Biology subjects

Karakuzu, A.

Publications and source records attributed to Karakuzu, A..

3 recordsLinked to original sources

bioRxiv2021

Vendor-neutral sequences (VENUS) and fully transparent workflows improve inter-vendor reproducibility of quantitative MRI

PurposeWe developed an end-to-end workflow that starts with a vendor-neutral acquisition and tested the hypothesis that vendor-neutral sequences decrease inter-vendor variability of T1, MTR and MTsat measurements. MethodsWe developed and deployed a vendor-neutral 3D spoiled gradient-echo (SPGR) sequence on three clinical scanners by two MRI vendors. We then acquired T1 maps on the ISMRM-NIST system phantom, as well as T1, MTR and MTsat maps in three healthy participants. We performed hierarchical shift function analysis in vivo to characterize the differences between scanners when the vendor-neutral sequence is used instead of commercial vendor implementations. Inter-vendor deviations were compared for statistical significance to test the hypothesis. ResultsIn the phantom, the vendor-neutral sequence reduced inter-vendor differences from 8 - 19.4% to 0.2 - 5% with an overall accuracy improvement, reducing ground truth T1 deviations from 7 - 11% to 0.2 - 4%. In vivo we found that the variability between vendors is significantly reduced (p = 0.015) for all maps (T1, MTR and MTsat) using the vendor-neutral sequence. ConclusionWe conclude that vendor-neutral workflows are feasible and compatible with clinical MRI scanners. The significant reduction of inter-vendor variability using vendor-neutral sequences has important implications for qMRI research and for the reliability of multicenter clinical trials.

bioengineering↗

bioRxiv2020

The quest for measuring myelin with MRI - An interactive meta-analysis of quantitative comparisons with histology

Several MRI measures have been proposed as in vivo biomarkers of myelin, each with applications ranging from plasticity to pathology. Despite the availability of these myelin-sensitive modalities, specificity and sensitivity have been a matter of discussion. Debate about which MRI measure is the most suitable for quantifying myelin is still ongoing. In this study, we performed a systematic review of published quantitative validation studies to clarify how different these measures are when compared to the underlying histology. We analysed the results from 43 studies applying meta-analysis tools, controlling for study sample size and using interactive visualization (https://neurolibre.github.io/myelin-meta-analysis). We report the overall estimates and the prediction intervals for the coefficient of determination and find that MT and relaxometry-based measures exhibit the highest correlations with myelin content. We also show which measures are, and which measures are not statistically different regarding their relationship with histology.

neuroscience↗

bioRxiv2018

Let’s talk about cardiac T1 mapping

BackgroundRecent reports have shown that T1 mapping sequences agree in phantoms, but exhibit significant differences in vivo. To characterize these differences in the heart, one needs to consider the effects of magnetization transfer (MT) and the T2 relaxation time in the most commonly used cardiac T1 mapping sequences (MOLLI, ShMOLLI and SASHA).\n\nMethodsSix explanted pig hearts were scanned weekly over a period of six weeks on a 3T system with the MOLLI, ShMOLLI, SASHA sequences and an inversion recovery sequence as reference. The T1 bias was computed as the difference between MOLLI, ShMOLLI, SASHA and the reference T1 values. We applied robust correlation statistics to assess the relationships between T1, T2 and MT. All data are publicly available at: http://neuropoly.pub/pigHeartsData.\n\nResultsA systematic T1 bias was present for all sequences, with MOLLI and ShMOLLI underestimating T1 and SASHA slightly overestimating T1 compared to the reference. The correlation of T1 bias with T2 was weak and insignificant. However, MT showed significant associations with T1 bias for all sequences. Our analysis is also available at: http://neuropoly.pub/pigHeartsInteractive.\n\nConclusionWe investigated cardiac T1 mapping sequences in a setting that allowed us to explore their accuracy and their dependence on T2 and MT effects. The T2 effects were not significant, and could not explain the T1 bias of MOLLI, ShMOLLI, SASHA with respect to the reference. On the other hand, the T1 biases exhibited a strong correlation with MT. We conclude that inaccuracies in cardiac T1 mapping are primarily due to magnetization transfer.

biophysics↗