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Brain magnetic resonance image segmentation using novel improvement for expectation maximizing

Balafar MA, Ramli AR, Mashohor S

Neurosciences (Riyadh), 2011 Jul;16(3):242-7.
PMID: 21677615

To improve the quality of expectation maximizing (EM) for brain image segmentation, and to evaluate the accuracy of segmentation results.

Matched MeSH terms: Brain/anatomy & histology*
Brain size evolution in pipefishes and seahorses: the role of feeding ecology, life history and sexual selection

Tsuboi M, Lim AC, Ooi BL, Yip MY, Chong VC, Ahnesjö I, et al.

J Evol Biol, 2017 Jan;30(1):150-160.
PMID: 27748990 DOI: 10.1111/jeb.12995

Brain size varies greatly at all taxonomic levels. Feeding ecology, life history and sexual selection have been proposed as key components in generating contemporary diversity in brain size across vertebrates. Analyses of brain size evolution have, however, been limited to lineages where males predominantly compete for mating and females choose mates. Here, we present the first original data set of brain sizes in pipefishes and seahorses (Syngnathidae) a group in which intense female mating competition occurs in many species. After controlling for the effect of shared ancestry and overall body size, brain size was positively correlated with relative snout length. Moreover, we found that females, on average, had 4.3% heavier brains than males and that polyandrous species demonstrated more pronounced (11.7%) female-biased brain size dimorphism. Our results suggest that adaptations for feeding on mobile prey items and sexual selection in females are important factors in brain size evolution of pipefishes and seahorses. Most importantly, our study supports the idea that sexual selection plays a major role in brain size evolution, regardless of on which sex sexual selection acts stronger.

Matched MeSH terms: Brain/anatomy & histology*
A comparison of brain phantom relative permittivity with CST simulation library and existing research

Chew KM, Seman N, Sudirman R, Yong CY

Biomed Mater Eng, 2014;24(6):2161-7.
PMID: 25226914 DOI: 10.3233/BME-141027

The development of human-like brain phantom is important for data acquisition in microwave imaging. The characteristics of the phantom should be based on the real human body dielectric properties such as relative permittivity. The development of phantom includes the greymatter and whitematter regions, each with a relative permittivity of 38 and 28 respectively at 10 GHz frequency. Results were compared with the value obtained from the standard library of Computer Simulation Technology (CST) simulation application and the existing research by Fernandez and Gabriel. Our experimental results show a positive outcome, in which the proposed mixture was adequate to represent real human brain for data acquisition.

Matched MeSH terms: Brain/anatomy & histology*
Periodic lateralized epileptiform discharges in neuropsychiatric lupus: association with cerebritis in magnetic resonance imaging and resolution after intravenous immunoglobulin

Lim KS, Cheong KL, Tan CT

Lupus, 2010 May;19(6):748-52.
PMID: 20133346 DOI: 10.1177/0961203309351539

A 13-year-old girl with a known diagnosis of systemic lupus erythematosus presented with seizures and psychosis. An electroencephalogram (EEG) revealed continuous, non-evolving periodic lateralized epileptiform discharges (PLEDs) in the left temporal region, which did not resolve with benzodiazepine. A magnetic resonance imaging (MRI) brain scan demonstrated a focal hyperintensity in the left medial temporal and left occipital lobes, left thalamus and bilateral cerebellar white matter, with evidence of vasculitis in the magnetic resonance angiography. Intravenous immunoglobulin was given because of failed steroid therapy, which resulted in a full resolution of clinical, EEG and MRI abnormalities. Lupus cerebritis should be considered as a possible aetiology in PLEDs, and immunoglobulin can be effective in neuropsychiatric lupus.

Matched MeSH terms: Brain/anatomy & histology
Medical image compression using 3-D Hartley transform

Shyam Sunder R, Eswaran C, Sriraam N

Comput Biol Med, 2006 Sep;36(9):958-73.
PMID: 16026779

In this paper, 3-D discrete Hartley transform is applied for the compression of two medical modalities, namely, magnetic resonance images and X-ray angiograms and the performance results are compared with those of 3-D discrete cosine and Fourier transforms using the parameters such as PSNR and bit rate. It is shown that the 3-D discrete Hartley transform is better than the other two transforms for magnetic resonance brain images whereas for the X-ray angiograms, the 3-D discrete cosine transform is found to be superior.

Matched MeSH terms: Brain/anatomy & histology
Fulltext Automatic Region-Based Brain Classification of MRI-T1 Data

Yazdani S, Yusof R, Karimian A, Mitsukira Y, Hematian A

PLoS One, 2016;11(4):e0151326.
PMID: 27096925 DOI: 10.1371/journal.pone.0151326

Image segmentation of medical images is a challenging problem with several still not totally solved issues, such as noise interference and image artifacts. Region-based and histogram-based segmentation methods have been widely used in image segmentation. Problems arise when we use these methods, such as the selection of a suitable threshold value for the histogram-based method and the over-segmentation followed by the time-consuming merge processing in the region-based algorithm. To provide an efficient approach that not only produce better results, but also maintain low computational complexity, a new region dividing based technique is developed for image segmentation, which combines the advantages of both regions-based and histogram-based methods. The proposed method is applied to the challenging applications: Gray matter (GM), White matter (WM) and cerebro-spinal fluid (CSF) segmentation in brain MR Images. The method is evaluated on both simulated and real data, and compared with other segmentation techniques. The obtained results have demonstrated its improved performance and robustness.

Matched MeSH terms: Brain/anatomy & histology*
Shape-based interpolation method in measuring intracranial volume for pre- and post-operative decompressive craniectomy using open source software

Abdullah JY, Rajion ZA, Martin AG, Jaafar A, Ghani ARI, Abdullah JM

Neurocirugia (Astur : Engl Ed), 2019 02 16;30(3):115-123.
PMID: 30782505 DOI: 10.1016/j.neucir.2018.12.004

INTRODUCTION: Intracranial volume (ICV) is an important tool in the management of patients undergoing decompressive craniectomy (DC) surgery. The aim of this study was to validate ICV measurement applying the shape-based interpolation (SBI) method using open source software on computed tomography (CT) images.
METHODS: The pre- and post-operative CT images of 55 patients undergoing DC surgery were analyzed. The ICV was measured by segmenting every slice of the CT images, and compared with estimated ICV calculated using the 1-in-10 sampling strategy and processed using the SBI method. An independent t test was conducted to compare the ICV measurements between the two different methods. The calculation using this method was repeated three times for reliability analysis using the intraclass correlations coefficient (ICC). The Bland-Altman plot was used to measure agreement between the methods for both pre- and post-operative ICV measurements.
RESULTS: The mean ICV (±SD) were 1341.1±122.1ml (manual) and 1344.11±122.6ml (SBI) for the preoperative CT data. The mean ICV (±SD) were 1396.4±132.4ml (manual) and 1400.53±132.1ml (SBI) for the post-operative CT data. No significant difference was found in ICV measurements using the manual and the SBI methods (p=.983 for pre-op, and p=.960 for post-op). The intrarater ICC showed a significant correlation; ICC=1.00. The Bland-Altman plot showed good agreement between the manual and the SBI method.
CONCLUSION: The shape-based interpolation method with 1-in-10 sampling strategy gave comparable results in estimating ICV compared to manual segmentation. Thus, this method could be used in clinical settings for rapid, reliable and repeatable ICV estimations.

Matched MeSH terms: Brain/anatomy & histology
Establishment of Reference Ranges for Normal Organ Weights in Malaysian Adults at Autopsy

Jothee S, Shafie MS, Vijayaretnam SV, Nor FM

Am J Forensic Med Pathol, 2020 Jun;41(2):110-114.
PMID: 32205487 DOI: 10.1097/PAF.0000000000000539

Organ weights are routinely measured during autopsies as a crude screening tool to detect possible organ pathology. In several centers, inclusion of major organ weights indicates whether an autopsy report has achieved its standard of practice, which in turn should be subjected to an audit. Previous studies show statistical variation in organ weights across different populations. Malaysian pathologists have relied on Western data and crude subjective determination in the interpretation of normal organ weights. Hence, the need for a reference range as a guide for pathologists is acute. Organ weights from traumatic deaths between 2004 and 2017 were analyzed in the UKM Medical Centre. Statistical analysis was performed to form reference ranges for normal weights of the brain, heart, lung, liver, spleen, and kidneys. In addition, the data were compared between sexes, races, and body mass index values to determine whether organ weights were affected by these parameters. In this study, reference ranges for organ weights are presented for Malaysian adult men and women.

Matched MeSH terms: Brain/anatomy & histology
Fulltext An EEG Database and Its Initial Benchmark Emotion Classification Performance

Seal A, Reddy PPN, Chaithanya P, Meghana A, Jahnavi K, Krejcar O, et al.

Comput Math Methods Med, 2020;2020:8303465.
PMID: 32831902 DOI: 10.1155/2020/8303465

Human emotion recognition has been a major field of research in the last decades owing to its noteworthy academic and industrial applications. However, most of the state-of-the-art methods identified emotions after analyzing facial images. Emotion recognition using electroencephalogram (EEG) signals has got less attention. However, the advantage of using EEG signals is that it can capture real emotion. However, very few EEG signals databases are publicly available for affective computing. In this work, we present a database consisting of EEG signals of 44 volunteers. Twenty-three out of forty-four are females. A 32 channels CLARITY EEG traveler sensor is used to record four emotional states namely, happy, fear, sad, and neutral of subjects by showing 12 videos. So, 3 video files are devoted to each emotion. Participants are mapped with the emotion that they had felt after watching each video. The recorded EEG signals are considered further to classify four types of emotions based on discrete wavelet transform and extreme learning machine (ELM) for reporting the initial benchmark classification performance. The ELM algorithm is used for channel selection followed by subband selection. The proposed method performs the best when features are captured from the gamma subband of the FP1-F7 channel with 94.72% accuracy. The presented database would be available to the researchers for affective recognition applications.

Matched MeSH terms: Brain/anatomy & histology
Quantification of diffusion tensor imaging in normal white matter maturation of early childhood using an automated processing pipeline

Loh KB, Ramli N, Tan LK, Roziah M, Rahmat K, Ariffin H

Eur Radiol, 2012 Jul;22(7):1413-26.
PMID: 22434420 DOI: 10.1007/s00330-012-2396-3

OBJECTIVES: The degree and status of white matter myelination can be sensitively monitored using diffusion tensor imaging (DTI). This study looks at the measurement of fractional anistropy (FA) and mean diffusivity (MD) using an automated ROI with an existing DTI atlas.
METHODS: Anatomical MRI and structural DTI were performed cross-sectionally on 26 normal children (newborn to 48 months old), using 1.5-T MRI. The automated processing pipeline was implemented to convert diffusion-weighted images into the NIfTI format. DTI-TK software was used to register the processed images to the ICBM DTI-81 atlas, while AFNI software was used for automated atlas-based volumes of interest (VOIs) and statistical value extraction.
RESULTS: DTI exhibited consistent grey-white matter contrast. Triphasic temporal variation of the FA and MD values was noted, with FA increasing and MD decreasing rapidly early in the first 12 months. The second phase lasted 12-24 months during which the rate of FA and MD changes was reduced. After 24 months, the FA and MD values plateaued.
CONCLUSION: DTI is a superior technique to conventional MR imaging in depicting WM maturation. The use of the automated processing pipeline provides a reliable environment for quantitative analysis of high-throughput DTI data.
KEY POINTS: Diffusion tensor imaging outperforms conventional MRI in depicting white matter maturation. • DTI will become an important clinical tool for diagnosing paediatric neurological diseases. • DTI appears especially helpful for developmental abnormalities, tumours and white matter disease. • An automated processing pipeline assists quantitative analysis of high throughput DTI data.

Matched MeSH terms: Brain/anatomy & histology*
Brain white and gray matter anatomy of MRI segmentation based on tissue evaluation

Salih QA, Ramli AR, Mahmud R, Wirza R

MedGenMed, 2005;7(2):1.
PMID: 16369380

Different approaches to gray and white matter measurements in magnetic resonance imaging (MRI) have been studied. For clinical use, the estimated values must be reliable and accurate when, unfortunately, many techniques fail on these criteria in an unrestricted clinical environment. A recent method for tissue clusterization in MRI analysis has the advantage of great simplicity, and it takes the account of partial volume effects. In this study, we will evaluate the intensity of MR sequences known as T1-weighted images in an axial sliced section. Intensity group clustering algorithms are proposed to achieve further diagnosis for brain MRI, which has been hardly studied. Subjective study has been suggested to evaluate the clustering group intensity in order to obtain the best diagnosis as well as better detection for the suspected cases. This technique makes use of image tissue biases of intensity value pixels to provide 2 regions of interest as techniques. Moreover, the original mathematic solution could still be used with a specific set of modern sequences. There are many advantages to generalize the solution, which give far more scope for application and greater accuracy.

Matched MeSH terms: Brain/anatomy & histology*
Fulltext Brain area-specific diurnal and photic regulation of val-opsinA and val-opsinB genes in the zebrafish

Hang CY, Kitahashi T, Parhar IS

J Neurochem, 2015 May;133(4):501-10.
PMID: 25727787 DOI: 10.1111/jnc.13084

Zebrafish possess two isoforms of vertebrate ancient long (VAL)-opsin, val-opsinA (valopa) and val-opsinB (valopb), which probably mediate non-visual responses to light. To understand the diurnal and light-sensitive regulation of the valop genes in different cell groups, the current study used real-time quantitative PCR to examine the diurnal changes of valopa and b mRNA levels in different brain areas of adult male zebrafish. Furthermore, effects of the extended exposure to light or dark condition, luminous levels and the treatment with a melatonin receptor agonist or antagonist on valop transcription were examined. In the thalamus, valop mRNA levels showed significant diurnal changes; valopa peaked in the evening, while valopb peaked in the morning. The diurnal change of valopa mRNA levels occurred independent of light conditions, whereas that of valopb mRNA levels were regulated by light. A melatonin receptor agonist or antagonist did not affect the changes of valop mRNA levels. In contrast, the midbrain and hindbrain showed arrhythmic valop mRNA levels under light and dark cycles. The differential diurnal regulation of the valopa and b genes in the thalamus and the arrhythmic expression in the midbrain and hindbrain suggest involvement of deep brain VAL-opsin in time- and light-dependent physiology. We show diurnal expression changes of vertebrate ancient long (VAL) opsin genes (valopa and valopb), depending on brain area, time of day and light condition, in the adult male zebrafish. Differential regulation of the valop genes in the thalamus and arrhythmic expression in the midbrain and hindbrain suggest their involvement in time- and light-dependent physiology to adjust to environmental changes.

Matched MeSH terms: Brain/anatomy & histology
Sequence and localization of kcnk10a in the brain of adult zebrafish (Danio rerio)

Loganathan K, Moriya S, Sivalingam M, Ng KW, Parhar IS

J. Chem. Neuroanat., 2017 Dec;86:92-99.
PMID: 29074372 DOI: 10.1016/j.jchemneu.2017.10.004

kcnk10a has been predicted in zebrafish to be a member of the two-pore domain potassium ion (K+) channel-related K+ (TREK) channel family known as a thermoreceptor. Since reproduction is affected by temperature, Kcnk10a could be involved in the regulation of reproduction. However, expression of kcnk10a in the zebrafish brain and association with reproduction has not been identified. In this study, the full length sequence and localization of kcnk10a in the brain was investigated and gene expressions of the TREK channel family were examined to investigate association with reproduction. We initially identified the full length cDNA sequence of kcnk10a using Rapid Amplification of cDNA Ends and localization in the zebrafish brain using in situ hybridization. Furthermore, we examined the gene expression differences of kcnk2b, kcnk10a and kcnk10b mRNA between genders as well as developmental stages by real-time PCR. The deduced amino acid sequence of the identified kcnk10a mRNA contains highly conserved two pore domains and four transmembrane regions and was higher similarity to zebrafish Kcnk10b than zebrafish Kcnk2a and 2b. kcnk10a mRNA was widely distributed in the brain such as the preoptic area, hypothalamus and the midbrain. kcnk10a mRNA expression exhibited significant difference between mature male and female, and increase during puberty. Kcnk10a could be involved in the regulation of reproductive function.

Matched MeSH terms: Brain/anatomy & histology*
Effects of a neurotensin analogue (PD149163) and antagonist (SR142948A) on the scopolamine-induced deficits in a novel object discrimination task

Azmi N, Norman C, Spicer CH, Bennett GW

Behav Pharmacol, 2006 Jun;17(4):357-62.
PMID: 16914954

Various lines of evidence suggest a role in cognition for the endogenous neuropeptide, neurotensin, involving an interaction with the central nervous system cholinergic pathways. A preliminary study has shown that central administration of neurotensin enhances spatial and nonspatial working memory in the presence of scopolamine, a muscarinic receptor antagonist which induces memory deficits. Utilizing similar methods, the present study employed a two-trial novel object discrimination task to determine the acute effect of a neurotensin peptide analogue with improved metabolic stability, PD149163, on recognition memory in Lister hooded rats. Consistent with previous findings with neurotensin, animals receiving an intracerebroventricular injection of PD149163 (3 microg) significantly discriminated the novel from familiar object during the choice trial. In addition, a similar dose of PD149163 restored the scopolamine-induced deficit in novelty recognition. The restoration effect on scopolamine-induced amnesia produced by PD149163 was blocked by SR142948A, a nonselective neurotensin receptor antagonist, at a dose of 1 mg/kg (intraperitonial) but not at 0.1 mg/kg. In conclusion, the present results confirm a role for neurotensin in mediating memory processes, possibly via central cholinergic mechanisms.

Matched MeSH terms: Brain/anatomy & histology

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