Questions tagged [neuroimaging]
For questions about techniques to directly or indirectly image the structure, function, or pharmacology of the brain.
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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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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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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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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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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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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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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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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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