Attention-based convolutional neural network for perfusion T2-weighted MR images preprocessing

Accurate skull-stripping is crucial preprocessing in dynamic susceptibility contrast-enhanced perfusion magnetic resonance data analysis. The presence of non-brain tissues impacts the perfusion parameters assessment. In this study, we propose different integration strategies for the spatial and channel squeeze and excitation attention mechanism into the baseline U-Net+ResNet neural network architecture to provide automatic skull-striping i.e., Standard scSE, scSE-PRE, scSE-POST, and scSE Identity strategies of plugging of scSE block into the ResNet backbone. We comprehensively investigate the performance of skull-stripping in Т2* weighted MR images with abnormal brain anatomy. The comparison that utilizing any of the proposed strategies provides the robustness of skull-stripping. However, the scSE-POST integration strategy provides the best result with an average Dice Coefficient of 0.9810 +/- 0.006

Peritumoral perfusion and proton spectroscopic MR imaging in the differentiation of gliomas and solitary metastases

Purpose: To asses the value of peritumoural perfusion-weighted and proton spectroscopic MR imaging in preoperative grading of gliomas and in differentiating between primary gliomas and solitary metastases. Methods and Materials: Ten low-grade gliomas, eight high-grade gliomas, and ten metastases were prospectively evaluated with MR imaging, dynamic susceptibility contrast-enhanced perfusion imaging, and single-voxel proton MR spectroscopy before surgical resection or stereotactic biopsy. Maximal rCBV values and maximal Cho/Cr ratios were calculated from peritumoural region surrounding the tumour. Tumour grade presumed with these values was compared to histopathologic grading. Differences in the study parameters between groups were assessed using the Mann-Whitney test. A Receiver Operating Characteristic analysis was performed to determine cutoff values. Results: A clear rCBV cutoff value of 1.88 was detected for differentiating low-grade gliomas from high-grade gliomas (sensitivity 100%, specificity 90%, area under the ROC curve .994, p< 0.0001). A clear rCBV cutoff value of 1.20 was detected for differentiation of metastases from gliomas (sensitivity 100%, specificity 90%, area under the ROC curve .972, p< 0.0001). The differences in the Cho/Cr ratios in the peritumoural regions of high-grade gliomas and of solitary metastasis were statistically significant (p<.001) but a clear cutoff value was not found. Conclusion: Our preliminary data support that peritumoural perfusion-weighted imaging can assist in preoperative differentiation between a glioma and a solitary metastasis, along with separating high-grade gliomas from low-grade gliomas

Application of resting-state fMRI methods to acute ischemic stroke

Diffusion weighted imaging (DWI) and dynamic susceptibility contrast-enhanced (DSC) perfusion-weighted imaging (PWI) are commonly employed in clinical practice and in research to give pathophysiological information for patients with acute ischemic stroke. DWI is thought to roughly reflect the severely damaged infarct core, while DSC-PWI reflects the area of hypoperfusion. The volumetric difference between DWI and DSC-PWI is termed the PWI/DWI-mismatch, and has been suggested as an MRI surrogate of the ischemic penumbra. However, due to the application of a contrast agent, which has potentially severe side-effects (e.g., nephrogenic systemic fibrosis), the DSC-PWI precludes repetitive examinations for monitoring purposes. New approaches are being sought to overcome this shortcoming. BOLD (blood oxygen-level dependent) signal can reflect the metabolism of blood oxygen in the brain and hemodynamics can be assessed with resting-state fMRI. The aim of this thesis was to use resting-state fMRI as a new approach to give similar information as DSC-PWI. This thesis comprises two studies: In the first study (see Chapter 2), two resting-state fMRI methods, local methods which compare low frequency amplitudes between two hemispheres and a k-means clustering approach, were applied to investigate the functional damage of patients with acute ischemic stroke both in the time domain and frequency domain. We found that the lesion areas had lower amplitudes than contralateral homotopic healthy tissues. We also differentiated the lesion areas from healthy tissues using a k-means clustering approach. In the second study (see Chapter 3), time-shift analysis (TSA), which assesses time delays of the spontaneous low frequency fluctuations of the resting-state BOLD signal, was applied to give similar pathophysiological information as DSC-PWI in the acute phase of stroke. We found that areas which showed a pronounced time delay to the respective mean time course were very similar to the hypoperfusion area. In summary, we suggest that the resting-state fMRI methods, especially the time-shift analysis (TSA), may provide comparable information to DSC-PWI and thus serve as a useful diagnostic tool for stroke MRI without the need for the application of a contrast agent

Cerebral perfusion MR imaging using FAIR-HASTE in chronic carotid occlusive disease: comparison with dynamic susceptibility contrast-perfusion MR imaging.

To determine the efficacy of flow-sensitive alternating inversion recovery using half-Fourier single-shot turbo spin-echo (FAIR-HASTE) in detecting cerebral hypoperfusion in chronic carotid occlusive disease, we subjected 12 patients with various degrees of cervical internal carotid artery stenoses and/or occlusion (Stenosis group) and 24 volunteers (Normal group) to FAIR-HASTE. In addition, 10 out of 12 patients in the Stenosis group underwent dynamic susceptibility contrast-perfusion magnetic resonance imaging (DSC-pMRI) before and after revascularization in the dominantly affected side. The absolute asymmetry indexes (AIs) of both cerebral hemispheres in the Normal and Stenosis groups were compared in FAIR-HASTE. In addition, the AIs were compared with those in the Stenosis group before and after revascularization in both FAIR-HASTE and regional cerebral blood flow (rCBF), calculated with DSC-pMRI. A statistically significant difference was recognized between the AIs in the Normal and Stenosis groups (AI = 2.25 +- 1.92, 8.09 +- 4.60, respectively ; p &#60; 0.0001). Furthermore, in the Stenosis group the AIs on both FAIR-HASTE (8.88 +- 4.93, 2.22 +- 1.79, respectively ; p = 0.0003) and rCBF (7.13 +- 3.57, 1.25 +- 1.33, respectively ; p = 0.0003) significantly decreased after revascularization. In the Stenosis group, before revascularization, signal intensity on both FAIR-HASTE and rCBF had a tendency to be lower in the dominantly affected side. FAIR-HASTE imaging was useful in the detection and evaluation of cerebral hypoperfusion in chronic occlusive carotid disease

Mystery(n) Phenotypic Presentation in Europeans: Report of Three Further Novel Missense RNF213 Variants Leading to Severe Syndromic Forms of Moyamoya Angiopathy and Literature Review

Moyamoya angiopathy (MMA) is a rare cerebral vasculopathy in some cases occurring in children. Incidence is higher in East Asia, where the heterozygous p.Arg4810Lys variant in RNF213 (Mysterin) represents the major susceptibility factor. Rare variants in RNF213 have also been found in European MMA patients with incomplete penetrance and are today a recognized susceptibility factor for other cardiovascular disorders, from extracerebral artery stenosis to hypertension. By whole exome sequencing, we identified three rare and previously unreported missense variants of RNF213 in three children with early onset of bilateral MMA, and subsequently extended clinical and radiological investigations to their carrier relatives. Substitutions all involved highly conserved residues clustered in the C-terminal region of RNF213, mainly in the E3 ligase domain. Probands showed a de novo occurring variant, p.Phe4120Leu (family A), a maternally inherited heterozygous variant, p.Ser4118Cys (family B), and a novel heterozygous variant, p.Glu4867Lys, inherited from the mother, in whom it occurred de novo (family C). Patients from families A and C experienced transient hypertransaminasemia and stenosis of extracerebral arteries. Bilateral MMA was present in the proband's carrier grandfather from family B. The proband from family C and her carrier mother both exhibited annular figurate erythema. Our data confirm that rare heterozygous variants in RNF213 cause MMA in Europeans as well as in East Asian populations, suggesting that substitutions close to positions 4118-4122 and 4867 of RNF213 could lead to a syndromic form of MMA showing elevated aminotransferases and extracerebral vascular involvement, with the possible association of peculiar skin manifestations

Quality of Radiomic Features in Glioblastoma Multiforme: Impact of Semi-Automated Tumor Segmentation Software.

ObjectiveThe purpose of this study was to evaluate the reliability and quality of radiomic features in glioblastoma multiforme (GBM) derived from tumor volumes obtained with semi-automated tumor segmentation software.Materials and methodsMR images of 45 GBM patients (29 males, 16 females) were downloaded from The Cancer Imaging Archive, in which post-contrast T1-weighted imaging and fluid-attenuated inversion recovery MR sequences were used. Two raters independently segmented the tumors using two semi-automated segmentation tools (TumorPrism3D and 3D Slicer). Regions of interest corresponding to contrast-enhancing lesion, necrotic portions, and non-enhancing T2 high signal intensity component were segmented for each tumor. A total of 180 imaging features were extracted, and their quality was evaluated in terms of stability, normalized dynamic range (NDR), and redundancy, using intra-class correlation coefficients, cluster consensus, and Rand Statistic.ResultsOur study results showed that most of the radiomic features in GBM were highly stable. Over 90% of 180 features showed good stability (intra-class correlation coefficient [ICC] ≥ 0.8), whereas only 7 features were of poor stability (ICC &lt; 0.5). Most first order statistics and morphometric features showed moderate-to-high NDR (4 &gt; NDR ≥1), while above 35% of the texture features showed poor NDR (&lt; 1). Features were shown to cluster into only 5 groups, indicating that they were highly redundant.ConclusionThe use of semi-automated software tools provided sufficiently reliable tumor segmentation and feature stability; thus helping to overcome the inherent inter-rater and intra-rater variability of user intervention. However, certain aspects of feature quality, including NDR and redundancy, need to be assessed for determination of representative signature features before further development of radiomics

Regional association of pCASL-MRI with FDG-PET and PiB-PET in people at risk for autosomal dominant Alzheimer's disease.

Autosomal dominant Alzheimer's disease (ADAD) is a small subset of Alzheimer's disease that is genetically determined with 100% penetrance. It provides a valuable window into studying the course of pathologic processes that leads to dementia. Arterial spin labeling (ASL) MRI is a potential AD imaging marker that non-invasively measures cerebral perfusion. In this study, we investigated the relationship of cerebral blood flow measured by pseudo-continuous ASL (pCASL) MRI with measures of cerebral metabolism (FDG PET) and amyloid deposition (Pittsburgh Compound B (PiB) PET). Thirty-one participants at risk for ADAD (age 39&nbsp;±&nbsp;13&nbsp;years, 19 females) were recruited into this study, and 21 of them received both MRI and FDG and PiB PET scans. Considerable variability was observed in regional correlations between ASL-CBF and FDG across subjects. Both regional hypo-perfusion and hypo-metabolism were associated with amyloid deposition. Cross-sectional analyses of each biomarker as a function of the estimated years to expected dementia diagnosis indicated an inverse relationship of both perfusion and glucose metabolism with amyloid deposition during AD development. These findings indicate that neurovascular dysfunction is associated with amyloid pathology, and also indicate that ASL CBF may serve as a sensitive early biomarker for AD. The direct comparison among the three biomarkers provides complementary information for understanding the pathophysiological process of AD

Role of magnetic resonance spectroscopy in grading of gliomas- a tertiary care centre study

Background: Grading of gliomas is important for the determination of appropriate treatment strategies. MR spectroscopy has found increasing utility in grading of gliomas.Methods: MR spectroscopic imaging was done for the referred patients to obtain Cho/NAA and Cho/Cr ratios. After analyzing histopathology reports, gliomas were classified into low grade and high grade. Histologically proven 54 low grade and 54 high grade gliomas were included in the study. The mean and standard deviation of these variables were obtained and compared between two groups.  ROC curve analyses were performed in order to identify the optimal cut-off value for metabolite ratios for prediction purposes of high grade versus low grade gliomas.Results: The mean and SD of Cho/NAA ratio in low grade glioma was 1.93±1.19. The mean and SD of Cho /NAA ratio in high grade glioma was 3.16±1.73 was significantly higher. The optimal cut-off for differentiating low grade and high grade gliomas was 2.15 with a sensitivity of 74.07% and specificity of 66.67%. The mean and SD of CHO/Cr in low grade glioma was 2.05±0.76. The mean and SD of Cho/NAA in high grade glioma was 2.87±1.65 was significantly higher. The optimal cut-off for differentiating low grade and high grade gliomas was 1.98 with a sensitivity of 64.8% and specificity of 64.1%.Conclusions: MR spectroscopy imaging plays a pivotal role in prediction of glioma grade preoperatively and helps in deciding appropriate treatment strategies