Neuroscience is the study of nervous systems. This tag is broadly applied to questions from the various subbranches like brain imaging, neural engineering, computational and systems neuroscience.
Questions tagged [neuroscience]
162 questions
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Are rank checks allowed for spike recording in Arbor simulations?
In the Arbor simulator one can specify whether to record no, local, or all spikes when working with distributed MPI simulations. Are there any reasons to record locally on each MPI and broadcasting results versus recording all spikes on just 1 rank…
Robin De Schepper
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Material-UI prevent Accordion default collapse on AccordionDetails click
I have a React web with two equal menus, so I've made a component with the menu and I render it twice in App component.
For the menu I use Material UI Accordion but when I click on the menu details, the menu colapses by defaul. How can I prevent…
PauCasademont
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Datajoint: suggestions for how to handle stages needing manual review in a neuroscience data pipeline?
Wondering if there are good examples or suggestions for how to handle steps that require manual review in a database-based scientific data pipeline (datajoint). For example, we'd like to handle the pre-processing and denoising/demixing of our…
jbussell
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Is there a way to make a plot clickable so it will tell me what EEG channel I am looking at?
Note: This is a question relating to mouse EEG data plotting.
I made a plot showing the averaged trial signals for filtered EEG electrode channels. While plotting this I saw a few signals that I want to exclude from my plot, but I don't have a way…
Jackie
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Neuroimage MRI scan CNN model preparation
I would like to know a couple of things to clear my confusion. I want to work on a medical neuroimage MRI image scans dataset from the ADNI database.
Each Alzheimer's Disease (AD) MRI image scan has multiple slices.
Do I have to separate each image…
Mjachowdhury
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multi-threading problem for NEST simulator
I want to use multi-threading function in NEST simulator (version 2.20.1). However, it gives a warning No multithreading available, using single threading. Can anyone help me to solve it?
I install NEST simulator using conda command
conda create…
Edward
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installing Brain Scaffold Builder with broken rtree dependency
I have recently installed NEST on my MAC. I have to install the Brain Scaffold Builder. I followed the instructions and wrote bsb==3.6.0b6 and I received the following error message
Using cached bsb-3.6.0b6-py3-none-any.whl (189 kB)
ERROR: Could not…
VDF
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How can I use PyMC3 to estimate a discrete value A over which a for loop must be constructed?
This is a properly articulated version of an old question.
I'm working on condensing some code written for a neuroscience paper: https://doi.org/10.1371/journal.pcbi.1007481. Without delving into unnecessary detail, here are some…
MurderOfCrows
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Using PyMC3 to uncover various qualities of a simulated neurological system
I'd like to preface this by making it clear that I am not interested in someone doing all of this work for me - I'm only interested in guidance.
I am reading a paper: https://doi.org/10.1371/journal.pcbi.1007481 in which the authors write C code…
MurderOfCrows
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How to plot multiple slices of a 3D brain image with nilearn and matplotlib subplots
I'm new to coding, so if I'm completely wrong just tell me.
I want to plot 25 slices of a brain scan using nilearn. These 25 slices should go along the z axis in steps of value=2. I want to use subplots to present them using subplots.
Here is what I…
Lightnjer
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How to set a Connection's synapse type in the NEST simulator?
Following the tutorial for the Python interface to the NEST simulator I have created 2 neuron populations and connected them:
import nest
ndict = {"I_e": 200.0, "tau_m": 20.0}
nest.SetDefaults("iaf_psc_alpha", ndict)
neuronpop1 =…
Robin De Schepper
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General Linear mode mri data
General Linear model analysis is usually done for fMRI data. I have applied the same analysis to MRI data and found the clusters which are linearly related to columns of behavioral scores(design matrix). I wanted to know if this analysis will give…
Algo_enthusiast
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In Brainrender is there a way to at labels and stop the brain from load upside down?
I am using brainrender to show where I've placed some electrodes. However, whenever I load brainrender my brain always loads upside down:
brainrender
Is there a way to fix this? Or do I just have to manually flip it every time?
I was also…
Jackie
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Is there a way to plot EEG electrodes onto a model of a mouse brain?
I am trying to figure out a way to plot EEG electrode coordinates onto a 3D image of a mouse brain, similar to this:
Sorry there are a lot of pictures showing what's been done. I'm a bit new to python, so I'm still trying to figure out what is the…
Jackie
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How to fit time series data as sum of time-shifted kernels
I have some voltage data recorded from brain electrophysiology that look like this:
Raw voltage trace
Notice that the fluctuations <200 uV is the actual data and the huge peaks are artifacts that might arise from occasional touching of the reference…
Jialiang Lu
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