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We present a Python library (Phybers) for analyzing brain tractography data. Tractography datasets contain streamlines (also called fibers) composed of 3D points representing the main white matter pathways. Several algorithms have been proposed to analyze this data, including clustering, segmentation, and visualization methods. The manipulation of tractography data is not straightforward due to the geometrical complexity of the streamlines, the file format, and the size of the datasets, which may contain millions of fibers. Hence, we collected and structured state-of-the-art methods for the analysis of tractography and packed them into a Python library, to integrate and share tools for tractography analysis. Due to the high computational requirements, the most demanding modules were implemented in C/C++. Available functions include brain Bundle Segmentation (FiberSeg), Hierarchical Fiber Clustering (HClust), Fast Fiber Clustering (FFClust), normalization to a reference coordinate system, fiber sampling, calculation of intersection between sets of brain fibers, tools for cluster filtering, calculation of measures from clusters, and fiber visualization. The library tools were structured into four principal modules: Segmentation, Clustering, Utils, and Visualization (Fibervis). Phybers is freely available on a GitHub repository under the GNU public license for non-commercial use and open-source development, which provides sample data and extensive documentation. In addition, the library can be easily installed on both Windows and Ubuntu operating systems through the pip library.

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Resumen El ataque cerebrovascular (ACV) es la primera causa de discapacidad y la tercera causa de muerte en la Argentina y en el mundo. La etiología del stroke es isquémica en su mayoría (más del 80% de los casos), siendo las causas más frecuentes las lesiones isquémicas de pequeños vasos de tipo lacunar y las tromboembólicas debido a ateroesclerosis de grandes arterias o cardioembolia. Las secuencias utilizadas en nuestro protocolo de estudio incluyen DWI, FLAIR, angio-RM 3D-TOF, SWI y FSE-T1 (tiempo aproximado de exploración de 13 minutos). Pueden observarse diferentes hallazgos en cada una de estas secuencias que son orientativos para determinar la etiología subyacente y estimar el tiempo de evolución de la lesión. En la actualidad, la trombectomía mecánica se ha convertido en el tratamiento de elección en pacientes seleccionados con accidente cerebral isquémico agudo. La transformación hemorrágica es la complicación más temida luego de la terapia de reperfusión intraarterial. La técnica de difusión de la resonancia magnética (RM) posee una mayor sensibilidad para detectar lesiones isquémicas, permite sospechar la etiología según el patrón lesional y aporta información valiosa para la selección de los pacientes candidatos a la reperfusión arterial.

Abstract Stroke or cerebrovascular attack (CVA) is the first cause of disability and the third cause of death in Argentina and in the world. The etiology of strokes is mostly ischemic (more than 80% of cases), with the most frequent causes being lacunar-type ischemic lesions of small vessels and thromboembolic lesions due to atherosclerosis of large arteries or cardioembolism. The sequences used in our study protocol include DWI, FLAIR, angio-RM 3D-TOF, SWI, and FSE-T1 (approximate scan time of 13 minutes). Different findings can be observed in each of these sequences that are indicative to determine the underlying etiology and estimate the time of evolution of the lesion. Currently, mechanical thrombectomy has become the treatment of choice in selected patients with acute ischemic stroke. Hemorrhagic transformation is the most feared complication after intra-arterial reperfusion therapy. The diffusion magnetic resonance technique is more sensitive for detecting ischemic lesions, allows one to suspect the etiology based on the lesion pattern, and provides valuable information for the selection of patients who are candidates for arterial reperfusion.

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SUMMARY OBJECTIVE: Minor ischemic events and silent ischemic lesions are more common in carotid stenting than in endarterectomy. These silent ischemic lesions are also associated with stroke risk and cognitive impairment, so it is important to understand the factors that increase the risk and develop strategies to reduce the risk. We aimed to evaluate the association between carotid stent design and silent ischemic lesion development. METHODS: The files of the patients who underwent carotid stenting between January 2020 and April 2022 were scanned. Patients with diffusion MR images taken within the postoperative 24 h were included in the study, while those undergoing acute stent placement were excluded. The patients were divided into two groups: those with open-cell stents and those with closed-cell stents. RESULTS: A total of 65 patients, including 39 patients undergoing open-cell stenting and 26 patients undergoing closed-cell stenting, were included in the study. There was no significant difference in demographic data and vascular risk factors between the groups. New ischemic lesions were detected in 29 (74.4%) patients in the open-cell stent group and 10 (38.4%) patients in the closed-cell stent group and were significantly higher in the open-cell group. There was no significant difference between the two groups in terms of major and minor ischemic events and stent restenosis at the 3-month follow-up. CONCLUSION: The rate of new ischemic lesion development was found to be significantly higher in carotid stent procedures performed with an open-cell Protégé stent than in those performed with a closed-cell Wallstent stent.

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BACKGROUND: Most studies using diffusion-weighted MRI (DW-MRI) in Alzheimer's disease (AD) have focused their analyses on white matter (WM) microstructural changes using the diffusion (kurtosis) tensor model. Although recent works have addressed some limitations of the tensor model, such as the representation of crossing fibers and partial volume effects with cerebrospinal fluid (CSF), the focus remains in modeling and analyzing the WM. OBJECTIVE: In this work, we present a brain analysis approach for DW-MRI that disentangles multiple tissue compartments as well as micro- and macroscopic effects to investigate differences between groups of subjects in the AD continuum and controls. METHODS: By means of the multi-tissue constrained spherical deconvolution of multi-shell DW-MRI, underlying brain tissue is modeled with a WM fiber orientation distribution function along with the contributions of gray matter (GM) and CSF to the diffusion signal. From this multi-tissue model, a set of measures capturing tissue diffusivity properties and morphology are extracted. Group differences were interrogated following fixel-, voxel-, and tensor-based morphometry approaches while including strong FWE control across multiple comparisons. RESULTS: Abnormalities related to AD stages were detected in WM tracts including the splenium, cingulum, longitudinal fasciculi, and corticospinal tract. Changes in tissue composition were identified, particularly in the medial temporal lobe and superior longitudinal fasciculus. CONCLUSION: This analysis framework constitutes a comprehensive approach allowing simultaneous macro and microscopic assessment of WM, GM, and CSF, from a single DW-MRI dataset.

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OBJECTIVE: Diffusion-weighted magnetic resonance imaging (DWI) has shown promise in predicting response to therapy in several malignancies. This systematic review and meta-analysis aimed to evaluate DWI in the prediction of response to treatment in patients with cervical cancer. METHODS: A systematic search was conducted on PubMed, Web of Science, Cochrane and Google Scholar databases Studies that evaluated DWI and apparent diffusion coefficient (ADC) for response evaluation before, during and after treatment with a correlation to conventional response criteria were included. The primary endpoint was the mean ADC values of cervical cancer at these timepoints. The Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) was used to assess the quality of the studies. RESULTS: Nine studies, comprising 270 patients, were included. Pre-treatment ADC values showed no correlation with eventual response. However, in our meta-analysis, there was a significant correlation with early treatment ADC values obtained within the first 3 weeks of therapy and response, as well as a significant correlation with the percentage change in ADC (ΔADC) and response. In addition, the pooled mean ΔADC percentage was also significantly higher in responders than in non-responders (49.7% vs 19.7%, respectively, p = 0.016). CONCLUSION: DWI shows potential as a biomarker of early treatment response in patients with cervical carcinoma. Use of the change in ADC particularly within the first 3 weeks of therapy seems to be predictive of response and may serve as a suitable marker in the determination of early response.

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The aging process is associated with many brain structural alterations. These changes are not associated with neuronal loss but can be due to cortical structural changes that may be related to white matter (WM) structural alterations. In this study, we evaluated age-related changes in WM and gray matter (GM) parameters and how they correlate for specific brain tracts in a cohort of 158 healthy individuals, aged between 18 and 83 years old. In the tract-cortical analysis, cortical regions connected by tracts demonstrated similar thinning patterns for the majority of tracts. Additionally, a significant relationship was found between mean cortical thinning rate with fractional anisotropy (FA) and mean diffusivity (MD) alteration rates. For all tracts, age was the main effect controlling diffusion parameter alterations. We found no direct correlations between cortical thickness and FA or MD, except for in the fornix, for which the subcallosal gyrus thickness was significantly correlated to FA and MD (p < 0.05 FDR corrected). Our findings lead to the conclusion that alterations in the WM diffusion parameters are explained by the aging process, also associated with cortical thickness changes. Also, the alteration rates of the structural parameters are correlated to the different brain tracts in the aging process.

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Stroke is a leading cause of disability worldwide. Motor impairments occur in most of the patients with stroke in the acute phase and contribute substantially to disability. Diffusion tensor imaging (DTI) biomarkers such as fractional anisotropy (FA) measured at an early phase after stroke have emerged as potential predictors of motor recovery. In this narrative review, we: (1) review key concepts of diffusion MRI (dMRI); (2) present an overview of state-of-art methodological aspects of data collection, analysis and reporting; and (3) critically review challenges of DTI in stroke as well as results of studies that investigated the correlation between DTI metrics within the corticospinal tract and motor outcomes at different stages after stroke. We reviewed studies published between January, 2008 and December, 2018, that reported correlations between DTI metrics collected within the first 24 h (hyperacute), 2-7 days (acute), and >7-90 days (early subacute) after stroke. Nineteen studies were included. Our review shows that there is no consensus about gold standards for DTI data collection or processing. We found great methodological differences across studies that evaluated DTI metrics within the corticospinal tract. Despite heterogeneity in stroke lesions and analysis approaches, the majority of studies reported significant correlations between DTI biomarkers and motor impairments. It remains to be determined whether DTI results could enhance the predictive value of motor disability models based on clinical and neurophysiological variables.

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PURPOSE: To investigate the association of hypoenhancement on dynamic Contrast enhanced (DCE) with prostate cancer patient outcomes. MATERIAL AND METHODS: This was a single-institution retrospective Institutional Review Board (IRB)-approved cohort study of 54 men who had prostate Magnetic Resonance Imaging (MRI) within 6 months of cancer diagnosis between 01/2012 to 03/2014. Two readers independently identified the dominant MRI-lesions utilizing Prostate Imaging-Reporting and Data System-version2- guidelines. These lesions were classified as hypoenhancing or hyperenhancing, compared to normal peripheral zone using quantitative DCE analysis. The t test for unequal sample sizes and the two-sample Wilcoxon rank-sum tests were used to compare groups. Logistic regression determined if DCE characteristics predict the development of metastases or prostate cancer death. RESULTS: Time-to-progression was significantly shorter for hypoenhancing tumors (6.2 vs. 24.8 months, p = 0.05). Men with these lesions had a higher odds of having poor outcome (univariate logistic regression, odds ratio (OR) 6.79, 95% confidence interval (CI) 1.45-31.72, p = 0.02; multivariate analysis, OR 2.05, 95% CI 0.30-13.72, p = 0.47). Hypoenhancing tumors were larger (33.1 vs. 19.1 mm, p < 0.001) and more likely to be intermediate (Gleason scores 3 + 4 and 4 + 3) and high-grade (Gleason scores ≥ 4 + 4) prostate cancers (p = 0.05). Men in the hypoenhancing group had a higher mean prostate-specific antigen (PSA) value (87.6 vs. 24.8 ng/dL, p = 0.01) and PSA density (1.54 vs. 0.72, p = 0.03). The mean Ktrans and kep of hypoenhancing lesion were lower when compared to hyperenhancing lesions (p = 0.03 and p = 0.04). Ve values did not differ (p = 0.25). CONCLUSION: Men with hypoenhancing prostate cancers may have a worse prognosis than men with hyperenhancing tumors.

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BACKGROUND: The aim of the study was to evaluate the added value of the apparent diffusion coefficient (ADC) of diffusion-weighted magnetic resonance imaging (DW-MRI) in patients with rectal cancer who received neoadjuvant chemoradiotherapy (CRT). The use of DW-MRI for response evaluation in rectal cancer still remains a widely investigated issue, as the accurate detection of pathologic complete response (pCR) is critical in making therapeutic decisions. PATIENTS AND METHODS: Thirty-three patients with locally advanced rectal cancer were evaluated retrospectively by MRI in addition to diffusion-weighted images (DWI) and its ADC pre- and post-neoadjuvant CRT. These patients subsequently underwent curative-intent surgery. Tumor staging by MRI and ADC value were compared with histopathological findings of the surgical specimen. RESULTS: MRI in addition to DWI had a sensitivity of 96.1%, specificity of 71.4%, positive predictive value of 92.5%, and negative predictive value of 83.3% in the detection of pCR. The pre-CRT ADC alone could not reliably predict the pCR group. Post-CRT ADC cutoff value of 1.49 x 10-3 mm2/s had the highest accuracy and allowed a 16.7% increase in negative predictive value and 3.9% increase in sensitivity. Patients with pCR to neoadjuvant treatment differed from the other groups in their absolute values of post-CRT ADC (p < 0.01). CONCLUSIONS: The use of post-CRT ADC increased the diagnostic performance of MRI in addition to DWI in predicting the final pathologic staging of rectal carcinoma.

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The purpose of this study is to determine the relationship between the structural integrity of the corpus callosum (CC) and clinical feeding/swallowing performance in children with unilateral spastic cerebral palsy (USCP). Twenty children with USCP, (11 males, 5.11-17.6 yoa) were assessed via the Dysphagia Disorder Survey (DDS) and diffusion tensor imaging. Children were grouped into left hemisphere lesion (LHL; n = 13) and right hemisphere lesion (RHL; n = 7) groups. DTI variables analyzed for three CC regions (anterior, middle, posterior) were: fractional anisotropy (FA), radial diffusivity (RD), mean diffusivity (MD), and fibers count. Children with RHL presented with higher clinical dysphagia severity (p = 0.03). Six of seven children with RHL had lesions affecting periventricular/subcortical areas, and 8/13 children with LHL had lesions affecting the sensorimotor cortex. In the LHL group, as FA and fiber count of the anterior CC decreased and RD increased (all indicating reduced CC structural integrity), signs of dysphagia increased (r = -0.667, p = 0.013; r = -0.829, p ≤ 0.001; r = 0.594, p = 0.032, respectively). Reduced fiber count in the middle and posterior CC was also significantly associated with increased DDS scores (r = -0.762, p = 0.002; r = -0.739, p = 0.004, respectively). For the RHL group no significant correlations were observed. We provide preliminary evidence that corpus callosum integrity correlates with feeding/swallowing performance in children with USCP, especially when cortical sensorimotor areas of the left hemisphere are impacted. In this sample, CC integrity appeared to enable interhemispheric cortical plasticity for swallowing, but was not as critical when intrahemispheric connections were disrupted, as seen in the RHL group.

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Human brain connection map is far from being complete. In particular the study of the superficial white matter (SWM) is an unachieved task. Its description is essential for the understanding of human brain function and the study of pathogenesis triggered by abnormal connectivity. In this work we automatically created a multi-subject atlas of SWM diffusion-based bundles of the whole brain. For each subject, the complete cortico-cortical tractogram is first split into sub-tractograms connecting pairs of gyri. Then intra-subject shape-based fiber clustering performs compression of each sub-tractogram into a set of bundles. Proceeding further with shape-based clustering provides a match of the bundles across subjects. Bundles found in most of the subjects are instantiated in the atlas. To increase robustness, this procedure was performed with two independent groups of subjects, in order to discard bundles without match across the two independent atlases. Finally, the resulting intersection atlas was projected on a third independent group of subjects in order to filter out bundles without reproducible and reliable projection. The final multi-subject diffusion-based U-fiber atlas is composed of 100 bundles in total, 50 per hemisphere, from which 35 are common to both hemispheres.

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Parkinson's disease (PD) affects at least 10 million people worldwide. It is a neurodegenerative disease, which is currently diagnosed by neurological examination. No neuroimaging investigation or blood biomarker is available to aid diagnosis and prognosis. Most effort toward diagnosis using magnetic resonance (MR) has been focused on the use of structural/anatomical neuroimaging and diffusion tensor imaging (DTI). However, deep brain stimulation, a current strategy for treating PD, is guided by MR imaging (MRI). For clinical prognosis, diagnosis, and follow-up investigations, blood oxygen level-dependent MRI, DTI, spectroscopy, and transcranial magnetic stimulation have been used. These techniques represent the state of the art in the last 5 years. Here, we focus on MR techniques for the diagnosis and treatment of Parkinson's disease.

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PURPOSE: To measure both transversal relaxation time (T2 ) and diffusion coefficients within a single scan using a multi-shot approach. Both measurements have drawn interest in many applications, especially in skeletal muscle studies, which have short T2 values. Multiple echo single-shot schemes have been proposed to obtain those variables simultaneously within a single scan, resulting in a reduction of the scanning time. However, one problem with those approaches is the associated long echo read-out. Consequently, the minimum achievable echo time tends to be long, limiting the application of these sequences to tissues with relatively long T2 . MATERIALS AND METHODS: To address this problem, we propose to extend the multi-echo sequences using a multi-shot approach, so that to allow shorter echo times. A multi-shot dual-echo EPI sequence with diffusion gradients and echo navigators was modified to include independent diffusion gradients in any of the two echoes. RESULTS: The multi-shot approach allows us to drastically reduce echo times. Results showed a good agreement for the T2 and mean diffusivity measurements with gold standard sequences in phantoms and in vivo data of calf muscles from healthy volunteers. CONCLUSION: A fast and accurate method is proposed to measure T2 and diffusion coefficients simultaneously, tested in vitro and in healthy volunteers.

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