CerebNet: A fast and reliable deep-learning pipeline for detailed cerebellum sub-segmentation

Quantifying the volume of the cerebellum and its lobes is of profound interest in various neurodegenerative and acquired diseases. Especially for the most common spinocerebellar ataxias (SCA), for which the first antisense oligonculeotide-base gene silencing trial has recently started, there is an urgent need for quantitative, sensitive imaging markers at pre-symptomatic stages for stratification and treatment assessment. This work introduces CerebNet, a fully automated, extensively validated, deep learning method for the lobular segmentation of the cerebellum, including the separation of gray and white matter. For training, validation, and testing, T1-weighted images from 30 participants were manually annotated into cerebellar lobules and vermal sub-segments, as well as cerebellar white matter. CerebNet combines FastSurferCNN, a UNet-based 2.5D segmentation network, with extensive data augmentation, e.g. realistic non-linear deformations to increase the anatomical variety, eliminating additional preprocessing steps, such as spatial normalization or bias field correction. CerebNet demonstrates a high accuracy (on average 0.87 Dice and 1.742mm Robust Hausdorff Distance across all structures) outperforming state-of-the-art approaches. Furthermore, it shows high test-retest reliability (average ICC >0.97 on OASIS and Kirby) as well as high sensitivity to disease effects, including the pre-ataxic stage of spinocerebellar ataxia type 3 (SCA3). CerebNet is compatible with FreeSurfer and FastSurfer and can analyze a 3D volume within seconds on a consumer GPU in an end-to-end fashion, thus providing an efficient and validated solution for assessing cerebellum sub-structure volumes. We make CerebNet available as source-code (https://github.com/Deep-MI/FastSurfer)

Early stages of pediatric bipolar disorder: retrospective analysis of a Czech inpatient sample

Michal Goetz,1 Tomas Novak,2 Marie Vesela,1 Zdenek Hlavka,3 Martin Brunovsky,2 Michal Povazan,4 Radek Ptacek,5 Antonin Sebela21Department of Child Psychiatry, Second Faculty of Medicine, Motol University Hospital, Charles University in Prague, Prague, Czech Republic; 2National Institute of Mental Health, Klecany and Third Faculty of Medicine, Charles University in Prague, Prague, Czech Republic; 3Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University in Prague, Prague, Czech Republic; 4Children’s Department, Bohnice Psychiatric Hospital, Prague, Czech Republic; 5Department of Psychiatry, First Faculty of Medicine, General Teaching Hospital, Charles University in Prague, Czech RepublicBackground: Approximately 30%–60% of adults diagnosed with bipolar disorder (BD) report onset between the ages 15 and 19 years; however, a correct diagnosis is often delayed by several years. Therefore, investigations of the early features of BD are important for adequately understanding the prodromal stages of the illness.Methods: A complete review of the medical records of 46 children and adolescents who were hospitalized for BD at two psychiatric teaching centers in Prague, Czech Republic was performed. Frequency of BD in all inpatients, age of symptom onset, phenomenology of mood episodes, lifetime psychiatric comorbidity, differences between very-early-onset (<13 years of age) and early-onset patients (13–18 years), and differences between the offspring of parents with and without BD were analyzed.Results: The sample represents 0.83% of the total number of inpatients (n=5,483) admitted during the study period at both centers. BD often started with depression (56%), followed by hypomania (24%) and mixed episodes (20%). The average age during the first mood episode was 14.9 years (14.6 years for depression and 15.6 years for hypomania). Seven children (15%) experienced their first mood episode before age 13 years (very early onset). Traumatic events, first-degree relatives with mood disorders, and attention deficit hyperactivity disorder were significantly more frequent in the very-early-onset group vs the early-onset group (13–18 years) (P≤0.05). The offspring of bipolar parents were significantly younger at the onset of the first mood episode (13.2 vs 15.4 years; P=0.02) and when experiencing the first mania compared to the offspring of non-BD parents (14.3 vs 15.9 years; P=0.03). Anxiety disorders, substance abuse, specific learning disabilities, and attention deficit hyperactivity disorder were the most frequent lifetime comorbid conditions.Conclusion: Clinicians must be aware of the potential for childhood BD onset in patients who suffer from recurrent depression, who have first-degree relatives with BD, and who have experienced severe psychosocial stressors.Keywords: children, adolescents, inpatient

Magnetic Resonance in Medicine / (2+1)DCAIPIRINHA accelerated MR spectroscopic imaging of the brain at 7T

Purpose To compare a new parallel imaging (PI) method for multislice proton magnetic resonance spectroscopic imaging (1HMRSI), termed (2+1)DCAIPIRINHA, with two standard PI methods: 2DGRAPPA and 2DCAIPIRINHA at 7 Tesla (T). Methods (2+1)DCAIPIRINHA is a combination of 2DCAIPIRINHA and sliceCAIPIRINHA. Eight healthy volunteers were measured on a 7T MR scanner using a 32channel head coil. The best undersampling patterns were estimated for all three PI methods. The artifact powers, gfactors, CramérRao lower bounds (CRLB), and root mean square errors (RMSE) were compared quantitatively among the three PI methods. Metabolic maps and spectra were compared qualitatively. Results (2+1)DCAIPIRINHA allows acceleration in three spatial dimensions in contrast to 2DGRAPPA and 2DCAIPIRINHA. Thus, this sequence significantly decreased the RMSE of the metabolic maps by 12.1 and 6.9%, on average, for 4<R<11, compared with 2DGRAPPA and 2DCAIPIRINHA, respectively. The artifact power was 22.6 and 8.4% lower, and the CRLB were 3.4 and 0.6% lower, respectively. Conclusion (2+1)CAIPIRINHA can be implemented for multislice MRSI in the brain, enabling higher accelerations than possible with twodimensional (2D) parallel imaging methods. An eightfold acceleration was still feasible in vivo with negligible PI artifacts with lipid decontamination, thus decreasing the measurement time from 120 to 15min for a 64644 matrix. Magn Reson Med 78:429440, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.(VLID)483935

Comparison of Multivendor Single-Voxel MR Spectroscopy Data Acquired in Healthy Brain at 26 Sites

Background: The hardware and software differences between MR vendors and individual sites influence the quantification of MR spectroscopy data. An analysis of a large data set may help to better understand sources of the total variance in quantified metabolite levels. Purpose: To compare multisite quantitative brain MR spectroscopy data acquired in healthy participants at 26 sites by using the vendor-supplied single-voxel point-resolved spectroscopy (PRESS) sequence. Materials and Methods: An MR spectroscopy protocol to acquire short-echo-time PRESS data from the midparietal region of the brainwas disseminated to 26 research sites operating 3.0-T MR scanners from three different vendors. In this prospective study, healthy participants were scanned between July 2016 and December 2017. Data were analyzed by using software with simulated basis sets customized for each vendor implementation. The proportion of total variance attributed to vendor-, site-, and participant-related effects was estimated by using a linear mixed-effects model. P values were derived through parametric bootstrapping of the linearmixed-effects models (denoted P-boot). Results: In total, 296 participants (mean age, 26 years +/- 4.6; 155 women and 141 men) were scanned. Good-quality data were recorded from all sites, as evidenced by a consistent linewidth of N-acetylaspartate (range, 4.4-5.0 Hz), signal-to-noise ratio (range,174-289), and low Cramer-Rao lower bounds ( .90), N-acetylaspartate and N-acetylaspartylglutamate (P-boot =.13), or glutamate and glutamine (P-boot =.11). Among the smaller resonances, no vendor effects were found for ascorbate (P-boot =.08), aspartate (P-boot >.90), glutathione (P-boot > .90), or lactate (P-boot =.28). Conclusion: Multisite multivendor single-voxel MR spectroscopy studies performed at 3.0 T can yield results that are coherent across vendors, provided that vendor differences in pulse sequence implementation are accounted for in data analysis. However, the site related effects on variability were more profound and suggest the need for further standardization of spectroscopic protocols. (C) RSNA, 202