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Brain Imaging - Science topic
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Questions related to Brain Imaging
I have been trying to analyse neurons for spine density and size using ImageJ.The images are from fixed brain section taken using confocal microscope. but the background fluorescence is interfering with the analysis as the software is unable to distinguish between actual spine and background noise. What plugins/macros can be used to reduce noise and clearly outline the structure of the neuron. Please do not hesitate to ask for more details in case you think you could help me out ! Please find the iimage attached. Many Thanks, - Raj
Brain Tumor Imaging Protocol will reduce variability and increase accuracy in determining progression and response of investigational therapies.
In the pictures below, with the FFT and DFT methods and the PCA phase recovery, which is common in optical microscopes, I obtained the magnetic resonance imaging (MRI) phase of the human brain tumor and the phase obtained.
Can the process be performed on MRI without prescribing Jumpstarting Drugs (JBTDDC)?
I am working on a project where I am able to perform conversion of NIFTI to JNIFTI file. These are neuroimaging files that require conversion so that I could integrate this into NiBabel, which is a package that gives access to some common medical and neuroimaging file formats. How can I perform this conversion in Python?
I am new to fMRI and I am working with rat fMRI data. I am performing the preprocessing steps in fsl (FMRIB Software Library) and since it designed for human brain, I must scale up the voxel size of rat brain image by 10.
I know that I probably must work with scl_slope and scl_inter in nifti header and I use fsledithd command to change the scl_slope to 10 (Now it is set to 1). but when I change the scl_slope in nifti header, the image doesn't change ( the voxel size remains unchanged.) and I think I must use fslcreatehd command to make these change to my image but I don't know how to do that. if this procedure is right please tell me how I must do that.
Also, I edit the voxel size directly with fsledithd(edit pixdim1, pixdim2 and pixdim3 instead of scl_slope and scl_inter) and it seems that it works, but, I don't know that it is correct to edit those parameter instead of scl_slope or not.
1. Science folks unanimously agree about a fixed definition for “Theory of Mind” or "Mentalizing"! That I think is a philosophical paradox as theory of mind has this very pivotal cannon of being open in empathizing and understanding different beliefs through attribution of mental state as in beliefs, intentions, knowledge and emotion. Thus, how could we all agree to establish one definition for “Theory of Mind” which conveys elimination of all other definitions or disregard openness to other definitions of “Theory of Mind” itself that might be quite different from the typical definition of theory of mind. As if one might staunchly emphasize that they believe in animal advocacy and rights but still keeps a songbird in a cage! I believe that some definitions cannot be strictly defined as a single omnipresent definition and depending on the subject and application would vary in definition. Theory of Mind can have one definition in mentally healthy human and yet another but not incorrect definition in mentally disordered people. Not to mention that theory of mind has been reported to be a personality trait in non-human primates as well!
Do you agree... or disagree?
2. There are neuropsychological assessments through sessions or interviews... But what about an efficient or statistically reliable "experimental" method of assessment for theory of mind in humans and non-human primates?! Theory of mind is a rather complex behavior which not only includes one's own beliefs or intents but also deciphers those of the others.
We have used "eyes task", etc. during neuroimaging to evaluate theory of mind. Scientists using such simple tasks and fMRI with all its limitations in terms of noise, resolution and processing to test mentalizing. Results are amazing but couldn't we develop better tasks and less limited modalities to assess a behavior with such complexity that involves numerous brain regions at once?
3. This is a social trait! When someone fails to develop mentalizing (either due to neurological disorders such as schizophrenia, autism... or due to still unknown mechanisms of acquired behaviors and social environment) which can be represented as a wide spectrum of complex behaviors from misunderstanding/incomprehension of beliefs or intentions which are different, unempathetic adamancy to disrespecting or denigrating and disparaging others' beliefs; wouldn't it be quite tricky to merely observe and assess underlying brain functions in a singled out subject via current imaging or experimental modalities?
I am using brain image database which is .mat format.
I has 3000 images in .mat format.
I want to convert data into .csv format.
Hi, I am conducting a Diffusion Tensor Imaging study on three groups of subjects, first-episode psychosis (FEP) group (Group 1), their siblings (S) (Group 2), and control group (C) (Group 3). I would like to infer the differences of their diffusivity values. I'm using TBSS to do this. I will also use F-Test and then T-Tests as post-hoc. However, I do not know how I can design my matrix in GLM because I have different sample sizes in my 3 group such as 19 FEP, 20 S, and 21 C. Could you help me on this issue, please?
Thank you so much,
I have been trying to find studies of adults who experienced adverse childhood events/childhood trauma that assess the link between ACEs and outcomes (bipolar disorder, PTSD/cPTSD, etc) using multiple measures to determine cause and effect.
A hypothetical example would be a study that assesses whether childhood emotional abuse/neglect (ACE) is associated with any 5-HTTLPR polymorphism (genetics), SLC6A4 hypermethylation (epigenetics), AND amygdala activity (fxn) in people with bipolar disorder (negative outcome) but not healthy controls who experienced similar severity of childhood emotional abuse/neglect
I know this is a huge lift and would require a somewhat large study but right now the story is missing a comprehensive view of the molecular and functional changes due to ACEs causes leads to negative outcomes.
Thank you in advance for any help you can give
I read a research paper investigating brain electrical waves using EEG. In this paper, the authors stated that participants were ineligible to involve if they had a history of neurological disorders, reported using drugs, or if they were left-handed. I am curious about the correlation between EEG and handedness? Especially, why left-handedness was excluded in this research?
Thank you for any answer
I need a CT images database of brain (both normal cases and abnormal cases ) for calculating the midline shift in CT images.
brain image data set using CT scans available free of charge?
I'm a college student and now I'm doing research in medical imaging. I need normal image dataset for my research. Where can I get normal CT/MRI brain image dataset? I really need this dataset for data training and testing in my research. Your help will be helpful for my research. Thank a lot:).
I'm a phd student my research is about medical image classification .. i need a dataset and i'm interestiin in brain image ( brain tumor) or if its not available can you provide me a dataset for prostate cancer or lung cancer
Dear all, motivated by a variety of MoBI studies currently being conducted in our group, I am thinking of proposing a new Brain Imaging Data Structure (BIDS) extension that addresses MoBI-specific needs for data sharing. This would also encompass flatscreen navigation data or 2D position streams from more conventional studies, so we can easily compare between recordings from different setups. I believe that the community will benefit a lot from clarifying properties specific to recording of spatial data. What are your thoughts on this idea? Is there any ongoing work for BIDS extension for movement data, or would you be interested in creating a new one?
can any one know the MRI brain image database.
I've been trying various iba1 antibodies with either Alexa 488 or 647 and am getting a lot of background and have never once seen anything close to resembling a microglia. I've tried blocking with various combinations of 0, .3 or 3.0% milk, 0, .3 or 1.0% BSA, with 4% normal donkey serum and nothing has worked.
Any suggestions would be very much appreciated. Perhaps there are better membrane-bound proteins I could stain for?
I've recently started pursuing PhD in Medical Image Processing. I am struggling to find a suitable problem to carry out research.
I was initially interested in working on brain images but after doing studies and according to peers' advices lots of works have already done with brain, but still work can be done on:
1. Retinal images
2. Chest radiography
3. Estimating probability of lung cancer etc.
I would be obliged if somebody suggests me some relevant topics(related to brain or other organs) where still there are lots of scopes to work on.
I hope you are doing well.
I am working with imaging systems. I am confused about the effects of linear polarizer in such systems ( I mean how a linear polarizer can improve the resolution?) and why working with one polarization is better than two polarization in image processing systems?
I use EEGLAB for processing EEG/ERP data. EEGLAB individually has some functions for topography plot (i.e. pop-topoplot which is popular for Neuroscience researchers). My question is there any additional tools which we could use jointly with EEGLAB to show the brain responses topography in a much better way which we could find in recent publications (i.g. could be a 3D view)? I would appreciate if you could introduce such tools in MATLAB or R.
Dear Colleagues, I'm currently on my PhD research in Deep Learning for Brain Image Analysis. Kindly help me check the attached Problem Statement and advise if those problem researchable. If they are not, kindly provide with suggestions on current debates, discussions and issues in deep learning. Thank you
I am working on a project related to neuro-degenerative diseases. Can any one guide me toward a PSP&MSA (MRI) Dataset? I searched over the internet but was unable to find.
OR if any of you have in your drive, is it possible to share that with me?
That can help me a lot.
I am working on ultrasound image quality that's why i need some vital link.
Plz suggest from where i can get mri brain image dataset for parkinson disease.
Although i have applied from ppmi, but it will take time.
Stroke is possibly the second most common disease that causes death, apart from disability. With BILLIONS spent on research, etc, one would imagine (and with NINDS getting a large chunk of federal dollars) that a basic, simple, publicly available research tool such as a databank for MRI of brain with acute stroke is available. I have scoured the ends of the Earth for this. Any suggestions ? Thanks,
I have a series of data from MRI brain database in MNC & DICOM format.
how can i open them in Matlab? Or how can i convert them into a jpeg ?
I'm using TMRE 100 nM in hippocampal slices following OGD. I know that this dye can give a stronger or lower signal in polarized mitochondria, depending on its concentration. At 100 nM it should give a stronger signal in polarized mito. right?
Since Biological Parametric Mapping (BPM) is no more supported, I would like to find another tool to combine several brain images acquired for each subjects or different groups.
I saw fusion ICA but it is not convenient for my data....
any other idea ?
Can you explain about it? Since software simulations have certain limitations, validation of new segmentation methods can be done using human-like phantoms, whose physical properties (e.g., geometry of the tissue structures and material properties) are known and are similar to the in vivo properties. The phantom images are generated using the MRI scanner and are more realistic than images generated with software simulations.
I want to write a paper about MRI brain segmentation . Can you state your suggestions that I can use them to start working on this topic?
When I am using the gray2rgb I get an error that it does not exist?
I know magnetoencephalography (MEG) records magnetic fields-which are very small- produced by electrical currents in brain to map brain activities. how effective the external magnetic fields can be on the response? can we also use them (external magnetic fields) to change brains activity on a good way-such as improving memory?
There are different types of diagnostic tests for Alzheimer's disease. as far as I know, one of them is positron emission tomography (PET) scanning. what exactly does cause the sign of the disease on a PET image? what percentage of Alzheimer's disease can be diagnosed by this procedure? do prescription drugs affect these signs after we take the test again?
How to find ROI from MRI brain image , perform segmentation and convert into 2d?
I have an MRI brain image in Lab color space and I want to do contrast limited adaptive histogram equalization on L channel and then do k means on a and b channels.
I am looking for an implementation of EnFCM (Enhanced Fuzzy C-Means) algorithm. I know it is not that difficult to implement, but I am looking for fast way. Kindly, if some one has information, share it here.
Szilagyi, László, et al. "MR brain image segmentation using an enhanced fuzzy c-means algorithm." Engineering in Medicine and Biology Society, 2003. Proceedings of the 25th Annual International Conference of the IEEE. Vol. 1. IEEE, 2003.
To what extent do you believe that psychogenic amnesia is distinct from organic amnesia? What would be the differences and similarities between psychogenic amnesia and organic amnesia?
What are the current research areas and challenges in brain image segmentation?
What is chisquare attack and how do i perform chisquare attack for Least significant bit Image steganography
What software or method could be applied for segmentation of hippocampus from MR DIcoms?
I am new to rodents MRI image processing. I have two questions:
1. What is the best program for registering structural rat images and its diffusion Images to its structural atlases and vice versa? Is landmark registration a reliable method in this field?
2.Is it necessary to extract the rodent brain before registration? Does FSL-bet do the job?
Thanks for considering my question!
There is the old IEEE article on MRI measurement of neuronal current by Dr. Ueno:
"Neuronal current distribution imaging using Magnetic Resonance" , IEEE Transactions on Magnetics, Vol. 5, No 35, 1999, p.4109
Now Bruker biospec resolution is about 30 micrometers in plane. Can we now make an image of neuronal currents in animal brain? Thank you for the articles.
Image processing and neural network
I would like to perform IVIM analysis of prostate diffusion-weighted images. Osirix UMM plugin doesn't work on my MacBook Air. Do you know alternative software?
I have some T2 hemosiderin images of a brain tumor and I need to know if I can use such images for finding out about relative blood distribution. Thanks for your help in advance.
My question is whether positron emission tomography measures the binding of the radioligand to a receptor that is specifically located at the cytoplasmic membrane or to all receptors regardless where they are located in the cell. I guess it depends on the tracer physiochemical characteristics, whether it penetrates the cellular membrane or not, and on the binding site within the protein. I just need a confirmation from an expert.
I need to use blood signal intensity in T1 MRI as reference in my project about brain tumors.What I have, are slices of MRI for entire brain. Is it possible to define blood signal in T1 MRI of brain? Your help is deeply appreciated in advance.
We have a GE 3T 750w
I have a problem with the contrast-enhanced MR angio of the neck (see screenshot)
- we have a ring, like a "donut" around the vessels
Sometimes it is difficult to exclude e.g. a dissection, notably of smaller vessels such as the non-dominant vertebral artery
We use the standard CE MRA sequence
Do you see the same "donut" on your CE-MRA?
If not, which kind of sequence, and which rate of Gd injection do you use?
Thanks for your help - very much appreciated to improve the image quality !
Happy new year !
I've got a set of resting data and found activations outside the head. I realised that a very large FOV was used during acquisition. Can this affect connectivity results?
We have a GE 3T 750w
I have a problem with a skin artifact(see attached images)
- may appear occipital or parietal (oftentimes more or less symmetric)
- appears 1mm iso-voxel 3DT1, evident on post-Gd (due to enhancement of epicranial structures
- appears more frequently on 32CH head only coil, and sometimes on 24CH head&neck coil
Is our scanner the only scanner with this problem? Or has someone seen this artifact as well?
Thanks for your help - very much appreciated to find the origin of the problem!
Happy new year!
I have a set of data (325 repeated slices) of Perfusion MRI with specific TR and TE (but I don't know what kind of perfusion (DSC,DCE or ASL) it is!). Does any one knows what I can get from these images? is it possible to obtain CBV maps from them? Indeed, I need to get information about blood distribution in a tumor; do you think that I can use these images?How?
one of the slices is attached.
I have just started researching about brain imaging techniques for early Alzheimer's Disease - something I know little about at present. It is often stated that short term memory is the first area that is affected for the patient. However, is there any research into how often this is actually the case, and how often it isn't? I haven't come across any so far in the literature I read. It is just often stated that it is the first sign, but I want something more substantive than that.
Short term memory from an imaging point of view, can be assessed by monitoring changes to the hippocampus. I am therefore investigating the existing techniques, and also seeing whether or not they can be improved on in anyway using my experience of imaging for other neurological conditions.
There is increasing evidence that global brain signal measured by resting-state fMRI contains potential physiologic basis. My question is, how to characterize the global brain signal, can it be achieved by computing the mean amplitude of low frequency fluctuations? Or other ways?
Is there any toolbox/software available? Thanks in advance.
Would like to know the feasibility and actual depth (areas of the brain) which could be reached with rTMD
We have a philips 3T achieva resonance and we are doing a sequences to use NODDI and HARDI with:
- b= 400 (15 directions)
- b=700 ( 30 directions)
- b= 2800 (65 directions)
We generate the gradients in the whole sphere with a program that obtain the optimal. And we have b=0 interleaved every ten directions.
The question is what is the best parameters to do that? I mean voxel size, TE, TR, use SENSE, gradient timing, EPI factor, ...
We tried with 2.5 isotropic voxel size a we obtain a value of one of SNR (same voxel size in reconstruction and acquisition) But when we used a voxel isotropic size of 2 (2x2x2) the SNR decrease a lot and the size in reconstruction and acquisition are different in the resonance.Perhaps obtaining the perfect combination of parameters we get a good sequence.
So we have a lot of question. What voxel size should we use? On the other hand, should we have the same size voxel acquisition that voxel reconstruction?
What TE, TR, EPI factor, gradient timing... are best?
We use SE sequences and EPI readout but there are other sequences (SE, IR, MIX, FFE) and different scan mode (SE, STE).
Thank you very much.
To define it as spontaneous production, the selection and the execution of new auditory-motor sequences appears insufficient. On the other hand, compared to numerous brain imaging studies on musical cognition, perception and musical development, there are few of them on musical invention which are, for the most part, confined to the study of already memorised performances and very few on musical improvisation in real time. In a brilliant work, a number of years ago Limb (2008) asked ten pianists to memorise a melody and, after having them lie in the tube of a suitably modified magnetic resonance machine and connected to a keyboard, he managed to have them reproduce a melody they had just learned, make a simple scale and, finally, improvise. Limb saw that the improvisation was correlated to the activation of a nerve network that included, among other things, structures such as the inferior left frontal gyrus, the anterior cingulated cortex and the medial prefrontal cortex. The most interesting evidence was the widespread ‘turning-off’ of the prefrontal areas, which are generally correlated to the conscious control of the activities in progress and responsible for interference in the capacity to concentrate. This experience of ‘turning-off’ is not yet sensorial and not yet perceptive; it is not an experience of emptiness, but corresponds to the activation of mental images that anticipate the specific action that leads to an internal emulation of the planned motor actions, very similar to what takes place in reality. As has been shown recently by Ridderinkhof and Brass, (2015), also with reference to the sphere of football, the comparison between the effects of the anticipated action and those of the internal emulation may generate an error signal that may encourage the improvement of the motor performance, even without the execution of the real movement.
i am working on feature extraction of MRI brain images for classification in normal and abnormal(having tumor) image. i need a MRI brain database (T1 or T2) of atleast 100 healthy patients as well as patients with tumor. please send me the link to either purchase or download database.
I have a set of 22 brain images provided by MRI technique.
Now I want to compress them by JPEG 3D method. I am little confused with the method. Shall I compress every single image by JP3D method? if so, then what makes it different from JPEG2000 or JPEG method?
i need information about FSL technique and scripts to extract features from MRI brain image to detect dementia
I am doing some simulations of monitoring bleeding at the brain using a microwave technology.
I would like to move to a realistic data. (currently I am modeling the bleeding as a simple sphere)
Do you know where I can find some data sets that following up the bleeding size over days?
(I can find at the publications nice graphs that describing the hematoma size over days but I want the images themselves).
Thanks a lot
Do you know how to measure cortical thickness and cortical concentration in the MRI images?
what kind of moralities are usually used for this procedure to see plasticity? (T1 or T2 or FA etc ?)
which software is the best and most user friendly for this processing?
I have f-MRI brain images(in .nii format). I wish to obtain all voxel coordinates as 3 columns with the 4th column giving the corresponding intensity value in float for observation purposes.
1st column :- X coordinate
2nd column :- Y coordinate
3rd column :- Z coordinate
4th column :- corresponding intensity value
Is there any software that can automatically do that ?
how can i extend this to ROI analysis ?
Your help is appreciated.
I am looking for a reference for the first report of beta oscillations. Does anybody know of one?
Thanks in advance, Ben
How to detect the edge of brain image with low contrast?
I have diffusion MR image (brain image) data sets with high b value, I want to find the boundary but CNR and SNR are relatively low. Is there any process I can do to make the boundary clear so that I can tell the brain tissue from background?
I need to validate my method with previous method on brain MRI images, I am unable to find ground truth of images. most database do not provide ground truth. let me know if you have any idea
How should I perform my analysis with probtrackx to obtain the number of voxels in the target mask that show connectivity to a seed mask? Something like the figure attached.
I have a small ROI as seed (2mm radius) and a single target mask that it is also waypoint and termination mask.
Currently, I'm assessing the feasibility of collecting brain wave data during use of a mobile learning app. The NeuroSky head set isn't very costly, whereas the "research tool" is.
As far as I know, there is no review or test rating available for the research tool in combination with the head set.
Can you provide your personal experience with the tool and the app?
I'd like to gain knowledge in order to prevent from purchasing nonsense. Thank you very much in advance for your support!
I am wondering what are the ideal MRI scan parameters for both pre and postoperative DBS surgery for use with the software LEAD-DBS. I currently have postop scans that are not ideal and LEAD-DBS is having difficulty reading them.
Our center uses a 1.5T with low SAR, but we are not opposed to increasing SAR slightly.
Any Good MRI-CT DICOM Image Database including 1.Axial (Horizontal-Transversal), 2. Coronal, and 3. Sagittal Brain Images to use for my 3D Brain Image Reconstruction and 3D Segmentation Algorithms ?
MRI-CT Brain Images have to be from same person-patient and should include the following 3 Brain Views-Planes:
2. Coronal, and
3. Sagittal Brain Images
so that a Full 3D Volume Pixel-Interpolation Reconstruction Algorithm can be deployed and tested.
Any web-links are more than welcome.
I am using SPM to coregister MRI and PA brain images. How can I store the co-registered image displayed in graphics window as 3D image?
I'm working on brain annotation of brain 3D MRI and in order to get the best result, the image enter must to be well segmented, so for that I’m looking for a software for automatic segmentation of brain with tumor in 3D-MRI images
or if anyone know any data base that has 3D-MRI brain images well segmented as BRATS.
I would like to scan one short sequence (90 seconds) multiple times on one subject, and then co-register and average images to get rid of artifacts and motion distortions. Can you recommend some tool for this ? Is it possible with SPM12 ? Or should I do it in photoshop ?
Thank you for answers
i want a scanned images of brain for my research work,so that i can use for comparitive analysis