Questions tagged [neuroimaging]
For questions about techniques to directly or indirectly image the structure, function, or pharmacology of the brain.
102
questions
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5 views
Working with neuroimages and visualize them as JPG, PNG, GIF and so on
I am very new in this area, i am trying to visualize a good dataset of neuroimages to work with. I am stuck to visualize the images and save OpenNeuro files, it is totally saved in JSON format and ...
2
votes
1answer
29 views
Temporally truncate BOLD data
I'm analyzing some resting-state data and some of the scans are 10 min while others are 7 min. I need to cut the last 3 min off of those with 10 min scans so everyone has 7 min of resting-state data. ...
1
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1answer
34 views
Find volume of lesion mask
I have drawn a lesion mask using FSLeyes on a T1-weighted image for MS patients. Is there tool to get the lesion volume from the mask?
7
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79 views
Supplementary Motor Area or Juxtapositional Lobule Cortex
Harvard-Oxford Cortical Structural Atlas now calls the 'Supplementary Motor Area' the 'Juxtapositional Lobule Cortex (formerly Supplementary Motor Cortex)'. I've looked for papers that explain the ...
3
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1answer
58 views
Publicly accessible database for the Autistic brain under MRI and/or fMRI
American neuroscientist James H. Fallon released many of the images of MRIs from diagnosed psychopaths and was able to identify a pattern when compared to the average individual. Is there a database ...
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24 views
Noise ceiling estimate is lower than model prediction in RSA?
I am using representational similarity analyses (RSA) to compare models to some fMRI data. As part of this analysis I have computed noise ceilings for each of my regions of interest (ROIs). What's ...
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2answers
33 views
Does the duration of the epoch of interest in fMRI need to be a multiple of TR?
I am designing an fMRI experiment whereby, for each trial, subjects need to listen to an auditory stimulus (of arbitrary duration), and subsequently give a rating for each stimulus.
I intend to ...
0
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0answers
4 views
fiber connection in DTI to distance matrix
I have a question regarding the DTI fiber connection matrix. In fMRI, we can use 1-|correlation coeff| to build a connectivity matrix based on distance. How can I do so in DTI data?
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0answers
25 views
Active Sources Extraction
I am using the LORETA-KEY software for source localization, which gives as an output the current density of each voxel.
No voxel has zero current density, so which method should be used to decide the ...
2
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37 views
Relaxing your concepts in meditation
I am using the app Waking up from Sam Harris. A lot of his guided meditations tell you to perceive the world as the raw data of experience, instead of perceiving objects and concepts. To illustrate ...
1
vote
1answer
25 views
task-fMRI to determine TMS site (online stimulation with that same task)?
I am planning an experiment whereby rTMS would be administered to subjects while they perform a language task, with the hopes of improving performance on this task as compared to sham stimulation.
...
3
votes
1answer
48 views
Is sign language handled differently by the brain than spoken laguage?
The human's ability to process language in the abstract is somewhat linked to our ability to both produce and understand sounds (see Broca's area), with that in mind, is Sign Language handled ...
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0answers
29 views
What is the term for mimicking other behaviors? [closed]
Say you see an actor playing someone insane, for the next few hours you feel kind of crazy too, especially if you are tired. You may feel annoyed and overwhelmed and mad for no reason, and kind of ...
8
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2answers
758 views
How do we know human brain development stops around age 25?
I've heard this stated as a fact more times than I can keep track of, but I haven't been able to find papers that actually demonstrate this. This seems to be the most cited paper on the topic, but it ...
1
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0answers
15 views
What methods exist for converting channel-wise directed (effective) connectiviy estimates to ROI-wise connectivity estimates?
I am reading up on directed connectivity estimates (e.g. Granger causality, DTF, dDTF) in an attempt to find a method that allows me to appropriately convert channel-wise connectivity estimates into ...
6
votes
1answer
836 views
Are scintillating scotomas really caused by cortical spreading depression? If so, how is this known to be true?
I have just read about a visual effect called a scintillating scotoma.
Many variations occur, but scintillating scotoma usually begins as a spot of flickering light near or in the center of the ...
2
votes
1answer
62 views
What is the difference between an Atlas and a Parcellation?
I come from a computer science background and am just starting out in the area of analyzing brain imaging data (fMRI predominantly) and while going through some of the literature, I am kind of ...
2
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0answers
23 views
Can a CT scan have advserse cognitive effects on the brain? [closed]
If the normal Xrays scans, despite the low amount of radiation (equivalent to a few hours of background radiation, can be sufficient to cause a burning sensation, then I wonder if the much higher dose ...
3
votes
1answer
38 views
What does “they tend within and between classes” mean in 'The Irreducible Mind'?
I am a philosophy student but I'm also interested in philosophy of mind, a field that overlaps issues in psychology and neuroscience these days. This passage is taken from a similar multidisciplinary ...
8
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1answer
329 views
Frissons on demand
Have you ever listened to music and it gives you "chills?" This response is called a "frisson," a french word meaning "to shiver."
When I want to access certain emotional and inspirationally charged ...
4
votes
0answers
27 views
Timing accuracy in presentation of videos with different frame rates (with COGENT)
For our fMRI study we want to present videos of 3 seconds duration. The videos have different frame rates:
48 videos were recorded with 50 fps
16 videos were recorded with 25fps
64 videos were ...
8
votes
1answer
64 views
In fMRI analyses, what is the t-test actually comparing?
In a 1st-level fMRI analysis, it is unclear to me what the t-test performed for each voxel is actually comparing. I've seen this being described in one of two different ways:
The t-test estimates how ...
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0answers
16 views
Has there been any substantive neuroimaging done to study Gendler's belief/alief distinction?
Tamar Gendler proposed a distinction between the concept of "belief" and "alief", "belief" being the more commonly held, intuitive conception of a certain type of propositional attitude and "alief" ...
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1answer
233 views
Jung's Anima and Neurological Basis in Split-Brain Patients; Left-Persona and Right-Anima
So, having skimmed some studies on split-brain patients, it makes me wonder about the whole "left-brain/right-brain" dichotomy that made its rounds in public perception some time ago.
I'm not sure ...
2
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0answers
55 views
Is synchronization between the MRI scanner and the stimulus presentation necessary for every trial?
I'm planning an event-related fMRI-experiment to investigate the difference in processing natural and computer-generated facial emotion expressions.
I've seen a lot of studies that synchronize the ...
2
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0answers
33 views
Compute single patient Z-Scores from atlas anatomical zone
I have one brain image from a single patient. I have a set of normal pateints. Both, single patient and normal patients are normalised to an SPM template and the NMI space.
I also have a brain atlas (...
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0answers
98 views
ROI analysis of a Z-Score map [closed]
I have a brain z-score image wich is the result of some test. The image is in the SPM space.
How can I perfrom a ROI analisis of different zones? And obtain some statistics for each place.
2
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0answers
23 views
(Flavours of) Psychophysiological Interactions
The paper by Fischmeister et al. 2016 (Cortex) analysed fMRI task-related connectivity patterns, for two tasks that relied vs did not rely on recursive reasoning. Namely, they found "increased ...
3
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0answers
40 views
Task-based vs task-positive networks
Do the terms "task-positive network" and "task-based network" refer to the same thing, such as the Fronto-Parietal Control Network (FPCN), as distinct from the task-negative networks such as the ...
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0answers
22 views
Does MEG measure the sum of neural activity or the maximum?
According to Wikipedia, neurons give a response that generates a readable MEG signal when they are firing in a relatively synchronized manner and their current carrying dendrites/axons are all aligned....
4
votes
1answer
316 views
What does 'Mean Diffusivity' tell me about the connectivity of cortical areas?
I am reading an article about changes in thalamic volume and connections in relation to age and I understand that thalamic volume decreases with age. The authors find that mean diffusivity (MD) in ...
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0answers
45 views
How to cope with the problem of noise in fMRI?
The sounds and noises that a typical MRI scanner produces are problematic for several reasons:
they give - annoying as they are - a strong feel of uncomfortableness to any subject or patient
they are ...
4
votes
1answer
309 views
During body-scan ('sweeping') meditation, what does brain-imaging (e.g. fMRI) look like?
I do not know how extensive body scans have been studied with brain-imaging techniques, e.g. fMRI.
Body scan is a meditation technique developed by Jon Kabat-Zinn. It was derived from a meditation ...
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2answers
88 views
Can we identify specific emotions on the basis of fMRI scans?
I am looking for fMRI studies in which the emotional response of a person listening to music is visible in the fMRI scans, paralleled by a retrospective think aloud report of the person describing his/...
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0answers
54 views
Single person with largest number of fMRI scans [closed]
Is there a known single test person of whom the largest number of fMRI scans (while performing different tasks) have been recorded? Are these publicly available?
I assume some overarching patterns ...
5
votes
1answer
256 views
How can I visualize DTI tractography streamlines generated from FSL's probtrackX in 3D?
I currently have track files of diffusion tensor imaging (DTI) data generated from FSL's probtrackX tractography tool. What is the best software to visualize the streamlines from FSL in 3D?
7
votes
1answer
124 views
How to stain for orexin neurons in mice?
I am interested in studying possible depletion of orexin levels in the brains of some mice, and am wondering if anyone knows of a staining substance/technique for use on slices of fixed mouse brains ...
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0answers
27 views
How does processing of T1 images affect tractography after registering the DWI to T1?
At the moment I believe that registering (aligning) Diffusion Weighted Images (DWI) to T1 images only allows for the DWI to have a parcellation basis, and otherwise it does not give much information.
...
2
votes
1answer
60 views
Why the brain region with less activity is not more responsible for some action?
From my naive understanding, it seems that when people try to find correlations between a human action and a certain pattern of activity in the brain, they measure the brain activity with some device ...
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0answers
54 views
How to convert fmri brain volumes to brain graph [closed]
I am working with fMRI data of Alzheimer's Disease (AD) patients. I want to convert brain volumes to brain graph and then using different graph metrics, I want to classify the brain volumes in AD and ...
4
votes
1answer
430 views
where can i find preprocessed fmri data set for alzheimer's disease
I want to work on identification of Alzheimer's patients based on given fMRI data.Basically, I want to implement the following paper https://www.ncbi.nlm.nih.gov/pubmed/25907414. Where can I get ...
3
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0answers
70 views
NiftyReg reg_resample results in strange artifacts when registering MNI-ICBM-152 atlas
I'm using NiftyReg for image registration, and I have several artifacts when applying the warp from a non-linear registering of de facto standard MNI-ICBM-152 atlas.
Here are a few slices showing the ...
5
votes
2answers
2k views
Difference between reverse inference and decoding (e.g. MVPA) in fMRI
Reverse inference, i.e. the use of brain activation (fMRI) data to infer the engagement of a certain mental function, is heavily criticised (e.g., Poldrack 2011, Neuron).
At the same time, decoding, ...
5
votes
1answer
84 views
Is there a complete connectome of a minicolumn of the neocortex?
I know that there are projects that try to map brain connectivity. My question is whether there is a dataset available with the complete connectivity of just a single minicolumn of the neocortex. ...
4
votes
0answers
38 views
Library (or manual creation) of ERP components
I'm looking to test some computational models using ERP components as inputs (eg. p300, n170)
I'm wondering if there is an existing library anywhere that would have a bank of wave/component examples ...
3
votes
1answer
67 views
What are the main differences between the FreeSurfer volumetric approach and the statistical parametric mapping from SPM?
In modern research of brain volume and function there are two main players. FreeSurfer which is free of cost and open source and the older, but more frequently used, statistical parametric mapping ...
5
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0answers
120 views
Is there a tangible benefit of synchronising the sample clock to the laser pulses in a resonant scanning two-photon microscope?
NI data acquisition cards offer a possibility of synchronising data acquisition with the pulses of a 80 MHz Ti:Sapphire laser. This supposedly helps improve the signal to noise ratio, since the true ...
2
votes
0answers
121 views
EEG electrode cluster selection
Is there a good review paper on electrode selection in EEG analysis to avoid the problem of double dipping (Kilner, 2013)? This is a well documented issue in neuroimaging (Kriegeskorte et al, 2009; ...
3
votes
1answer
63 views
Voltage sensitive dyes technique: What is the underlying measure?
I just discovered voltage sensitive dyes technique:
I have seen that figures are labelled with dF/F0, what does it stands for?
3
votes
1answer
967 views
LAURA/LORETA source localization in Matlab
Is there a Matlab toolbox for doing source localization using LAURA or sLORETA within Matlab (not requiring additional software like LORETA-KEY, etc.)?
