Questions tagged [neuroimaging]
For questions about techniques to directly or indirectly image the structure, function, or pharmacology of the brain.
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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 ...
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"runs" or "sessions" in Structural MRI - Purpose and Implications for Quality Control
I am working on a graduate research project using the ABIDE I and II autism datasets.
MRIQC has been run on these data - and I now must remove participants marked as outliers on 3 specific quality ...
CommunityBot
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Why do fNIRS devices commonly use two different frequencies?
One of the most common techniques used for functional neuroimaging nowadays is functional near infra-red spectroscopy (fun fact: IIRC Natalie Portman worked on a research paper involving fNIRS as the ...
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automated co-registration of PET CT
Hi all:) I've acquired Whole body PET CT data from form which I would like to generate brain co-registered PET and CT nifti files - has anyone implemented something similar? I have experience with ...
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Eddy Current Correction without reverse-phase encoding Data
I'm a beginner to dMRI analysis and am attempting to prepress data from the ABIDE-2 database (San Diego State Uni's DTI scan data) using the FSL pipeline (TOPUP->EDDY->DTIFIT). The TOPUP step ...
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MNI vs. study-specific template in ABIDE ASD datasets
I'm new to MRI analysis and don't think I can properly gauge the implications to subsequent spatial analysis of performing registration to the MNI152 template. The form of analysis I'm conducting ...
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Correlation of Gene Expression with Dynamic Imaging Phenotypes
I've been researching the process of performing a spatial correlation between gene expression in the brain and particular imaging phenotypes such as structural white matter connectivity. My research ...
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How to estimate calcium concentration from fluorescence images
Is there a way to get a rough estimate of a [Ca2+] based on fluorescence microscopy images (obtained using GCaMP for example)? Usually what we get is the ratio f/f0, but is there a way to estimate the ...
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Neuroimaging vs. Gene Expression for Neurological Disorders
As someone who has recently started learning about how we study the brain, the two most common forms of data I've encountered are neuroimaging data (fMRI scans, etc.) of the brain's distribution of ...
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Interpreting Negative Z-Scores Gene Expression
When examining ISH heatmaps of gene expression in the brain, I'm typically looking for above-average expression in the form of high z-scores but have also encountered imaging with negative z-scores. ...
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Time duration of the scanning (nifti file, .nii)
How to calculate/read the information about the time duration of the particular .nii file? Such information is not stored in the header (I checked the header with MATLAB niftiinfo function).
Thanks!
M
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Error "File too small" When using spm_slice_vol, Fieldtrip MATLAB
When I was trying to convert a CT scan file's coordinate system into an approximation of the ACPC coordinate system on Fieldtrip MATLAB, there was error prompting that:
...
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Seminal Books of fMRI
I would like to know what books about fMRI do people consider as key or seminal. I am very familiar with a great amonut of MRI techniques, but I am sort of looking for a book in fMRI that really ...
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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 ...
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Question about How to assign the order of vertices of a pial surface in FreeSurfer
I'm a CIVET user but I recently started to use FreeSurfer.
As far as I know, for a surface from CIVET, its vertices are ordered by upsampling a polygon. So I could access downsampled surface by ...
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A tool to compare structural MRIs recorded at different times
I have two MRI's from the same person with a Huntington disease, recorded at different time points (with different MRI machines).
I would like to compare the MRIs to see how the disease progresses. ...
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why structural studies of the cerebellum (atrophy, segmentation, etc.) always reports LEFT and RIGHT even when laterality is absent from the study?
I have noticed that structural studies of the cerebellum, regardless of the focus of the study (neurodegenerative, autism, alcoholism, drummers) usually report left-sided and right-sided results. Even ...
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How many possible states does a brain have?
Suppose I have a box, inside of which is a light which can be either on or off: it has exactly two states.
Suppose I wanted to take some "snapshot" of the state of this device, and store all the ...
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What does it mean if a neuron is "expressing" something?
Sorry for the simple question, not a neuroscientist just trying to understand a paper for school. In a study with mice, there was 2-photon calcium imaging done, and part of it read:
We used single- ...
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Does only the time-series data of fMRI matter or does spatial distribution of the signal values also matter?
I was denoising fMRI data using GLM and had a question regarding the “data” of fMRI in general.
(For reference you can look at the “GLM” part of https://fmriprep.org/en/stable/outputs.html or https://...
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BOLD->functional connectivity->spectral graph theory (e.g. Atasoy 2016) vs BOLD->Fourier Analysis
My read of "Human brain networks function in connectome-specific harmonic waves" (Atasoy 2016) seems to be that you can model brain activity in terms of standing waves of the connectome (...
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What are the brain regions related to tinnitus shown in this figure?
I am interested in learning about the neural mechanisms behind tinnitus, and was wondering if someone could help me to name the parts of the brain on the image below from a site of the University ...
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Is it possible to detect the mental flow state with EEG?
I know that it is possible to detect "focus" with a consumer EEG with a single electrode and a reference point (ear clip), even without conductive gel, but is it possible to detect a flow state with ...
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Why memory studies was a strong area of research during 90's?
Memory studies seemed to have flourished during nineties - particularly early nineties.
Not only in Psychology, but in neuroscience, in social sciences, in History, there was a period in which a lot ...
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Why does Cross-sex hormone therapy have an opposite effect on cortical thickness?
In a recent lecture I was informed that cross-sex hormone therapy increases the cortical thickness in FtMs, but decreases CTh in MtFs. Why does this happen when studies find females have increased ...
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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 ...
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Cognitive impairment in fibromyalgia
People suffering from Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) often have memory and cognitive complaints. (Glass, 2006)
In FM as in CFS, some abnormalities of cerebral blood flow have ...
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What is the size limit of molecules entering the intracellular sections of a neuron?
As voltage sensitive organic dyes enter the inside of neurons and quantum dots are seeking to replace these due to their higher quantum yield, I was wondering what the seize limit is, as quantum dot ...
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Measuring postsynaptic potential vs action potential at axon hillock?
I have been reading literature regarding Neuronal potential measurement. Conventionally, researchers use electrode-based method to measure action potential. However, as it's of high invasiveness and ...
CommunityBot
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Are there equivalent calcium imaging molecules that fluoresce in the presence of neurotransmitters between axons?
Molecules like GCaMP fluoresce when calcium ions attach to them. I was wondering if this can work with the other neurotransmitters in the brain or compounds that transmit signals outside of neurons.
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How close are fluorescent dyes to individual neurons in two photon microscopy?
Considering the minute electrical excitation produced by neural cells needed to excite fluorescent dyes, how close are they to these cells, considering that being too close will disrupt cell processes....
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Opening an aparc+aseg.nii.gz file programmatically in Python
How do you programmatically in Python open and read segmentation data in an aparc+aseg.nii.gz file programmatically?
Is this correct?
...
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Can the administration of self-report measures of craving prompt participants with addiction to experience craving during the experiment?
My research focuses on measuring the neural correlates (through resting-state EEG) pre-post an improvisational music therapy session (MT sessions) in clients with substance misuse.
One of my variable ...
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Is there any maping between the AAL to Brodmann areas (BA)?
I am trying to find any correspondence between BA6 (Premotor cortex) and AAL, but there are no information about it. Is there any equivalence table for Brodmann areas and other related anatomic labels?...
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Has anyone tried using functional near-infrared spectropathy to quantitively measure sodium concentrations in the brain?
Functional near-infrared spectropathy "fNIRS", is a biophysics/medical technique that uses the near-infrared part of the electromagnetic spectrum (around 680nm to 810nm in wavelength) to ...
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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 ...
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Do I report all anatomical regions in a large significant cluster identified in functional connectivity seed-to-voxel analysis?
I am conducting a resting-state functional connectivity seed-to-voxel analysis on the 25 participants from the NYC test-retest dataset using the CONN toolbox with the Posterior Cingulate Cortex of the ...
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Choice of reference/mid-slice during SPM slice-timing-correction
I'm trying to figure out the simultaneous-multi-slice (SMS) factor for my MR acquisition, to use during slice-timing correction, in SPM12.
The DICOM header obtained during conversion (with the ...
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How firing of neurons stimulate reality? [duplicate]
Iam just an enthusiast.When I look for how does our brain works it boils down to firing of neurons in a pattern. I read that all of our thoughts, memory is due to firing of networks of neurons in a ...
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Which characteristics of neural activity patterns underlie conscious experience?
Which specific characteristics of neural activity patterns are unique for the cortex and neocortex as the presumed "seat of consciousness" and can only be observed there? Activity patterns having ...
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How well is biofeedback understood?
From an answer to the question Research suggesting conscious control over brain region activation? I have learned:
»[S]ubjects become better at up-regulating or down-regulating
activation in ...
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Is there an equivalence table between the Desikan-Killiany atlas to brodmann areas?
FreeSurfer makes inferences about volume, through the calculation of the surface of the brain. The parametric method (used in SPM) is a voxel-based statistics.
FreeSurfer analysis does not map the ...
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What is the brain doing when someone tries to solve a physics or math problem that they can’t make any progress on?
Is their brain actually working or is it day dreaming and not functioning if they’re staring at a physics problem and not capable of making any progress on it?
When a student who can’t come up with ...
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Is what psychologists define as subconsciousness proven in neuroscience and can the psychological subconsciousness be visualized by neuroscientists?
We read phrases like
The subconsciousness makes up 90% of our brain.
The subconsciousness makes up 95% of our brain.
The subconsciousness can be influenced by hypnosis.
I have yet to see a study in ...
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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 ...
CommunityBot
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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. ...
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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 ...
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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 ...
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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?
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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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