial position accuracy in magnetic resonance imaging.

Similar Datasets

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