A library for fMRI real-time processing systems in python (RTPSpy) with comprehensive online noise reduction, fast and accurate anatomical image processing, and online processing simulation

We introduce a python library for real-time fMRI (rtfMRI) data processing systems, Real-Time Processing System in python (RTPSpy), to provide building blocks for a custom rtfMRI application with extensive and advanced functionalities. RTPSpy is a library package including 1) a fast, comprehensive, and flexible online fMRI denoising pipeline comparable to offline processing, 2) utilities for fast and accurate anatomical image processing to define a target region on-site, 3) a simulation system of online fMRI processing to optimize a pipeline and target signal calculation, 4) interface to an external application for feedback presentation, and 5) a boilerplate graphical user interface (GUI) integrating operations with RTPSpy library. Since online fMRI data processing cannot be equivalent to offline, we discussed the limitations of online analysis and their solutions in the RTPSpy implementation. We developed a fast and accurate anatomical image processing script with fast tissue segmentation (FastSeg), image alignment, and spatial normalization, utilizing the FastSurfer, AFNI, and ANTs. We confirmed that the FastSeg output was comparable with FreeSurfer, and could complete all the anatomical image processing in a few minutes. Thanks to its highly modular architecture, RTPSpy can easily be used for a simulation analysis to optimize a processing pipeline and target signal calculation. We present a sample script for building a real-time processing pipeline and running a simulation using RTPSpy. The library also offers a simple signal exchange mechanism with an external application. An external application can receive a real-time neurofeedback signal from RTPSpy in a background thread with a few lines of script. While the main components of the RTPSpy are the library modules, we also provide a GUI class for easy access to the RTPSpy functions. The boilerplate GUI application provided with the package allows users to develop a customized rtfMRI application with minimum scripting labor. Finally, we discussed the limitations of the package regarding environment-specific implementations. We believe that RTPSpy is an attractive option for developing rtfMRI applications highly optimized for individual purposes. The package is available from GitHub (https://github.com/mamisaki/RTPSpy) with GPL3 license.

Analisis Variasi Flip Angle terhadap Informasi Citra Anatomi pada Sekuen 3D TOF MRA Brain dengan MRI 3 Tesla

Background : Magnetic Resonance Angiography is a diagnostic imaging method that can display images of blood vessels. MRA imaging on MRI 3 Tesla provides high spatial resolution making blood vessel contrast increased so that the intracranial vessels are clearer. The efficient technique that does not use contrast media in MRA is Time of Flight. 3D TOF imaging is good for visualizing intracranial vessels. In this method the appropriate flip angle will produce a hyperintense picture of the blood vessels. This study aims to determine the effect of flip angle on anatomical image information on 3D TOF MRA Brain.Methods : This type of research is a quantitative experimental approach, conducted in February 2020 in Pertamina Central Hospital, South Jakarta. Research by conducting flip angle variations of 15°, 20°, 25°, 30° in the 3D TOF sequence of the Brain against 10 volunteers. Criteria for volunteers are healthy people aged 18-25 years. The results of the images were assessed by 3 respondent, including Internal Carotid Artery, Vertebral Artery, Basilar Artery, Anterior Cerebral Artery, Posterior Cerebral Artery, Middle Cerebral Artery, Anterior Communicating Artery, Posterior Communicating Artery. Then the Kappa test was carried out followed by the Friedman test to find the highest mean rank and comparison of flip angle in anatomical information of 3D TOF MRA Brain.Results : The results showed that there was an effect of changes in the values of the flip angle to the anatomical information on 3D TOF MRA Brain with p 0,05. The optimal Flip angle value is obtained based on the highest mean rank value which is flip angle 25° with a value of 3,22. The higher the value of flip angle, the greater the signal and contrast, but many slow flowing blood vessels will hypointens.Conclussion : There are difference in anatomical image information of 3D TOF sequence among 4 variation flip angle on examination MRA Brain. Flip angle 25° is better than 15°, 20° and 30° at anatomy information on 3D TOF sequences to show intracranial artery because it has a higher mean rank value.

SERUM EXPRESSION OF MICRORNA-142 IN A COHORT OF BULGARIAN PATIENTS WITH INFLAMMATORY BOWEL DISEASES

The focus of the research was to investigate the anatomical location of the rabbit liver. Thus, we applied a topographic algorithm, using dorsal frozen cuts and CT algorithm with coronary slices. The used animals were 13 matured, healthy clinically white New Zealand rabbits. We measured the metric CT parameters – transverse and craniocaudal sizes. At the level of the dorsal plane, located 15 mm ventrally from the spine, dorsal part of lobus hepatis sinister was found, and on the right and laterally - lobus hepatis dexter. At the level of the dorsal plane, located 30 mm ventrally from the spine, lobus hepatis dexter was located cranially relative to lobus hepatis sinister medialis and reached caudally to pars pylorica. Lobus hepatis sinister lateralis remained caudal to lobus hepatis sinister medialis and touched corpus ventriculi. Lobus hepatis sinister lateralis was found cranially to corpus ventriculi and pars pylorica. Lobus caudatus caudally touched the right kidney. At the level of the dorsal plane, located 45 mm ventrally from the spine, lobus hepatis dexter was found to be in the same dorsal plane with the left lobe of the liver. CT normodense heterogeneous anatomical image of lobus hepatis dexter was parallel to that of lobus hepatis sinister, which determined the transverse location of the organ. The obtained imaging analysis of the liver’s anatomical parts and their proximity to other organ structures were interpreted depending on their attenuation profile. The transverse size of the organ at 15 mm ventrally from the spine showed a value of 76.16 mm, and at 30 mm ventrally, this parameter reached a value of 81.48 mm. The highest values were obtained at 45 mm ventrally - 85.21 mm. CT anatomical study added and confirmed the results of the topographic investigation.

USING 4-[18F]-ADAM MEASURE SEROTONIN TRANSPORTER VARIATIONS WITH HAMD SCALE RELATED TO MAJOR DEPRESSIVE DISORDER IN CT/PET THREE-DIMENSIONAL IMAGE

The medical image can be divided into two major classes: anatomical image and functional image. Magnetic resonance image (MRI) and computed tomography (CT) belong to the anatomical image, which can show an outline of an organ and a tissue clearly. The functional image can show the image of the organ and the tissue metabolism situation. Positron emission tomography (PET) and single photon emission computed tomography (SPECT) are also part of the functional image. In this paper, we use 4-[[Formula: see text]F]-ADAM to measure serotonin transporter changes and find the relation with major depressive disorder in CT/PET three-dimensional image. In clinical diagnosis, based on the video imaging methods can be divided into the anatomy and function of these two categories. Therefore, the combination of anatomical and functional imaging can provide more useful information. In the study, we use the CT image to get the reference position and combine it with the isotope metabolic situation from PET. We use the fused image to construct 3D image and count serotonin transporter with different times, and measure the variance about serotonin transporter changes in the organization of the metabolism and distribution. We use the variance to find the relation and compare the score using Hamilton Depression Rating Scale by experienced psychiatrists. After the test cases, we measure the serotonin transporter distribution of depressed patients can do a preliminary classification. We can get the gray-level value changes in major depressive disorder patients at different times. The advantage of this method is to offer more information to diagnose or analyze the difference between the brain organs, such as pons, midbrain, thalamus, corpus striatum, and prefrontal cortex.

ADAPTIVE STATISTICAL ITERATIVE RECONSTRUCTION FOR OPTIMIZATION IMAGE QUALITY OF CT SCAN ABDOMEN

Adaptive Statistical Iterative Reconstruction is software used to reduce noise. In several hospital uses the ASIR application with varying percentages between radiographers. The purpose of this study was to determine differences in noise and anatomical image information on variations in the percentage of ASIR and ASIR values that reveal optimal CT scan anatomic image information. This type of research is experimental, data are taken from 30 samples of reconstructive CT scan of the abdomen by giving four variations of ASIR (0%, 40%, 60%, and 80%). Noise measurement is done by placing the ROI size of 105.61 mm2 at three points, namely superior liver, inferior liver and middle of the aorta on the axial section. while the assessment of anatomical image information by observation of the results of variations in the value of ASIR by two radiologists. Data analysis uses the One way Anova test to determine differences in noise, Friedman test to determine differences in anatomical image information with a confidence level of 95%. The results showed that there were differences in the abdominal CT scan image noise on variations in the percentage of ASIR with p -alues 0.001. Noise decreased with increasing percentage ASIR. The highest noise value is 15.34 at ASIR 0% while the lowest noise is 8.57 at ASIR 80%. There are differences in anatomical image information on the variation of ASIR with p-values 0.001. The percentage ASIR of 40% is the optimal ASIR value for displaying CT images of abdominal with mean rank of 3.46.

PERBEDAAN INFORMASI CITRA ANATOMI SEKUEN DIFFUSION WEIGHTED IMAGING (DWI) ANTARA PENGGUNAAN PROPELLER DENGAN TANPA PROPELLER PADA PEMERIKSAAN MRI BRAIN DENGAN KASUS STROKE

Background: Stroke is a brain disease where an acute nerve function is occurred due to the cerebral vascular disorders. To establish a diagnosis the stroke, it can be identified by employing the Diffusion Weighted Imaging (DWI) sequence in the MRI examination. Artifacts still exist on the MRI image which in turn reduce the resolution when using the DWI sequence. Adding the PROPELLER data acquisition method in the DWI sequence possibly improves the quality of brain images. The purpose of this study is to know the difference on the quality of anatomical image information between the DWI sequences with PROPELLER and without PROPELLER methods, and to determine adequate anatomical image appearance that created in amongst of the two methods, specifically for the stroke disease.Methods: this research is quantitative research with experimental approach. This study was conducted using MRI 1.5 T at Bethesda Hospital Yogyakarta. Data were 16 images from 8 patients using DWI sequences using PROPELLER without PROPELLER on MRI Brain examination with stroke. The results of the image were evaluated on 7 criteria: cortex cerebri, basal ganglia, thalamus, pons, cerebellum, stroke (infarction) and artifacts using questionnaires given to 3 respondents. Data analysis was done by Wilcoxon test to know the difference of anatomical image information on DWI sequence using PROPELLER without PROPELLER and to know better anatomical image information from both sequences seen from mean rank value.Results: The results shown, there is a significant difference on the quality of anatomical image information and the artifacts between the use of DWI sequence with and without PROPELLER methods ( 0.05). Based on the mean rank results, the DWI PROPELLER sequence has a higher mean rank value 4.50 compared to the DWI sequence without PROPELLER 0.00.Conclusions: The DWI PROPELLER sequence has better image results compared to the DWI sequence without PROPELLER.

ANALISIS INFORMASI CITRA ANATOMI MSCT THORAX DENGAN KASUS EFUSI PLEURA KANKER PARU PADA WINDOW MEDIASTINUM POST KONTRAS MENGGUNAKAN VARIASI NILAI WINDOW WIDTH

Background: Malignancy of lung cancer is the biggest cause of pleural effusion. To diagnose lung cancer pleural effusion, a thorax MSCT can be examined. The MSCT parameter that affects image contrast is window width. The purpose of this study was to determine the differences in the anatomical information of thorax MSCT images in the post contrast mediastinal window to the use of window width range 350-600 HU values in cases of lung cancer pleural effusion, and to determine the appropriate window width value to obtain optimal anatomic image information on Thorax MSCT in cases of lung cancer pleural effusion.Methods: This type of research is quasi experimental. The research was conducted at the Radiology Installation of the Dr. Moewardi Hospital. The data were 60 images of the post contrast mediastinal window thorax MSCT axial slice from 10 patients with 6 window width variations (350 HU, 400 HU, 450 HU, 500 HU, 550 HU, 600 HU). An image assessment was conducted by 3 respondents regarding the resulting of 5 anatomical information. Data analysis used Friedman statistical test.Results: The results showed that there was a difference in the anatomical information of the thorax MSCT in the post contrast mediastinal window to the window width variation in cases of lung cancer pleural effusion with a significance level of p value 0,000 (ρ 0.05). Differences in anatomical image information occur in the anatomy of the aorta, limits of pleural effusion with lesions and clarity of lesions, where as there is no difference in anatomy of the right and left primary bronchus. The optimal use of the window width value for thorax MSCT in the post contrast mediastinal window cases of lung cancer pleural effusion is WW 350 HU with a rank value of 4.61.Conclusions: This study shows that the use of 350 HU window width produces better anatomical image information than the use of other window widths in the case of pleural effusion of lung cancer.