Practical methods for segmentation and calculation of brain volume and intracranial volume: a guide and comparison.

Background: Accurate segmentation and calculation of total brain volume (BV) and intracranial volume (ICV) (further-volumetry) may serve various clinical tasks and research studies in neuroscience. Manual segmentation is extremely time consuming. There is a relative lack of published broad recommendations and comparisons of tools for automated volumetry, especially for users without expertise in computer science, for settings with limited resources, and when neuroimaging quality is suboptimal due to clinical circumstances. Our objective is to decrease the barrier to entry for research and clinical groups to perform volumetric cranial imaging analysis using free and reliable software tools. Methods: Automated volumetry from computed tomography (CT)/magnetic resonance imaging (MRI) scans was accomplished using 3D Slicer (v. 4.11.0), FreeSurfer (v. 7.1.1), and volBrain (v. 1.0) in a cohort of 39 patients with ischemic middle cerebral artery territory brain infarcts in the acute stage. Visual inspection for accuracy was also performed. Statistical analysis included coefficient of determination (R2) and Bland-Altman (B-A) plots. A multifaceted comparison between 3D Slicer, FreeSurfer, and volBrain from practical user perspective was performed to compile a list of distinguishing features. Results: BV: FreeSurfer, 3D Slicer, and volBrain provide similar estimations when high quality T1-MRI scans with 1 mm slices (3D scans) are available, whereas 3 mm and thicker slices (2D scans) introduce a dispersion in results. ICV: the most accurate volumetry is provided by 3D Slicer using CT scans. volBrain uses T1-MRIs and also provides good results which agree with 3D Slicer. Both of these methods may be more trustworthy than T1 MRI-derived FreeSurfer calculations. Conclusions: All three studied tools of automated intracranial and brain volumetry-3D Slicer, FreeSurfer, and volBrain-are free, reliable, require no complex programming, but still have certain limitations and significant differences. Based on our investigation findings, the readers should be able to select the right volumetry tool and neuroimaging study, and then follow provided step-by-step instructions to accomplish specific volumetry tasks.

Surgical Treatment of Propriospinal Myoclonus: A Case Report.

Propriospinal myoclonus (PSM) is a rare segmental movement disorder characterized by repetitive irregular myoclonic jerks of the trunk and/or axial limbs at the resting state. It is imperative to make a correct diagnosis as other movement disorders can be mistaken for or mask PSM. Therefore, a battery of neuroimaging and neurophysiological testing must be undertaken. In our case report, we discuss a patient who was diagnosed with PSM concurrently with cervical degenerative stenosis and then had a successful outcome via surgical decompression and arthrodesis of the cervical spine. We documented the patient's postoperative course and achievement of complete remission, sustained at a 41-month follow-up. We then grouped our case together with five other PSM cases in the literature to offer readers a broader context of the role of surgical spinal intervention in ameliorating PSM.

Natural history of Chiari I malformation in children: a retrospective analysis.

PURPOSE: While there are increasing numbers of studies published regarding Chiari I malformation (CM1) in children, most of these focus on surgical indications, technique, and outcomes. Few studies examine the natural history of CM1 once the decision is made to treat a patient conservatively. In this study, we seek to determine the percentage of pediatric patients who undergo surgery for CM1, both after initial consultation and in a delayed fashion, the natural history of CM1 after a decision to pursue non-operative management, and attempt to identify patient factors that may predict development of new or worsening CM1 symptoms. METHODS: From our database of 465 pediatric patients with CM1, we identified those who were seen for initial consultation from July 1, 2011, to June 30, 2016. We examined rates of surgical intervention, types of surgical intervention, age, gender, and presence or absence of headache and syrinx, and looked carefully at the patients who had new or worsening symptoms prompting delayed surgical intervention. RESULTS: We identified 226 patients meeting inclusion criteria. Overall, 15% of patients had surgery, the majority being Chiari decompression. Just over half of these patients had surgery within 6 months of initial consultation. Of those with delayed surgery, only 4 patients had new symptoms/syrinx and 1 patient had symptom progression. The other patients had various reasons for surgical delay not related to symptom development or progression. There were no obvious commonalities among these 5 patients that could predict progression prospectively. All patients who had surgery did so within 2 years of initial consultation. CONCLUSION: Overall, the natural history of asymptomatic CM1 is benign. Patients treated non-operatively are unlikely to progress. If they do progress, this is likely to occur within 2 years of initial consultation. There were no factors identified in this study that predicted new or worsening symptoms over time.

Soft tissue density within the foramen magnum, a predictor for surgical intervention in pediatric patients with Chiari malformation type I.

OBJECTIVE: Chiari malformation type I (CMI) is diagnosed as herniation of the cerebellar tonsils by at least 5 mm below the foramen magnum. However, the degree of tonsillar herniation is a poor predictor of the need for decompression surgery. Exploration for an alternative morphological predictor for surgical intervention could provide greater insight into the development of an appropriate treatment plan for these patients. To investigate this issue, the authors calculated the soft tissue density within the foramen magnum as a measure of impaction of the cerebellar tonsils. Soft tissue density within the foramen magnum and degree of tonsillar herniation were then assessed for their correlation with the need for surgical intervention. METHODS: The authors conducted a retrospective, longitudinal chart review of pediatric patients with CMI. Those who had undergone surgical intervention were considered symptomatic and those who had been treated conservatively, as asymptomatic. Soft tissue density was found by dividing the soft tissue occupancy of the foramen magnum (brainstem and cerebellar tonsils) by the total area of the bony foramen magnum. The predictive value of these two measurements for the need of surgery was determined. RESULTS: Of the 465 patients seen for CMI at the authors' institution between July 1, 2011, and May 31, 2017, 80 underwent surgical intervention and 385 were asymptomatic. The average tissue density was significantly greater in the surgical group than in the asymptomatic group (83.3% and 78.6%, respectively, p < 0.0001). The average tonsillar descent for surgical patients was 10.8 mm compared to 9.8 mm for asymptomatic patients (p = 0.140). The point-biserial correlation coefficient was assessed, and soft tissue density was found to positively correlate with the need for surgical intervention (rpb = 0.199, p = 0.0001), whereas tonsillar herniation did not correlate with the need for surgery (rpb = 0.083, p = 0.115). Additionally, the degree of tonsillar herniation did not correlate with soft tissue density (r = 0.09), indicating that soft tissue density is an independent morphological parameter. CONCLUSIONS: The study findings suggest that the need for surgical intervention in CMI patients is positively correlated with increasing soft tissue density within the foramen magnum, whereas the degree of tonsillar herniation did not show a correlation with the need for surgical intervention. Additionally, soft tissue density is a factor independent of the degree of tonsillar herniation. Further investigation of tissue density within the foramen magnum is needed in the hope of discovering a clinically applicable parameter that would indicate a need for surgical intervention in patients with CMI.

The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2.

YidC, a bacterial member of the YidC/Alb3/Oxa1 insertase family, mediates membrane protein assembly and insertion. Cytoplasmic loops are known to have functional significance in membrane proteins such as YidC. Employing microsecond-level molecular dynamics (MD) simulations, we show that the crystallographically unresolved C2 loop plays a crucial role in the structural dynamics of Bacillus halodurans YidC2. We have modeled the C2 loop and used all- atom MD simulations to investigate the structural dynamics of YidC2 in its apo form, both with and without the C2 loop. The C2 loop was found to stabilize the entire protein and particularly the C1 region. C2 was also found to stabilize the alpha-helical character of the C-terminal region. Interestingly, the highly polar or charged lipid head groups of the simulated membranes were found to interact with and stabilize the C2 loop. These findings demonstrate that the crystallographically unresolved loops of membrane proteins could be important for the stabilization of the protein despite the apparent lack of structure, which could be due to the absence of the relevant lipids to stabilize them in crystallographic conditions.