TOPPE: A framework for rapid prototyping of MR pulse sequences

Nielsen, Jon Fredrik; Noll, Douglas C.

doi:10.1002/mrm.26990

Cited by 31 publications

(40 citation statements)

References 13 publications

(24 reference statements)

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“…All experiments were conducted in accordance with the local institutional review board, and all subjects were provided written informed consent. We implemented the OSSI pulse sequence using the vendor’s pulse programming language, EPIC, as well as our own in‐house pulse sequence development framework, TOPPE 11 . Single‐slice imaging with was performed using a single‐shot constant‐density spiral‐out trajectory ( n c = 6, TR = 17.5 ms, flip angle = 10 ◦ , FOV = 19 × 19 cm 2 , matrix = 45 × 45 reconstructed at 64 × 64, slice thickness = 2.5 mm, sampling BW = 250 kHz), with 16 extra k‐space center samples prior to readout.…”

Section: Methodsmentioning

confidence: 99%

A retrospective physiological noise correction method for oscillating steady‐state imaging

Cao

Noll

2020

Magnetic Resonance in Med

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Purpose Oscillating steady‐state imaging (OSSI) is an SNR‐efficient steady‐state sequence with T2∗ sensitivity suitable for FMRI. Due to the frequency sensitivity of the signal, respiration‐ and drift‐induced field changes can create unwanted signal fluctuations. This study aims to address this issue by developing retrospective signal correction methods that utilize OSSI signal properties to denoise task‐based OSSI FMRI experiments. Methods A retrospective denoising approach was developed that leverages the unique signal properties of OSSI to perform denoising without a manually specified noise region of interest and works with both voxel timecourses (oscillating steady‐state correction [OSSCOR]) or FID timecourses (F‐OSSCOR). Simulations were performed to estimate the number of principal components optimal for denoising. In vivo experiments at 3 T field strength were conducted to compare the performance of proposed methods against a standard principal component analysis‐based method, measured using mean t score within an region of interest, number of activations, and mean temporal SNR. Results Correction using OSSCOR was significantly better than the standard method in all metrics. Correction using F‐OSSCOR was not significantly different from the standard method using an equal number of principal components. Increasing the number of OSSCOR principal components decreased activation strength and increased the number of suspected false positives. However, increasing the number of principal components in F‐OSSCOR increased activation strength with little to no increase in false activation. Conclusion Both OSSCOR and F‐OSSCOR substantially reduce physiological noise components and increase temporal SNR, improving the functional results of task‐based OSSI functional experiments. F‐OSSCOR demonstrates a proof of concept utilization of coil‐localized FID signal information for physiological noise correction.

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Section: Methodsmentioning

confidence: 99%

A retrospective physiological noise correction method for oscillating steady‐state imaging

Cao

Noll

2020

Magnetic Resonance in Med

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“…One possibility would be to export the complete scan protocol used in a study and make it available to other research groups with the same scanner and software. Another interesting emerging possibility would be to develop and execute pulse sequences within a platform-or hardware-independent environment [Layton et al, 2017;Nielsen and Noll, 2018]. This would allow the tailored design of pulse sequences and imaging protocols that could be used to systematically vary the exposure in a very controlled manner, with the possibility of separating RF and SGF exposure in the experiments [Schreiber et al, 2001].…”

Section: Need For Details In Experimental Studiesmentioning

confidence: 99%

Valid Exposure Protocols Needed in Magnetic Resonance Imaging Genotoxic Research

Wilén

Olsrud

Frankel

et al. 2020

Bioelectromagnetics

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Several in vitro and in vivo studies have investigated if a magnetic resonance imaging (MRI) examination can cause DNA damage in human blood cells. However, the electromagnetic field (EMF) exposure that the cells received in the MR scanner was not sufficiently described. The first studies looking into this could be regarded as hypothesis‐generating studies. However, for further exploration into the role of MRI exposure on DNA integrity, the exposure itself cannot be ignored. The lack of sufficient method descriptions makes the early experiments difficult, if not impossible, to repeat. The golden rule in all experimental work is that a study should be repeatable by someone with the right knowledge and equipment, and this is simply not the case with many of the recent studies on MRI and genotoxicity. Here we discuss what is lacking in previous studies, and how we think the next generation of in vitro and in vivo studies on MRI and genotoxicity should be performed. Bioelectromagnetics. © 2020 Bioelectromagnetics Society.

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“…Previous attempts at bringing reproducibility and vendorindependence to the task of MRI sequence development 1,2 have been useful for early-prototype studies. These tools are great solutions for creating prototype sequences and allow for an easy exchange and reusal of pulse modules.…”

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confidence: 99%