sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f59f14660cd367f4eeb201812cb04b2e2026e5f606b363d3efc68107c4fe44c7 | MATLAB | 3,402 | 109 | % cfsWrite.m
% an example of writing a cfs file
% using INT2 format
% must have cfs32.dll in system directory
% calls matcfs32.dll
% note: must choose yScale with care
% (not very obvious in this example)
% unless data is already in required format
% 21.02.09: version 1 JGC
% 24.02.09: capitalis... |
4f4a210bf50d62615f52cc19af2da6ecf9365e299ab87c9f393f8072ac17a988 | MATLAB | 3,407 | 102 | %Calculate F-observed and the empirical F-distribution for a one-way
%between subjects ANOVA
%
%EXAMPLE USAGE
% >> [F_obs, F_dist, df_effect, df_res] = perm_crANOVA(data, [16, 16], 1e4)
%
%REQUIRED INPUTS
% data - An electrode x time points x conditions x subjects array of ERP
% data. A... |
c29b38cb639e4e1f63f59672f0dfca370aa0c1ff1468cb23b89c1b64084ca306 | MATLAB | 3,407 | 104 | % extractFictracTrialsOpto.m
%
% Helper function for computeAvgFictracOpto_1Fly() that takes in one
% trial's worth of data for one FicTrac parameter and divides it into
% reps based on the opto stimulation
% Output appends trials into cell array given as input
%
% INPUTS:
% reps - cell array of size # NDs x # dur... |
d918e915aba5e6e162fee3374abd3811a9b926422cb030e96ba055ab9279e7aa | MATLAB | 3,409 | 70 | function W0 = null_model_und_sign(W,ITER)
%NULL_MODEL_UND_SIGN Random graphs with preserved weight, degree and
% strength distributions
%
% W0 = null_model_und_sign(W,ITER);
%
% This function randomizes an undirected network with positive and
% negative weights, while preserving the deg... |
1170cb0e223c28bbdc2dd65b394f0da6449bf2daf8d64799bc96543e4e34e29e | MATLAB | 3,411 | 82 | function success = find_centerlines(folder_name)
% gets the centerlines given tracks and their associated individual worm
% images
addpath(genpath(pwd))
parameters = load_parameters(folder_name); %load experiment parameters
ImageSize = 2*round(parameters.TrackingWormBoxHalfSize * parameters.CameraPixel... |
1fde44a4ff3cc7431793794e421b268213064eec5e0eeaac1c39f9d6fbe3d94f | MATLAB | 3,412 | 121 | function status = besa_save2Swf(file_path, file_name, data_matrix, ...
time_samples, source_labels, data_scale_factor, time_scale_factor)
% BESA_SAVE2SWF writes a data matrix into ASCII-source waveform file format
%
% Parameters:
% [file_path]
% Full path to the folder where the file should be saved.... |
fa34eb8473b5a9b36fc0c2850f38c0559d36d46e844f5d0265b48c3dfa13a31e | MATLAB | 3,413 | 108 | function data_rcs=shortchannel_regression(cfg, datain);
% SHORTCHANNEL_REGRESSION
% shortchannelregression performs reference channel subtraction for fNIRS
% data. It is an adaptation from ft_nirs_referencechannelsubstraction
% (http://www.fieldtriptoolbox.org/reference/ft_nirs_referencechannelsubtraction/)
%
% Use as... |
9edb67c13f2c4c843765be403d745db3905f414133eaeb6dad32855224461120 | MATLAB | 3,416 | 83 | function [wEB,hprsML,logEv,postHess] = findEBestimate_GLM(w0,hprs0,mstruct)
% [wEB,hprsML,logEv,postHess] = findEBestimate_GLM(w0,hprs0,mstruct)
%
% Find empirical Bayes estimate for GLM regression weights (Poisson or
% logistic). Maximizes marginal likelihood (computed using Laplace
% approximation) for hyperparameter... |
ee1d993be1c400d893a6c38362972fc9a6ce40243494905b716a0581153f5b21 | MATLAB | 3,416 | 74 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function [sq] = mkSqRatemaps(ratemaps)
v = homography_solve([20 0 0 20; 0 0 30 30], [20 0 0 20; 0 0 20 20]); % transform
x_edges = 0:1:20;
y_edges = 0:1:20;
kern = ratemaps.cfg.smoothingKernel;
for a = 1:length(ratemaps.data)
s... |
3985027549717678b5537cbf29983168e0b6faad72f94823f6a7684ecea04ac5 | MATLAB | 3,418 | 116 | % plotRaw2ChImgFicTracData.m
%
% Function to plot raw traces of imaging data (dF/F) for all ROIs and
% FicTrac data (yaw angular velocity and forward velocity), each in its
% own separate subplot
%
% INPUTS:
% frameTimes - frame times of imaging data
% bksSignal - background subtracted fluorescence signal for a... |
4b138c5a8a8bf7d6cbb3b63938513cc0f22673aefafbf40d5d86652e83b69d58 | MATLAB | 3,419 | 111 | function [ama] = loadama(filename);
% LOADAMA read an inverted A-matrix and associated geometry information
% from an ama file that was written by Tom Oostendorp's DIPOLI
%
% Use as
% [ama] = loadama(filename)
%
% See also LOADTRI, LOADMAT
% Copyright (C) 2005, Robert Oostenveld
%
% This file is part of FieldTrip, ... |
6b998780c2b0baa7596470ffe9284af6c31bdcde4b4367d607081d49900639d9 | MATLAB | 3,419 | 85 | function mltp_compute_bfo_90_ac(obj, session)
% We have to use the shrunk data if the shape is a rectangle
if strcmpi(obj.getArena().shape, 'rectangle')
outputFolder = fullfile(session.getAnalysisDirectory(), obj.Config.placemaps.outputFolderShrunk);
else
outputFolder = fullfile(session.getA... |
932ef52bcdcb52f919a36925dfa55789caccdc897fd1b0ef8833c7cd183efead | MATLAB | 3,419 | 101 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function [v_max, vind_max, rotationsDegUsed ] = ml_alg_bfo(rotationsDeg, maps1, maps2, disjointMaps, MIN_DIFFERENCE_FOR_MAX_CORRELATION)
numRotations = length(rotationsDeg);
rotations90 = floor(rotationsDeg ./ 90);
rotati... |
3ef4dad8038a26f023e257eaeba8ae4e37182dd7865c8d1e4acf89e7ae517d7a | MATLAB | 3,421 | 137 | %fig_S12_ISI_histograms.m
%%
clear all;
close all;
clc;
warning('on','all')
%% addpath if not added yet
% assumes script run within local directory
scriptdirs = {pwd;
'..\..\plot';
'..\..\helper_functions';
'..\..\analyze'
};
addpath(scriptdirs{:})
%%
datadir = pwd;
datafile = 'fig9_fig10_unit_ex.mat';
datapath =... |
80927a0fb5c9d1129747f57436ea5e53a21bffec409589a7a93fd3d9c091cd6f | MATLAB | 3,421 | 104 | % VL_DEMO_HOG Demo: HOG features
% Author: Andrea Vedaldi
% AUTORIGHTS
prefix = fullfile(vl_root,'figures','demo') ;
randn('state',0) ;
rand('state',0) ;
figure(1) ; clf ;
% --------------------------------------------------------------------
% Load a figure
%... |
cc89dd8d16d033a161820880e7e986300b70d232596b4214595cff7f730d7536 | MATLAB | 3,427 | 87 | function [r,p,ot] = buttonResponses(iTrial,p,s,i,ot,r,stimOnset)
% collects response within time window
%remove all unwanted responses from queue
KbQueueFlush(p.keyboardIDSubject);
timeWindowEndT = stimOnset + p.maxStimDuration + p.respDurMax;
%-- initialize data vecs to missing value
r.button(iTrial) = 99... |
6b15e862b1bb729bd525ff0dc02c6b9b08db6754eea226a1775c38a25fb1c3b7 | MATLAB | 3,430 | 106 | function [ncs] = read_neuralynx_ncs(filename, begrecord, endrecord)
% READ_NEURALYNX_NCS reads a single continuous channel file
%
% Use as
% [ncs] = read_neuralynx_ncs(filename)
% [ncs] = read_neuralynx_ncs(filename, begrecord, endrecord)
% Copyright (C) 2005-2007, Robert Oostenveld
%
% This file is part of Field... |
c55d6a53d10d785fffbf1c2bd6224509c804bae459f9d43c64285dced85629e2 | MATLAB | 3,434 | 46 | function status = fillSystemInformation( obj, data )
% Fill system information
%
% Syntax:
% status = FILLSYSTEMINFORMATION( obj, data );
%
% Input parameters:
% * data - data from json file(s)
%
%
% Example:
% status = FILLSYSTEMINFORMATION( obj, data );
%
% Available at: https://github.com/NCN-Lab/DBScope
% Fo... |
7ece48b11e07b85c906659e8abe3c4b03e7173fe13dd9c44ee8aa7e0d50b285f | MATLAB | 3,437 | 95 | function hsvColorHistogram = hsvHistogram(image)
% input: image to be quantized in hsv color space into 8x2x2 equal bins
% output: 1x32 vector indicating the features extracted from hsv color
% space
[rows, cols, numOfBands] = size(image);
% totalPixelsOfImage = rows*cols*numOfBands;
image = rgb2hsv(image);
% split i... |
34479d198e6dc4693fed78927149693027a1ce25aecb7047058724210363bdcc | MATLAB | 3,438 | 59 | function boundary_index = pbgnessSeed( input_im, spnum, superpixels, pb_im)
%% background seeds
% L = imlab(:,:,1);
% A = imlab(:,:,2);
% B = imlab(:,:,3);
[row,col,~] = size(input_im);
row_thes = 0.1*row;
col_thes = 0.1*col;
pos_mat=zeros(spnum,2);
% color_mat=zeros(spnum,3);
pb_weight = zeros(spnum, 1);... |
441b3682496b3b416e1f3c863f9de70dbfb13f7c563db13286688257214f5a74 | MATLAB | 3,438 | 100 | % uThreshSelectROIs.m
%
% Function for the user to select the ROIs and background threshold for a
% single time series. Calculates raw signal (mean pixel intensity) in each
% ROI and performs background subtraction.
% ROI selection by pixels with mean pixel intensity relative to rest of
% image above threshold and ... |
c6a98f72de2ad7e78f4cc7599f2c741db8f5568ab2a6106ce75fe3d2ba910583 | MATLAB | 3,438 | 97 | classdef IZeroClampSeries < types.core.CurrentClampSeries & types.untyped.GroupClass
% IZEROCLAMPSERIES Voltage data from an intracellular recording when all current and amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There is no CurrentClampStimulusSeries associated with an IZero series beca... |
e7bfd51638c4289e503983e261e3102af3aaf7d306dc5578ddc0606f842e4fe3 | MATLAB | 3,438 | 75 | % get the optimal rectangles for bounding boxes that can perfectly enclose
% sliding window and corresponding dense sift bins
% assume that the outlier of bbs can be entirely obtained
function [roi, grids, pts_ds] = getDetectionRegion(I_pred, bb_I, patchSize, nStride, alignment)
% superpixel segmentation
% imseg... |
3aa10ef8869f7f989c693dbdde3d7b57724066afd1b531f49978a4bfd0c87dbd | MATLAB | 3,441 | 106 | % [results] = read_fig3_table(table_dir, sheet_name)
% read figure 3 data from .xlsx file.
% returns a struct with data, specifically
% results.means = means;
% results.sems = sems;
% results.x = x;
% results.pos_true = pos_true;
% results.neg_true = neg_true;
%
% Mackay et al. 2024 (DOI:10.1038/s41467-0... |
710e866d555bcc7183a8e56be39bcfdb02a150c8bbf77c82e4312c08bf92e7c2 | MATLAB | 3,442 | 118 | function testOpenMEEGeeg
% TEST testOpenMEEGeeg
% Test the computation of an EEG leadfield with OpenMEEG
addpath(cd) % Make sure current folder is in the path
%% Set the position of the probe dipole
pos = [0 0 70];
%% Set the radius and conductivities of each of the compartments
% 4 Layers
r = [85 88 92 100];
c = ... |
2abdad4f1f07b80107448894d0eb81397c34d35df554e5a0361f0fbb5cece13b | MATLAB | 3,444 | 122 | %% LOAD
load('ds_events.mat')
%%
[outcomes] = get_pop_sparseness(ds_events,2)
%% GET LIST OF BETA WEIGHTS FOR EACH NEURON
starts=-99:1:100;
bin=30;
ends=zeros(1,length(starts))+bin;
timepoints=[starts;ends];
t=100;
type='onsets';
param(1).type=type;param(1).stat='avg';param(1).extype='ratio';param(1).exthresh= 2;
b... |
888dd85ab16dc80a807339c5c1661c82cc1df1d26b616811ec88921cb54ec3c8 | MATLAB | 3,445 | 103 | % mglInstallSound: Install an .aiff file for playing with mglPlaySound
%
% $Id$
% usage: soundNum = mglInstallSound(soundName,<samplesPerSecond=8192>)
% by: justin gardner
% date: 02/08/07
% copyright: (c) 2007 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: Installs an aiff... |
fe3424bf376a4472d0954521d780ab780871471804006c451d1157d44c4a9313 | MATLAB | 3,445 | 78 | function output_calibration = core_tracker_fit_arena(output_calibration_file_name, ...
working_background_file_name, ...
input_calibration, ...
options)
... |
1a9841e18f60ae43712bd2b14db984d788f3bd7242a484ba12fa9052e1f4fb0f | MATLAB | 3,447 | 146 | % FIGURE 1
%% LOAD DATA
if ismac
load('/Users/christianpotter/Desktop/Analysis/pop_analysis_potter2023/fixed_outcomes.mat')
else
load('C:\Users\Runyan1\Desktop\Desktop Code\dimred_event_analysis\pop_analysis_potter2023\Figure 1\fixed_outcomes.mat')
end
%% GET INFO ABOUT WAVELENGTHS
iters=length(fixed_outcomes... |
e657b412f76cb405d5038238d91c1a0eeb309b00762c71fad8005030f7cd7549 | MATLAB | 3,449 | 96 | function response = slack_incoming(url, varargin)
%% response = slack_incoming(url, payload)
% url : [char] Webhook URL (you have to get Webhook URL from Slack)
% payload : [char, struct] payload must be JSON style string or struct
% # payload is a case when varagin is a single argument
% varargin :... |
049e6d44132a2869c737386a445d3de0cad716247ce3a880ec98fba0c9e69929 | MATLAB | 3,450 | 79 | % function write_fig2_results_to_xlsx(results_cell, file_name, sheet_name)
% writes the data necessary to plot figure 2 to .xlsx
%
% Inputs:
% results_cell: Cell array containing the data to be written.
% file_name (str): Name including path of the .xlsx document.
% sheet_name (str): Name of the wor... |
cfec76d25713d7fcd6ade0d6421e102d36c9c658c5df18e74a560759530124a4 | MATLAB | 3,451 | 102 | % initalizeVisualPanels.m
%
% Code that takes in all parameters for initalizing visual panels and calls
% the appropriate PControl commands.
%
% INPUTS:
% panelParams - struct containing all parameter values for initalizing
% visual panels appropriately. Fields are:
% panelMode - [X,Y] representing close... |
3aeb5bd8d79041543c5fb5130461c175390cd1448054121ef369b777b2b1be01 | MATLAB | 3,453 | 118 | function loc = getStimLocDeg(projectDir, subjnr, useStimFlag, forcedGridLoc, hemi, relativeSize, offset)
% Define pRF XY centers that fall within stimulus squares
if ~exist('useStimFlag','var') || isempty(useStimFlag)
useStimFlag = true;
forcedGridLoc = [];
end
if ~exist('relativeSize','var') || isempty(relat... |
b4b27b5f15cba79e64172b39cfd35d7fe9244fc6b481e613eee5785d6b5d4d5d | MATLAB | 3,453 | 67 | function DecayHalfTime = ExponentialFit_DecayHalfTime(fit_timevect,object_2fit,expfit_type,StartPoint)
% DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: ExponentialFit_DecayHalfTime
% Feb 2023 - Marie Labouesse, marie.labouesse@gmail.com
% Exponential Fit a function to get its DecayHalfTime
... |
fa991cd738484d5ca7d9286a008b6c7325dc62de511fb081664a66cf5083bfe8 | MATLAB | 3,454 | 108 | function [chi_res, chi_SA] = delta2chi_SAR(deltaB, D, chi_res0, maskErode, thresh_SAR, chi_ap)
% function [chi_res, chi_SA] = delta2chi_SAR(deltaB, D, chi_res0, maskErode, thresh_SAR, chi_ap)
% QSM with streaking artifact removal (SAR)
% Input:
% deltaB: relative field shift
% D: convolution kernel
% chi_res0: i... |
41b6355970b07b4225059e7e9f40083e2208334b79d95771ed9e5b59ff5b95ac | MATLAB | 3,459 | 63 | % Compare the spikes times of a list of mda files to a list of txt files
filenames = [
%"Z:\1_Maxwell_Gagnon\hannahProjectData\smrFiles\20170810_JC6_ephys_cell2\20170810_JC6_ephys_cell2_MS.smr",
%"Z:\1_Maxwell_Gagnon\hannahProjectData\smrFiles\20170810_JC6_ephys_cell3\20170810_JC6_ephys_cell3_MS.smr",
%"Z:... |
9629e61ca09723a5b7a76a71117cfc3d64ccd26b1355e9e5e63a025c84c8e591 | MATLAB | 3,459 | 94 | % preprocessUserDaq.m
%
% Function to take data saved in userDaqDat.mat, the output of run2PExpt
% for any experiment type, and convert it to a more useable form for later
% analyses
%
% INPUTS:
% exptCond - experimental condition string
% flyData - information about this fly
% inputParams - experiment-specific... |
1673f75b92e305e34c3774f1f3eb5fb8d69a9ac52bcf234bb7bd339bba0e1dbf | MATLAB | 3,460 | 99 | function simseq_init(sessionDir,clip, keep, runBase, rawFileDir)
% simseq_init(sessionDir, clip, keep, runBase, rawFileDir)
%
% Function to initialize workflow for mrVista
%
% Inputs:
% sessionDir : (str) base folder of session, where mrSESSION.mat
% will be created
% clip : (i... |
979024e09153e6f8093c2e3b04d2e49ff45d822ba6a786ac24bb73d1ed7cb59c | MATLAB | 3,461 | 103 | % mglCheckOS
%
% usage: mglCheckOS(majorVersion,minorVersion)
% by: justin gardner
% date: 05/13/2022
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: Checks os version and returns t/f if equal or better to
% arguments. Will also set mglGetParams to have the... |
fd23bd33077995dbcafde10026456a24360cf7e5e60298cbd3ca17c6b346c80c | MATLAB | 3,461 | 81 | %----FUNCTION:
% extract statistical color histogram using integral histogram(RGB, HSV, LAB, Opponent color space)
function [colorArr_c, colorArr_s] = sp_colorHist_grid_cs(chns, grid_x, grid_y, patch_size, surrWidth)
nPatch = numel(grid_x);
[imh, imw, ~] = size(chns.rgb);
colorArr_c.RGBHist = zeros(nPatch, chn... |
f9d370f91f857fdb580f8d665f6cbeb36c1fb0ccda2b6cc85882a0f5ea9c33e2 | MATLAB | 3,463 | 98 | function Net = setESN(Options)
% The recurrent neural network (RNN) we are setting is r-based rather than v-base
% referring to the notation introduce in (Miller & Fumarola, NC 2012).
% Although these two dynamics have been proven to be equivalent (Miller &
% Fumarola, NC 2012), the rate (r-)based is the one int... |
a005ae9836a68ee871f726a057973bf31724e6f881616de60de246c969f0e6aa | MATLAB | 3,465 | 97 | %function stsum(x,y,STS,elec,unit,cc);
function STS = stsum(x,y,STS);
% updates the STS global struct: .sts[odd/even/shuf,:], array 2x:; .Ns [2,1]
% computes STS for shuffled spike times, for odd only - .stsShuf
% input: x holds spike frames, y holds the signal
% bef_s and aft_s units are s
%
%sta, the STA funct... |
3da1172b4fb80226ed94b6aed3b1013a81da5412019c88888cb59ea09055f559 | MATLAB | 3,466 | 117 | close all
clear all
%% create figure 4D
%% janine.thome@zi-mannheim.de
%% paths
pato=['/###/Figures/']; %% add output path
if ~isdir(pato), mkdir(pato); end
%% load results
file = 'Multim_FI.mat'; % mod = 1
load(file)
Vi_mean = squeeze(mean(mean(Vi_kfold)));
labK =... |
3323583310e0d653150349ed557ed79cfb66f2da7030e01e3f087c2439a85e3d | MATLAB | 3,468 | 84 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function [F, success] = ml_alg_compute_best_aligned_map_table_v2(T, comparisonMethod, REFLECT_ONE_CONTEXT)
F = [];
success = true;
wb = [];
% Get unique animalName, sessionName, cellName combinations
R = get_... |
62e45d1bf8ee8f56c8b56e536f78abf6b4d916df718723a684643aed591c6719 | MATLAB | 3,469 | 95 | % plot_convolved(results, which_panel, plot_info, curr_ax)
%
% this function plots the main figures from summary source data saved in
% .xlsx format, rather than raw data
% it is a combination of elements of perm_multcompare_gm_publ.m and
% plot_signals.m, and was put together in response to final requests to
% combine... |
656a27d8460f2affc4b9751a4351da1a7d9fa3fe1db2215b3f8101fe554f2120 | MATLAB | 3,469 | 106 | % Supplement to touch decoding paper, Maallo et al, 2023 (submission year)
% read response mat files for each subject and perform multi-class SVM classification
clc
clear
close all
%% load data files in matlab format
% load 'SUBJ_responses' mat file
% contains info table and
% con't: stimresponses
responsefolder = p... |
6d449dab645043ba66d5f7a7fab6c2f292397dd6b3972904166cc65595747eb5 | MATLAB | 3,469 | 96 | function core_tracker_job_consolidate(output_track_file_name, ...
output_segmentation_file_name, ...
per_chamber_track_file_name_from_chamber_index, ...
per_chamber_segmentation_file_name_from_chamber_index... |
e8c2eff6f120b500e64181abdbab316325c4587fb020c93ca027eb6b1f89b739 | MATLAB | 3,471 | 104 | % This is a mesh processor script: it computes basis triangle parameters
% and necessary potential integrals, and constructs a combined mesh of a
% multi-object structure (for example, a head or a whole body)
%
% Copyright SNM/WAW 2017-2020
%clear all %#ok<CLALL>
[~,name,~]=fileparts(pwd); L = length(name)+1;
i... |
86ff6b63c57f2bdca1ebb42bd8c0b1b22ee5145dbfa6ddb0e4e2d8e6369f0852 | MATLAB | 3,472 | 67 | function Get_WPLI(ComputeParams,PLX_Path,filename,SaveFileDir)
%% Compute and get WPLI and cohrence for given plx file
%% Input
% Compute Params for the whole codes.
% ComputeParams.Method = 0;% 0: wpli 1:wpli_basied
% ComputeParams.wpli_ParaLength = 1; typically
% Comput... |
fc8b6d7715b3bb0678892bb522f8fe7a9f48f7cd56d64fdaf70c615abbe413a7 | MATLAB | 3,474 | 78 | %%% author: SK
%%% date: 28/03/2024
%%% reference :"Neural effects of dopaminergic compounds revealed by multi-site electrophysiology in mice and interpretable machine-learning"
clear all; close all; clc;
%%Specify the directory to save data
save_dir = '\\preprocessed';
%%Specify the path of chronux tool... |
ef47dfb66e4fe90f64eef2d9e8a367145e1cf645a3d89b931d10a3f8a6fe038e | MATLAB | 3,477 | 125 | % This code takes an individual TIFF stack and outputs a series of CSV files, each representing individual slices.
% It can handle up to 4 channels as long and by default name them as red, green, blue, and white (in that order)
slices = 25;
width = 1012;
height = 424;
redT = 0; %T is for the threshold of that channel
... |
f7e1710458d05ee14e609b3e120a0e4bcdd1e748427c9f6b42923114da49cdec | MATLAB | 3,477 | 155 | function [epochs] = fiff_read_epochs(fname)
%
% [epochs] = fiff_read_epochs(fname,setno)
%
% Read eochs from file
%
%
% Author : Martin Luessi, MGH Martinos Center
% License : BSD 3-clause
global FIFF;
if isempty(FIFF)
FIFF = fiff_define_constants();
end
me='MNE:fiff_read_epochs';
%
% Open the file
%
fprin... |
b10f769ebcf4bf8ca0f77039937bdba838d2ff47f26e337ed435b37e2d428d2e | MATLAB | 3,482 | 119 | % plotLRrunCorr.m
%
% Function for looking at correlation in activity between left and right
% cells in calcium imaging.
% Prompts user to select pData file through GUI and outputs graph showing
% two dF/F traces, FicTrac yaw and forward velocities, and running
% correlation. Also shows overall correlation b/w two c... |
1ed00744a27ded6610998b1cdff90021e9a661ecd72cfd065e67819375556195 | MATLAB | 3,483 | 110 | function R=latmio_und_connected(R, ITER)
%LATMIO_UND_CONNECTED Lattice with preserved degree distribution
%
% L = latmio_und_connected(A,ITER);
%
% This function "latticizes" an undirected network, while preserving the
% degree distribution. The function does not preserve the strength
% distribution in we... |
1f9c47b794ed6be80c96be57ca5389e8b3d8c313f9fc59c25f17a31b11d3f01a | MATLAB | 3,486 | 71 | % Final Regression Script
clear all
clc
%cd('M:\Matt Chilvers\Documents\PhD\Project3_WhiteMatterLesion\Scripts\Plots\ScatterPlots\FinalRegressionAnalysis')
cd('/Users/dukelowlab/Library/CloudStorage/OneDrive-UniversityofCalgary/PhD_Projects/Project3_WhiteMatterLesion/Scripts/Plots/ScatterPlots/FinalRegressionAnalys... |
4d91d54353dbca1c1626f1e03ea9eef7c6f66d7ffb975d75233100ebc8e0bcd1 | MATLAB | 3,486 | 94 | % preprocessOpto.m
%
% Function for processing raw voltage signals indicating when the
% optogenetic stimulation was active (feedback signal from shutter in
% front of mercury lamp; high = open). Extracts start and end times of
% opto stim. Also, logical for stim on or not. Saves parameters of opto
% stim that wer... |
c3c8530b953fd0c2cb1d1957c6d4f442b62024e7285e90526ee07fc649db750e | MATLAB | 3,489 | 83 | function fH = makeFigure4_SuppressionLevelsAcrossVisualAreas(ds,fLMM,lmmResults, ...
roisToPlot, cmapROIs, useSTRetParams, saveFigs, saveFigDir)
% Function to reproduce main manuscript figure 4:
% panel a: All 9 ROIs SEQ vs SIM amplitude voxel scatter plot for small & short stimulus condition
% panel b: Su... |
ced1dc07098dfc863b3aac8d772f151331cf19d3f314452377ee1ce97f738d9a | MATLAB | 3,492 | 112 | function simseq_2gray(sessionDir)
% simseq_2gray(sessionDir);
%
% Function to transforms the time series from the inplane to volume anatomy
% and averages the time series
%
% Inputs
% sessionDir : (str) path to subject's VistaSoft session
%
% Written by EK 2021, adapted from D Finzi toonotopy code
%% Load initial... |
917055a71e976e71d5696b01297c79fa06c81762ebe158db754c52594387956c | MATLAB | 3,493 | 107 | function val = ft_getopt(opt, key, default, emptymeaningful)
% FT_GETOPT gets the value of a specified option from a configuration structure
% or from a cell-array with key-value pairs.
%
% Use as
% val = ft_getopt(s, key, default, emptymeaningful)
% where the input values are
% s = structure or cell... |
ac5574ba4b5e22d61a8f4f2049f99a6d844d4c539c93400ad9ca96fee7eb40d9 | MATLAB | 3,493 | 86 | function normcorre_registration(parentDir, fileName, varargin)
%===================================================================================================
%
% Uses the NoRMCorre algorithm to apply a rigid motion correction to pre-processed imaging data. It
% must be saved as a .mat file containing the var... |
efe8729d634d538c391780e073efe95d7ca7b92731d74fef0f7352a1c142e44d | MATLAB | 3,494 | 68 | function PlotBEAM(MIEEGData,label,Fs,LowFreq,HighFreq)
channel = 1:30;
trigger = find(MIEEGData(:,33)==2);
left_MI = zeros(2000,30);
left_MI_cell = cell(20,1);
right_MI = zeros(2000,30);
right_MI_cell = cell(20,1);
k1 = 1;
k2 = 1;
for i = 1:length(trigger)
bp_data = BandpassFilter(MIEEGData(trigger(i)-8... |
9ac758b13afc45b6df9a0016337e7274adc3252104ba2f21a2f03a0cb4346bd3 | MATLAB | 3,495 | 72 |
function [Spikes,nose,Fs]=getSpikesEM(File, passNo);
%getSpikesOF, modified from getSpikes to read OpenField data. ehud, Oct
%2016
%
%1. parse the data according to gaps in Timestamps (> 1s)
%Session_str, e.g.,'20150906Thalamus36\20150906Thalamus36_1to...'
%
%Spikes{Nelecs,Nunits}, cell holding spike times i... |
ffbf7c8228a913a7aff944787e40de16ca423513fa7eed65642468cb6d90d57c | MATLAB | 3,495 | 106 | function [TChannel]= SONChannelInfo(fid,chan)
% SONCHANNELINFO reads the SON file channel header for a channel
% Output follows the CED disk header structure but a FileName field
% is added to tag the returned structure with its source file.
%
%
% INFO=SONCHANNELINFO(FID, CHAN)
% where FID is the matlab file han... |
b4a4a594621049f08f006975b1f332a0c967fb5673dd98d9364fcec3f08a07c1 | MATLAB | 3,496 | 117 | function [nst] = read_neuralynx_nst(filename, begrecord, endrecord)
% READ_NEURALYNX_NST reads a single stereotrode file
%
% Use as
% [nst] = read_neuralynx_nst(filename)
% [nst] = read_neuralynx_nst(filename, begrecord, endrecord)
% Copyright (C) 2005, Robert Oostenveld
%
% This file is part of FieldTrip, see ht... |
7826e4e7bbe43932d63fc309c0be7f55f41598844d08ff5a40acd9255337e1c5 | MATLAB | 3,498 | 97 | % oneStepOptoWCtrl.m
%
% Optogenetic Stimulation Function. Opens up shutter in front of mercury
% lamp for duration specified by user on X% of repeats. Other (100-X)% of
% repeats, shutter doesn't open. Which repeat shutter opens is random.
% Specify duration before and after steps when shutter is not open.
% Return... |
f282d45e2eb6a8e0e2f8d9de3241a85ad2972ea31a8edae8a8fd674c9bbc785d | MATLAB | 3,498 | 117 | function [ntt] = read_neuralynx_ntt(filename, begrecord, endrecord)
% READ_NEURALYNX_NTT reads a single tetrode file
%
% Use as
% [ntt] = read_neuralynx_ntt(filename)
% [ntt] = read_neuralynx_ntt(filename, begrecord, endrecord)
% Copyright (C) 2005, Robert Oostenveld
%
% This file is part of FieldTrip, see http:/... |
a0d60f49d2ced61ed0809932065c60827676ba29724f03742116baaa33779c32 | MATLAB | 3,499 | 104 | % getResidualSpikeRate_fly.m
%
% Function for calculating residual spike rate. Takes in input from
% getCorrelationEphysContParam_cond_fly() and generates residual spike
% rate. Uses behVals and ephysVals. Takes 1st column of behVals as
% variable to get mean curve and subtract from this to get residuals.
% Remaini... |
065754b419a031ad7a8428ac78cf7a5bc756a16f76a747cb55d12df783075fcd | MATLAB | 3,500 | 126 | function [B,tspred,tsorig,corr_pred_obs,MSE,local_error] = fcn_fit_model(sc,ts)
%fcn_fit_model reweight fiber tracts using functional data
%
% [B,tspred,corr_pred_obs,MSE, ocal_error] = fcn_fit_model(sc,ts)
% uses a matrix of interregional coupling (sc) to constrain regression
% model of brain activity. The ac... |
5900783a40281aaf27d277e34bb0f9a570a747bc81195a3160ed9e9694850eef | MATLAB | 3,500 | 106 | % plotScatterPCAStepParams.m
%
% Function to plot scatterplot of output of pcaCompStepParams()
% Plots each turn bout set 1 PC1 vs set 2 PC1.
% Select output file of pcaCompStepParams() through GUI
%
% INPUTS:
% datDir - path to folder containing pcaCompStepParams() output files
% plotType - string for type of plot... |
a05342b8e262a331ab92c12405fabadf7389238417da80bbde1fc3404cea2546 | MATLAB | 3,502 | 73 | function h = mk_doub_exp_ker(t_on, t_off, A, dt, varargin)
% h = mk_doub_exp_ker(t_on, t_off, A, dt)
%
% Function to create a double-exponential kernel. The kernel is defined as
%
% h(t) = A*(1-exp(-t/t_on))*exp(-t/t_off)
%
% The function is evaluated at increments of dt from t=0 to t=t_max defined
% as the time wher... |
2c696049dbea669da47c04a5c08b3a0a6f32114b5f7f4543fa45219f0e0ad012 | MATLAB | 3,504 | 75 | function scan_img = single_scan(neur_vol, psf_sz, psf2, varargin)
% scan_img = scan_volume(neur_vol, psf, varargin)
%
% Scan a 3D volume with a given point-spread function. This function takes
% in a neural volume (as generated by "simulate_neural_vol_v*.m"), a
% point-spread function, and a number of other optional s... |
e0c8b51b93016de8de093323a3590bf4aa4fcbcc3a84066836c2d972e69170c8 | MATLAB | 3,507 | 145 | function [fspec, fstem, fmt] = MRIfspec(fstring,checkdisk)
% [fspec fstem fmt] = MRIfspec(fstring,<checkdisk>)
%
% Determine the file specification (fspec), stem (fstem), and format
% (fmt) from the given file string.
%
% A specification is the name of a file as it could exist on disk. The
% specification has the form ... |
62b243aba782408f9648144e547ffab1772159e21eafcfe83ff5d018bc88a5ec | MATLAB | 3,509 | 114 | % plotNormAEPPEP_allFlies_v2.m
%
% Function that takes output files from saveAEPPEPbyCond_fly() and
% generates a plot of the AEP and PEP for each leg, normalized to the AEP
% of the unmanipulated condition. Plots mean +/- SEM for each fly.
% Uses line to connect AEP and PEP for each fly
% Subplots for each leg (lef... |
859abb1d74f94b36013c9ab30f07f5223497e72f5b1c8baa9a877becf4fb90a1 | MATLAB | 3,512 | 92 | function [filt] = ft_preproc_dftfilter_Opt(dat, Fs, Fl)
% FT_PREPROC_DFTFILTER applies a notch filter to the data to remove the 50Hz
% or 60Hz line noise components. This is done by fitting a sine and cosine
% at the specified frequency to the data and subsequently subtracting the
% estimated components. The longer th... |
77d2983f2828ee7dcae6f60854305485990909f54a55497c69edbb7c92d3d7a1 | MATLAB | 3,514 | 117 | function plot_accuracy(output,bin,starts,param,shuffle_yn)
%% UNPACK VARIABLES
sp_accuracy=output.sp_accuracy;
spn_accuracy=output.spn_accuracy;
sp_err=std(sp_accuracy)/sqrt(length(sp_accuracy));
spn_err=std(spn_accuracy)/sqrt(length(spn_accuracy));
pn_accuracy=output.pn_accuracy;
sn_accuracy=output.sn_accuracy;
... |
e3ef0bf359a1b2f3e4fa998d572badf09dc19b026d634b426b532f0f50ecd54a | MATLAB | 3,514 | 112 | classdef MLSession < MLSessionInterface
% MLSession Implementation for a session
% An implementation for an experiment session
properties (SetAccess=private, GetAccess = protected)
Config
SessionRecord
Name
Date
Trials
SessionDirectory
... |
e692f40444059b5819e842f69cca7c092c477f5be70c01c8cbc03178e332b800 | MATLAB | 3,515 | 91 | function [spikes, markers, all_strings] = get_all_data_from_level_h5(filename,str)
% The function extracts the spikes and the markers from a .h5 dataset
%% authors: Francesco E. Vaccari
%% date: 22nd February 2024
%
% INPUT:
% filename = a string that identify the h5 file from which extract data
% str... |
799ec0af2ee62c4e8c2924b4ca47873f346eed78e9ff07bf2b1e0a4b125781e4 | MATLAB | 3,516 | 122 | function [fhdr,chdr,ename,cnames,fcom,ftext] = read_egis_header(filename)
% READ_EGIS_HEADER reads the header information from an EGI EGIS format file
%
% Use as
% [fhdr chdr] = read_egia_header(filename)
% with
% fhdr - the file header information
% chdr - the cell header information
% ename ... |
92869780da95946f4f39e49d0f658fac4027e85498e6b65c569388f8b5291666 | MATLAB | 3,517 | 120 | function [median_total_error,std_error,estimated_duration]=decoding_movement_duration(score,idx_dir,idx_duration,ref_bin,Ndim,Nbins,do_plot)
%% decoding_movement_duration predicts the duration of trajectories
%% corresponding to the same movement direction than the sample trajectory
%
% INPUTS
%
% score: Projection of ... |
fa8560348ca8f96dc0c124e5c9dc171541e004c13de9fa179513458bff5e5e5e | MATLAB | 3,518 | 92 | function [psdPeaks, intpsd, gammaP, betaP, meanLevel, envLevel, osci] = record(r, allTime)
% RECORD give property of the parameter setting
% psdPeaksSheet = zeros(Delta_e_steps, Delta_i_steps, 16, 6); % XX peaks in psd, e.g. -1-NaN, 5 peaks, 12 peaks
% intpsdSheet = zeros(Delta_e_steps, Delta_i_steps, 16, 6); % integr... |
642af73c18e9a415e5133461216002b3d8241bd8ff0a1521aacd2d3317d28885 | MATLAB | 3,520 | 93 | function seqMaster = generateSequence(locations, dt, durations, ...
nrSeqRepetitions, conditionOrder, totalTrialsPerBlock, ...
hemifield)
% Stimulus order:
% Simultaneous trial order is one frame of 6 = all stim simultaneous,
% rest of frames are 1 = blank count, 1x4 s... |
30571b6c8fc4dc89a259a5f8ff4a4fe0c88b394cb7f3b67db16e19923ceef1f5 | MATLAB | 3,523 | 86 | classdef ExternalResources < types.hdmf_common.Container & types.untyped.GroupClass
% EXTERNALRESOURCES A set of four tables for tracking external resource references in a file. NOTE: this data type is in beta testing and is subject to change in a later version.
% REQUIRED PROPERTIES
properties
entities; % REQUIR... |
6a207f7db97d870bf372c916cb3227df0026661cba045f7b2da178cd2aa9d1c3 | MATLAB | 3,523 | 106 | % mglPostEvent.m
%
% $Id: mglOpen.m 385 2009-01-03 20:34:37Z justin $
% usage: mglPostEvent(command,<time>,<char/keyCode>)
% by: justin gardner
% date: 01/10/09
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: This is a mac specific command that is used ... |
b8ebdd5c71d80b93eb5fdf76a22e9c12fdf3cd6a3c19a5a29dd8ff68ec10c9fc | MATLAB | 3,523 | 106 | function [chi_res, flag, relres, iter] = delta2chi_NDI(deltaB, kernel, DPWeight, maskErode, NDIParams)
% [chi_res, flag, relres, iter] = delta2chi_NDI(deltaB, kernel, DPWeight, maskErode, NDIParams)
%
%% Author: Xu Li
% Affiliation: Radiology @ JHU
% Email address: xuli@mri.jhu.edu
%
% Quantitative Susceptibil... |
05830e2727cab56df747bdab93c9f1db2dcd1367c7a79a33a21f6d4bd0194358 | MATLAB | 3,524 | 83 | classdef RECORDINGMODE_CHRONIC < RECORDINGMODE_COMMONMETHODS
% Object with properties and methods to analyse chronic fields from PerceptPC json data at NCN lab
%
% Available at: https://github.com/NCN-Lab/DBScope
% For referencing, please use: Andreia M. Oliveira, Eduardo Carvalho, Beatriz Barros, Carol... |
e41f5edc4ec5e95a3467bc47df274f0b7047f74196a1a6d1c145650150d40952 | MATLAB | 3,525 | 106 | % eyeCalibrationASL.m
%
% $Id: eyeCalibDisp.m 486 2009-02-16 00:05:54Z dep $
% usage: eyeCalibDisp()
% by: justin gardner
% date: 12/10/04
% copyright: (c) 2006 Justin Gardner (GPL see mgl/COPYING)
% purpose: eye calibration - mgl version
% stimuli should be defined in visual a... |
dac55137737dd501cc8fb8ab1856ef16aef94a750f277f78ad5806c1808af36e | MATLAB | 3,531 | 131 | % plotSpikesPhaseDelays.m
%
% Function to plot amplitude of modulation of spike timing by phase, across
% temporal offsets
% Fits 1 period sine curve to values for each delay, plots amplitude (2*a)
% equation: a*sin(x+c) + d
% Data from getSpikesStepPhase_cell()
%
% INPUTS:
% datDir - directory with output files
%... |
f2e2d21015fcf6e0baaa174e7722e9bc2023a1df5634ec4693989cfc638f7aa1 | MATLAB | 3,531 | 106 | % This is a mesh processor script: it computes basis triangle parameters
% and necessary potential integrals, and constructs a combined mesh of a
% multi-object structure (for example, a head or a whole body)
%
% Copyright SNM/WAW 2017-2020
%clear all %#ok<CLALL>
[~,name,~]=fileparts(pwd); L = length(name)+1;
... |
147023dd94f91f6968d983b48e1ceeb14a8b3e83503095f3901ad1526655b846 | MATLAB | 3,532 | 85 | % blockRandomization.m
%
% usage: blockRandomization()
% by: justin gardner
% date: 01/22/07
% purpose: function that decides order of parameters,
% it needs to set block.parameter with relevant
% parameters and what they will be set to.
% e.g. block will end up... |
3cff4cb37d68d84dbfc090ee4a3e639658a0f434cb9e35891776ad16fcb3684d | MATLAB | 3,532 | 103 | % mglTestTexture: an automated and/or interactive test for rendering.
%
% usage: mglTestTexture(isInteractive)
% by: Benjamin Heasly
% date: 03/10/2022
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: Test rendering a smoothly varying texture.
% usage:
% ... |
54919c930b1e126342d220c1bcb6e2f896666d93da775961a0bbf947735cea10 | MATLAB | 3,534 | 120 | %{
Copyright (C) Cambridge Electronic Design Limited 2014
Author: James Thompson
Web: www.ced.co.uk email: james@ced.co.uk, softhelp@ced.co.uk
This file is part of CEDS64ML, a MATLAB interface to the SON64 library.
CEDS64ML is free software: you can redistribute it and/or modify
it under the t... |
a753bf805c2494be4237f7f191156951c56687b234ae4c93e878ad31e8a0b6b3 | MATLAB | 3,537 | 84 | function [micID, sampleID] = readRecipe(recipePath)
% Read the microscope ID and the sample ID from a recipe file
%
% function [micID, sampleID] = webupload.readRecipe(recipePath)
%
% Purpose
% The microscope ID is the value of ID directly under the top-level SYSTEM key and the
% sample ID i... |
5ad1e2feb19ed058ea84ee0bc11b51bca5b122babd685b8efe96140090e6a9df | MATLAB | 3,538 | 111 | clear
cd ./opto_sponlick
% C1S2:light;
control=dir('C*.mat');
inhibit=dir('I*.mat');
active=dir('A*.mat');
k=1;
for j=1:length(control)
load(control(j).name)
light=C1S2;
lickp.control(j,1)=0;lickp.control(j,2)=0;lickp.control(j,3)=0;
for i=1:20
t=light(i);
lick1=find(I... |
39037f09ff0ec0ef6caad08998a4f7fcd6568cf1d497382cd1188aa374f5976e | MATLAB | 3,539 | 70 | function subject_power_2014_motion_parse(movement_files,skip_seconds,epi_TR,expected_contiguous_frame_count)
% FD parsing Nipype wrapper pulling in list of motion files
% All variables (skips, TR, CurrentDirectory) set within Nipype
% Iterates over range of values from 0.1 to maximum of 0.5 FD threshold
% Outputs to .m... |
bf01458048f40002dbcb5bae96b38328c22d6f7b3edde5c55272c31565625f1a | MATLAB | 3,541 | 93 | % calculate the mean and variance of arbitery windows as well as its surroundings of an image using
% integral image computation
function [avg_c, var_c, avg_s, var_s] = calcMeanandVariance_cs(I, gridx, gridy, patchSize, surrWidth, varFlag)
[imh, imw, imc] = size(I);
% coordinates of center pixels for computing re... |
e7dfefc7767f0ac182859365262903f0cbf38286897c126ee9e4cb32dd712c37 | MATLAB | 3,541 | 152 | %% GET mDECONV FOR EACH DATASET
all_mSOM=cell(1,6);
all_mPV=cell(1,6);
all_mPYR=cell(1,6);
for ds=1:6
curdeconv=all_deconv{ds};
curct=all_cell_types{ds};
cursom=all_deconv{ds}(curct==1,:);
curpv=all_deconv{ds}(curct==2,:);
curpyr=all_deconv{ds}(curct==0,:);
all_mSOM{ds}=mean(cursom,1);
... |
50eeabaceb7ddd3ad67d8b22387d6ceb0af43287b535e6530ed2867939a89d5a | MATLAB | 3,545 | 94 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
% This loads celias tetrode data into a form that can be used by the
% population vector code
function [T] = load_celia_data_structure_as_table_v2(data)
%data = load(dataFilename);
%data = data.ratemaps;
animalNames = ex... |
03acc9cebf5aeff21eb83a3e3601bb38f4d1aec3736f5519f21a1f4d421557da | MATLAB | 3,546 | 99 | % stepParam2Vector.m
%
% Function that takes in legSteps struct and returns a vector of values for
% a single field, during either stance or swing, at a specified times.
% Holds the parameter value for the entire duration of the step (swing +
% stance). Since steps are defined max-min-max position (forward walking,
... |
614c2fa6cd387501a65a61843bf5e3f53b05c2407542cf16c31ae15444c240fd | MATLAB | 3,546 | 133 | close all
clear all
clc
sessionsToUse = [2];
project = ml_util_json_read('project_config.json');
expRich = dir(fullfile(project.dataFeatureRichFolder, '**', 'experiment_description.json'));
miceRich = initMice(expRich, project.analysisFeatureRichFolder);
plot_mice_groups(miceRich, sessionsToUse)
expPoor = dir(fullf... |
d62fd0f4277dfdd0a2db92469054a6da50422b90a9e38eb45ba6baa9dbd8f6bc | MATLAB | 3,548 | 71 | % run amapOFshow
clear all; runMode = 'batch';
globals; initglobals;
PRINT_ERRORS = 0; PRINT_INFO=0; PRINT_NAN=0;
DATA_TYPE = 'OF';
%DATA_TYPE = 'EM';
PLOT_TYPE = {'tuning'}; % {'map'}, {'trajectory'}, {'tuning'}, {'map';'trajectory'} ;
%PLOT_TYPE = {'map'}; % {'map'}, {'trajectory'}, {'tuning'}, {'map';... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.