sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
087f96797a8ada466a680082be529604fbb9d7ae3093bd17d143f097eccea68c | MATLAB | 3,827 | 114 | function [hdr] = ft_fetch_header(data)
% FT_FETCH_HEADER mimics the behavior of FT_READ_HEADER, but for a FieldTrip
% raw data structure instead of a file on disk.
%
% Use as
% hdr = ft_fetch_header(data)
%
% See also FT_READ_HEADER, FT_FETCH_DATA, FT_FETCH_EVENT
% Copyright (C) 2008, Esther Meeuwissen
%
% This fil... |
751bf8d70ebe312a9dfd129a834ecf9364b593aaac49232038b67d24c9207ea1 | MATLAB | 3,828 | 119 | close all
clear all
clc
%% compute choose connecting node for wrong answer
%% show that this number is significantly larger than 0.5
exp_root = 'C:\Users\User\Documents\fMRI_EXP\';
root = 'C:\Users\User\Documents\fMRI_EXP\Alon\';
behvioural_analysis_codes = 'C:\Users\User\Documents\psychExpLaptopOld';
addpath(genpat... |
e75797ecc6a7e10b086b46ac2d76a7e86973d8192d96a7305084858715fc4ea9 | MATLAB | 3,828 | 137 | function [pairs,p_pairs,pairs_ref,meanvals_dat,meanvals] = ...
PAIRS(fet_proc,kval,nset,saveops)
%calculates projection angle of response similarity statistic
%
%INPUTS:
% fet_proc: (nn x dim) features space for nn neurons, dim features.
% should processed features with pca to have zero mean and diag co... |
0bb106782c63a2beec45d44946d8fabf127260b5b73e32eb25a8e1cdba7ee8ab | MATLAB | 3,829 | 112 | function [RDM_fdtFolded_ltv, cv2RDM_fdt_sq] = fisherDiscrTRDM(Xa, Ya, Xb, Yb, condPredIs, RDMmask)
% USAGE
% [RDM_fdtFolded, sdRDM_fdt] = fisherDiscrTRDM(Xa, Ya, Xb, Yb[, condPredIs, RDMmask)
%
%
% computes a lower-triangular vector of Linear Discriminat t-statistics
% (RDM_fdtFolded_ltv) and a folded symmetric ... |
bdce0ecf452dd3cbdb684ca759f61326e6524d1b36b3eae549da09013f35af91 | MATLAB | 3,829 | 128 |
%% bin10
mypath = '/Users/bo/Documents/data_liujia_lab/manuscript_gridcell3hz/analysis_liuP1_greeble';
fold1 = 3;
fold2 = 12;
num_bin = 9;
timeFile = fopen([mypath, '/MRI_result_sinusoid/txt_barchart_',num2str(fold1),'_fold_effect_2025.txt'],'rt');
table_time = textscan(timeFile,'%s %s %s');
fclose(timeFile);
data... |
6da16a9dee1945826b40275d9c05e5e478d64b39f3d989b5d879da9000339fa9 | MATLAB | 3,830 | 132 | % op_alignISIS.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [out,fs,phs]=op_alignISIS(in,tmax,initPars);
%
% DESCRIPTION:
% Apply spectral registration to align ISIS subspectra prior to
% subtraction. This is intended to be used prior to averaging, so that the
% alignment can be performed independently for ... |
b8cbc535af7f04562bb7d00b2f243853de20c4e499eda74334f064a47b926cb5 | MATLAB | 3,830 | 96 | % STD_FINDSAMEICA - find groups of datasets with identical ICA decomposiotions
% (search identical weight*sphere matrices)
%
% Usage:
% >> clusters = std_findsameica(ALLEEG);
% >> clusters = std_findsameica(ALLEEG,icathreshold);
% Inputs:
% ALLEEG - a vector of loaded EEG ... |
bf46e5f58e8fd5eb739144ce5c867dc0ac68dfe245f217fd90e3ec70c91e7a0e | MATLAB | 3,830 | 103 | function [fitted_data] =improved_LFP_fit(name_of_data_file,epoch_length,fitting_range,frequency_resolution)
%Find power spectra for each epoch and run 1/f fit for average spectra per animal
% Output it a data structure with all spectra and fit information
% Input is name of data file to analyze, length of epochs... |
70aea0f891590aa1b3d65b4500a329f3fa7fa1bd33e387224064089473d61703 | MATLAB | 3,831 | 114 | function [pulseCleanedTemplate, cpulse2ndGuess, averageHeartRateInSamples, verbose] = ...
tapas_physio_get_cardiac_pulse_template(t, c, verbose, ...
varargin)
% determines cardiac template by a 2-pass peak detection and averaging of
% closest matches to mean and refinements
%
% [pulseCleanedTemplate, cpulse2ndG... |
99ac07687c75e6bb918b857ba20f96eb17ebb8b7b2af0c9eb5d1e1b93f50b144 | MATLAB | 3,831 | 88 | function [sequence,shuffled] = ReplayScore(matrix,varargin)
% ReplayScore
% This is a structure wrapper which calls "FindReplayScore"
%
% USAGE
%
% [r,p,a,b,rShuffled,c,cShuffled,jump,jumpShuffled,maxJump, maxJumpShuffled] = ReplayScore(matrix,threshold,<options>);
%
% INPUT
%
% matrix probability matrix fo... |
49b1c38eebaf7e470b369181ef2d925312be9d21bce74dbd0937d3bb3fe523e5 | MATLAB | 3,832 | 110 | function [coordidx,D,scoords,vORr]= surfing_circleROI(coords,faces,centervertex_idx,radius,distancemetric,n2f)
% Creates a circular region of interest (ROI) on the surface given a radius
%
% [coordidx,D,scoords]=surfing_circleROI(coords,faces,centervertex_idx,radius,distmetric,n2f)
% INPUTS:
% coords: 3xN coordi... |
2c380a357afceba6f0be954d25f4f75356c2fdde979ad237469f3757d9e01ea3 | MATLAB | 3,833 | 82 | function this = plot3d(this, varargin)
% Plots 3 orthogonal sections (with CrossHair) of 3D image interactively
%
% Y = MrImage()
% Y.plot3d(inputs)
%
% This is a method of class MrImage.
% This method interfaces with the general 3d plot utility of tapas_uniqc_view3d,
% offering similar capabilities in terms of dat... |
ea1ede1f7bd74134c42e6a27cdf97a321755494528f21a22a61e1beaf11f0b26 | MATLAB | 3,834 | 83 | % load anatomical data from the brainstorm_db folder, convert to MNI,
% extrapolate to high res, make leadfield, save to bs_results for each
% subject
anat_folder = [BrainstormDbDir '/anat/'];
data_folder = [BrainstormDbDir '/data/'];
AD_dir =main_path;
bs_dir = dir([anat_folder 'RSID*']);
bs_names = {bs_dir.name}'... |
2b4eb100a110f995218f4c9b51394dc255b935799158d8cd05ec8b5cf8526fcf | MATLAB | 3,835 | 109 | function figHandles = arrangeFigures(varargin)
% ARRANGEFIGURES Arrange multiple figure windows in a grid
%
% Syntax:
% arrangeFigures()
% arrangeFigures('Name', Value, ...)
% handles = arrangeFigures(...)
%
% Description:
% Automatically arranges open figure windows in a grid layout.
%
% Inputs (Nam... |
3ac6f52a457f58bbf1e663ccc8f45e0cf416969ea81b6876bdcab103c1c74278 | MATLAB | 3,836 | 111 | function [lamda,dif_av,Data]=SolveEquations(op,rate,nt,dif,tp,T,K,SName,app,Cb,clim,NameMask)
C0=app.Cin;
f=app.DiffusionModel;
ds2=app.ds.^2;
S0 = app.S0;
dt = app.dt;
M = app.M;
BC = app. bounds;
alpha=app.Alpha.Value;
aux=app.Aux.Value;
freq=app.freq;
%uni... |
744b602765b83008a95e515928f17d06699e5bb80506e08cb0e171883bc41367 | MATLAB | 3,836 | 137 | %fits a sample GLM
%written by dlh, Oct. 2021
%runtime is about 15 mintes on a laptop, with hyperparameter search incl.
%% add paths and set up load and save directories
%redefine these for your local machine!
%where the repo lives
codedir = '/Users/dhocker/projects/constantinoplelab/published/ofc_glm/';
%where y... |
d0062cc21d751de83dcb39cd3983006562d57e7f27ea9d941977f23fa526c1e2 | MATLAB | 3,836 | 151 | clear all
close all
clc
% Replace with your file name
filename = 'Data\wt1\ROT1\2023-01-09_10_28_55_048_+0100\output.h5';
% Get physical constants
speed_of_light = physconst('LightSpeed');
f_info= h5info(filename);
% Not all measurements contain both radar channels
% Check if channel 2 is available in this file
... |
029d5c47948448cc2b500f1c1fd528fb129b6cdb773d1bbdd10f3c888be2308f | MATLAB | 3,838 | 112 | function [refShift, refFWHM] = osp_CrChoReferencing(dataToFit)
%% [refShift, refFWHM] = osp_CrChoReferencing(dataToFit)
% Calculates the reference shift and full-width half-maximum (FWHM) of a
% spectrum according to the LCModel algorithm. The algorithm is described in:
% S.W. Provencher, "Estimation of metab... |
57371da36564cfe677b93bbf031219ef865307d82f923724515f3e8b2b752e5a | MATLAB | 3,839 | 116 | function Tmed = runMediation_simple_numeric_ageTOI_EIGC(EIG, T, sigAgeMask, outName)
% EIG: [Nobs x Ncomp x Nep x Ntime] (soggetti, componenti, epoche, tempo)
% T: table con almeno T.Age (numerico) e T.meanBIS
% sigAgeMask: logical 3D con TRUE dove Age è significativo nel tempo.
% Ammessi... |
bd5a4c5e45c7eab6f91b887aed4ebf92a6a719791a575c3d21ebcb272b34432b | MATLAB | 3,840 | 104 | function glscf = CO_GLSCF(y, alpha, beta, tau)
% CO_GLSCF The generalized linear self-correlation function of a time series.
%
% This function was introduced in Queiros and Moyano in Physica A, Vol. 383, pp.
% 10--15 (2007) in the paper "Yet on statistical properties of traded volume:
% Correlation and mutual informat... |
831ccf96bce8ee72cbf558b5d025dab1452a9779964e81cbdd51156bf7adfa17 | MATLAB | 3,847 | 104 | function initialize_display(hObject, eventdata, handles)
% Remove anything currently in the axes
cla(handles.contourWindow);
cla(handles.detectionAxes);
cla(handles.focusWindow);
cla(handles.spectogramWindow);
cla(handles.waveformWindow);
%
handles.data.currentcall = 1;
handles.data.current_call_valid = true;
handle... |
5474673e25764e17eb5cac6464fed76b64364d3f7675b32192c5fc7720c62bb7 | MATLAB | 3,848 | 131 | function plot_nodes_in_cortex_new (V)
figure
hold on
% % PLOT CORTEX
%
cortex.path='C:\Users\dk00549\OneDrive - University of Surrey\Documents\Surrey\MATLAB\PluginsProgramsToolboxes\LEiDA-master\LEiDA\TIDES\Atlas\MNI152_T1_2mm_brain_mask.nii';
cortex.pial=mapPial(cortex.path);
cortex.color=[0.9 0.9 0.9];
... |
a70e7326fa81ac771906fe0b4e2c48247060ebeef238d8412d655bfeb3e4cb3c | MATLAB | 3,848 | 143 | function a = circ_plot(alpha, format, formats, varargin)
%
% r = circ_plot(alpha, ...)
% Plotting routines for circular data.
%
% Input:
% alpha sample of angles in radians
% [format specifies style of plot
% pretty, histogram, density, []
% [formats standard matlab string for plot... |
c6af196b6ff3956d6da6d38077758b9a6feae7bdbc95050ac783a9bdf2f17e55 | MATLAB | 3,850 | 102 | function ChangeBinaryGain(filename,varargin)
%ChangeBinaryGain - Change gain in a multiplexed binary file.
%
% USAGE
%
% ChangeBinaryGain(filename,<options>)
%
% filename file to read
% <options> optional list of property-value pairs (see table below)
%
% =======================================... |
df2a76a8062a97fa5c284bea29b7419810a9add83acb8b8244b29721fce5f82c | MATLAB | 3,852 | 133 | function [hdlMeanSem,hdlDots,hdlLeg] = meanErrPlotDots(data,varargin)
% function [hdlMeanSem,hdlDots,hdlLeg] = meanErrPlotDots(data,varargin)
%
% Plots mean, all datapoints, and error in 3 possible forms: SEM, STD and
% 95% CI.
% Display variables
marker = '__os^v><dph*';
linespec = 'ob';
errorType = 'CI'; % alternat... |
efdd82a971b54c7bb3750c0e64ede3297f5661e5944117a1f5b68bbac60e1138 | MATLAB | 3,852 | 105 | function hess = getHessian(problem, x, d, storedb, key)
% Computes the Hessian of the cost function at x along d.
%
% function hess = getHessian(problem, x, d)
% function hess = getHessian(problem, x, d, storedb)
% function hess = getHessian(problem, x, d, storedb, key)
%
% Returns the Hessian at x along d of the cost ... |
97f53f96e572275a9ded7ddf2571b992bed7135d361a224a2ffcfe7c2fb4f89a | MATLAB | 3,853 | 117 | function [uniqueEntries,numberOfOccurences,whereIdx] = countEntries(m,isRow, keepNaN)
%COUNTENTRIES returns all unique entries (sorted) in the array m and how many times the respective entries occured
%
%SYNOPSIS [uniqueEntries,numberOfOccurences] = countEntries(m,isRow)
%
%INPUT m : any matrix (not cells or ... |
beb27cc373c56908973a57426e1dd6f15b10397c27fcb27e23fdef0c47ec5c57 | MATLAB | 3,853 | 147 | function slopeFit = plotChVals_linFit(params, dataStruct)
% plots values per channels with a linear fit
% returns slope of linear fits
% (c) Jiri, Sep16
%% basic check
nCh = size(dataStruct.yVals,2);
assert(size(dataStruct.yVals,1) == size(dataStruct.xVals,1));
%% load 'H'
load(params.storage.cacheFile, 'H');
%% y-... |
3c5e23d12f56636cf003e02c96cadbac463fbfc50dbbaeeabda7d8b9e9fcbd71 | MATLAB | 3,854 | 125 | function aaName = anatomicalArea_getName(atlasName, AA_list, H_ch, addLateralization, maxDist)
% based on atlasName & assignments in header H, returns name of the assigned anatomical area aaName
% works for multiple atlases (Yeo, Destrieux, neurologists labels = LabelsAK)
% assignment is NOT case sensitive (Visual = vi... |
64a95b19926d5edcd1aa03ec723add9b775d05f8ac04c1d0c426b4e8f930b13d | MATLAB | 3,854 | 105 | function [data, annotations, layer_numbers, layer_names, colours, colour_scheme] = RegionAnalysis_Unbiased(data, I, source, layer_numbers, layer_names) % by Julia Becker, 01/04/2020
%REGIONANALYSIS_UNBIASED User assigns ROIs without seeing the measurement
%points
% - annotations add up on top of each other (you ca... |
ad8f77ae4ed81726164f4c745364afe7718b5a86393d477840b8a34f6297c9d8 | MATLAB | 3,854 | 100 | function convertGallant(directory, stimuliType, dryRun)
if ~exist('dryRun', 'var')
dryRun = false;
end
if ~exist('stimuliType', 'var')
stimuliType = 'NatRev';
end
if ~exist('directory', 'var')
directory = 'V2Data';
end
fprintf('directory=%s, stimuliType=%s, dryRun=%b\n', directory, stimuliType, dryRun);
add... |
724f38bccfb3b63cba85632a65562bf2dbb044e72e5db8dacfb169be31b75177 | MATLAB | 3,856 | 129 | % notes: inherit some from examples_fullanalysis2.m
%%%%%%%%%%%%%%%%%%%%%%%%% Analyze, looping over subjects.
% define
totalnsdsessions = [40 40 32 30 40 32 40 30];
hemis = {'lh' 'rh'};
% do it
alltvals = {};
for subjix=1:8
nn = totalnsdsessions(subjix);
% load betas (b2, in PSC units)
alldata = zeros(327684,... |
a01821736fcea30608e49ead8ff638a63810f520e4da59149d0b0c185899d318 | MATLAB | 3,856 | 148 | function nmri_combine_exports(inputExports,pathOut)
%nmri_combine_exports(inputExports,pathOut)
% Function to combine multiple (>=2) export EEG/MEG export directories
% into a single one
%
% inputExports = cell array of paths to exports to combine
% pathOut = new output path to be generated
if ~exist('inputE... |
0bcf8df84bca728e1cf03687fda977d26fd7ba3b5a310eab0b9890c49d769408 | MATLAB | 3,857 | 107 | function [events,info] = FindSpikeTrains(spikes,varargin);
%FindSpikeTrains - Split long spike trains into 'active' periods.
%
% Split spike trains into 'active' events in which consecutive spikes remain
% in close temporal proximity. These events are separated by periods of
% silence, cannot exceed a certain duration... |
3ede46f95d7b6ebe3c8a44a920799d1b49888fad52d1080fc569f5b1b2043739 | MATLAB | 3,858 | 78 | function [fit, FitResults, gof, output, op] = setup_fitting(Params,res_step,sz)
%setup_fitting(Params 'struct', res_step 'double', sz 'double')
% setup variables for fitted parameters
%
% Params : Parameter struct
% res_step: idx for current step
% sz : is the final matrix size
fit = struct();
... |
c446b77086fc34ece064444633fce9eb06612940dbcd96164be0b1e71c6d4433 | MATLAB | 3,858 | 72 | %% load libraries
run('set_library_paths.m');
addpath(SPM_PATH); % per spm docs, do not genpath it
addpath(genpath(CANLABTOOLS_PATH));
pattern_mask_dir = CANLABMASKS_PATH; % store in var bc called later
addpath(genpath(pattern_mask_dir));
%% VARIABLES THAT MUST BE DEFINED BEFORE THE SCRIPT IS SOURCED
% THIS SCRIPT IS ... |
1a808f236e4274b7bf1ca39f5571ffa4011ad12be1530b3c7b735bdd6da42819 | MATLAB | 3,861 | 132 | % gridSearch - Perform a grid search to find the best mu and sigma for the pSFT model
%
% Syntax
% [best_params, best_sse] = gridSearch(init_params, fixed_params, which_search, param_bounds)
%
% Input Arguments
% init_params – initial pSFT parameters
% fixed_params – fixed parameters
% which... |
b764e587c627acd61495538ae642ed94f82693123824757e3247bd352d89f9a1 | MATLAB | 3,862 | 107 | function PlotSync(synchronized,indices,varargin)
%PlotSync - Plot successive occurrences of a multidimensional variable.
%
% Plot resynchronized samples such as spike rasters or successive evoked
% potentials.
%
% USAGE
%
% PlotSync(synchronized,indices,<options>)
%
% synchronized synchronized <a href="matlab... |
55f1d023428fc7a797e38857404ced806eaf8f1c4cc9519b384a4162cb8dd22d | MATLAB | 3,864 | 123 | function fig = ARTwarp_gui_csv_to_ctr
% This function generates a graphical user interface to enter the
% parameters for converting some .csv files to .ctr
% Initialise the freqCol and Tempres as empty arrays so their UI fields
% show as empty initially
freqCol = [];
tempres = [];
% Get folder_name from the user
fold... |
70106c2c8b5977332cec34615c247082bc6c1f80a0d15944050fffbb0da3ea8a | MATLAB | 3,865 | 111 | function [iti,iti_npv,iti_pv,startTime] = getITI(S)
% Calculates inter-trial interval and start time for each trial in a
% session. SSS 05/2020
%INPUTS:
% S = screened sessions from get_data (using poolRats to screen for
% current criteria 05/2020)
%OUTPUTS:
% iti = cell for each session containing the ITI ... |
a62b00e0ffd3bdef1fb3617035998d79c811b450b79b5b8722a6e9ed504434c0 | MATLAB | 3,866 | 107 | function run_match_indegree_simulation(params, options)
% RUN_MATCH_INDEGREE_SIMULATION - Run with in-degree matched connectivity
%
% H1 Line: Execute simulation with heterogeneous in-degrees
%
% Syntax:
% run_match_indegree_simulation(params, options)
%
% Description:
% Runs simulation where neurons have variable ... |
3f22c21387d7086a1f02728981d327d5d187d4707e8ab93c9efefac2af98f024 | MATLAB | 3,867 | 105 | function [data, annotations, layer_numbers, layer_names, colours, colour_scheme] = RegionAnalysis_Unbiased(data, I, source, layer_numbers, layer_names) % by Julia Becker, 01/04/2020
%REGIONANALYSIS_UNBIASED User assigns ROIs without seeing the measurement
%points
% - annotations add up on top of each other (you ca... |
3af34b03add41554cc5d531d3109924c87f8fc13d1bd7b02db410c2886fff135 | MATLAB | 3,870 | 108 | %op_iterativeWaterFilter.m
%Georg Oeltzschner, Johns Hopkins University 2020.
%
% USAGE:
% out=op_iterativeWaterFilter(out,wlim,Kinit,M,plot_bool);
%
% DESCRIPTION:
% This function is a wrapper to attempt error-free water removal using
% multiple instances of the op_removeWater function. This is necessary
% because at... |
3f5eb5447736a6d56254ef59ee6cdc5d30a47b7950e85dccb689445e27e0d575 | MATLAB | 3,870 | 132 | function [ choice ] = nf_uidialog( cfg )
%make our own dialog functions, maybe this can avoid MAtlab freezing the
%RDP interface on NMRI
% this one based on a figure NOT the dialog interface
if ~exist('cfg','var')
cfg=[];
end
if ~isfield(cfg,'title')
cfg.title='Dialog Box';
end
if ~isfiel... |
a950cc9a402ecaec39a185b37bb9ff3d00b2c99ce2d8a13127d4073b9924084b | MATLAB | 3,871 | 117 | function [m,aprime,corr,far,misclass, mprop, statstable] = confusion_matrix(true,cla)
% [m,aprime,corr,far,missclass, mprop, statstable] = confusion_matrix(true,cla)
%
% calculates a confusion matrix (m, mprop) and a-prime scores (AUC
% effect size) from true class assignments (true) and estimated class assignments (cl... |
5ec3e759cb43f4e49684f0412369b3062620f969602aadebdc9f73efac6e5171 | MATLAB | 3,872 | 98 | function [net, info] = cnn_stn_cluttered_mnist(varargin)
%CNN_STN_CLUTTERED_MNIST Demonstrates training a spatial transformer
% The spatial transformer network (STN) is trained on the
% cluttered MNIST dataset.
run(fullfile(fileparts(mfilename('fullpath')),...
'..', '..', 'matlab', 'vl_setupnn.m')) ;
opts.data... |
ebd5024ee746bf4ef478fc585035a8fddddd6b55165163b82e2cf51bf76d3321 | MATLAB | 3,872 | 94 | function [results] = analysis03A(config)
% Runs analysis 03A: Are human connectomes more emergent and/or better
% performing than randomly connected reservoirs? Load results from
% analysis01A and let the best individual from "sister" populations compete
% (evaluate on a set of train/test data). Sister populations were... |
10ad5a5fa2a7a3dda161e77ae80c7ad682e2574a646184ac155ac70e5537d334 | MATLAB | 3,876 | 145 | function [avr] = read_besa_avr(filename)
% READ_BESA_AVR reads average EEG data in BESA format
%
% Use as
% [avr] = read_besa_avr(filename)
%
% This will return a structure with the header information in
% avr.npnt
% avr.tsb
% avr.di
% avr.sb
% avr.sc
% avr.Nchan (optional)
% avr.label (optional)
%... |
71fb311a01dff8e3bd8f44865e29ef43d92c28031c08ec9c00252a6cee8d551e | MATLAB | 3,876 | 98 | function [ord,R,keepers] = BF_ClusterReorder(dataMatrix,distanceMetric,linkageMethod)
% BF_ClusterReorder A clustered reordering of the rows of an input data matrix.
%
% Computes a reordering of the rows of an input data matrix (under a given
% distance metric), placing similar rows close together in the output
% p... |
80639e2833adc0e59e9c1ef30e1f8f94ca8f5230ef68b39d3e42e06afa335043 | MATLAB | 3,878 | 124 | function h = plotbarcounts(countmat,numplots,testregion,varargin)
% function h = plotbarcounts(countmat,numplots,testregion,varargin)
% case 'critical', critical = varargin{i+1};,index = index+2;
% case 'title', mytitle = varargin{i+1};,i = i+2;
% case 'legend', mylegend = varargin{i+1};,i = i+2;
% case 'ylabel', myyla... |
4458962303a2dbe6c9f1419e7e9281cfc48e24795f2d7aa798bfc5427deeb214 | MATLAB | 3,880 | 93 | function [struct,filename] = getStruct(basepath,extension,fieldName)
%getStruct - Load custom data extensions associated with a given session.
% This is a helper function similar to CellExplorer's loadStruct.
% If multiple .mat files match your query, the function will return
% the first one (in alphabetical order).
... |
f6cb9ff5e8178fa17835cb409128f79b4c6ed576c3170f5d0fd832aa28c415bd | MATLAB | 3,880 | 99 | % CORRECTFIT - correct fit using observed p-values. Use this function
% if for some reason, the distribution of p values is
% not uniform between 0 and 1
%
% Usage:
% >> [p phat pci zerofreq] = correctfit(pval, 'key', 'val');
%
% Inputs:
% pval - input p value
%
% Optional inputs:
... |
b2eae57e80d3a2001990095e13105edf324795d50df26b348e3d7c7bae3bd059 | MATLAB | 3,884 | 120 | function cost = getCost(problem, x, storedb, key)
% Computes the cost function at x.
%
% function cost = getCost(problem, x)
% function cost = getCost(problem, x, storedb)
% function cost = getCost(problem, x, storedb, key)
%
% Returns the value at x of the cost function described in the problem
% structure.
%
% stored... |
ea886fe151de38e926ba27276b237f6a9600202deb2f1b9b2af4acd315c0104a | MATLAB | 3,884 | 108 | % setting parameters
dt = 0.01;
T_total = 1000;
t = 0:dt:T_total;
% Intrinsic angular velocities
omega_A = 2 * pi / 22.7; % A: AVP % change here (22.7 -> 23.7) for Sup. Fig. 11d
omega_B = 2 * pi / 24.3; % B: non-AVP (nA)
% Parameter search ranges
K_BtoA_values = linspace(0, 0.2, 41); % = K_nA_... |
f7141527cafb66215e63e2ce9b158abc300980944b0deb52861dea81cdbeeb5e | MATLAB | 3,885 | 109 | function F = spm_Tcdf(x,v)
% Cumulative Distribution Function (CDF) of Students t distribution
% FORMAT p = spm_Tcdf(x,v)
%
% x - T-variate (Student's t has range (-Inf,Inf)
% v - degrees of freedom (v>0, non-integer d.f. accepted)
% F - CDF of Student's t-distribution with v degrees of freedom at points x
%___________... |
278e14b3476d07da5759d7452f6dd24ed2fadfcd42bd2ac8acf479b9142333e0 | MATLAB | 3,887 | 66 | function [gui, MRSCont] = osp_processingWindow(gui,MRSCont)
%% osp_processingWindow
%This functions finds the handle to update the window in progress
%
%
% USAGE:
% osp_processingWindow(gui);
%
% INPUT:
% gui = gui class containing all handles and the MRSCont
% MRSCont = MRS co... |
67c93c242bcf66fb8a5a041db030511099103ee4c4537f30f4aa79677e8319d8 | MATLAB | 3,887 | 112 | function fitParams = readLCMFitParams(MRSCont, which, kk)
% Fall back to defaults if not provided
if nargin < 3
which = 'A';
if nargin < 2
kk = 1;
if nargin < 1
error('ERROR: no input Osprey container specified. Aborting!!');
end
end
end
% Determine output file strings... |
74c31521ef3db7215c97bea7ded8304bc2e85d80fefe29a209b117db66197a5f | MATLAB | 3,887 | 100 | function h=plplot(x, xmin, alpha)
% PLPLOT visualizes a power-law distributional model with empirical data.
% Source: http://www.santafe.edu/~aaronc/powerlaws/
%
% PLPLOT(x, xmin, alpha) plots (on log axes) the data contained in x
% and a power-law distribution of the form p(x) ~ x^-alpha for
% x >= xmin... |
dea2d7215ef26b753b0bfff0a6ded5d9e7a47ab9b4e6bc94db087e5cdef41542 | MATLAB | 3,887 | 103 | function [ nfe ] = vb_nfe( obj )
% Evaluate negative free energy for HUGE model given current parameter
% estimates.
%
% This is a protected method of the tapas_Huge class. It cannot be called
% from outside the class.
%
% Author: Yu Yao (yao@biomed.ee.ethz.ch)
% Copyright (C) 2019 Translational Neuromodeling Unit
%... |
c32655d0a2f8b2e8a14346aefd46ea262101c0c6c976a94f5d0e0b0ad9064f29 | MATLAB | 3,888 | 162 | function sol = prox_tv(b, gamma, param)
% Start the time counter
if ~isfield(param, 'tol'), param.tol = 10e-4; end
if ~isfield(param, 'verbose'), param.verbose = 0; end
if ~isfield(param, 'maxit'), param.maxit = 50; end
if ~isfield(param, 'weights'), param.weights = [1, 1]; end
[r, s] = gradient_op(b*0);
pold = r; qol... |
489af15f78378fa43c0bd2fafa15a67d3b2d2bc1f33bec9bc9436416fcb8bc8d | MATLAB | 3,889 | 135 | function tapas_uniqc_new_script(varargin)
% Creates a new script (e.g. tests/examples) including header.
% tapas_uniqc_new_script(funname) opens the editor and pastes the content
% of a user-defined template into the file funname.m.
% Note that the prefix tapas_uniqc_ is automatically added to the filename.
%
% Exa... |
9801d18faf7e041b7eeb333ca4f3115a9ae1772baeee8f4533debab78429e391 | MATLAB | 3,889 | 85 | classdef McsCmosFilterSource < handle
% Holds the contents of a CMOS-MEA filter source
%
% The filters in the filter pipeline are stored in the Pipeline field
%
% (c) 2017 by Multi Channel Systems MCS GmbH
properties (SetAccess = private)
Pipeline = {}; % (cell array) The filters in the pipeline
... |
c7d391e4c726f60ee97c24bf22f2211905efaee2cfcedf4a5cfd9d51f8d8cec7 | MATLAB | 3,889 | 104 | clear; close;
%specify ages to include in analysis
ages = {'05', '08', '12', '18', '24'};
%specify other info about data
tasks = {'hand', 'social'};
cohorts = {'gm', 'uk'};
% create empty table
columnNames = {'ID', 'Cohort', 'Task', 'Age', 'Channels', 'ROI_SNR'};
variableTypes = {'string', 'string', 'string', 'doubl... |
ef97533f22b4c4becd7f80daf758f834294701202e4e82d8727ff7b3be7df3ec | MATLAB | 3,889 | 84 | function [rgb hex] = wes_palettes(palettename)
%colors = wes_palettes(palettename)
%get color palettes from Wes Anderson movies. Available:
% 'GrandBudapest', 'Moonrise', 'Royal', 'Moonrise2', 'Cavalcanti',
% 'Royal2', 'GrandBudapest2', 'Moonrise3', 'Chevalier', 'Zissou',
% 'FantasticFox', 'Darjeeling', 'Rushmore', 'Bo... |
3bb2e3de7f1546c1f34b7102756f5775b30b2bbb1dd3ded356aed2d8115ee791 | MATLAB | 3,892 | 93 | function pool_chnls2table(params, groupInfo)
% writes a list of iEEG into Excel table
% 1 row = 1 channel
% (c) Jiri, Oct23
%% check if output dir exists
if exist([params.storage.dir_results filesep params.storage.outName],'dir') ~= 7
error(['output directory for results not found, dir = ' params.storage.dir_resu... |
352026e40fe47b545023a30acad4825601ae6bd72032367be700db500ce747ff | MATLAB | 3,895 | 126 | function plot_nodes_in_cortex_new (V)
figure
hold on
% % PLOT CORTEX
cortex.path='C:\Users\dk00549\OneDrive - University of Surrey\Documents\Surrey\MATLAB\PluginsProgramsToolboxes\LEiDA-master\LEiDA\TIDES\Atlas\MNI152_T1_2mm_brain_mask.nii';
cortex.pial=mapPial(cortex.path);
cortex.color=[0.9 0.9 0.9];
corte... |
5cabe1ec40e80baaeca552b1d6a2ae1b335ff31f5c816ce877228f58b01d9181 | MATLAB | 3,895 | 135 | function [WTOpt, WTMdl, BlkInf, Belief, Kappa, Prior] =...
GenerateSynthData_Bayes_subopt_onlylambda_nonflat(params, ratTrial,...
noise_arg, gen_arg, noise_params)
%GenerateSynthData_Bayes_subopt_onlylambda_nonflat - generates synthetic
% wait times for Bayes SubOpt model with lambda over a WEAKLY INFORMATIVE ... |
f15f08d465b5bb4f5fe3b9d94de2dc9659803b366382ee5c7601ecc14c9c1f0a | MATLAB | 3,898 | 104 | classdef MrCompare < MrCopyData
% This class loads and compares different objects, e.g. images/rois
%
% EXAMPLE
% MrCompare(imageArray, extraDimInfo)
%
% See also MrDimInfo MrImage
% Author: Saskia Klein & Lars Kasper
% Created: 2019-02-25
% Copyright (C) 2019 Institute f... |
2a0a64ae684df561c1e86efe31794885a84380108fe565f31e6a25d09afc36b7 | MATLAB | 3,899 | 124 | % op_get_Multispectra_LW.m
% Helge Zoellner, Johns Hopkins University 2014.
%
% USAGE:
% [FWHM]=op_get_Multispectra_LW(in);
%
% DESCRIPTION:
% Estimates the linewidth of a reference peak in the spectrum. By default,
% the reference peak is water, between 4.4 and 5.0 ppm. Two methods are
% used to estimate the linewid... |
3778e5ef15b04cae51b16b5242e0b7c27331fb9a1fb290ca33669f11fde1e542 | MATLAB | 3,900 | 126 | function plot_nodes_in_cortex_SchaeferShen_2016ROI (V)
figure
hold on
% % PLOT CORTEX
cortex.path='C:\Users\dk818\OneDrive - Imperial College London\INS\TIrsfMRI_BrainStateTopologyAndDynamics\AtlasAndOtherInputs\MNI152_T1_2mm_brain_mask.nii';
cortex.pial=mapPial(cortex.path);
cortex.color=[0.9 0.9 0.9];
cort... |
58140fd5309c1ae14a9d4a69326bc22cffc4aa0cc54cb50d848bbb1b238417be | MATLAB | 3,900 | 133 | function [xc,mode] = XCorr1(x,y,varargin)
%XCorr1 - Compute cross-correlograms and their modes for pairs of curves.
%
% USAGE
%
% [xc,mode] = XCorr1(x,y,<options>)
%
% x first set of curves (MxN matrix: M curves, N bins)
% y second set of curves
% <options> optional list of ... |
616190cb59060614bf3402d591f58fce77dee61186434dd1ded1432da72ad27d | MATLAB | 3,900 | 126 | %%% Create Video and save it %%%
function SaveVideo(Data,NameVideo,ECS,nt,rate,dt,originalTime,unitC,unitT,clim,Cbasal,fps,NameMask,MS)
% Define scaling factors for time and concentration units
scale=convertFromSIunit(unitC);
scaleT=convertFromSIunit(unitT);
% Convert basal concentration units fro... |
b7ff3926e7daefdb5b0c46be117eb3c8124e44e5fea678f60679f533232cc38c | MATLAB | 3,900 | 145 | function signal=MPRAGEfunc(nimages,MPRAGE_tr,inversiontimes,nZslices,FLASH_tr,flipangle,sequence,T1s,varargin);
if strcmp(sequence,'normal')
normalsequence=true;
waterexcitation=false;
else
normalsequence=false;
waterexcitation=true;
B0=7;
FatWaterCSppm=3.3;% ppm
gamma=42.576;%MHz/T
pulseSpace=1/2... |
1ca7389985bf3c5567db074a26d6bbff5830df8438a5cfb7a3d0c19586955ff6 | MATLAB | 3,903 | 193 | function Pipeline_plotData(params, plt)
% For plotting of general timeseries data
analysisDir = getAnalysisDir(params);
ExpInfoFn = getFileName(params, 'ExpInfo');
tsFn = getFileName(params, 'TS');
wsFn = getFileName(params, 'WSData');
load(fullfile(analysisDir, ExpInfoFn));
load(fullfile(analysisDir, ts... |
59947dd02bd0e749c3dd574fe2467480232551bff4b6a85692182ab94fd05a91 | MATLAB | 3,904 | 156 | function [err,ErrMessage, NameList] = zglobb (Identifiers, Opt)
%
% [err, ErrMessage, List] = zglobb (Identifiers, [Opt])
%or
% [List] = zglobb (Identifiers, [Opt])
%Purpose:
% returns the list of files specified in Identifiers
%
%
%Input Parameters:
% Identifiers is a cellstr identifying which briks to use
% ... |
47e562adfe2342cca7a0460fbadde9d696b1d2ea38c35cdbc8263fc433b57af5 | MATLAB | 3,907 | 101 | %Global metrics
% using subset1 as an example
% For multicenter fitting, using multi_center_multimodelnlm_global.m instead of multimodelnlm_global.m
% For multicenter fitting, network atrriobutes should be harmonized (Adj_site_effect.m) before using multi_center_multimodelnlm_global.m
%
% load graph theoritica... |
4cc8dea9fc9671f2cc2490e888aac88f7eaa2068581a71c466f0f1ba67bbd96b | MATLAB | 3,908 | 122 | % CORRCOEF_CELL - compute pairwise correlations using arrays and
% cell array inputs.
%
% Usage:
% >> c = corrcoef_cell( data );
% >> c = corrcoef_cell( data );
%
% Inputs:
% data - [cell array] data consisting of PAIRED arrays to be compared.
% The last dimension of emb... |
0ec2c9b1abf5e1009310ca6e7b4d0fa58e63e65a719f02342487fb57e39f6bb0 | MATLAB | 3,909 | 112 | function [varargout] = rfAnatVisInterp(interParams,varargin)
if length(varargin) == 2
interpHSVA = 1;
hsvImageMatrix = varargin{1};
alphaImageMatrix = varargin{2};
elseif length(varargin) == 1
interpHSVA = 0;
valuesImageMatrix = varargin{1};
else
error('(rfAnatVisInterp) Wrong number of varargi... |
410761d4ee6dfc80b18348f4e4276b1653541166b3ba9c6f7241de4f95eeb292 | MATLAB | 3,909 | 119 | function [spikeMatrix,spikeTimes,Params,Info] = formatSpikeTimes(File, ...
Params, Info, spikeDataFolder, expMatData, electrodesToGround)
% this function loads in the spike detection result and creates a
% spike matrix and spike times structure for the chosen spike detection
% method and chosen length of record... |
766af7cd0f4f37565f8c26dc48eb20ca53c2cec23976d0ce8cc795b2acf96a1d | MATLAB | 3,909 | 114 | % assign circles to each point in a rectangle
% for each point in the matirx, create a list of circle centers that it
% belongs to
% save the file at base path
% filename = imagewidth_imageheight_radius.mat
classdef assigncircles < handle
properties
width = 0 ;
height = 0 ;
radius... |
906e543f03171948b3dad3a841364cbd743ccb8f04b40f16097bbaf63dc82161 | MATLAB | 3,910 | 130 | function [c, r, t, cpulse] = tapas_physio_read_physlogfiles_custom(log_files, ...
verbose)
% reads out physiological time series and timing vector from custom-made logfiles
% of peripheral cardiac monitoring (ECG
% or pulse oximetry)
%
% [c, r, t, cpulse] = tapas_physio_read_physlogfiles_custom(logfiles)
%
% I... |
ec760df44983264b29692413c8eedcf97287cdcecd82512522430d2978658617 | MATLAB | 3,910 | 82 | % Main script for the SANDI analysis using random forest regression
%
% Reference:
% Lee H, ..., Huang S, Communications Biology, 2026
% Based on Palombo M. et al. Neuroimage 2020: https://doi.org/10.1016/j.neuroimage.2020.116835
%
% Requirements:
% - SANDI-Matlab-Toolbox v1.0 (https://github.com/palombom/SANDI-Matlab-... |
ff158dfaa638392d1c6349553b726cb4304141e81fbabf8aff677edb14edd029 | MATLAB | 3,910 | 74 | % "surfing" toolbox for surface-based voxel selection, useful for
% SURFace-based information mappING" of the cerebral cortex.
%
% Authors: Nikolaas N. oosterhof [NNO] <n.oosterhof@bangor.ac.uk>
% Tobias Wiestler [TW] <tobias.wiestler.09@acl.ac.uk>
% Joern Diedrichsen [JD] <j.diedri... |
5cfe1f021bf001bf0f688ef1558026b8167708cb6df710770687bef05f1fcdde | MATLAB | 3,911 | 111 | function getTriggers_emoReco_stimuliTypes(params)
% determines trials which contained the selected keyword (in params.thisCategory)
% saves result into respective column of 'trials_events' in each sessionCacheFile
% - rows = trials
% - values = zeros (event not found) and ones (event found)
% (c) Jiri, Mar16
disp... |
f207460286f33aec90dad18a54184949cf30ad69dfe6d914f525505d48b622ec | MATLAB | 3,912 | 112 | function fast_rcnn_demo(varargin)
%FAST_RCNN_DEMO Demonstrates Fast-RCNN
%
% Copyright (C) 2016 Abhishek Dutta and Hakan Bilen.
% All rights reserved.
%
% This file is part of the VLFeat library and is made available under
% the terms of the BSD license (see the COPYING file).
run(fullfile(fileparts(mfilename('fullpa... |
038ecf6a84a757ae256cb1964b648c261746bfb56f17057ff1387936f370ac87 | MATLAB | 3,914 | 114 | function GenCocktailList(CodedVectors)
% Function converts coded target and trial vector factor-dose
% combinations that require testing (in numFact x numComb array V) and
% output 'to test' list as excel spreadsheet.
global numFact destRowWells destColWells numDose run CombList DoseList
global Factors w... |
fb3bfcb01bac8bc4d1944cfd9d3ff5e66ee1c86275f2e6e7fe0bc0ced7b30e15 | MATLAB | 3,916 | 112 | function [err,XYZdic] = AFNI_Index2XYZcontinuous (Indx, Info, CoordCode)
%
% [err,XYZdic] = AFNI_Index2XYZcontinuous (Indx, Info, [CoordCode])
%
%Purpose:
% Change from voxel XYZindex (called Voxel Coords in AFNI) to XYZ in mm
% The mm and voxel coordinates refer to the values displayed
% on the top left corner... |
44659db058949f1ea0baa9288ce89af8869edc7d7dc3a28168202261db574486 | MATLAB | 3,918 | 103 | function [rt,intervalID] = RelativeTimes(t,intervals,values)
%Relative times - compute the relative times of samples within intervals
% For example, a sample with a timestamp in the middle of an interval
% would have relative time 0.5. A sample that falls outside of the provided
% intervals would return as NaN. Multip... |
aa86b4d1d94963577dc8df2e20e754e398a86a22aaf357851377ade8a0b93c0a | MATLAB | 3,919 | 138 | function [ odorOrder, ORNOrder ] = GetBestOrder( data3D )
% use simulated annealing algorithm to find the order of ORN and odor to
% gather the large responses close to the diagonal.
%% design a punishment matrix
[odorNum, ornNum, zDim] = size(data3D);
pM = zeros(odorNum, ornNum);
for i = 1: odorNum
for j = 1: o... |
d4e9960d60f47020a04bafdc0279feb966ac0d558b11b82bb1c714384789577f | MATLAB | 3,919 | 137 | %script Test_TellAfni
%
%
%
%Purpose:
%
% A script to demonstrate the use of the matlab AFNI driver tools (TellAfni).
% Make sure no current AFNI session is running with the -yesplugouts option.
%
% The script is not fancy and some steps might go by too quickly but it should
% be a simple read to figure it all ... |
a27eae03125d9a3cf2648e0012dec422181256de08457b0e1f98cc920c3ff690 | MATLAB | 3,921 | 94 | function params = initialize_network_parameters()
% INITIALIZE_NETWORK_PARAMETERS - Set up default network parameters
%
% H1 Line: Initialize default parameters for spiking neural network
%
% Syntax:
% params = initialize_network_parameters()
%
% Description:
% Creates a structure containing all default parameters ... |
de39af137598d45cf9c1bf175b3565b5f97fbdff7196db60b8ea4d4c0d3e6421 | MATLAB | 3,922 | 88 | function placefield = place_field_dombeck(dFoT,ytrace,bins,movingAverage,...
Foutfield,Finfield,minwidth,Ftransient,dFrelThresh)
% Function to detect place fields according to Dombeck et al., 2010,2014.
% Parameters: 'minwidth' in bins, 'dFabsThresh': minimum mean dF that must
% occur in at least one bin in the... |
83e0df48c422b4e48506292936a69747d1f6d55ce870a1b84b2cf1e4fd2d3be9 | MATLAB | 3,923 | 148 | function plotTrials(params, trialsData)
% plots values in 'trialsData' struct with fields:
% yVals: [sample x ch x clz]
% yErrs: [sample x ch x clz] -> optional (plotband)
% xVals: x-Axis values (vector), typically time in [s]
% info: struct with supplementary information
% (c) Jiri, Jan11 (in whitenoise),... |
9e1cacb5c4b0b4d49756f9a68bab405dd90e05719d84bfecf682854e9d03f040 | MATLAB | 3,923 | 111 | function PlotExtendedData9(datadir, codedir)
%PlotExtendedData9 - Plots Extended Data 4.
% INPUTS:
% datadir - Local directory where ProcessData_ExtendedData9.mat was saved after running ProcessData_ExtendedData9
% codedir - Local directory where code (e.g., published/EstrousRPE/) was saved
%% Set up paths
s = pa... |
a4dca75ad616fcfb4eb975ab46cf54d54175129be6d128216ce827e2797e926d | MATLAB | 3,923 | 99 | function [dimInfoArray, sfxArray, selectionArray] = split(this, splitDims)
% splits dimInfo along specified dimensions, creating an array of reduced
% dimInfos and corresponding string suffixes for index-specific object naming
%
% Y = MrDimInfo()
% Y.split(splitDims)
%
% This is a method of class MrDimInfo.
%
% IN
... |
384f71c886c34631acebf2ab03ec2729c239aa27fcc9df455d7c48b599f53c0d | MATLAB | 3,924 | 121 | function [Y, I, J] = randswap(X, dimmode)
% RANDSWAP - randomly swap elements of a matrix
%
% For vectors, Y = RANDSWAP(X) randomly swaps the elements of X. For
% N-D matrices, RANDSWAP(X) randomly swaps the elements along the first
% non-singleton dimension of X.
%
% RANDSWAP(X,DIM) randomly swaps the ... |
33c17f1cf329a1002751eff37b582dcb62c3cd5230caf8c6c227965521e04987 | MATLAB | 3,925 | 136 | % parse up the beliefs into a 2d discrete distribution
function [output] = dSTR_decode_parsedata(varargin)
%% general appraoch that should work for all cases
% for each neuron, get the following
% session_id
% neurons' average firing over time (2s after reward)
% p_mix and p_high for that trial
% which bin it is in... |
c97f08e90fc8c472828f7733f311a43a9e9f39b412937678d9b9422dd274ff31 | MATLAB | 3,925 | 141 |
function [h5cropIndex,imcropRect]=h5movieCropping(h5Path,varargin)
options.BandPx=[3 25];
options.verbose=true;
options.autoCropping=false;
options.windowsize=1000;
options.dataset='mov';
options.diary=true;
options.diary_name='diary_crop';
options.processWholeMovie=true;
disps('Starting movie cropping')
if isstr... |
e70406f27148901404754cf233a063207d806854b2609619fd93917e5393e20b | MATLAB | 3,928 | 139 | function [summaryLoading] = loading(allPaths,varargin)
% converting two dcimg movies to h5 files and passing all metadata
% this is a high-level functions outputting diagnostic data too!
%
% SYNTAX
% [movieG,movieR,summary] = loadingMovies(dcimgpathG,dcimgpathR,varargin)
% [movieG,movieR,summary] = loadingMovies(dcimgp... |
0ffe380657d0f945f0e75f2ba6377b9c3c223d4f118ed428f68ac467bb2b041d | MATLAB | 3,931 | 148 | % Batch script for sparse prediction
clear all
% --- training method for variable sample size data
method_id = 1;
%case 1 linear_sparse_space_sw
%case 2 linear_sparse_space_vec_sw
%case 3 linear_sparse_stepwise_sw
%case 4 linear_sparse_stepwise_em_sw
% --- Basic Learning Parameters
parm.Ntrain = 2000; % # ... |
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