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Questions tagged [neuroscience]

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.

162 questions
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Class with too many parameters: better design strategy?

I am working with models of neurons. One class I am designing is a cell class which is a topological description of a neuron (several compartments connected together). It has many parameters but they are all relevant, for example: number of axon…
Mike Vella
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topoplot in ggplot2 – 2D visualisation of e.g. EEG data

Can ggplot2 be used to produce a so-called topoplot (often used in neuroscience)? Sample data: label x y signal 1 R3 0.64924459 0.91228430 2.0261520 2 R4 0.78789621 0.78234410 1.7880972 3 R5 0.93169511…
Harold Cavendish
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Brain modelling

Just wondering, since we've reached 1 teraflop per PC, yet we are still not able to model an insect's brain. Has anyone seen a decent implementation of a self-learning, self-developing neural network?
Andy
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1 answer

Down-sample mri T1 image in python with Nipy

I have a T1 image (NIFTI), already aligned, with dimension 121 x 145 x 121. The image is loaded by nibabel. The voxel size is 1.5 x 1.5 x 1.5 mm. I want to down-sample it to an image with 2.0 x 2.0 x 2.0 mm resolution and keep the images aligned. I…
RemiDav
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2 answers

Downsampling of fMRI image with FSL

I have a set of fMRI images. One group has a dimensionality of 90 x 60 x 12 x 350 with voxel dimension 1 x 1 x 1 mm (350 volumes). The other group has a dimensionality of 80 x 35 x 12 x 350 with voxel dimension 0.2 x 0.2 x 0.5 mm. I'm using one of…
machinery
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1 answer

How to Plot an exponential distribution of spike times over a histogram of them, in R?

So my question follows the development after my last one. I have been trying to work on getting the spike times as a rastor plot for a spike train. I took a firing rate of 100 and got spike train for 20 trials: The code for that is: fr = 100 dt =…
14thTimeLord
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Spark MLLib's Word2Vec cosine similarity greater than 1

http://spark.apache.org/docs/latest/mllib-feature-extraction.html#word2vec On the spark implementation of word2vec, when the number of iterations or data partitions are greater than one, for some reason, the cosine similarity is greater than 1. In…
Jason Xie
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4
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2 answers

How to read .eeg file from BrainVision Core Data Format in python?

I have a dataset in BrainVision Core Data Format which consists of the header file (.vhdr), marker file (.vmrk), and raw EEG data (.eeg) file for each subject. I know that python has mne.io.read_raw_brainvision() function which reads header file and…
bipvan
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2 answers

How to plot a peristimulus time histogram (PSTH) in R with ggplot2

Say that I have two conditions, 'a' and 'b'. A neuron fires on average 40 spikes / second (Hz) in condition 'a' and 80 spikes / second in condition 'b'. The response to condition 'a' is presented 20 times and condition 'b' is presented 10 times,…
Jonathan
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1 answer

Count protuberances in dendrite with openCV (python)

I'm trying to count dendritic spines (the tiny protuberances) in mouse dendrites obtained by fluorescent microscopy, using Python and OpenCV. Here is the original image, from which I'm starting: Raw picture: After some preprocessing (code below)…
Lucas Miranda
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Allen Brain Institute - brain observatory example

I'm trying to follow the example of brain observatory ipython notebook. However, I became stuck loading the nwb file like below. from allensdk.core.brain_observatory_cache import BrainObservatoryCache boc =…
Hyunsu Lee
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1 answer

Having a neural network output a gaussian distribution rather than one single value?

Let's consider I have a neural network with one single output neuron. To outline the scenario: the network gets an image as input and should find one single object in that image. For simplifying the scenario, it should just output the x-coordinate…
daniel451
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2 answers

Loading a Nifti through Nibabel and using the shape function

I have a nifti file 1.nii.gz Now, i never dealt with nifti files. So, just opening it using this software i realized that a nii.gz is a sort of container that contains 3 arrays of 2d pictures. In fact, if i scroll the mouse i can see 448 2d…
AleWolf
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3 answers

Analysis of Eye-Tracking data in python (Eye-link)

I have data from eye-tracking (.edf file - from Eyelink by SR-research). I want to analyse it and get various measures such as fixation, saccade, duration, etc. Is there an existing package to analyse Eye-Tracking data? Thanks!
Cranjis
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Python: Writing a small neural network with matrices

I'm trying to simulate a two neuron network in python. It's simple enough to do writing separate equations for each neuron, but since I would like to generalize the code a bit more so that it's easy to increase the number of neurons without…
Brenton
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