Questions tagged [neuroimaging]

For questions about techniques to directly or indirectly image the structure, function, or pharmacology of the brain.

Filter by
Sorted by
Tagged with
0 votes
0 answers
5 views

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 ...
Greg's user avatar
  • 1
1 vote
0 answers
7 views

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 ...
Lambda's user avatar
  • 199
1 vote
0 answers
14 views

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 ...
Lambda's user avatar
  • 199
0 votes
0 answers
17 views

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 ...
Lambda's user avatar
  • 199
0 votes
0 answers
7 views

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 ...
Johncowk's user avatar
  • 135
0 votes
0 answers
20 views

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. ...
Lambda's user avatar
  • 199
1 vote
0 answers
49 views

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 ...
Lambda's user avatar
  • 199
0 votes
0 answers
8 views

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
Mary's user avatar
  • 31
0 votes
0 answers
29 views

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: ...
Peter Wang's user avatar
2 votes
0 answers
13 views

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 ...
yanghee Im's user avatar
0 votes
0 answers
33 views

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. ...
demitau's user avatar
  • 161
0 votes
0 answers
13 views

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 ...
Pauliinaa's user avatar
3 votes
1 answer
546 views

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- ...
Bn.F76's user avatar
  • 133
2 votes
1 answer
35 views

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 ...
JFR's user avatar
  • 76
4 votes
1 answer
50 views

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://...
Danny  Han's user avatar
  • 143
4 votes
1 answer
77 views

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 (...
llllvvuu's user avatar
  • 143
0 votes
0 answers
47 views

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 ...
Saturno's user avatar
5 votes
0 answers
38 views

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 ...
blahyeah's user avatar
0 votes
1 answer
18 views

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 ...
C-Consciousness's user avatar
1 vote
1 answer
24 views

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.
C-Consciousness's user avatar
0 votes
1 answer
33 views

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....
C-Consciousness's user avatar
2 votes
0 answers
214 views

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? ...
Paul Reiners's user avatar
2 votes
0 answers
43 views

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?...
Bob Satikin's user avatar
3 votes
0 answers
47 views

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 ...
Fil's user avatar
  • 1,524
2 votes
1 answer
77 views

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 ...
Science123's user avatar
0 votes
1 answer
73 views

"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 ...
Ruth Minkov's user avatar
1 vote
0 answers
33 views

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 ...
RhinoPak's user avatar
4 votes
0 answers
49 views

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 ...
Tsvetoslav Ivanov's user avatar
1 vote
0 answers
30 views

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 ...
z8080's user avatar
  • 919
0 votes
0 answers
22 views

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 ...
user42757's user avatar
  • 111
1 vote
1 answer
86 views

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 ...
Hans-Peter Stricker's user avatar
1 vote
0 answers
24 views

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 ...
Hans-Peter Stricker's user avatar
0 votes
1 answer
319 views

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 ...
BornPerson's user avatar
0 votes
2 answers
131 views

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 ...
Alex's user avatar
  • 1
2 votes
1 answer
71 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. ...
G Warner's user avatar
  • 141
1 vote
1 answer
315 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?
SpinUp __ A Davis's user avatar
7 votes
0 answers
448 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 ...
PCS's user avatar
  • 173
3 votes
1 answer
64 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 ...
Red's user avatar
  • 43
2 votes
0 answers
312 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 ...
switchup621's user avatar
1 vote
2 answers
161 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 ...
z8080's user avatar
  • 919
1 vote
0 answers
28 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 ...
Lena Pappa's user avatar
3 votes
0 answers
49 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 ...
Borut Flis's user avatar
1 vote
1 answer
32 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. ...
z8080's user avatar
  • 919
3 votes
1 answer
78 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 ...
Shmuel Newmark's user avatar
1 vote
0 answers
33 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 ...
James Liase's user avatar
8 votes
2 answers
3k 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 ...
eyeExWhy's user avatar
  • 446
1 vote
0 answers
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 ...
qualiaMachine's user avatar
6 votes
1 answer
2k 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 ...
uhoh's user avatar
  • 473
2 votes
1 answer
593 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 ...
Fahad's user avatar
  • 21
2 votes
0 answers
30 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 ...
Bastien Altorg's user avatar