sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1030368b0079ccc8b21508eb98144938d5beeb4f65c3bbf9650423f8c8555794 | MATLAB | 1,632 | 22 | function [output_mat] = lorenzliver(input_x,rho,tmax)
% Solve over time interval [0,100] with initial conditions [input_x,1,-input_x]
% ''f'' is set of differential equations
% ''a'' is array containing x, y, and z variables
% ''t'' is time variable
sigma = 10;
beta = 2.667;
[t,a1] = co... |
309e00ee58d8117ffc623cd674b549d4c9aad9fb6eee9c2796df578d0cdf7322 | MATLAB | 1,632 | 87 | clear
load a2_1_averagingSaccades
iMonkey = 3;
close all
figure(1)
clf
for iMuscimol = [0,9,12] +1
%for iMuscimol = [0,9,12] +1
%for iMuscimol = [0,1,4] +1
k = 1;
amp = [1:k:20];
clear m u l
for iAmp =1:numel(amp)-1
cAmp = amp(iAmp);
I = sacAllAmp{iMonkey, iMuscimol}>amp(iAmp) & sacAllAmp{iMonkey, iMuscimol}<a... |
11cef1a013159ee2a3735c1c94b2cae9f6d4d5af70f938f8125f1d354817e269 | MATLAB | 1,634 | 48 | function [imgAB, alphaAB] = alpha_comp_over(imgA, imgB, alphaA, alphaB)
%alpha_comp_over - Alpha composite one image over another
%
% [IMG_AB, ALPHA_AB] = alpha_comp_over(IMG_A, IMG_B, ALPHA_A, ALPHA_B)
% alpha composites IMG_B on top of IMG_A, using the alpha masks ALPHA_A
% and ALPHA_B.
%
% This function is n... |
33c8e493fceadd5a888cc9254cc678e68e4fdde8b395a4976bdf4fa05479770e | MATLAB | 1,636 | 49 | function plot_frame(self, varargin)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the Licens... |
f87db304a4d26c756bdeeb4b40315b6aa8a3a2c2a936b2474286bd3c3184cf4b | MATLAB | 1,639 | 81 | clear
close all
%save(mfilename);
imSize = [733, 977];
hmSize = [210, 280];
hmSize = [733, 977];
hmScale = mean(hmSize./imSize);
pix2deg = 34.910;
filesAll = dir('../../Images_Movies_Functions/analyze1/data0_Image/image_*');
I = arrayfun(@(x) x.isdir, filesAll);
filesAll = filesAll(I);
nFile = numel(filesAll);
im... |
f8dbf05dba5b1d5385b8d3f728df552776336e6decd7e8e2411405605abad9bb | MATLAB | 1,639 | 39 | classdef (HandleCompatible) ICalcVelocityStreaks
%ICalcVelocityStreaks - Interface for classes that calculate velocity
%
% The ICalcVelocityStreaks class is an abstract superclass that
% implements (or requires implementation in its subclasses via abstract
% methods or properties) functionality related to calcul... |
35bfabdff41b2ea24af1e794e1f35fa3221896b91c9fc5da5455c92a4ac7fdc3 | MATLAB | 1,640 | 81 | %{
clear
close all force
warning on
imSize = [733, 977];
load('a0_0_bhv2trialStrct.mat');
UMonkey = [1,3];
NIImage_IndividualAndGroup5 = [...
7
11
25
27
38
39
40
47
49
53
56
60
9
22
28
41
42
43
44
50
52
55
59
];
% no... |
570b976450b7eeaedca1ec7d347358310fbc9912b9f6f20410e55295724e4479 | MATLAB | 1,643 | 50 | function t2n_renameNrnmech(newname,path)
% This function renames the nrnmech dll file to the name specified in newname.
% Also deletes all .o and .c files created during dll compilation by
% NEURON.
%
% INPUTS
% newname string with new name for dll file
% path (optional) path to the main folder of the model (cont... |
977430f185803a5c32535b096dccd0653d9cf8e8350d79b116bae2474aecd87e | MATLAB | 1,645 | 43 | %calculating the average vaule of each individual fiber bundle core
%Last modification: 02/01/2023
% by Peisheng Ding (peisheng.ding@mpi-halle.mpg.de, peisheng.ding@mail.utoronto.ca)
function A_cores= average_cores(Image, Cores_Stats,blank_field,radii)
% %------------------------------------------------------... |
9c093f797209f8e483dbdfd90c6eaf01d2e4d71c4677a6b73a032695e4f250d5 | MATLAB | 1,645 | 54 | function simulate_EEG(masterFolder,arrayID,S)
addpath('/lustre04/scratch/nbrake/code/simulation_code');
baseFolder = '/lustre04/scratch/nbrake/data/simulations/parameter_sensitivity_analysis_2';
load(fullfile(baseFolder,'parameters.mat'));
fid = fopen(fullfile('/lustre04/scratch/nbrake/code/simulation_code','mod_file... |
2b63d8fccc7ec8d40d06056aae2d5923ddd38e0691e912c3d3d8b37423a85fb5 | MATLAB | 1,647 | 43 | function [] = iso_compl_v5(RespMatComb,Quantity,CSel,RelHumidities)
% Comparison of the responses towards the highest concentration - ISO compliance
%
area([0,7],[RespMatComb(CSel,3)*1.3 RespMatComb(CSel,3)*1.3], RespMatComb(CSel,3)*0.7,'FaceColor','r','FaceAlpha',0.3, ...
'LineStyle', 'none'); % ISO bound... |
4a63cf5401b05f77f06fa96a102a9639df9cdbdceea4eccc21bdf887674a19bd | MATLAB | 1,647 | 51 | function live2pHoloSocket
global ExpStruct
global websocket
seqNum = numel(find(diff(ExpStruct.triggerPuffer)==1));
if seqNum > numel(ExpStruct.bigListofSequences)
sendThis = [1000];
sendThisSI = [];
elseif seqNum ==0
disp('0 trials')
sendThis = [];
... |
565b3aa1700aee1ee8ef9f08f34a684d6d734ecb4b07e1005abab2e744159582 | MATLAB | 1,648 | 47 | function check_plotList(self)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
... |
762af680ad7e3a29bdf6704da5c62e5118cbb25c9a8f71f2d4eee226a239585c | MATLAB | 1,648 | 35 | function [fluor, stillScans] = LoadROIfluor(expt, fluor, loco)
% Load ROI-level fluorescence signals from file generated by GetROIfluor, without needing memory-hog ROI structure
savePath = strcat( expt.dir, expt.name, '_ROIfluor.mat' );
tic
fprintf('\nLoading %s', savePath);
if exist(savePath, 'file')
load(sa... |
32e1aea77959ba985d44a91cff8b58ef608e4895a6491f282bdc76d7f17096ca | MATLAB | 1,653 | 42 | function [DataMatrix, Labels,MouseIDs,Days,sessionNames] = AverageSessionDataOld(DataMatrixSrc, LabelsSrc ,MouseIDsSrc,DaysSrc,sessionNamesSrc)
sessionNum = zeros(1,length(sessionNamesSrc));
SessionNameWithoutBout = cell(1,length(sessionNamesSrc));
for k=1:length(sessionNamesSrc)
curName = sessionNamesSrc{k};... |
82cc3145668dad1e36f8793e909c376599ecade50c162efc70955beb8e40d540 | MATLAB | 1,654 | 49 | function releases = getGitHubReleaseHistory(verbose)
% Return a structure containing the release history on GitHub
%
% gURL = zapit.updater.getGitHubReleaseHistory(verbose)
%
% Purpose
% Return the project's GitHub release history. This can be used to determine
% if the installed version is... |
0b359c710b52482a2cc11d4c1593253fae69a3a5f8d5c368fffa64fc2bfd9a56 | MATLAB | 1,657 | 53 | %% Run Experiment For Set Duration
%
% <html>
% This examples shows how to use Matlab to control the Synapse mode and
% monitor recording status <br>
% This uses the 'ExperimentSetTime' example experiment, but it could run with any
% experiment <br>
% </html>
%% Housekeeping
% Clear workspace and close exist... |
7e2597bb5a1118b9f4951f6312472c9181f2708c95250c2fea94f4b95e6f9048 | MATLAB | 1,659 | 55 | function mycolor = getmycolors(colorSet)
% myCOLORsHEX = {'#009ADE','#C77CFF','#FF1F5B','#FFC61E','#F28522','#A0B1BA'};
if nargin < 1 || isempty(colorSet); colorSet = 1; end
if colorSet == 1
% myCOLORsHEX = {'#009ADE','#C77CFF','#FF1F5B'};
myCOLORsHEX = {'#0E4BEF','#5a005a','#FF0090'};
myCOLORsHEX = {... |
645e075225fd678b2f7a17370b19cbf964df5942e52da9f7bee5b7e3537c05f0 | MATLAB | 1,660 | 71 | function [h]=rmHrfTwogammas(t,params)
% Create an HRF based on the SPM two gamma model.
%
% [h]=rmHrfTwogammas(t,params)
%
% t: a range of latencies
% params(1): peak gamma 1
% params(2): fwhm gamma 1
% params(3): peak gamma 2
% params(4): fwhm gamma 2
% params(5): dip
% Final hrf is: gamma1/max(gamma1)-dip*gamma2... |
9f36d75869d185e21d6aa89569df7b0f2ace1f136ad351a2a0f9fc0a4aabd1a1 | MATLAB | 1,664 | 68 | %% rsquared
%
% [R^2] and adjusted [R^2] statistics
%
% <matlab:open('rsquared.m') code>
%
%% Syntax
%
% [RSQ,RSQADJ] = rsquared(X,E)
%
%% Arguments
%
% See also <mvgchelp.html#4 Common variable names and data structures>.
%
% _input_
%
% X multi-trial time series data
% E ... |
4222c3338ded5c2285ed4ec2105e9aabd4161658b37c4a1c886a705eb858b5bf | MATLAB | 1,665 | 37 | classdef (SharedTestFixtures={matlab.unittest.fixtures.PathFixture(...
fullfile(fileparts(mfilename('fullpath')), '..', '..', '..', 'inputOutput'), ...
'IncludeSubfolders', true)}) ...
testio_CSIloadtwix < matlab.unittest.TestCase
properties
dataFile
end
methods(TestMethodSetup... |
e8ec78037e51cdc3ed9c4b2cdb7d2b4ef32996767ad06626273b2f4818d1162b | MATLAB | 1,666 | 22 | function J = customcolormap_preset(preset_name)
switch(preset_name)
case 'pasteljet'
J = customcolormap([0 .25 .5 .75 1], {'#9d0142','#f66e45','#ffffbb','#65c0ae','#5e4f9f'});
case 'red-yellow-blue'
J = customcolormap(linspace(0,1,11), {'#a60026','#d83023','#f66e44','#fa... |
950af36b54bba4ea95715fc04ea49fa07bf4c6c86ded2fb42ceca3c3137a0755 | MATLAB | 1,668 | 42 | function annotate_signals(self, objPI, hFig, currROI, params)
%annotate_signals - Add annotations to 'signals' plot
%
% The function 'annotate_signals' calls function 'annotate_traces' with
% adjusted parameters to produce annotations for ROI responses
% one-by-one.
%
% See also CalcDetectSigs, CalcDetectSigsCl... |
9eb2b3d74a87397860d039f9757b6273e0efd89d07483f400667bab764c23824 | MATLAB | 1,668 | 52 | function varargout = plot_imgs(self, objPI, hAxes, varargin)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, eithe... |
6aeb06ef24f2735da970a6b6b6df6e06264e6c61fd5ebee7d9fa12bb2cf2de06 | MATLAB | 1,669 | 54 | function[simsig simsigmod snr] = gen_simsig(sigy1_freq, sigy2_freq, Fs, ...
numsec, noise_ratio, amp_ratio)
% function[simsig simsigmod snr] = gen_simsig(sigy1_freq, sigy2_freq, Fs,...
% numsec, noise_ratio, amp_ratio)
%
% This function generates a PAC containing signal 'simsig' and a
% corresponding modulating s... |
91067051a316382081536d00377c51bdd249d06d96d25c8fe68c82811428487c | MATLAB | 1,669 | 39 | function [calibratedPoints,rotMat] = rotateAndScaleCoords(template, refPointsStereotaxic, refPointsSample)
% Calculate rotation and displacement of sample with respect to stereotaxic coords and apply to data
%
% function [calibratedPoints,rotMat] = zapit.utils.rotateAndScaleCoords(template, refPointsStereot... |
05ef5a5ca655bcbcff7d36d68474de1a80a7d2154d9b64124a6b7ca4e82102bc | MATLAB | 1,670 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
393511005cc08ebba04a3779dd5f0aca8fa106fba9cc7ce775fc2534e97fb939 | MATLAB | 1,670 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
3af442e285f284143140736969d34daaa0f187183aebbe2169db684b173c809e | MATLAB | 1,670 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
49a8db15090df949c83037a2d9fee6cefa91c547a3cb921bc33d5d1aa4247863 | MATLAB | 1,670 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
7231198474c8af7203d12c6687bf8bd204603197d01b32d5ffdcef68a45e640c | MATLAB | 1,670 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
7f76c9d079a27f04e4bcddead013878673fc1045ee549e22bfa4dbdfa176fa0e | MATLAB | 1,670 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
d757a529e20db06c5fe29dafcb4b96e4a98ca48c5bb8b1917d0249cc25fad3a5 | MATLAB | 1,670 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
f9eb1a2071ed6e69ac0b872881876a25301f78e21443f15605a260c17da88798 | MATLAB | 1,670 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
bcb2653f5ccace2b6bd345f29a595127ec48686be711d4d361229faca44da239 | MATLAB | 1,671 | 53 | function [data, bgLevel] = subtract_bg(data, bgPct)
%subtract_bg - Helper function to subtract the image background
%
% This function is not intended to be called directly.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modif... |
4bbc7b65f60eac286231713d7c3527fc2d00d941a5816d8620063c6b996229af | MATLAB | 1,672 | 62 | function getIPaddress
% Get the IP address of the local machine
%
% function zapit.interfaces.getIPaddress
%
% Purpose
% Return IP address(es) to help user connect to TCP/IP server from a different PC on
% the same network. It is common for PCs to have multiple IP addresses. e.g. A Windows
... |
568e6518c0456b4ee4f49f7c07df643b195b4a7094323489367d8ee7964bb02e | MATLAB | 1,673 | 58 |
clear
close all force
imSize = [733, 977];
hWB = waitbar(0,'checking the trials ...');
%load tirals info
load('a0_0_bhv2trialStrct.mat');
I = arrayfun(@(x) isfield(x.analyze,mfilename), dataTrl);
if any(I)
I(I) = arrayfun(@(x) x.analyze.(mfilename), dataTrl(I));
end
NTrial = find(~I);
nTrial = numel(NTrial);
... |
b80b665d58503e02168677a2df508c03c32c779ee23f38ccec1dadb85126080e | MATLAB | 1,673 | 56 | % the pattern separation toolbox: analyse spike train ensembles
% Copyright (C) 2022 Alexander D Bird
function [estRR_obj] = estimate_RR(input,output,options)
%ESTIMATE_RR Estimates the redundancy of the input and output ensembles.
if nargin<3 || isempty(options)
options='-par';
end
n_trial_in=size(in... |
cb8c57f2d09ee550dcd7b7f71758cc0f9c187cce812c8d4afbba848e7ddfa101 | MATLAB | 1,673 | 47 | function stats = get_ROI_stats(roiMask, pixelSize)
%get_ROI_stats - Extract descriptive statistics about ROIs
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as pub... |
2c8c568f91a29f20a47b032ddbc47b8cadca9f1501028e6ea97a0cc625f87ca7 | MATLAB | 1,677 | 56 | %% check_delete_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 10
for counter = 1 : length (dLPTCs{1})
delete_tree (dLPTCs{1}{counter}, ...
find (BO_tree (dLPTCs{1}{counter}) > 5), 'none');
end
end
%% test 2
tree = sample2_tree;
delete_tree (t... |
502c1772d82e031fefc22d12eb3ee83644f5455e3ec838d9cf0f9d18f175918e | MATLAB | 1,680 | 84 | clear all
load('RvsVData')
G = [-157.5:45:157.5]';
v = reshape(RvsV(:,1),10,8)';
r = reshape(RvsV(:,2),10,8)';
nCase = zeros(8,1);
for i=1:8
nCase(i) = sum(~isnan(r(i,:)));
end
vDat = reshape(v',80,1);
rDat = reshape(r',80,1);
iOut = find(isnan(rDat));
vDat(iOut) =[];
rDat(iOut) = [];
sym = ['bo';'b+';'bs';'bx';... |
bdc4e457cf74b2ea1be4baf2d003f0559ee7c1ac8d1b709f9d5f2f6eb089d03c | MATLAB | 1,680 | 48 | % op_filter.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [MRSIStruct,lorenzianFilter]=op_filter(MRSIStruct,lineBroadening);
%
% DESCRIPTION:
% Perform lMRSIStructe broadening by multiplying the time domain signal by an
% exponential decay function.
%
% INPUTS:
% MRSIStruct = input data in matlab struct... |
291b0e81751d13f077751c8ad33bcd94fb36528641039a41bc165faf5806499d | MATLAB | 1,681 | 53 | function pparam = mv_rearrange_preprocess_dimensions(pparam, dim_order, max_dim)
% mv_classify and mv_regress rearrange the data dimensions such that the
% dimensions are in the order [samples, search dimensions, features].
% The preprocess parameters have some fields referring to dimensions; these
% need to be adapted... |
0aec0cfc940b80b1d25ca1e388c27656d6fa0269806f5ae0726ca6b446420d69 | MATLAB | 1,682 | 49 | function Y = MovingPercentile(X, pct, win, alignment)
% X = matrix to calculate moving percentile on (along first dimension)
% pct = percentile to calculate
% window = width of window to calculate percentile of
% alignment = 'pre', 'post' or 'center' position of window relative to index
tic
if mod(win,2) == 0
... |
dcd21d69ccb05b6b6d8b63d744ea1518d62377a62d78413af7586dee539c3811 | MATLAB | 1,682 | 46 | function [hRaw, strRawImgType] = create_constructor_rawImg(varargin)
%create_constructor_rawImg - Class method to create a concrete RawImg
% subclass constructor.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it u... |
bb87a10ede4103dee13f92e45288f78693f3a6646311ce8cd4e8f974213bb8e1 | MATLAB | 1,683 | 46 | function subclassOut = choose_subclass(classParent, strType, varargin)
%choose_subclass - Helper function for choosing a subclass
%
% This function is not intended to be called directly.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute i... |
95368875965343fcee0a72dcfd159a7a950be41ab3312373f980f1013a45e68e | MATLAB | 1,684 | 46 | cd 'C:/Work/MatlabCode/projects/BrainMetabolismModeling/BrainMetabolismModeling'
load('data/MinModel.mat')
%Data for Fig. 4E, S2
simulateCombSimpleModel(minModel, 'data/simpleModelOutputRedMitMob.mat', 0.15, 0.1, 0.1, 0.1, 0.1, 0.5, 0.4, 0.2);
simulateCombSimpleModel(minModel, 'data/simpleModelOutputTransport.mat', 0.... |
9ae040ad48a2dfd6fb08731f93eda0e39c3be14c0cdc758172de764f9b697b0c | MATLAB | 1,684 | 42 | function bMask = LK_MaskBehavioralSampling(cfg)
%
% LK_MaskBehavioralSampling creates a mask based on the number of discrete
% observations per factor level. Each factor is checked separately and
% independently from the other factors.
%
% Input is a structure with fields
% data --> time x n matrix (for n fact... |
9218d96a229d22c0182d7531cf45cfafa82a9d19b722a7143eb0ac5974a76d51 | MATLAB | 1,685 | 66 | clear
clc
close all
filename = [pwd,'\temporary data\test_block','.cnt'];
cnt1 = loadcnt(filename,'dataformat','int32');
for epoch = 1:length(cnt1.event)
type(epoch) = cnt1.event(epoch).stimtype;
typeoffset(epoch) = cnt1.event(epoch).offset;
end
trigger=cnt1.event.stimtype;
stimTime = 5;
epochTime =... |
47ebf96e4d7d83b52188f3eef9eaf33fc753412872e7294f93687cfe16206648 | MATLAB | 1,686 | 48 | function [pixelMask, groupMask, significantMask] = ROIsToMask(self)
%ROIsToMask - Create mask from ROI pixel data
%
% [pixelMask, groupMask, significantMask] = ROIsToMask(OBJ) requires a
% CalcFindROIsFLIKA object and returns three subsequent stages of ROI
% masks produced by the FLIKA algorithm.
%
% See also C... |
35c81a028c10db39d189834a03f69fd01f1840f4c62f915268927a2038360683 | MATLAB | 1,687 | 41 | function vec_gNa = range_conductanceNa(nainfo,tree,options)
% nainfo: gbar, slope
if nargin < 1 || isempty(nainfo)
warning ('You need to define the information for the Na conductance disribution')
end
if numel(nainfo.region) == 1
isregion = find(strcmp(tree.rnames,nainfo.region));
isregion = tree.R == isr... |
887026221c8938c7e8fadbb9fd31d7cd757686368195b9249a80280df185970a | MATLAB | 1,687 | 50 | function cleanUp
% Example - run a sub-function automatically when the caller function ends
%
% function cleanUp
%
% Purpose
% Demo of how to run a sub-function when the main function ends.
% The use of try/catch statements means that the "cleanUp" function
% will run even if the calle... |
01687d2d4b17d4a6294c137a96347513ea61a5c6f282e67a82ad1a857dc38b7d | MATLAB | 1,688 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
05755e48dbf241237a43ee6ee53b6546ebb78387db0eda480334de52f97011ea | MATLAB | 1,688 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
29633ea5b73c2081783050f7a7a722db8b6ff14b8ed3ec2b03c37bbabb452dc3 | MATLAB | 1,688 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
533b19e250345a020c7325feea62b3ccc6ac1e456ac524b700f2c40dd5721e3a | MATLAB | 1,688 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
542561cd661b80a27efba000746f223a31f56cc0deb6b176b5b64a794b2f1212 | MATLAB | 1,688 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
5e0a013ffb87722f71e26f5ff9d6cbd2f68aa505216c663660c973bc46e5f05a | MATLAB | 1,688 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
88ba08e7aebda9773f852e4f3a1fdc3299fac97c1169d8b0438cb1ca39c57a45 | MATLAB | 1,688 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
befc137ca92859e8d1752440230d02e48688a41ad1a9ad13cd2764530c4aced6 | MATLAB | 1,688 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
5cc1a553291c5bfc3a5a09a56919a4744b81ef80d6d70b0669db7398272d223d | MATLAB | 1,689 | 50 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
8a07116d1361f7670e47300b88dee9c6c296bca4c9c7a0f442a0d0940f11c7cf | MATLAB | 1,689 | 48 | function params = getExtraParams(params)
params.recomputePredictionsFlag = true;
params.analysis.zeroPadPredNeuralFlag = true;
params.analysis.reluFlag = true;
params.analysis.spatial.sparsifyFlag = 0;
params.saveDataFlag=0;
params.verbose = 0;
% normalization falg
params.analysis.normNeuralChan = 0;
params.analysis.... |
4ba839b958dd9f24107245076cdd41de710fbcf845a367037ad28f50b222d569 | MATLAB | 1,693 | 54 | function refreshImage(obj)
% Add an image to empty axes or re-plot an image with new XData and YData
%
% zapit.gui.main.controller.refreshImage
%
% Purpose
% Insert and empty image into axes. Calling this method with no image in hImAx or an
% image with empty CData will cause a new image to ... |
74f74b5a240ed6bfbe7cd693a92375cb4bb5a78cbc8e8c413be9b8fd5fd99162 | MATLAB | 1,693 | 63 | %% check_plot_tree
tree = sample_tree;
%% test 1
clf; hold on; shine;
axis off
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 10
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
plot_tree (tree, rand (1, 3), [], [], [], '-p');
... |
3fed6e09a405a532181e702910844a78eb616714d4b9267ec8af479c3499f75c | MATLAB | 1,694 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
4bbc7fcc7ca625075a1491114c45c6fb0500b0594c0430837499b950c204d554 | MATLAB | 1,694 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
7f71ddae30e3f3745a0884fb73e7033d0344ef6f1897a34517ce1b269f7b8386 | MATLAB | 1,694 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
ac9858ff51fdf2bfbde98b92f7ccd57b71f5f3cb34c1322972ff4cec5cc6cfbb | MATLAB | 1,694 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
5505b5791c969b8d30c3230a177d676aac8b6ec4a4a4ee117c4ab0d13b1a9d0c | MATLAB | 1,695 | 45 | function [Corrs,Pvals] = abcd_edgewise_correlation_iterative_reliability_single_factor(rmats,factor,binsize,iter)
%UNTITLED Summary of this function goes here
% Input: rmats = 2D matrix (subject x edge)
% factor = behavioral item to correlate with RSFC
% Should be n x 1, where n = subje... |
40d8a26f7f6819fca612d86881d784fa3acb998c3d71b1ddb5df3a2ace8179df | MATLAB | 1,696 | 61 | function [All, outVars] = getTuningCurve(All, opts, outVars)
% general settings
visAlpha = opts.visAlpha;
numExps = numel(All);
for ind=1:numExps
uVisID = unique(All(ind).out.vis.visID);
uVisID(uVisID==0)=[];
oriCurve=[];
oriCurveSEM = [];
oriTrialCount =[];
for i=1:numel(uVisID)
... |
683aa410d10adfb6f2e148ce90b67821bab6424b46f1511f7d4048948d580701 | MATLAB | 1,697 | 44 | function cpObj = copyElement(obj)
%copyElement - Customised copyElement class method to ensure that the
% rawImg property and the children (which are both handle objects) are
% recursively copied.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you ca... |
7646b3ca2ab23b2ff25e8885dff2f21b46bdd42d17d26d6532f7f6825ba89122 | MATLAB | 1,697 | 43 | function checkScannerCalibClocked(obj)
% Run through the scanner calib locations using a clocked AO task.
%
% zapit.pointer.checkScannerCalibClocked()
%
% Purpose
% Run the beam rapidly over all of the coordinates in the scanner calibration
% grid. This method starts the scanners but does no... |
31290559b5deb1f1873e001b9596c5aff083096f45603a693e58ac22645cca03 | MATLAB | 1,699 | 37 | function channelToUse = choose_channel(self)
%CHOOSE_CHANNEL - Compares image channels to a set of processable channels
%and in case there is more than one appropriate channel, asks the user
%which channel to use. Can deal with a single RawImg object or an array of
%RawImg objects.
% Copyright (C) 2017 Matthew J.P.... |
321aafae9dcb6375cdc945c1c2b3f24e496c1d538de4fe06a117dd6390b8f07b | MATLAB | 1,700 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
3d7ee90bef42b27d26e7e4c4c818cc3660130432d4886e4c33ded1c437eff805 | MATLAB | 1,700 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
48bfce00ce155dd6d68b1ece7367ca28c62bf5c847dc77898a898d78acb8e882 | MATLAB | 1,700 | 61 | %% check_rot_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 50
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
rot_tree (tree, [], '-m3d');
end
end
%% test 2
rot_tree (sample_tree, [], '-s -m3dX');
tprint ('./panels/ro... |
48dd7226ae93b05d70b38d576066a0c78c454ce830004fe17b657697710bbf3d | MATLAB | 1,700 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
4ec03ca59a0496817eaf48277f7a48c06e32f5045c8a03e000496118cd98f28f | MATLAB | 1,700 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
5d211ddb11ebd73b10d4863e863f89bda94737f2c28f44d67d16f22b14b1a0cd | MATLAB | 1,700 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
ad7338ec24485c4f75f54008171abb28e41c8218592f9b3d4bb6b3f3492721b3 | MATLAB | 1,700 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
c54e032759242511390c677b2ec8511ba80d623cdfec9a28bdbc4113c3151013 | MATLAB | 1,700 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
d04013de2eade0ce515dc236bf07ae1b3afc2aa6593b612d7fa65f0e1231001c | MATLAB | 1,700 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
ac74bca61f862803f220e8bff0d6a408945411496f0e4ee6d81118a4f6ca1db5 | MATLAB | 1,701 | 42 | function params = st_cleanParams(params)
%-----------------------------------
%--- For speed we do our computations in single precision.
%--- But we output in double (for compatibility).
%-----------------------------------
params.analysis.x0 = single(params.analysis.x0);
params.analysis.y0 ... |
0275a6d161c1d8eb6fa38b82a3e86b1802174bd051b0cd24a9a28a5ae2ad826a | MATLAB | 1,703 | 79 | % op_lorentzianPeak.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_lorentzianPeak(n,sw,Bo,lw,ppm0,amp);
%
% DESCRIPTION:
% Generate a noiseless spectrum containing a single lorentzian peak with
% desired parameters (frequency, amplitude, linewidth, etc.).
%
% INPUTS:
% n = Number of points in spect... |
2dc187f35faf9a9c9604392c2353281b752cfa6862c986bebd1124d248fc20ea | MATLAB | 1,703 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
8d1d38622ef5812e337dc1b4278d84b310bfaac590b1df9a726f177d69052e3f | MATLAB | 1,703 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
e49cadeed0b0608d9d7be2c7110b9f299297e234e9202fc17dfc015290c20c70 | MATLAB | 1,703 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% -------------... |
1ce7487baa30d68d01c5c7b9a493ef57f5e17c752664162ffe0a5a03aa11c7aa | MATLAB | 1,706 | 80 | % op_gaussianPeak.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_gaussianPeak(n,sw,Bo,lw,ppm0,amp);
%
% DESCRIPTION:
% Generate a noiseless spectrum containing a single gaussian peak with
% desired parameters (frequency, amplitude, linewidth, etc.).
%
% INPUTS:
% n = Number of points in spectrum.
%... |
17297eb7267b670034b64ce533d2e42e44bbd75617a1368bdc638071f200ceb4 | MATLAB | 1,708 | 53 | tfce = tfceMex_maxtree(t, E, H, calc_neg, faces)
% Apply threshold-free cluster enhancement (TFCE), computed exactly
% FORMAT tfce = tfceMex_maxtree(t, E, H, calc_neg, faces)
% t - T map (3D volume, or Nx1 vector for surface data)
% E - TFCE parameter for extent
% H - TFCE parameter for height
%... |
057c16bd43b854a97d3f33516bb946602a88aace20db045de27a8176a9291bdc | MATLAB | 1,714 | 46 | %rf_single2dualBand.m
%Peter Truong, Sunnybrook Research Institute 2021.
%
% USAGE:
% [rf,AMPINT]=rf_single2dualBand(rf_struct,tp,df);
%
% DESCRIPTION:
% Creates a dualband RF pulse from user a single band RF pulse with a duration
% of tp(ms). If the original rf pulse set at frequency = f_orig, the
% second band wil... |
d0286cb16f7ef1c51714c8ea9c5a74e06b2393c5ebeb5df0fb929ae05c2ae3cb | MATLAB | 1,714 | 51 | function qc = motionQc(result, motionFile, motionModel)
%MOTIONQC Compare phase regressors and selected SVD component with motion.
arguments
result struct
motionFile {mustBeTextScalar}
motionModel (1,1) string = "motion+derivatives"
end
motion = readmatrix(motionFile);
if size(motion, 1) ~= size(result.re... |
339aad1e31b694e0cf68fcc129a2c6c3ab15ffda2c8dc0b9f387553b699e602c | MATLAB | 1,717 | 45 | load(fullfile(dataFolder,'EEG_data','data_sample_time_series.mat'),'time','eeg','ptID');
load(fullfile(dataFolder,'EEG_data','data_time_information.mat'));
t0 = timeInfo.infusion_onset-timeInfo.object_drop;
red = clrsPT.qualitative_CM.red;
CM = clrsPT.iridescent(1e3);
black = CM(end,:);
marsh_model_analysis;
fig =... |
7f3cbb500162f0d762f13f187cb523cbd1af4cba7b3a59ea6736da1405c03d56 | MATLAB | 1,717 | 71 | % CPLOTTER Plots a contour.
% (scheme package)
%
% HP = cplotter (c, color, DD)
% ----------------------------
%
% Plots a 2D contour obtained from contourc (see "contourc"). A contour is
% defined by:
% c = [contour1 x1 x2 x3 ... contour2 x1 x2 x3 ...;
% #number_of_pairs y1 y2 y3 ... #number_of_... |
a153c63f4d97a40efa8a7964c8bfcd4ee079fdc339fac8e38b2d25eb5cae0a2c | MATLAB | 1,719 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% ------------... |
c17500426f93232b11e6bc5b5904c20c68a686358e34fc39d7630626e8f774a7 | MATLAB | 1,719 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% ------------... |
c5f18af0335d84575af426393b3d022ee674574b7c8384678bc025b8bccf9c0d | MATLAB | 1,719 | 51 | % Parameter configuration for TS extraction for resting state fmri
% Parameter configuration for TS extraction for resting state fmri
% _________________________________________________________________________
% Stanford Cognitive and Systems Neuroscience Laboratory
%
% $Id rest_ts_extraction_config.m $
% ------------... |
7f9764cfc8833bef1f5bf3abbaa5e031162e27261cd5457d6b5e044f14ea5d20 | MATLAB | 1,720 | 52 | function soundAsync(y,fs,bits)
% soundAsync Play vector as sound, asynchronously.
% soundAsync(Y,FS) sends the signal in vector Y (with sample frequency
% FS) out to the speaker on platforms that support sound. Values in
% Y are assumed to be in the range -1.0 <= y <= 1.0. Values outside
% that range are clippe... |
aa18929095603a4475f88cd1458703a17c7fdcda540aa80885f9fe8cdfe44da2 | MATLAB | 1,721 | 60 | clear;
clc;
close all
%% Figure9
subs=30;
frequency=60;
condition=2;
category=3;
load([pwd,'\temporary data\Sub_score.mat']);
size(Sub_score);
%30 subject *2 condition *60 frequency *3 comfort/flicker/preference
aver_subs=squeeze(mean(Sub_score,1));%2*60*3
for fre=1:frequency
for criterion=1:catego... |
e1a7a349360456e66070e1c18a04feeff060a4385ab2e1acf9d548a5cba47c43 | MATLAB | 1,721 | 67 | % op_addphase.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_addphase(in,ph0,ph1,ppm0,suppressPlot);
%
% DESCRIPTION:
% add zero and first order phase to a spectrum.
%
% INPUTS:
% in = input spectrum in matlab structure format
% ph0 = zero order phase to add (degrees)
% ph1 ... |
bc5ef9cf25f0c271df13ce0f82f1972a2e0182d54d71cc1319290cb1fbdcf665 | MATLAB | 1,723 | 37 | classdef test_respiration < matlab.unittest.TestCase
methods (Test)
function extractsDominantChangingComponent(testCase)
t = linspace(0, 2 * pi, 12);
image = zeros(3, 3, 2, numel(t));
image(1, 1, 1, :) = sin(t);
image(2, 2, 1, :) = 0.1 * cos(t);
r... |
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