GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. If nothing happens, download GitHub Desktop and try again. If nothing happens, download Xcode and try again. If nothing happens, download the GitHub extension for Visual Studio and try again. MRIcroGL is an open source volume ray caster. Most users will want to use the pre-compiled executable see the previous section. However, you can compile this yourself.
Lazarus 2. This software includes a BSD license. Skip to content. Dismiss Join GitHub today GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. Sign up. Pascal PHP Other. Pascal Branch: master. Find file. Sign in Sign up. Go back.
A Role for the Action Observation Network in Apraxia After Stroke
Launching Xcode If nothing happens, download Xcode and try again. Latest commit Fetching latest commit…. Available from Github. Compiling Most users will want to use the pre-compiled executable see the previous section. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window.GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.
If nothing happens, download GitHub Desktop and try again. If nothing happens, download Xcode and try again. If nothing happens, download the GitHub extension for Visual Studio and try again. Correction thresholds for temporal and spatial auto-correlations in the data can be individually adjusted.
The currently available STEN toolbox is a beta version. All statistical computations and their outcomes have been extensively validated. However, some minor bugs at the visualization level still need to be fixed. The most commonly used input data for STEN so far are evoked potential files with header. STEN produces outputs in the. STEN 2. Now to run STEN, you first need to activate the right conda environment. So, again, open a conda terminal and run the following command:. The team of the LINE www.
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So, again, open a conda terminal and run the following command: Windows: activate sten macOS and Linux: source activate sten Now that you're in the right environment, start STEN with the following command: ipython --c "import sten; sten. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window.Draper, Muriel M.
Bruchhage, Ruth G. Williams, Marcus S. Neuroimaging methods have recently been used to investigate plasticity-induced changes in brain structure. However, little is known about the dynamic interactions between different brain regions after extensive coordinated motor learning such as drumming.
In this article, we have compared the resting-state functional connectivity rs-FC in 15 novice healthy participants before and after a course of drumming min drumming sessions, 3 days a week for 8 weeks and 16 age-matched novice comparison participants.
To identify brain regions showing significant FC differences before and after drumming, without a priori regions of interest, a multivariate pattern analysis was performed. Drum training was associated with an increased FC between the posterior part of bilateral superior temporal gyri pSTG and the rest of the brain i. These regions were then used to perform seed-to-voxel analysis. The pSTG presented an increased FC with the premotor and motor regions, the right parietal lobe and a decreased FC with the cerebellum.
Perspectives and the potential for rehabilitation treatments with exercise-based intervention to overcome impairments due to brain diseases are also discussed. Neuroplasticity NP is defined as the ability of the nervous system to respond to intrinsic or extrinsic stimuli by reorganizing its structure, function, and connections.
Neuroplasticity underlies not only normal development and maturation but also skill learning and memory, as well as the consequences of sensory deprivation or environmental enrichment Kolb and Muhammad Even if NP was initially thought to be limited to critical periods in development, it is now largely accepted to occur throughout the lifespan. Moreover, several famous neuroimaging investigations demonstrate adaptative neuroplastic modifications in the structure Maguire et al.
Interestingly, few of these neuroimaging studies have investigated neuroplastic modifications following physical activity. These existing studies have mainly focused on cognitive facilitation by cardiovascular exercise in older adults, failing to investigate young participants or different types of physical activity Voelcker-Rehage and Niemann Over the past decades, musical training has gained increasing interest as a paradigm to study human experience-related NP in the same general model framework Herholz and Zatorre Playing a musical instrument is a highly complex task and requires multimodal skills such as bimanual motor activity dependent on multi-sensory feedback, fine motor skills coupled with metric precision, musical memorization Wan and Schlaugand improvization Pinho et al.
These skills involve complex interactions, between sensory and motor systems and high-order cognitive processes, which have to be coordinated at a high degree of synchrony and accuracy Zatorre et al. There is increasing evidence from several different neuroimaging modalities that NP is associated with musical training.
By using structural neuroimaging, Gaser and Schlaug reported gray matter volume differences in motor, auditory, and visual—spatial brain regions when comparing professional musicians keyboard players with matched groups of amateur musicians and nonmusicians Gaser and Schlaug Cerebral activity patterns associated with musical perception in musicians have also been studied by using functional MRI fMRI.
A significant difference in the degree of activation between musicians and nonmusicians was noted in the temporal regions and for musicians the degree of activation was correlated with the age at which the person had begun musical training Ohnishi et al. Functional MRI was also used to explore the brain activations of novices trained to play sequences on a piano keyboard Lahav et al. These studies showed complex interactions between auditory and motor brain regions that were associated with musical training.
Only expert drummers have been studied thus far. While Tsai et al. Recently, resting-state functional connectivity rs-FC analyses have been widely used to investigate neuroplastic modifications.
Rs-FC corresponds to the temporally correlated, low-frequency spontaneous fluctuations of blood oxygen level-dependent signals across brain regions that occur when a participant is not performing an explicit task Fox and Raichle Temporal correlations do not appear to be random, as patterns of connectivity have been reliably identified across studies and participant. Moreover, it is now widely accepted that the strength of correlations within and between networks has behavioral relevance Guerra-Carrillo et al.
Interestingly, it has been proposed that rs-fMRI is an effective measure of plasticity and that rest activity patterns reflect the history of repeated synchronized activation between brain regions. Thus, the study of rs-FC is particularly adapted to highlight neuroplastic modifications Buckner and Vincent ; Guerra-Carrillo et al. In this article, we have compared the rs-FC in 15 novice healthy participants, by using a fully data-driven approach, before and after a course of drumming with another 16 novice participants who were again evaluated longitudinally but with no intervention.
This longitudinal design was used to disentangle cause and effect by investigating the same participants before and after the course of drumming.Skip to main content.
MRIcro visibleHuman. This can help scientists visualize data or students learn anatomy. The software uses the computers graphics card, so computers with better cards and drivers will be able to view higher resolution images as described in the troubleshooting section. You can view multiple images simultaneously. Initially, this is set to black-white, but you have many options such as blue-green. For example, in Figure 2 the color range for the blue-green overlay is from 2 to 5.MRIcron vlog
Drag the 3D rendering to rotate the object. Roll the scroll wheel up and down or pull two fingers up and down on a touch pad to adjust the clipping depth of the 3D rendering for example, in Figure 2 we have clipped the top of the brain from the rendering.
Creating 3D visualizations of MRI data: A brief guide
Right-click and drag over the 3D rendering to adjust the position of the clipping plane for example, in Figure 2 we have set the clip plane to remove the top of the head. If you have an overlay loaded described belowright-click and drag over the 2D slices to adjust the transparency of the overlay.
If you have a 4D dataset loaded described belowroll the scroll wheel left and right or swipe left and right with two fingers to adjust which volume is displayed. It was designed to be a simple, intuitive tool for displaying medical images. However, just like there are different types of car to suit different drivers, there are different programs that are suited for different applications.
It includes great features like a nice DTI fiber tracking view. It has nice tools for DTI and connectivity mapping. Scriptable, fast, and flexible. In our car analogy it is our BMW — lots of performance and features. It does not require a graphics card and so it can run anywhere. In our car analogy, this is like a pickup truck that has tremendous utility drawing tools, peristimulus plots, etc.Case Report New Apr 13, v35 n Author Summary in Korean.
Editorial New Apr 13, v35 n Opinion New Apr 6, v35 n Original Article New Apr 6, v35 n Brief Communication New Apr 6, v35 n Cartoon Editorial New Mar 30, v35 n Gains from the Novel Corona Virus. Opinion New Mar 30, v35 n Original Article New Mar 30, v35 n Opinion New Mar 23, v35 n Brief Communication New Mar 23, v35 n Brief Communication New Mar 16, v35 n Opinion New Mar 16, v35 n Cartoon Editorial New Mar 9, v35 n9.
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Editorial Apr 13, v35 n Original Article Apr 13, v35 n Case Report Apr 13, v35 n Forthcoming Issues. JKMS on. Search Advanced Search. Address Change. Journal of Korean Medical Science. Beginning January 1,JKMS will cease its print edition and switch to online-only weekly publishing schedule. New format of articles will be implemented as well to attract global readership. Style Guide: NEW. Please download files of the Style Guide on " Information for Contributors " page and use the files for writing your manuscript.
Permission Request Form.Volume models made from magnetic resonance images on computed tomographs can produce horizontal, coronal, sagittal, and oblique planes that are used widely in clinics, although detailed structures cannot be identified.
Creating 3D visualizations of MRI data: A brief guide
Existing real color volume models are mostly commercial and their production methods have not been released. The aim of this study was to distribute free of charge, real-color volume models produced from sectioned images with the production method. The original voxel size of sectioned images was increased appropriately so that the volume model could be handled by typical personal computers.
By adjusting variables of the software, desired oblique planes could be produced instantly. With overlay function, a model of segmented structure can be overlapped to the entire volume models.
The sectioned images with high quality and the segmentation data of Visible Korean enabled the identification of detailed anatomical structures on the planes. The volume models can be used by medical students and doctors for learning sectional anatomy. Other researchers can utilize the method of this study to produce volume models from their own sectioned images.
Three-dimensional 3D volume models consist of pixel information of two-dimensional 2D medical images with spacing information between the 2D images. Based on the pixel and spacing information, volume models enable the observation of structures in a body not only on classical horizontal, coronal, and sagittal planes for the diagnosis of common diseases, 1 but also on various oblique planes for specific clinical fields, such as a probe's eye and trajectory view on the magnetic resonance images MRIs in deep brain stimulation surgery, 23 neuro-ocular plane on computed tomographs CTs of ophthalmology, 45 and ultrasonographic view for heart and liver diagnoses.
Most volume models for medicine are usually produced from MRIs and CTs with a gray color and low resolution. Moreover, owing to the small number of segmented structures, it was difficult to identify detailed anatomical structures. In case of the Anatomage Table, its expensive price limited the utilization by students with low economic status.
Crucially, both projects did not release the volume rendering methods from the sectioned images. The aim of this study was to release a real-color volume model along with a segmented volume model and its production methods. The real-color volume models with high resolution and detailed segmentation will enhance the understanding of sectional anatomy by medical students and doctors.
Another aim is to inform the purpose of the oblique planes in various medical fields.
For this study, real-color sectioned images and segmented images with structures from Visible Korean were reconstructed by volume modeling. Horizontal sectioned images of a human male head had been prepared in a previous study.
Therefore, the voxel size was increased to 0. One of every five sectioned images were selected to align the images at 0. The file format of the sectioned images was converted using Photoshop as follows.
Using the skin segmentation data, the embedding agent surrounding the head in the images was removed and the pixel size was resized from 0.
In the conversion process, the study times of the DICOM header should be different from each other by more than one second for further alignment process. Therefore, a pause of 1 second was inserted between each image in the action tool.
After changing the instance number, the study time and study date in the DICOM files were unified automatically to produce images considered as a single study in a further reconstructing process. Using auto-batch processing by the commands in Scripting tool of MRIcroGL, the oblique planes could be captured automatically. In the commands, the clipazimuthelevation command, the values of the depth depth from the surface, 0 to 1, by 0.
The planes were captured and saved as bitmap BMP format using the savebmp command. Using the identical process to produce a real-color volume model, a segmented volume model of the head was produced based on the segmented images of head structures.
Among the segmented structures, the cerebellum, brainstem, putamen, and globus pallidus were selected in this study to produce individual segmented volume models.
Informed consent was waived by the board. In the real-color volume model, three classical planes and oblique planes of a real color and real shape in a body could be shown vividly unlike MRIs Fig.
A segmented volume model was made voxel size, 0. In the segmented volume model, the accurate boundary of a real shape in the body could be shown Fig. The real-color volume model revealed the actual color of the anatomical structures, while the segmented volume model showed the precise location and outline of the structures.
Experts can utilize a real-color volume model solely, while novice students can utilize the segmented volume model together.
Classical three horizontal, coronal, and sagittal sectional planes on a real-color volume model A and segmented volume model B from Visible Korean.The datasets generated for this study are available on request to the corresponding author and contingent on the approval of sharing this dataset by the BCOS team and local ethics committee.
Limb apraxia is a syndrome often observed after stroke that affects the ability to perform skilled actions despite intact elementary motor and sensory systems. In a large cohort of unselected stroke patients with lesions to the left, right, and bilateral hemispheres, we used voxel-based lesion-symptom mapping VLSM on clinical CT head images to identify the neuroanatomical correlates of the impairment of performance in three tasks investigating praxis skills in patient populations.
These included a meaningless gesture imitation task, a gesture production task involving pantomiming transitive and intransitive gestures, and a gesture recognition task involving recognition of these same categories of gestures. Neocortical lesions associated with poor performance in these tasks were all in the left hemisphere.
They involved the pre-striate and medial temporal cortices, the superior temporal sulcus, inferior parietal area PGi, the superior longitudinal fasciculus underlying the primary motor cortex, and the uncinate fasciculus, subserving connections between temporal and frontal regions.
No significant lesions were identified when language deficits, as indicated via a picture naming task, were controlled for. The implication of the superior temporal sulcus and the anatomically connected prestriate and inferior parietal regions challenges traditional models of the disorder.
The network identified has been implicated in studies of action observation, which might share cognitive functions sub-serving praxis and language skills. Limb apraxia refers to a range of deficits in skilled action that are not consequences of motor weakness, sensory impairment, or lack of comprehension or coordination Heilman and Rothi, Patients with the disorder have difficulties performing skilled actions, such as shaving or making a cup of tea.
In stroke patients, limb apraxia can be demonstrated by impairments both when they use the affected and the unaffected hand. Traditional theories of the disorder have categorized praxis deficits according to errors made by patients in tasks involving 1 Imitation of both meaningless and meaningful gestures e.
Whereas pantomime and object-use tasks pertain to deficits implicating conceptual semantic planning for meaningful gestures, imitation of meaningless gestures tests the implementation or production systems Cubelli et al. Most screening batteries for apraxia involve the use of pantomiming and imitation of meaningless hand gestures, because these tasks are particularly sensitive for detecting praxis deficits Niessen et al. Lesion-mapping studies investigating limb apraxia agree that left hemisphere damage plays a role in this disorder, implicating the fronto-temporo-parietal network Mengotti et al.
They report a significant role for the inferior parietal lobe in tool-use pantomime and in imitation of meaningless gestures Buxbaum et al.
However, there is no clear dichotomy between the two, as the neural correlates of pantomime are widespread Daprati and Sirigu, ; Goldenberg et al. Several factors could account for these findings.
Lesion-mapping studies of apraxia have been limited by methodological issues, notably in the analysis methods used, and variability in the tasks used to study the disorder. There have been inconsistencies in the screening tools used to assess various subtypes of the disorder Goldenberg, The lesion-symptom mapping methods employed have included the use of manual delineation of abnormal brain tissue, which can produce inconsistencies across operators Gillebert et al.