Pub Date : 2024-04-05DOI: 10.1007/s10334-024-01154-x
Wenbo Sun, Dan Xu, Huan Li, Sirui Li, Qingjia Bao, Xiaopeng Song, Daniel Topgaard, Haibo Xu
Objective
To assess the performance of hybrid multi-dimensional magnetic resonance imaging (HM-MRI) in quantifying hematoxylin and eosin (H&E) staining results, grading and predicting isocitrate dehydrogenase (IDH) mutation status of gliomas.
Materials and methods
Included were 71 glioma patients (mean age, 50.17 ± 13.38 years; 35 men). HM-MRI images were collected at five different echo times (80–200 ms) with seven b-values (0–3000 s/mm2). A modified three-compartment model with very-slow, slow and fast diffusion components was applied to calculate HM-MRI metrics, including fractions, diffusion coefficients and T2 values of each component. Pearson correlation analysis was performed between HM-MRI derived fractions and H&E staining derived percentages. HM-MRI metrics were compared between high-grade and low-grade gliomas, and between IDH-wild and IDH-mutant gliomas. Using receiver operational characteristic (ROC) analysis, the diagnostic performance of HM-MRI in grading and genotyping was compared with mono-exponential models.
Results
HM-MRI metrics FDvery-slow and FDslow demonstrated a significant correlation with the H&E staining results (p < .05). Besides, FDvery-slow showed the highest area under ROC curve (AUC = 0.854) for grading, while Dslow showed the highest AUC (0.845) for genotyping. Furthermore, a combination of HM-MRI metrics FDvery-slow and T2Dslow improved the diagnostic performance for grading (AUC = 0.876).
Discussion
HM-MRI can aid in non-invasive diagnosis of gliomas.
{"title":"Quantifying H&E staining results, grading and predicting IDH mutation status of gliomas using hybrid multi-dimensional MRI","authors":"Wenbo Sun, Dan Xu, Huan Li, Sirui Li, Qingjia Bao, Xiaopeng Song, Daniel Topgaard, Haibo Xu","doi":"10.1007/s10334-024-01154-x","DOIUrl":"https://doi.org/10.1007/s10334-024-01154-x","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Objective</h3><p>To assess the performance of hybrid multi-dimensional magnetic resonance imaging (HM-MRI) in quantifying hematoxylin and eosin (H&E) staining results, grading and predicting isocitrate dehydrogenase (IDH) mutation status of gliomas.</p><h3 data-test=\"abstract-sub-heading\">Materials and methods</h3><p>Included were 71 glioma patients (mean age, 50.17 ± 13.38 years; 35 men). HM-MRI images were collected at five different echo times (80–200 ms) with seven <i>b</i>-values (0–3000 s/mm<sup>2</sup>). A modified three-compartment model with very-slow, slow and fast diffusion components was applied to calculate HM-MRI metrics, including fractions, diffusion coefficients and T2 values of each component. Pearson correlation analysis was performed between HM-MRI derived fractions and H&E staining derived percentages. HM-MRI metrics were compared between high-grade and low-grade gliomas, and between IDH-wild and IDH-mutant gliomas. Using receiver operational characteristic (ROC) analysis, the diagnostic performance of HM-MRI in grading and genotyping was compared with mono-exponential models.</p><h3 data-test=\"abstract-sub-heading\">Results</h3><p>HM-MRI metrics <i>F</i><sub><i>D</i>very-slow</sub> and <i>F</i><sub><i>D</i>slow</sub> demonstrated a significant correlation with the H&E staining results (<i>p</i> < .05). Besides, <i>F</i><sub><i>D</i>very-slow</sub> showed the highest area under ROC curve (AUC = 0.854) for grading, while <i>D</i>slow showed the highest AUC (0.845) for genotyping. Furthermore, a combination of HM-MRI metrics <i>F</i><sub><i>D</i>very-slow</sub> and T2<sub><i>D</i>slow</sub> improved the diagnostic performance for grading (AUC = 0.876).</p><h3 data-test=\"abstract-sub-heading\">Discussion</h3><p>HM-MRI can aid in non-invasive diagnosis of gliomas.</p>","PeriodicalId":18067,"journal":{"name":"Magnetic Resonance Materials in Physics, Biology and Medicine","volume":"21 1 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140574550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Objectives: CT and MR are often needed to determine the location and extent of brain lesions collectively to improve diagnosis. However, patients with acute brain diseases cannot complete the MRI examination within a short time. The aim of the study is to devise a cross-device and cross-modal medical image synthesis (MIS) method Cross2SynNet for synthesizing routine brain MRI sequences of T1WI, T2WI, FLAIR, and DWI from CT with stroke and brain tumors.
Materials and methods: For the retrospective study, the participants covered four different diseases of cerebral ischemic stroke (CIS-cohort), cerebral hemorrhage (CH-cohort), meningioma (M-cohort), glioma (G-cohort). The MIS model Cross2SynNet was established on the basic architecture of conditional generative adversarial network (CGAN), of which, the fully convolutional Transformer (FCT) module was adopted into generator to capture the short- and long-range dependencies between healthy and pathological tissues, and the edge loss function was to minimize the difference in gradient magnitude between synthetic image and ground truth. Three metrics of mean square error (MSE), peak signal-to-noise ratio (PSNR), and structure similarity index measure (SSIM) were used for evaluation.
Results: A total of 230 participants (mean patient age, 59.77 years ± 13.63 [standard deviation]; 163 men [71%] and 67 women [29%]) were included, including CIS-cohort (95 participants between Dec 2019 and Feb 2022), CH-cohort (69 participants between Jan 2020 and Dec 2021), M-cohort (40 participants between Sep 2018 and Dec 2021), and G-cohort (26 participants between Sep 2019 and Dec 2021). The Cross2SynNet achieved averaged values of MSE = 0.008, PSNR = 21.728, and SSIM = 0.758 when synthesizing MRIs from CT, outperforming the CycleGAN, pix2pix, RegGAN, Pix2PixHD, and ResViT. The Cross2SynNet could synthesize the brain lesion on pseudo DWI even if the CT image did not exhibit clear signal in the acute ischemic stroke patients.
Conclusions: Cross2SynNet could achieve routine brain MRI synthesis of T1WI, T2WI, FLAIR, and DWI from CT with promising performance given the brain lesion of stroke and brain tumor.
{"title":"Cross<sup>2</sup>SynNet: cross-device-cross-modal synthesis of routine brain MRI sequences from CT with brain lesion.","authors":"Minbo Jiang, Shuai Wang, Zhiwei Song, Limei Song, Yi Wang, Chuanzhen Zhu, Qiang Zheng","doi":"10.1007/s10334-023-01145-4","DOIUrl":"10.1007/s10334-023-01145-4","url":null,"abstract":"<p><strong>Objectives: </strong>CT and MR are often needed to determine the location and extent of brain lesions collectively to improve diagnosis. However, patients with acute brain diseases cannot complete the MRI examination within a short time. The aim of the study is to devise a cross-device and cross-modal medical image synthesis (MIS) method Cross<sup>2</sup>SynNet for synthesizing routine brain MRI sequences of T1WI, T2WI, FLAIR, and DWI from CT with stroke and brain tumors.</p><p><strong>Materials and methods: </strong>For the retrospective study, the participants covered four different diseases of cerebral ischemic stroke (CIS-cohort), cerebral hemorrhage (CH-cohort), meningioma (M-cohort), glioma (G-cohort). The MIS model Cross<sup>2</sup>SynNet was established on the basic architecture of conditional generative adversarial network (CGAN), of which, the fully convolutional Transformer (FCT) module was adopted into generator to capture the short- and long-range dependencies between healthy and pathological tissues, and the edge loss function was to minimize the difference in gradient magnitude between synthetic image and ground truth. Three metrics of mean square error (MSE), peak signal-to-noise ratio (PSNR), and structure similarity index measure (SSIM) were used for evaluation.</p><p><strong>Results: </strong>A total of 230 participants (mean patient age, 59.77 years ± 13.63 [standard deviation]; 163 men [71%] and 67 women [29%]) were included, including CIS-cohort (95 participants between Dec 2019 and Feb 2022), CH-cohort (69 participants between Jan 2020 and Dec 2021), M-cohort (40 participants between Sep 2018 and Dec 2021), and G-cohort (26 participants between Sep 2019 and Dec 2021). The Cross<sup>2</sup>SynNet achieved averaged values of MSE = 0.008, PSNR = 21.728, and SSIM = 0.758 when synthesizing MRIs from CT, outperforming the CycleGAN, pix2pix, RegGAN, Pix2PixHD, and ResViT. The Cross<sup>2</sup>SynNet could synthesize the brain lesion on pseudo DWI even if the CT image did not exhibit clear signal in the acute ischemic stroke patients.</p><p><strong>Conclusions: </strong>Cross<sup>2</sup>SynNet could achieve routine brain MRI synthesis of T1WI, T2WI, FLAIR, and DWI from CT with promising performance given the brain lesion of stroke and brain tumor.</p>","PeriodicalId":18067,"journal":{"name":"Magnetic Resonance Materials in Physics, Biology and Medicine","volume":" ","pages":"241-256"},"PeriodicalIF":2.3,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139692224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2024-01-22DOI: 10.1007/s10334-023-01139-2
Zhen Tang, Sasan Mahmoodi, Di Meng, Angela Darekar, Brigitte Vollmer
Objective: Susceptibility weighted imaging (SWI) of neonatal hypoxic-ischemic brain injury can provide assistance in the prognosis of neonatal hypoxic-ischemic encephalopathy (HIE). We propose a convolutional neural network model to classify SWI images with HIE.
Materials and methods: Due to the lack of a large dataset, transfer learning method with fine-tuning a pre-trained ResNet 50 is introduced. We randomly select 11 datasets from patients with normal neurology outcomes (n = 31) and patients with abnormal neurology outcomes (n = 11) at 24 months of age to avoid bias in classification due to any imbalance in the data.
Results: We develop a rule-based system to improve the classification performance, with an accuracy of 0.93 ± 0.09. We also compute heatmaps produced by the Grad-CAM technique to analyze which areas of SWI images contributed more to the classification patients with abnormal neurology outcome.
Conclusion: Such regions that are important in the classification accuracy can interpret the relationship between the brain regions affected by hypoxic-ischemic and neurodevelopmental outcomes of infants with HIE at the age of 2 years.
{"title":"Rule-based deep learning method for prognosis of neonatal hypoxic-ischemic encephalopathy by using susceptibility weighted image analysis.","authors":"Zhen Tang, Sasan Mahmoodi, Di Meng, Angela Darekar, Brigitte Vollmer","doi":"10.1007/s10334-023-01139-2","DOIUrl":"10.1007/s10334-023-01139-2","url":null,"abstract":"<p><strong>Objective: </strong>Susceptibility weighted imaging (SWI) of neonatal hypoxic-ischemic brain injury can provide assistance in the prognosis of neonatal hypoxic-ischemic encephalopathy (HIE). We propose a convolutional neural network model to classify SWI images with HIE.</p><p><strong>Materials and methods: </strong>Due to the lack of a large dataset, transfer learning method with fine-tuning a pre-trained ResNet 50 is introduced. We randomly select 11 datasets from patients with normal neurology outcomes (n = 31) and patients with abnormal neurology outcomes (n = 11) at 24 months of age to avoid bias in classification due to any imbalance in the data.</p><p><strong>Results: </strong>We develop a rule-based system to improve the classification performance, with an accuracy of 0.93 ± 0.09. We also compute heatmaps produced by the Grad-CAM technique to analyze which areas of SWI images contributed more to the classification patients with abnormal neurology outcome.</p><p><strong>Conclusion: </strong>Such regions that are important in the classification accuracy can interpret the relationship between the brain regions affected by hypoxic-ischemic and neurodevelopmental outcomes of infants with HIE at the age of 2 years.</p>","PeriodicalId":18067,"journal":{"name":"Magnetic Resonance Materials in Physics, Biology and Medicine","volume":" ","pages":"227-239"},"PeriodicalIF":2.3,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139513241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2024-01-12DOI: 10.1007/s10334-023-01141-8
Malte Roehl, Miriam Conway, Sarah Ghonim, Pedro F Ferreira, Sonia Nielles-Vallespin, Sonya V Babu-Narayan, Dudley J Pennell, Peter D Gatehouse, Andrew D Scott
Objective: The excellent blood and fat suppression of stimulated echo acquisition mode (STEAM) can be combined with saturation recovery single-shot acquisition (SASHA) in a novel STEAM-SASHA sequence for right ventricular (RV) native T1 mapping.
Materials and methods: STEAM-SASHA splits magnetization preparation over two cardiac cycles, nulling blood signal and allowing fat signal to decay. Breath-hold T1 mapping was performed in a T1 phantom and twice in 10 volunteers using STEAM-SASHA and a modified Look-Locker sequence at peak systole at 3T. T1 was measured in 3 RV regions, the septum and left ventricle (LV).
Results: In phantoms, MOLLI under-estimated while STEAM-SASHA over-estimated T1, on average by 3.0% and 7.0% respectively, although at typical 3T myocardial T1 (T1 > 1200 ms) STEAM-SASHA was more accurate. In volunteers, T1 was higher using STEAM-SASHA than MOLLI in the LV and septum (p = 0.03, p = 0.006, respectively), but lower in RV regions (p > 0.05). Inter-study, inter-observer and intra-observer coefficients of variation in all regions were < 15%. Blood suppression was excellent with STEAM-SASHA and noise floor effects were minimal.
Discussion: STEAM-SASHA provides accurate and reproducible T1 in the RV with excellent blood and fat suppression. STEAM-SASHA has potential to provide new insights into pathological changes in the RV in future studies.
{"title":"STEAM-SASHA: a novel approach for blood- and fat-suppressed native T1 measurement in the right ventricular myocardium.","authors":"Malte Roehl, Miriam Conway, Sarah Ghonim, Pedro F Ferreira, Sonia Nielles-Vallespin, Sonya V Babu-Narayan, Dudley J Pennell, Peter D Gatehouse, Andrew D Scott","doi":"10.1007/s10334-023-01141-8","DOIUrl":"10.1007/s10334-023-01141-8","url":null,"abstract":"<p><strong>Objective: </strong>The excellent blood and fat suppression of stimulated echo acquisition mode (STEAM) can be combined with saturation recovery single-shot acquisition (SASHA) in a novel STEAM-SASHA sequence for right ventricular (RV) native T1 mapping.</p><p><strong>Materials and methods: </strong>STEAM-SASHA splits magnetization preparation over two cardiac cycles, nulling blood signal and allowing fat signal to decay. Breath-hold T1 mapping was performed in a T1 phantom and twice in 10 volunteers using STEAM-SASHA and a modified Look-Locker sequence at peak systole at 3T. T1 was measured in 3 RV regions, the septum and left ventricle (LV).</p><p><strong>Results: </strong>In phantoms, MOLLI under-estimated while STEAM-SASHA over-estimated T1, on average by 3.0% and 7.0% respectively, although at typical 3T myocardial T1 (T1 > 1200 ms) STEAM-SASHA was more accurate. In volunteers, T1 was higher using STEAM-SASHA than MOLLI in the LV and septum (p = 0.03, p = 0.006, respectively), but lower in RV regions (p > 0.05). Inter-study, inter-observer and intra-observer coefficients of variation in all regions were < 15%. Blood suppression was excellent with STEAM-SASHA and noise floor effects were minimal.</p><p><strong>Discussion: </strong>STEAM-SASHA provides accurate and reproducible T1 in the RV with excellent blood and fat suppression. STEAM-SASHA has potential to provide new insights into pathological changes in the RV in future studies.</p>","PeriodicalId":18067,"journal":{"name":"Magnetic Resonance Materials in Physics, Biology and Medicine","volume":" ","pages":"295-305"},"PeriodicalIF":2.3,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10995026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139432685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2024-01-10DOI: 10.1007/s10334-023-01138-3
Nicolas Boulant, Caroline Le Ster, Alexis Amadon, Guy Aubert, Alexander Beckett, Jean Belorgey, Cédric Bonnelye, Dario Bosch, David Otto Brunner, Guillaume Dilasser, Olivier Dubois, Philipp Ehses, David Feinberg, Sajjad Feizollah, Vincent Gras, Simon Gross, Quentin Guihard, Hervé Lannou, Denis Le Bihan, Franck Mauconduit, Frédéric Molinié, François Nunio, Klaas Pruessmann, Lionel Quettier, Klaus Scheffler, Tony Stöcker, Christine Tardif, Kamil Ugurbil, Alexandre Vignaud, An Vu, Xiaoping Wu
Objective: To assess the possible influence of third-order shim coils on the behavior of the gradient field and in gradient-magnet interactions at 7 T and above.
Materials and methods: Gradient impulse response function measurements were performed at 5 sites spanning field strengths from 7 to 11.7 T, all of them sharing the same exact whole-body gradient coil design. Mechanical fixation and boundary conditions of the gradient coil were altered in several ways at one site to study the impact of mechanical coupling with the magnet on the field perturbations. Vibrations, power deposition in the He bath, and field dynamics were characterized at 11.7 T with the third-order shim coils connected and disconnected inside the Faraday cage.
Results: For the same whole-body gradient coil design, all measurements differed greatly based on the third-order shim coil configuration (connected or not). Vibrations and gradient transfer function peaks could be affected by a factor of 2 or more, depending on the resonances. Disconnecting the third-order shim coils at 11.7 T also suppressed almost completely power deposition peaks at some frequencies.
Discussion: Third-order shim coil configurations can have major impact in gradient-magnet interactions with consequences on potential hardware damage, magnet heating, and image quality going beyond EPI acquisitions.
目的:评估三阶垫片线圈对 7 T 及以上的梯度场行为和梯度磁相互作用的可能影响:评估三阶垫片线圈对 7 T 及以上梯度场行为和梯度磁场相互作用的可能影响:在场强从 7 到 11.7 T 的 5 个地点进行了梯度脉冲响应函数测量,所有地点均采用完全相同的全身梯度线圈设计。为了研究磁体的机械耦合对磁场扰动的影响,在一个地点对梯度线圈的机械固定和边界条件进行了多种改变。在法拉第笼内连接和断开三阶垫片线圈时,在 11.7 T 下对振动、氦浴中的功率沉积和磁场动态进行了表征:对于相同的全身梯度线圈设计,所有测量结果都因三阶垫片线圈的配置(连接或不连接)而有很大不同。根据共振情况,振动和梯度传递函数峰值可能会受到 2 倍或更多的影响。在 11.7 T 时断开三阶垫片线圈也几乎完全抑制了某些频率的功率沉积峰值:讨论:三阶垫片线圈配置可对梯度磁铁相互作用产生重大影响,其对潜在硬件损坏、磁铁加热和图像质量的影响超出了 EPI 采集的范围。
{"title":"The possible influence of third-order shim coils on gradient-magnet interactions: an inter-field and inter-site study.","authors":"Nicolas Boulant, Caroline Le Ster, Alexis Amadon, Guy Aubert, Alexander Beckett, Jean Belorgey, Cédric Bonnelye, Dario Bosch, David Otto Brunner, Guillaume Dilasser, Olivier Dubois, Philipp Ehses, David Feinberg, Sajjad Feizollah, Vincent Gras, Simon Gross, Quentin Guihard, Hervé Lannou, Denis Le Bihan, Franck Mauconduit, Frédéric Molinié, François Nunio, Klaas Pruessmann, Lionel Quettier, Klaus Scheffler, Tony Stöcker, Christine Tardif, Kamil Ugurbil, Alexandre Vignaud, An Vu, Xiaoping Wu","doi":"10.1007/s10334-023-01138-3","DOIUrl":"10.1007/s10334-023-01138-3","url":null,"abstract":"<p><strong>Objective: </strong>To assess the possible influence of third-order shim coils on the behavior of the gradient field and in gradient-magnet interactions at 7 T and above.</p><p><strong>Materials and methods: </strong>Gradient impulse response function measurements were performed at 5 sites spanning field strengths from 7 to 11.7 T, all of them sharing the same exact whole-body gradient coil design. Mechanical fixation and boundary conditions of the gradient coil were altered in several ways at one site to study the impact of mechanical coupling with the magnet on the field perturbations. Vibrations, power deposition in the He bath, and field dynamics were characterized at 11.7 T with the third-order shim coils connected and disconnected inside the Faraday cage.</p><p><strong>Results: </strong>For the same whole-body gradient coil design, all measurements differed greatly based on the third-order shim coil configuration (connected or not). Vibrations and gradient transfer function peaks could be affected by a factor of 2 or more, depending on the resonances. Disconnecting the third-order shim coils at 11.7 T also suppressed almost completely power deposition peaks at some frequencies.</p><p><strong>Discussion: </strong>Third-order shim coil configurations can have major impact in gradient-magnet interactions with consequences on potential hardware damage, magnet heating, and image quality going beyond EPI acquisitions.</p>","PeriodicalId":18067,"journal":{"name":"Magnetic Resonance Materials in Physics, Biology and Medicine","volume":" ","pages":"169-183"},"PeriodicalIF":2.3,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10995016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2023-11-29DOI: 10.1007/s10334-023-01133-8
Chuanli Cheng, Bingxia Wu, Lei Zhang, Qian Wan, Hao Peng, Xin Liu, Hairong Zheng, Huimao Zhang, Chao Zou
Objective: The study aims to propose an accurate labelling method of interscapular BAT (iBAT) in rats using dynamic MR fat fraction (FF) images with noradrenaline (NE) stimulation and then develop an automatic iBAT segmentation method using a U-Net model.
Materials and methods: Thirty-four rats fed different diets or housed at different temperatures underwent successive MR scans before and after NE injection. The iBAT were labelled automatically by identifying the regions with obvious FF change in response to the NE stimulation. Further, these FF images along with the recognized iBAT mask images were used to develop a deep learning network to accomplish the robust segmentation of iBAT in various rat models, even without NE stimulation. The trained model was then validated in rats fed with high-fat diet (HFD) in comparison with normal diet (ND).
Result: A total of 6510 FF images were collected using a clinical 3.0 T MR scanner. The dice similarity coefficient (DSC) between the automatic and manual labelled results was 0.895 ± 0.022. For the network training, the DSC, precision rate, and recall rate were found to be 0.897 ± 0.061, 0.901 ± 0.068 and 0.899 ± 0.086, respectively. The volumes and FF values of iBAT in HFD rats were higher than ND rats, while the FF decrease was larger in ND rats after NE injection.
Conclusion: An automatic iBAT segmentation method for rats was successfully developed using the dynamic labelled FF images of activated BAT and deep learning network.
目的:利用去甲肾上腺素(NE)刺激下的动态MR脂肪部分(FF)图像,建立大鼠肩胛间BAT (iBAT)的准确标记方法,并建立基于U-Net模型的iBAT自动分割方法。材料和方法:34只大鼠分别饲喂不同的饲料或饲养在不同的温度下,在注射NE前后进行连续磁共振扫描。iBAT通过识别在NE刺激下FF变化明显的区域来自动标记。此外,这些FF图像与识别的iBAT掩模图像一起用于开发深度学习网络,以在各种大鼠模型中实现iBAT的鲁棒分割,即使没有NE刺激。然后在高脂饲料(HFD)和正常饲料(ND)喂养的大鼠中验证训练模型。结果:临床3.0 T MR扫描共采集FF图像6510张。自动标记结果与手工标记结果的骰子相似系数(DSC)为0.895±0.022。对于网络训练,DSC、准确率和召回率分别为0.897±0.061、0.901±0.068和0.899±0.086。HFD大鼠iBAT体积和FF值均高于ND大鼠,NE注射后ND大鼠iBAT体积和FF值下降幅度更大。结论:利用激活BAT的动态标记FF图像和深度学习网络,成功建立了大鼠iBAT自动分割方法。
{"title":"Automatic segmentation of the interscapular brown adipose tissue in rats based on deep learning using the dynamic magnetic resonance fat fraction images.","authors":"Chuanli Cheng, Bingxia Wu, Lei Zhang, Qian Wan, Hao Peng, Xin Liu, Hairong Zheng, Huimao Zhang, Chao Zou","doi":"10.1007/s10334-023-01133-8","DOIUrl":"10.1007/s10334-023-01133-8","url":null,"abstract":"<p><strong>Objective: </strong>The study aims to propose an accurate labelling method of interscapular BAT (iBAT) in rats using dynamic MR fat fraction (FF) images with noradrenaline (NE) stimulation and then develop an automatic iBAT segmentation method using a U-Net model.</p><p><strong>Materials and methods: </strong>Thirty-four rats fed different diets or housed at different temperatures underwent successive MR scans before and after NE injection. The iBAT were labelled automatically by identifying the regions with obvious FF change in response to the NE stimulation. Further, these FF images along with the recognized iBAT mask images were used to develop a deep learning network to accomplish the robust segmentation of iBAT in various rat models, even without NE stimulation. The trained model was then validated in rats fed with high-fat diet (HFD) in comparison with normal diet (ND).</p><p><strong>Result: </strong>A total of 6510 FF images were collected using a clinical 3.0 T MR scanner. The dice similarity coefficient (DSC) between the automatic and manual labelled results was 0.895 ± 0.022. For the network training, the DSC, precision rate, and recall rate were found to be 0.897 ± 0.061, 0.901 ± 0.068 and 0.899 ± 0.086, respectively. The volumes and FF values of iBAT in HFD rats were higher than ND rats, while the FF decrease was larger in ND rats after NE injection.</p><p><strong>Conclusion: </strong>An automatic iBAT segmentation method for rats was successfully developed using the dynamic labelled FF images of activated BAT and deep learning network.</p>","PeriodicalId":18067,"journal":{"name":"Magnetic Resonance Materials in Physics, Biology and Medicine","volume":" ","pages":"215-226"},"PeriodicalIF":2.3,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138451854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2024-01-09DOI: 10.1007/s10334-023-01137-4
Marianne Nabbout, Michael C Langham, Christiana Cottrell, Felix W Wehrli
Objective: Neurovascular compliance (NVC) is the change in the brain's arterial tree blood volume, ΔV, divided by the change in intra-vascular blood pressure, ΔP, during the cardiac cycle. The primary aim of this work was to evaluate the performance of MRI measurement of NVC obtained from time-resolved measurements of internal carotid artery (ICA) and vertebral artery (VA) flow rates. A secondary aim was to explore whether NVC could be estimated from common carotid (CCA) flow in conjunction with prior knowledge of mean ICA and VA fractional flow rates, given the small cross-section of ICA and VA in some populations, in particular small children.
Methods: ΔV was quantified from the blood flow rate measured at the ICA and VA for actual NVC derivation. It was further estimated from individually measured CCA flow rate and mean flow fractions ICA/CCA and VA/CCA (which could alternatively be obtained from literature data), to yield estimated NVC. Time-resolved blood flow rate in CCA, ICA and VA was obtained via retrospectively-gated 2D PC-MRI at 1.5 T in healthy subjects (N = 16, 8 women, mean age 36 ± 13 years). ΔP was determined via a brachial pressure measurement.
Results: Actual and estimated mean NVC were 27 ± 15 and 38 ± 15 μL/mmHg, respectively, and the two measurements were strongly correlated (r = 0.80; p = 0.0002) with test-retest intra-class correlation coefficients of 0.964 and 0.899.
Conclusion: Both methods yielded excellent retest precision. In spite of a large bias, actual and estimated NVC were strongly correlated.
{"title":"Quantification of neurovascular compliance with retrospectively gated phase-contrast MRI.","authors":"Marianne Nabbout, Michael C Langham, Christiana Cottrell, Felix W Wehrli","doi":"10.1007/s10334-023-01137-4","DOIUrl":"10.1007/s10334-023-01137-4","url":null,"abstract":"<p><strong>Objective: </strong>Neurovascular compliance (NVC) is the change in the brain's arterial tree blood volume, ΔV, divided by the change in intra-vascular blood pressure, ΔP, during the cardiac cycle. The primary aim of this work was to evaluate the performance of MRI measurement of NVC obtained from time-resolved measurements of internal carotid artery (ICA) and vertebral artery (VA) flow rates. A secondary aim was to explore whether NVC could be estimated from common carotid (CCA) flow in conjunction with prior knowledge of mean ICA and VA fractional flow rates, given the small cross-section of ICA and VA in some populations, in particular small children.</p><p><strong>Methods: </strong>ΔV was quantified from the blood flow rate measured at the ICA and VA for actual NVC derivation. It was further estimated from individually measured CCA flow rate and mean flow fractions ICA/CCA and VA/CCA (which could alternatively be obtained from literature data), to yield estimated NVC. Time-resolved blood flow rate in CCA, ICA and VA was obtained via retrospectively-gated 2D PC-MRI at 1.5 T in healthy subjects (N = 16, 8 women, mean age 36 ± 13 years). ΔP was determined via a brachial pressure measurement.</p><p><strong>Results: </strong>Actual and estimated mean NVC were 27 ± 15 and 38 ± 15 μL/mmHg, respectively, and the two measurements were strongly correlated (r = 0.80; p = 0.0002) with test-retest intra-class correlation coefficients of 0.964 and 0.899.</p><p><strong>Conclusion: </strong>Both methods yielded excellent retest precision. In spite of a large bias, actual and estimated NVC were strongly correlated.</p>","PeriodicalId":18067,"journal":{"name":"Magnetic Resonance Materials in Physics, Biology and Medicine","volume":" ","pages":"307-314"},"PeriodicalIF":2.3,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2023-12-21DOI: 10.1007/s10334-023-01136-5
Peter David Gatehouse, Gabriella Captur, Sonia Nielles-Vallespin, Dudley John Pennell
Introduction: Quality assurance (QA) of measurements derived from MRI can require complicated test phantoms. This work introduces a new QA concept using gradient and transmit RF recordings by a limited field camera (FC) to govern the previous Virtual Phantom (ViP) method. The purpose is to describe the first technical implementation of combined FC+ViP, and illustrate its performance in examples, including quantitative first-pass myocardial perfusion.
Materials and methods: The new QA concept starts with a synthetic test object (STO) representing some arbitrary test input. Using recordings of the unmodified standard sequence by a gradient and RF waveform camera (FC), ViP calculates by Bloch simulation the continuous RF signal emitted by the STO during this sequence (hence FC+ViP). During nominally identical repetition of the sequence acquisition, ViP transmits the RF signal for scanner reception, reconstruction and any further parametric derivations by the unmodified standard scanner image reconstruction and analysis software.
Results: The scanner outputs were compared against the input STOs.
Conclusion: First proof-of-principle was discussed and supported by correlation between scanner outputs and the input STO. The work makes no claim that its examples are valid QA methods. It concludes by proposing a new industrial standard for QA without the FC.
简介:磁共振成像测量的质量保证(QA)需要复杂的测试模型:磁共振成像测量的质量保证(QA)需要复杂的测试模型。这项研究引入了一种新的质量保证概念,即利用有限场相机(FC)的梯度和发射射频记录来控制以前的虚拟模型(ViP)方法。其目的是描述 FC+ViP 组合的首次技术实施,并在实例中说明其性能,包括定量的第一通道心肌灌注:新的质量保证概念从代表任意测试输入的合成测试对象(STO)开始。利用梯度和射频波形照相机(FC)记录未经修改的标准序列,ViP 通过布洛赫模拟计算出 STO 在此序列中发出的连续射频信号(因此称为 FC+ViP)。在名义上完全相同的重复序列采集过程中,ViP 将射频信号发送给扫描仪接收、重建,并通过未修改的标准扫描仪图像重建和分析软件进行进一步的参数推导:结果:将扫描仪的输出与输入的 STO 进行了比较:通过扫描仪输出与输入 STO 之间的相关性,讨论并支持了第一个原理证明。这项工作并未声称其示例是有效的质量保证方法。最后,它提出了一种不使用 FC 的质量保证新工业标准。
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Pub Date : 2024-04-01Epub Date: 2024-02-17DOI: 10.1007/s10334-024-01149-8
Christian Karl Eisen, Patrick Liebig, Jürgen Herrler, Dieter Ritter, Simon Lévy, Michael Uder, Armin Michael Nagel, David Grodzki
Objective: To compensate subject-specific field inhomogeneities and enhance fat pre-saturation with a fast online individual spectral-spatial (SPSP) single-channel pulse design.
Methods: The RF shape is calculated online using subject-specific field maps and a predefined excitation k-space trajectory. Calculation acceleration options are explored to increase clinical viability. Four optimization configurations are compared to a standard Gaussian spectral selective pre-saturation pulse and to a Dixon acquisition using phantom and volunteer (N = 5) data at 1.5 T with a turbo spin echo (TSE) sequence. Measurements and simulations are conducted across various body parts and image orientations.
Results: Phantom measurements demonstrate up to a 3.5-fold reduction in residual fat signal compared to Gaussian fat saturation. In vivo evaluations show improvements up to sixfold for dorsal subcutaneous fat in sagittal cervical spine acquisitions. The versatility of the tailored trajectory is confirmed through sagittal foot/ankle, coronal, and transversal cervical spine experiments. Additional measurements indicate that excitation field (B1) information can be disregarded at 1.5 T. Acceleration methods reduce computation time to a few seconds.
Discussion: An individual pulse design that primarily compensates for main field (B0) inhomogeneities in fat pre-saturation is successfully implemented within an online "push-button" workflow. Both fat saturation homogeneity and the level of suppression are improved.
目的通过快速在线单通道频谱-空间(SPSP)脉冲设计,补偿特定受试者的场不均匀性并提高脂肪预饱和度:方法:利用特定受试者的场图和预定义的激发 k 空间轨迹在线计算射频形状。探索了计算加速选项,以提高临床可行性。将四种优化配置与标准高斯频谱选择性预饱和脉冲进行了比较,并使用模型和志愿者(N = 5)的数据在 1.5 T 下通过涡轮自旋回波(TSE)序列与 Dixon 采集进行了比较。对不同身体部位和图像方向进行了测量和模拟:模型测量结果表明,与高斯脂肪饱和度相比,残余脂肪信号最多可减少 3.5 倍。体内评估显示,在颈椎矢状图采集中,背侧皮下脂肪信号最多可提高 6 倍。矢状脚/脚踝、冠状和横向颈椎实验证实了定制轨迹的多功能性。其他测量结果表明,在 1.5 T 时可以忽略激励场 (B1) 信息:讨论:在一个在线 "按钮 "工作流程中,成功实现了主要补偿脂肪预饱和主场(B0)不均匀性的单脉冲设计。脂肪饱和的均匀性和抑制水平都得到了改善。
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Pub Date : 2024-02-22DOI: 10.1007/s10334-024-01152-z
Paweł Wierzba, Anna Sękowska-Namiotko, Agnieszka Sabisz, Monika Kosowska, Lina Jing, Robert Bogdanowicz, Małgorzata Szczerska
{"title":"Reply to Comment on ‘Nanodiamond incorporated human liver mimicking phantoms: prospective calibration medium of magnetic resonance imaging’","authors":"Paweł Wierzba, Anna Sękowska-Namiotko, Agnieszka Sabisz, Monika Kosowska, Lina Jing, Robert Bogdanowicz, Małgorzata Szczerska","doi":"10.1007/s10334-024-01152-z","DOIUrl":"https://doi.org/10.1007/s10334-024-01152-z","url":null,"abstract":"","PeriodicalId":18067,"journal":{"name":"Magnetic Resonance Materials in Physics, Biology and Medicine","volume":"14 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139920567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}