sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ec9705366a374eeb99856eb533dcbfa31ff0b6c19b7278025ec124cba2b15486 | MATLAB | 4,697 | 144 | % Name: Robert Kim
% Date: 11-15-2023
% Email: robert.f.kim@gmail.com
% plot_one_modality.m
% Description: Render the 4x4 lesion-effect boxplot grid for the two-layer
% one-modality (instr) RNNs (Fig. 6 / supplementary). Reads the per-lesion
% .mat files written by one_modality_two_layer_lesion_across_models.m and
% ru... |
e06f1b68ebe7b02bf3725fc77af0976085b922a19a09487e62337c51712b5c66 | MATLAB | 4,699 | 110 | function handles = plot_arrow( x1,y1,x2,y2,varargin )
%
% plot_arrow - plots an arrow to the current plot
%
% format: handles = plot_arrow( x1,y1,x2,y2 [,options...] )
%
% input: x1,y1 - starting point
% x2,y2 - end point
% options - come as pairs of "property","value" as defined fo... |
ccc249a261f354639abcbc597e2832cb808882d7caedd742f5e7ce575b1dfaae | MATLAB | 4,700 | 122 | % pop_plottopo() - plot one or more concatenated multichannel data epochs
% in a topographic array format using plottopo()
% Usage:
% >> pop_plottopo( EEG ); % pop-up
% >> pop_plottopo( EEG, channels );
% >> pop_plottopo( EEG, channels, title, singletrials);
% >> pop_plottopo( EEG, channels, t... |
643b598a539009c412f69e9f9935fa0e28b578dd1369f8fd45eff9587b670a21 | MATLAB | 4,702 | 95 | function [dS,t,f]=mtdspecgrampb(data,movingwin,phi,params)
% Multi-taper derivatives of time-frequency spectrum - binned point process
%
% Usage:
%
% [dS,t,f]=mtdspecgrampb(data,movingwin,phi,params)
% Input:
% Note that all times can be in arbitrary units. But the units have to be
% consistent. So, if E i... |
99fe631e1da9ec13d8bf99399b10542b52e70094cd7488c068f5e886d8144381 | MATLAB | 4,704 | 94 | function [dS,t,f]=mtdspecgramc(data,movingwin,phi,params)
% Multi-taper derivative of the time-frequency spectrum - continuous process
%
% Usage:
%
% [dS,t,f]=mtdspecgramc(data,movingwin,phi,params)
% Input:
% Note that all times can be in arbitrary units. But the units have to be
% consistent. So, if E is... |
848723323fe89ba92ce378004f0680c9a87a052104bc7f375846a5b023d80211 | MATLAB | 4,705 | 86 | function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencyc(data1,data2,params)
% Multi-taper coherency,cross-spectrum and individual spectra - continuous process
%
% Usage:
% [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencyc(data1,data2,params)
% Input:
% Note units have to be consistent. See chronux.m for more informat... |
8a9c827e367131d069a9466d13c4c169755f2ecf537ed9d765e575bfd0fa9fae | MATLAB | 4,707 | 102 | function [S,t,f,Serr]=mtspecgramc(data,movingwin,params)
% Multi-taper time-frequency spectrum - continuous process
%
% Usage:
% [S,t,f,Serr]=mtspecgramc(data,movingwin,params)
% Input:
% Note units have to be consistent. Thus, if movingwin is in seconds, Fs
% has to be in Hz. see chronux.m for more information.
% ... |
a9c6a935fefe481412579e88f408c99b10747ecc8e53950da6f33d4ae0f5047a | MATLAB | 4,708 | 261 | % This function takes a problem in SeDuMi MATLAB format and writes it out
% in SDPpack format.
%
% Usage:
%
% writesdp(fname,A,b,c,K)
%
% fname Name of SDPpack file, in quotes
% A,b,c,K Problem in SeDuMi form
%
% Notes:
%
% Problems with complex data are not allowed.
%
% ... |
e9bb3b148924cb3305a8ad540597751b43083a8f95a905269ae8f751792b5f57 | MATLAB | 4,708 | 164 | % Tri-state bus sizing and topology design
% Section 5.4, L. Vandenberghe, S. Boyd, and A. El Gamal
% "Optimizing dominant time constant in RC circuits"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 11/27/05
% Modified by Michael Grant - 3/8/06
%
% We optimize a tri-state bus connecting six node... |
471fc29134c7fbeebe64fd5aaf7a9775b0a737894f0d6c78711469b22ac06180 | MATLAB | 4,711 | 131 | function postprocess_write_file_for_parameters(filename_prefix, ...
Theta, Theta_samples, bayes_factors, names)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically re... |
e605b300e4b7a6cb9208880f6f84b62151a1b921b95378f4cfca1454a78a5130 | MATLAB | 4,711 | 197 | function out=test_benchmark
%
% David Gleich
% Copyright, Stanford University, 2007
%
%
% 9 July 2007
% Initial version
%
%% History
%%
% 2008-10-07, Version 2.1, Matlab 2007b, boost 1.33.0,
% g++-3.4 (lib), gcc-? (mex)
% airfoil west cs-stan minneso tapir
% large 0.223 s 0.... |
44e62f45b30a07b69aec749f30530957e1decc4dd2dbb6489f1423645bd52e7f | MATLAB | 4,713 | 149 | function [ redred, localred ] = DoubleRedundancyMMIDiscrete(varargin)
%%DOUBLEREDUNDANCYMMIDISCRETE Compute the PhiID double-redundancy of discrete
% input data using the MMI PID. It uses a plug-in MI estimator first to find
% the MIB, and then uses a data-efficient quasi-Bayesian estimator to compute
% the double-redu... |
dff44cf1864deab1d91e209510ebb9512314046672a83798abdc7c98228c871c | MATLAB | 4,713 | 132 | function [dist,angles,stats] = PhaseDistribution(phases,varargin)
%PhaseDistribution - Compute phase distribution.
%
% USAGE
%
% [dist,angles,stats] = PhaseDistribution(phases,<options>)
%
% phases phases
% <options> optional list of property-value pairs (see table below)
%
% ================... |
4bfbc74361ccb3dc9a753214c70c0db2e96c24ac0a3aacef154577c04b320f3c | MATLAB | 4,714 | 131 | function nii_deface(in)
% Syntax: NII_DEFACE(in)
% input can be a single anat 3D NIfTI, or BIDS folder containing sub-* folders.
% If no input is provided, a file/folder dialog will pop up.
%
% NII_DEFACE removes face and neck structure from T1w/T2w NIfTI.
%
% How does this code deface?
% 1. A xform matrix is est... |
07bc601ee90e76606e63abacdca3d7995a22b793ec8864eb6162ddd5b39e7053 | MATLAB | 4,717 | 94 | function [dS,t,f]=mtdspecgrampt(data,movingwin,phi,params)
% Multi-taper derivative time-frequency spectrum - point process times
%
% Usage:
%
% [dS,t,f]=mtdspecgrampt(data,movingwin,phi,params)
% Input:
% Note that all times can be in arbitrary units. But the units have to be
% consistent. So, if E is in secs, wi... |
22a2563e71ca2d1c817470f7f255c62cdb8389ff740e9bcba3404dc4c27645f9 | MATLAB | 4,719 | 126 | function ea_lcm_func(options)
if strcmp(options.lcm.func.connectome,'No functional connectome found.')
return
end
disp('Running functional connectivity...');
if iscell(options.lcm.seeds)
if length(options.lcm.seeds)==1
options.lcm.seeds=options.lcm.seeds{1}; % supply as char
end
end
try
exportgmt... |
c4a3bc5d5d1112cefb550fe310ff0b648aee6b8ac7291ccbb54241e60edd8552 | MATLAB | 4,719 | 99 | function [dense,Adotdden] = getdense(At,Ablkjc,K,pars)
% [dense,Adotdden] = getdense(At,Ablkjc,K,pars)
%
% GETDENSE Creates dense.{l,cols,q}.
% Try to find small proportion of the cone primitives that appear
% in a large proportion of the primal constraints.
%
% ******************** INTERNAL FUNCTION OF SEDUMI ***... |
fc8d0b63092537a630ac43f0822cf833ebbb2365a5c7691b066500b2ad19f436 | MATLAB | 4,719 | 110 | % %% Load data for 'P_replay' (Fig.4F) and '|Lseq|' (Fig.4G)
% load('candidates_excluded.mat'); % candidates based on pupil width
% load('result_replay_CA1.mat'); result_replay_CA1 = result_replay;
% load('result_replay_VIS.mat'); result_replay_VIS = result_replay;
% n_ses = size(result_replay_CA1,1);
% n_candidat... |
61102208afd06dc8913266bfa210b14ae863fffeaf477b8ceb213a310b445058 | MATLAB | 4,723 | 137 | function [f, pp] = make_box_plot2_swarm_title(plot_an, plot_aw, colL, colR, titlename, markerSize, markerAlpha, jitterWidth, null99_an, null99_aw)
% make_box_plot2 : swarmchartを使った簡易ヒゲなし箱ひげ図
% MATLABのswarmchart関数でデータをプロットし、Q1-Q3を太い線で表示、中央値を〇で表示します。
% null distributionの99%ラインを点線で表示します。
% ※ MATLAB R2020b以降が必要です
%... |
aeb499c80aab90989740b51f20c074337427c38c50bdb66c588b187a99034885 | MATLAB | 4,723 | 129 | function [coeff,local] = CV(timestamps,varargin)
%CV - Compute coefficient of variation for a point process.
%
% Three alternative measures can be computed: regular CV, CV in operational time
% (Gestri and Petracchi, 1970; Nawrot et al., 2008) or CV2 (Holt et al., 2006).
%
% While the CV is typically computed for cons... |
0f73cea496b730583bbf7a2bf6a06a044c956b7b2e6a5827d31f9ddf2911125d | MATLAB | 4,739 | 119 | function [map,stats] = FiringMap(positions,spikes,varargin)
%FiringMap - Compute firing map (e.g. for a place cell).
%
% Compute firing map (e.g. for a place cell), as well as occupancy and spike
% count maps. Optionnally, field statistics can also be computed, including
% in-field peak and mean firing rates, firin... |
7ee1dbbf41407ffe147d44f072bc1d662308ae37f23ed6efa6277dad2a99b884 | MATLAB | 4,742 | 157 | typeArray = [allflies.trtype];
for i = 1:16
inds{i} = find(typeArray==i);
end
flyArray = [allflies.flyID];
for i = 1:max(flyArray)
inds{i} = find(flyArray==i);
end
%% Left Turns
% TO DO THIS, YOU NEED TO RUN THE CONTENT OF COMPUTETURNBOUTS2.M
Lturns = {}; leftPB = []; rightPB = []; turnLdata =... |
48a17b14b426d5c0bfe765e9483b8dffa2ae8bfffb966a7bb32813584b5bc9d9 | MATLAB | 4,743 | 153 | classdef ( Hidden, Sealed ) PointerManager < handle
%uix.PointerManager Pointer manager
% Copyright 2016 The MathWorks, Inc.
% $Revision: 1435 $ $Date: 2016-11-17 17:50:34 +0000 (Thu, 17 Nov 2016) $
properties( SetAccess = private )
Figure % figure
end
properties( Acces... |
9e166acde9ad78bc64605e0a9aa0e672d70e8f9095685670ac1ffa7cfdfa7c57 | MATLAB | 4,744 | 88 | function ClincFreq_AffVolStat(INDIR,OutAffVoldir,SetUpPara,Para,AtlasTempU)
for i = 1:length(SetUpPara.ParaOut)
LabName = SetUpPara.ParaOut(i).LabName;
AffVoldir{i} = [OutAffVoldir,filesep,LabName,filesep];
if length(dir([AffVoldir{i},'ROIWise',filesep,AtlasTempU{1,3},filesep,'Group*AffVol... |
b5ce535eb5fae97694eb298e51dcd0ef5f82e9332c545c96f9f8649d0e5f7e53 | MATLAB | 4,744 | 169 | % THIS SCRIPT extracts region averages and local pattern expression in each
% parcel of the Shen 2013 atlas
%
% - extracts local parcel means and all local pattern expression for all signatures.
% - Preps file Parcellation_data.mat saved in "results" folder.
% - Allow us to compare local pattern expression across pa... |
5221c8535515345aac3c953a92f7c12674ed81b8f642750fb961e0f06fdafffe | MATLAB | 4,745 | 146 | % qqdiagram() - Empirical quantile-quantile diagram.
%
% Description:
% The quantiles (percentiles) of the input distribution Y are plotted (Y-axis)
% against the corresponding quantiles of the input distribution X.
% If only X is given, the corresponding quantiles are plotted ... |
62c95fb118bed6da4af2396e831244965c0a8e01a3a7b80e8cb4cc4cbd1ca04f | MATLAB | 4,746 | 93 | function data=rmlinesc(data,params,p,plt,f0)
% removes significant sine waves from data (continuous data).
%
% Usage: data=rmlinesc(data,params,p,plt,f0)
%
% Inputs:
% Note that units of Fs, fpass have to be consistent.
% data (data in [N,C] i.e. time x channels/trials or a single vector) - required.
% ... |
996ff78c35ea3244b0cc865e11bc33d0158aefda543b82ea430d718a23a11717 | MATLAB | 4,747 | 129 | function [n_cnt,con_mat,pval]=ea_NBSfdr(varargin)
%NBSfdr Simes procedure to determine edges surviving a false discovery
%rate (FDR) threshold. A p-value for each edge is determined using
%permuted data that has been supplied as part of the structure STATS.
%
% [N_CNT,CON_MAT,PVAL]=NBSfdr(STATS) operates on th... |
52370faf5c20c03bf97c77c6582a88337c02db33f0453dd4d7a9c39f7c456683 | MATLAB | 4,749 | 110 | function [sm,dE2_mat] = get_shear_modulus_LE(Npts,P0,V,newC,gamma,ka)
% GET_SHEAR_MODULUS_LE Compute the athermal (zero-temperature) shear
% modulus of the tissue at a given strain, splitting it into affine and
% non-affine contributions, under Lees-Edwards (sheared) periodic
% boundary conditions.
%
% [sm, dE2_mat]... |
fd63173d2e89e22ac6a3ef8f304b52b02736d03a9612b6d405a352c7c575c365 | MATLAB | 4,750 | 127 | function upSetPlot(data, labels, figH, setSizeColor)
% More info on UpSet plots in the original publication:
% Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot,
% Hanspeter Pfister. UpSet: Visualization of Intersecting Sets
% IEEE Transactions on Visualization and Computer Graphics (InfoVis),
% 20(12)... |
5b6c3e601042d8e85484bb16d8cfe71fd113218c7750a42a194b01ee6e82763d | MATLAB | 4,752 | 150 | function output = ea_checkStimParams(stimFile)
% Check if "S" is compatible with the latest format. Fix when necessary.
%
% Input can be stimparameters file or group analysis file.
% Output will be "S" or "M" (with "M.S" updated).
updated = 0;
stimFile = GetFullPath(stimFile);
vars = who('-file', stimFile);
if ismemb... |
65752ce5ed227c24da5ce2ac69e563ed7fa5fdfcd05d8d86e0ce7526c0a06cd5 | MATLAB | 4,754 | 142 | function speedTable = cellSpeeds(compiledData, outputFolder, options)
% CELLSPEEDS Calculate speed metrics for each tracked cell from
% compiled tracking data produced by compileResultsCSV.
%
% For each cell track, computes average speed, cumulative speed, and
% speed variance over the full period, as well as the firs... |
47e8d6f695ea4bef270ccef7401aeee8473995dbec8a6bcd201ba02ecc05bb5a | MATLAB | 4,755 | 180 | figtitlebase = 'BucknerLab rsFMRI Cosine Similarity Wedge';
image_set_name = 'bucknerlab'; % keyword for named set to pass into load_image_set
[mapset, netnames] = load_image_set(image_set_name);
mycolors = seaborn_colors(length(netnames));
k = length(DAT.conditions);
myfontsize = get_font_size(k); % This is a fu... |
6789bafbdddb4516034e6106f45ffe0986e496da6f54818018c59f7c2f6fc928 | MATLAB | 4,761 | 142 | function showMovie(data,subim,wl,pausetime,mycmap,do_write)
% Usage ... showMovie(data,subIm,wl,pauseTime,cmap,writeims)
%
% data is a 3-dim variable with time images to show
% when subIm is supplied, subtracted images will be showed
% wl will fix the windowing to [min max] if specified
% pauseTime will show the ... |
787d9d53672a20579148e00ec108ebb2fddbbca369e30735fbeef67b2305f526 | MATLAB | 4,776 | 172 | % Optimal interconnect wire sizing
% Section 5.1, L. Vandenberghe, S. Boyd, and A. El Gamal
% "Optimizing dominant time constant in RC circuits"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 11/25/05
% Modified by Michael Grant - 3/8/06
%
% we consider the problem of sizing an interconnect wire t... |
e4e87be5a475da2b2eaf6baaeeef0f06278af53fb28addeb1517a13a5c089995 | MATLAB | 4,776 | 121 | %% Core numbers in MatlabBGL
% This example illustrates the concept of the core number of a vertex.
% Mathematically, the core number of a vertex v is the largest integer c
% such that v has degree > 0 when all vertices of degree < c are removed.
% Equivalently, the core number of vertex v is the largest integer c such... |
0ebe59aae92d3b55017f185568b418ee98a922026432d1c0958a621b4fb4aa87 | MATLAB | 4,786 | 120 | function settings = ea_switch2VATgrid(options, S, settings, side, outputPaths)
% Change connectome fibers to a regular grid aligned with the electrode
% (classic VAT).
% For parameters, see ea_till_creategridforelectrode.
% By Dembek, Butenko and Li, konstantinmgtu@gmail.com
arguments
options % Lead-DBS option... |
e6af5f19a71d82bf6446b98248ed67fa24d7ca2d00b412f83000c215df4a5012 | MATLAB | 4,790 | 105 | function [S,t,f,R,Serr]=mtspecgrampb(data,movingwin,params,fscorr)
% Multi-taper time-frequency spectrum - binned point process
%
% Usage:
%
% [S,t,f,R,Serr]=mtspecgrampb(data,movingwin,params,fscorr)
% Input:
% data (in form samples x channels/trials or single vector) -- required
% movingwin ... |
a3c16749c91ffa2f5976fb3977089e64d58c2cb8de4f03552425485ddbb17417 | MATLAB | 4,791 | 86 | function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencyc(data1,data2,params)
% Multi-taper coherency,cross-spectrum and individual spectra - continuous process
%
% Usage:
% [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencyc(data1,data2,params)
% Input:
% Note units have to be consistent. See chronux.m for more in... |
d6cb589d043328e3bc5198243e9c94dfca49cc62d6c9a1e5ba34267e7a015b62 | MATLAB | 4,791 | 116 | function ivals = glmnetControl(pars)
% DESCRIPTION:
% View and/or change the factory default parameters in glmnet
%
% USAGE:
% glmnetControl; (with no input or output arguments)
% displays all inner parameters and their current values.
% glmnetControl(pars);
% sets the internal parameters that appear in the... |
c7153ee35aa1b863739ad718a9620c55b9efc6e4ab93524f2048ec63610cf655 | MATLAB | 4,793 | 152 | function [d, xd, bw] = kernelDensity(x, bins, h, kernel)
%KERNELDENSITY Calculate the kernel density of a data set
%
% [D, XD] = IOSR.STATISTICS.KERNELDENSITY(X) calculate the kernel density
% D of a dataset X for query points XD. The kernel density is calculated
% for 100 query points equally spaced between t... |
4096a8dcd070533f808b4f83538f03ed9d349e4bb8cddd4d3f0bdff1dd90060e | MATLAB | 4,794 | 129 | function [vertices, label, colortable] = read_annotation(filename)
% [vertices, label, colortable] = Read_Brain_Annotation(annotfilename.annot)
%
% vertices expected to be simply from 0 to number of vertices - 1;
% label is the vector of annotation
%
% colortable is empty struct if not embedded in .annot. Else, it will... |
bfbfb48edd68d3c0401119bc80568144b7c0bca20e1fe2a6b9c0cb1b841d823c | MATLAB | 4,800 | 129 | function [vertices, label, colortable] = Read_Brain_Annotation(filename)
% [vertices, label, colortable] = Read_Brain_Annotation(annotfilename.annot)
%
% vertices expected to be simply from 0 to number of vertices - 1;
% label is the vector of annotation
%
% colortable is empty struct if not embedded in .annot. Else, i... |
56a0ca549a4bc127ba90628fc81987c01debe6f4f09ba5847c0ab488a9cad77a | MATLAB | 4,802 | 137 | function CBIG_pMFM_step5_generate_STDFCD_correlation_main()
% This function is used to generate the correlation between the empirical
% and simualted SWSTD of timecourse. The results corresponds to the figure
% 6A, 6B and 6C in the paper.
%
% There is no input for this function as it can automatically get the
% output... |
c03e3b7cb90b6aa4bc57be0750c903ec783f0fbd1f30d8ea035d1e55418fd397 | MATLAB | 4,809 | 102 | function [S,t,f,Serr]=mtspecgramc(data,movingwin,params)
% Multi-taper time-frequency spectrum - continuous process
%
% Usage:
% [S,t,f,Serr]=mtspecgramc(data,movingwin,params)
% Input:
% Note units have to be consistent. Thus, if movingwin is in seconds, Fs
% has to be in Hz. see chronux.m for more information... |
417a8cd11fc55ad515d60b2db8d79bda88cb10697df598dfa6803a8e59e901f5 | MATLAB | 4,811 | 94 | function [dS,t,f]=mtdspecgrampt(data,movingwin,phi,params)
% Multi-taper derivative time-frequency spectrum - point process times
%
% Usage:
%
% [dS,t,f]=mtdspecgrampt(data,movingwin,phi,params)
% Input:
% Note that all times can be in arbitrary units. But the units have to be
% consistent. So, if E is in ... |
fdfc454ca1b1e2c5689b89d5bc755fe4730d1ab767fd327663ea54e8be97ad5f | MATLAB | 4,813 | 148 | function [maps,stats] = SurveyFiringMaps(units,varargin)
%SurveyFiringMaps - Compute and plot firing maps for all subsessions.
%
% USAGE
%
% [maps,stats] = SurveyFiringMaps(units,<options>)
%
% units optional list of units, i.e. [electrode group, cluster]
% pairs; set cluster to -1 to... |
a81ad38a43a5b6465dd3fb4833de408d083eb9d59b14ae4644ac2714e1ae3af8 | MATLAB | 4,815 | 101 | function [datafit,Amps,freqs,Fval,sig]=fitlinesc(data,params,p,plt,f0)
% fits significant sine waves to data (continuous data).
%
% Usage: [datafit,Amps,freqs,Fval,sig]=fitlinesc(data,params,p,plt,f0)
%
% Inputs:
% Note that units of Fs, fpass have to be consistent.
% data (data in [N,C] i.e. time x cha... |
88ebbee537d3240b1f1d2293b95719d3d099156ee7a79784b9282e4b7ddcc2c8 | MATLAB | 4,816 | 107 | function [pamlist,FilesExist] = ea_discfibers_getpams(obj)
% Return list of PAM results
% always initialize with entries for mirrorred stims
% mirror flag will be checked in ea_discfibers_calcvals_pam
numPatient = length(obj.allpatients);
pamlist = cell(numPatient*2,2);
FilesExist = zeros(numPatient,2); % no sense to... |
9cda1f61baa35743a56f15319b3ede983be1736589a42eaf4c1d27b82c9168ee | MATLAB | 4,816 | 126 | function mTrackChopped = simpleTrackChop(simpleTrack, m)
% SIMPLETRACKCHOP : chops the simpleTrack into m tracklets and return the chopped tracklets.
%
% SYNOPSIS: mTrackChopped = simpleTrackChop(simpleTrack, m)
%
% INPUT: simpleTrack : (structure) contains 1 row (1 track) with fields
% .t... |
4b886bc1d221165af2cbe70a57dd279888fbd5c3cbbb1211f766a33056b6e88e | MATLAB | 4,817 | 128 | function [Temptrace, tempRoi, handles] = Segmentation_autoThresh(handles, disppara)
if nargin<2
disppara=1;
end
scrsz = get(groot,'ScreenSize');
pos_seg = round([scrsz(3)*0.1 scrsz(4)*0.55 scrsz(3)*0.4 scrsz(4)/3]);
mov = handles.mov;
mov2d_filt = handles.mov2d_filt;
%%%%%% setup parameters
areathreshold = handles... |
290c65f7e4188814d2eb85757ab47fe8340d8a09cace33ae3d919cf8714bb462 | MATLAB | 4,821 | 135 | % pop_savestudy() - save a STUDY structure to a disk file
%
% Usage:
% >> STUDY = pop_savestudy( STUDY, EEG ); % pop up and interactive window
% >> STUDY = pop_savestudy( STUDY, EEG, 'key', 'val', ...); % no pop-up
%
% Inputs:
% STUDY - STUDY structure.
% EEG... |
b53f80dd3f837c740a244872fdaab4cb5acf34788bf1c572b4437f751931ad8c | MATLAB | 4,821 | 104 | function [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)
% Multi-taper time-frequency spectrum - point process times
%
% Usage:
%
% [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)
% Input:
% data (structure array of spike times with dimension channels/trials;
% also ... |
46866bfb52d12513ef120a578450555800d4b46571fefc592eb357df0427b834 | MATLAB | 4,822 | 95 | function ClincFreq_CalHeatNum(INDIR,OutHeatdir,SetUpPara,Para,AtlasTempU,dbmask)
[V,D,namelist] = Dynamic_read_dir_NIFTI_sparse(INDIR);
D(isnan(D)) = 0;
D(isinf(D)) = 0;
D = D>0;
for i = 1:length(SetUpPara.ParaOut)
LabName = SetUpPara.ParaOut(i).LabName;
HeatDir{i} = [OutHeatdir,filesep,LabName,filesep];
m... |
4f56c2b93106602d7ea92a9cecf4e9cb947d36a60320b7bbb41eabcda3872023 | MATLAB | 4,822 | 113 | % plotsphere() - This function is used to plot a sphere and
% project them onto specific surfaces. This may
% be used for plotting dipoles for instance.
%
% Usage:
% >> handle = plotsphere(pos, rad, 'key', 'val')
%
% Inputs:
% pos - [x y z] 3-D position of the sphere center
% ... |
ceb4b81b4a7f2467707b1627ef9d4523c80525bda71e71cd97168667a7354a09 | MATLAB | 4,825 | 126 | % eegthresh() - reject trials with out-of-bounds channel values within a
% specified epoch time range.
%
% Usage:
% >> [Iin, Iout, newsignal, elec] = eegthresh( signal, frames, ...
% elecs, negthresh, posthresh, timerange, starttime,endtime);
%
% Required inputs:
% signal - 2-D da... |
e3314200b3603edbaa69a6f9fc0f861ba8dd93d5a4ef0c521d0c6d8552abad29 | MATLAB | 4,827 | 120 | % Name: Robert Kim
% Date: 05-13-2023
% Email: robert.f.kim@gmail.com
% one_modality_intact_across_models.m
% Description: Evaluate the INTACT one-layer one-modality (instr) RNN models
% across all 5 trained networks. Generates 400 random instruction-task trials
% per network, scores anti-DMS / pro-DMS performance, and... |
8fdceea4ad6b2cfca45f12e1f3949b2b5271a9e75a0b72c9e3230fa594ede3eb | MATLAB | 4,829 | 133 | %% Preprocess Data
%Run one animal's data through this pipeline at a time
%Input = directory containing full recording data from a single animal.
%This should consist of raw intan files where each file contains one
%minute of data from all channels.
%Output = an experiment directory for this animal/recordi... |
dcf34080a9cb449560370e6fd6dcf8e00b40189b81d1fcea4992d04732f46c0d | MATLAB | 4,830 | 129 | function varargout = save(tree, filename)
% XMLTREE/SAVE Save an XML tree in an XML file
% FORMAT varargout = save(tree,filename)
%
% tree - XMLTree
% filename - XML output filename
% varargout - XML string
%
% Convert an XML tree into a well-formed XML string and write it into
% a file or return it as a string i... |
ebf235b7bf01cdd8212278363d4b854467fcdae51572257ecd4fdce869cf219d | MATLAB | 4,831 | 93 | function data=rmlinesc(data,params,p,plt,f0)
% removes significant sine waves from data (continuous data).
%
% Usage: data=rmlinesc(data,params,p,plt,f0)
%
% Inputs:
% Note that units of Fs, fpass have to be consistent.
% data (data in [N,C] i.e. time x channels/trials or a single vector) - requi... |
b6daa48b164a164fb6f9bc744a2d7ce572d5bebb17bc5f96131c75a14c44cd94 | MATLAB | 4,832 | 124 | function [TypeOfSpike,BurstStarts,BurstEnds,BurstDurations,NumSpikesInBursts,numberBursts] = BurstDetect(spikeTimes_msec, BurstThreshold_msec, TailThreshold_msec, minNoSpikes)
TypeOfSpike = zeros(1,length(spikeTimes_msec));
if spikeTimes_msec(2) - spikeTimes_msec(1) < BurstThreshold_msec
TypeOfSpike(1) = 1; % 1 fo... |
e25b85412b0ab4dfde200f0fbcf61e92bb36d64d3944e25de2b37efbe03ce793 | MATLAB | 4,833 | 143 | % pop_dipfit_gridsearch() - scan all ICA components with a single dipole
% on a regular grid spanning the whole brain. Any dipoles that explains
% a component with a too large relative residual variance is removed.
%
% Usage:
% >> EEGOUT = pop_dipfit_gridsearch( EEGIN ); % pop up interactive window
% >> EEGO... |
236494c93140d842901e6076374c76eb1b2a2acd1359a228514bf6a42307d888 | MATLAB | 4,838 | 129 | function varargout = save(tree, filename)
% XMLTREE/SAVE Save an XML tree in an XML file
% FORMAT varargout = save(tree,filename)
%
% tree - XMLTree
% filename - XML output filename
% varargout - XML string
%
% Convert an XML tree into a well-formed XML string and write it into
% a file or return it as a string i... |
843f4f7c89c9217e89beac06be9c80f90355fb3fb485e51d1c33348312290fa6 | MATLAB | 4,839 | 140 | function [matched,only1,only2] = Match(list1,list2,varargin)
%Match - Replace values in one list with closest values in a second list.
%
% USAGE
%
% [matched,only1,only2] = Match(list1,list2,<options>)
%
% list1 first list
% list2 second list
% <options> optional list of property-va... |
313ae29fa83bb14dc66ed29b4bb2d487a6791375fb29badb7da1f43bc82dabe3 | MATLAB | 4,840 | 112 | function ea_CaptureFigVid(ViewZ, FileName,OptionZ)
% CaptureFigVid(ViewZ, FileName,OptionZ)
% Captures a video of the 3D plot in the current axis as it rotates based
% on ViewZ and saves it as 'FileName.mpg'. Option can be specified.
%
% ViewZ: N-rows with 2 columns, each row are the view angles in
% ... |
110c1061c9d2c92e22e80e579e6549b64388735030230b229fd226112529da5a | MATLAB | 4,842 | 135 | % Minimize order of a lowpass FIR filter (magnitude design)
% "FIR Filter Design via Spectral Factorization and Convex Optimization"
% by S.-P. Wu, S. Boyd, and L. Vandenberghe
% (figures are generated)
%
% Designs an FIR lowpass filter using spectral factorization method where we:
% - minimize the filter order
% - hav... |
ef93ea3768c015ee225abae2c3978b5a498d971496abf17c60ec74e9bb2d6819 | MATLAB | 4,843 | 108 | function [stress_tensor, cell_stress] = get_viscous_qvm_stress(V, C, topo, KP, P0, KA, A0, strain, Fvx, Fvy)
% GET_VISCOUS_QVM_STRESS Compute the tissue-level and per-cell stress
% tensors, including the viscous (cell-cell adhesion) force contribution,
% under Lees-Edwards (sheared) periodic boundary conditions.
%
% ... |
e6f98645d0df3335fb2ef0a5538cce3cc5393c74027b6e739ce7a406b3580662 | MATLAB | 4,848 | 64 | function para_default = defaultparameter
% ------------------ edit with caution ---------------------------------
%% movie denoise for feature detection (Don't change these parameters unless you are confident)
para_default.GaussKernel = [4, 4, 2]; % movie denoise kernel (kernel size, kernel size, kernel SD)
para_def... |
c6df346186f808b0e66bcf08d1a70f28032fbf7b755056a7ef0c58a4fae9441f | MATLAB | 4,849 | 43 | %Admin functions (adminfunc folder):
% <a href="matlab:helpwin abouteeglab">abouteeglab</a> - No help information
% <a href="matlab:helpwin eeg_checkchanlocs">eeg_checkchanlocs</a> - Check the consistency of the channel locations structure...
% <a href="matlab:helpwin eeg_checkset">eeg_checkset</a> ... |
dc1e4b704067367a679e636c7d295f6534629fc5b756e8a15e9f03ccb7e90310 | MATLAB | 4,850 | 157 | function [data,t] = SurveyCCG(units,varargin)
%SurveyCCG - Compute and plot cross-correlograms (CCGs) for all subsessions.
%
% USAGE
%
% [data,t] = SurveyCCG(units,<options>)
%
% units optional list of units, i.e. [electrode group, cluster]
% pairs; set cluster to -1 to process all cl... |
f0d721e5ae9f009a2ae5deab348b607ce6ae90823d5a151ec6e1a4d8045d5121 | MATLAB | 4,857 | 174 | function [t,amps,data,aux] = read_intan_data(filename)
% [t,amps,data,aux] = read_intan_data
%
% Opens file selection GUI to select and then read data from an Intan
% amplifier data file (*.int).
%
% t = time vector (in seconds)
% amps = vector listing active amplifier channels
% data = matrix of electrode-r... |
3ff21b080efe6125eb5335bf42b8e7c02c3b7e9dd3e573437d46c0ad603e7179 | MATLAB | 4,864 | 173 | function keep_con = bz_PlotMonoSyn(ccgR,sig_con,Pred,Bounds,completeIndex,binSize,duration)
% Manual sorting
%click to delete the ccg (turns pink)
keep_con = sig_con;
window =false(size(ccgR,1),1);
window(ceil(length(window)/2) - round(.004/binSize): ceil(length(window)/2) + round(.004/binSize)) = true;
halfBins =... |
204a4fbf8a31520a3c80c45be5bad9c08704a5e02dbf466dc7923bd357763552 | MATLAB | 4,865 | 175 | function [ SM ] = WriteTopicsMult( WPM , BETAM , WOM , K , E , M , FILENAME )
%% Function WriteTopicsMult
%%
% |[ SM ] = WriteTopicsMult( WPM , BETAM , WOM )| writes the most likely entities
% (e.g. words, authors) per topic to a cell array of strings |SM|. The
% difference with function WriteTopics is that for ea... |
2b8e75bc3b23a98a9906eb0a41d9a551e733fa7732d173864951c10d83c3d0ac | MATLAB | 4,869 | 178 | function hpol = myPolar(theta,rho,maxrho,line_style)
% this is same as polar, but you can set the maximum rho value.
if nargin < 1
error('Requires 2 or 3 input arguments.')
elseif nargin == 2
if isstr(rho)
line_style = rho;
rho = theta;
[mr,nr] = size(rho);
if mr == 1
... |
cb17c32da6d884885118a9f67c88a7cca4e5ad2f74e50d0e04e27a5aa564c664 | MATLAB | 4,874 | 128 | function [colormap]=cbrewer(ctype, cname, ncol, interp_method)
%
% CBREWER - This function produces a colorbrewer table (rgb data) for a
% given type, name and number of colors of the colorbrewer tables.
% For more information on 'colorbrewer', please visit
% http://colorbrewer2.org/
%
% The tables were generated fr... |
15c612ac9d80ea6f52212df68d3357137593286ce29dd99f01b21b16d8060d35 | MATLAB | 4,877 | 148 | function [node,elem,face,success]=surf2mesh(v,f,p0,p1,keepratio,maxvol,regions,holes,forcebox)
%
% [node,elem,face]=surf2mesh(v,f,p0,p1,keepratio,maxvol,regions,holes,forcebox)
%
% create quality volumetric mesh from isosurface patches
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2007/11/24
%
% input paramete... |
b2d573b84b95c07608e73e7aa8ca877f6a3d705e677ab403e16e8ca8ef48000a | MATLAB | 4,878 | 138 | % GETPROBLEM Script for locating, reading and convert to SeDuMi, a problem
% with the name specified by the variable `pname'. You have to define the
% variable 'pname' before using this script.
%
% Usage: pname = 'problemname'; getproblem
% Problem returned in (At,b,c,K).
%
% IMPORTANT
% 1. If you have an envi... |
513d49e317af0ef1bac8ad9e052ae995193ad2be0beccbaf269547c5575c30d9 | MATLAB | 4,879 | 162 | function mat_epochs = G_EpochTS( mat, events, seg, varargin)
% Epoch time series into segments
%
% Input
% mat, channel x samples
% events, vector of events locations (in samples)
% epoch_range, [lo_boundary, hi_boundary] relative to each event (in
% samples) where a negative number m... |
130114fc0f4b3cb42a751939bfc9f681a36624958dd99281a1222b67e6c24737 | MATLAB | 4,886 | 183 | function D = ea_pdist2( X, Y, metric )
% Calculates the distance between sets of vectors.
%
% Let X be an m-by-p matrix representing m points in p-dimensional space
% and Y be an n-by-p matrix representing another set of points in the same
% space. This function computes the m-by-n distance matrix D where D(i,j)
% is t... |
b9391b1b94a437ff017b0fd54ee89965fda04113c0a185d57fef78296bdbc9e4 | MATLAB | 4,887 | 145 | % ConvertBasler2pos - Convert Basler data to pos file format
%
% USAGE
%
% ConvertBasler2pos(filebasename,<options>)
%
% filebasename basename of the video file (should be filebasenmae.avi)
% <options> optional list of property-value pairs (see table below)
%
% ======================================... |
eaa528049e743f6a61ebea47b357699a618abf644b4d39afb6d86041231f6cc3 | MATLAB | 4,888 | 122 | %% FORMATTOOL - converts simple data format to dataraster format
% Organizes data from simple formats (e.g. voltage value vectors) to the
% dataraster format for processing in the information analysis. For each
% point in timelocks, data will be binned around the time lock point. One
% bin will start for time values eq... |
f8fb91ca7047a2e4247f009e01d6fb592b4051a733cc5683bb09f9cc39c70a5b | MATLAB | 4,888 | 110 | function linelabel(vectors)
%LINELABEL Labels plotted lines.
% LINELABEL(LIBRARY), allows the user to select points and labels each
% with the row number of its closest (Euclidean) match among the rows of
% the matrix LIBRARY. When the mouse is clicked in the axis, the
% nearest point is selected and l... |
515489e8b2d08889c83024cf00260a596ff0461ae38224751b5995244d401222 | MATLAB | 4,890 | 110 | function cifti = cifti_struct_create_from_template(ciftitemplate, data, type, varargin)
%function cifti = cifti_struct_create_from_template(ciftitemplate, newdata, type, ...)
% Create a new cifti struct using an existing cifti as a template for the dense or
% parcels dimension.
%
% The 'type' ... |
45be163d3a4ccb5f04c64da6c659f672d55aba30b5eee9c17a26339437bc7a2f | MATLAB | 4,893 | 104 | function [S,t,f,R,Serr]=mtspecgrampb(data,movingwin,params,fscorr)
% Multi-taper time-frequency spectrum - binned point process
%
% Usage:
%
% [S,t,f,R,Serr]=mtspecgrampb(data,movingwin,params,fscorr)
% Input:
% data (in form samples x channels/trials or single vector) -- required
% movingwi... |
2ebbd164d1c14efbbe1c622d19bb429de60d3d1955fc2c6311fb378c24a27b6d | MATLAB | 4,896 | 131 | function [database_train, database_train_noisy, params_train, sigma_mppca, bunique, Ndirs_per_Shell] = build_training_set(SANDIinput)
% Builds the dataset for supervised training of the machine learning models
% for SANDI fitting.
%
% Author:
% Dr. Marco Palombo
% Cardiff University Brain Research Imaging Centre (CUBR... |
23e10098a80be538821cd9e0706eab1bb404adf4982bddfa282c45a6d48062f6 | MATLAB | 4,900 | 150 | function obj=stat_boxplot(obj,varargin)
%stat_boxplot() Create box and whiskers plots
%
% stat_boxplot() will create box and whisker plots of Y values for
%unique values of X. The box is drawn between the 25 and 75
%percentiles, with a line indicating the median. The wiskers
%extend above and below the box to the most ... |
4d9dd51ad293c1094a46e7136a9f638158f4b7833a0697c4da3651ab92312b29 | MATLAB | 4,900 | 131 | % this script reads all the spike timestamp and a/d info from a plx file into matlab
% variables.
% Open a plx file
% this will bring up the file-open dialog
StartingFileName = '';
%StartingFileName = 'c:\plexondata\NSSample.plx';
%StartingFileName = 'c:\plexondata\au101602a.plx';
[OpenedFileName, Version, Fre... |
f702d8afb3098fb222ace628b3af80a47f799d788af9fe885a55f068178a23ba | MATLAB | 4,903 | 162 | function h = mArrow3(p1,p2,varargin)
%mArrow3 - plot a 3D arrow as patch object (cylinder+cone)
%
% syntax: h = mArrow3(p1,p2)
% h = mArrow3(p1,p2,'propertyName',propertyValue,...)
%
% with: p1: starting point
% p2: end point
% properties: 'color': color accordin... |
4287e0e677b17409863fd2d0c5a2fa8eac4f0ff7610ee019ba009c6d34465d1d | MATLAB | 4,905 | 140 | %% LaBGAScore_pet_prep_1_dat_behavioral_data.m
%
%
% *USAGE*
%
% This script sets up the DAT structure for second level analysis of PET
% data using CANlab tools in a single PET session design
%
%
% *OPTIONS*
%
% * behavioral_data_filename name of the .tsv file in BIDS/phenotype containing subject ratings, default '... |
93c84fa74aa7927133d19472a9942e9db686d902a140de99f3b3b70f7fb46198 | MATLAB | 4,906 | 131 | function [phaseamplitude] = bz_PhaseAmplitudeDist(lfp,phaserange,amprange,varargin)
% [phaseamplitudemap,ampfreqs,phasecenters] = bz_PhaseAmplitudeDist(lfp,phaserange,amprange)
%This function calculates the mean amplitude of multiple higher frequency bands at
%a the phase for a single lower frequency band signal
%
%%IN... |
05624d265f6b040d1f632e3110c820c998dd4dd296062efd84b0bceb60a2292e | MATLAB | 4,907 | 86 | function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencysegc(data1,data2,win,params)
% Multi-taper coherency, cross-spectrum and individual spectra with segmenting - continuous process
% computed by segmenting two univariate time series into chunks
%
% Usage:
% [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencysegc(data... |
dc7145e6971decb8150fc0dd3bbf1d5a30069063eab97190b805e3cf6e0512a9 | MATLAB | 4,908 | 101 | function [datafit,Amps,freqs,Fval,sig]=fitlinesc(data,params,p,plt,f0)
% fits significant sine waves to data (continuous data).
%
% Usage: [datafit,Amps,freqs,Fval,sig]=fitlinesc(data,params,p,plt,f0)
%
% Inputs:
% Note that units of Fs, fpass have to be consistent.
% data (data in [N,C] i.e. tim... |
5c3bd8844564027ef60aa203bf0b093f16eff59fc966942828593fe431a855d5 | MATLAB | 4,909 | 116 | %% Step 2 Tiny Dancers: Epoching and artefact rejection
clear all
clc
addpath 'C:\Users\tnguyen\OneDrive - Fondazione Istituto Italiano Tecnologia\Documenti\MATLAB\functions'
addpath 'D:\MUSICOM_EEG/onsets'
addpath('D:\MUSICOM_EEG/EEG/')
addpath('C:/Users/tnguyen/OneDrive - Fondazione Istituto Italiano Tecnolog... |
48c07a88d7b1c2394f26da16a9e51e8018b7e541c1f68835270ca3e238a696e1 | MATLAB | 4,919 | 143 | function spikes = GetSpikeTimes(units,varargin)
%GetSpikeTimes - Get spike timestamps.
%
% USAGE
%
% spikes = GetSpikeTimes(units,<options>)
%
% units optional list of units, i.e. [electrode group, cluster] pairs;
% special conventions:
% cluster = -1 all cluster... |
2086f879d2cc22e1cb3cdd7194137cd266d6d2672a7b009844496278e35dd681 | MATLAB | 4,922 | 146 | function [output,status] = urlwrite(urlChar,location,method,params)
%URLWRITE Save the contents of a URL to a file.
% URLWRITE(URL,FILENAME) saves the contents of a URL to a file. FILENAME
% can specify the complete path to a file. If it is just the name, it will
% be created in the current directory.
%
% F =... |
a59f79dfd47572ee113059188676c5812e2e039b4f48de2cbb0776685ac78dd1 | MATLAB | 4,925 | 104 | function [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)
% Multi-taper time-frequency spectrum - point process times
%
% Usage:
%
% [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)
% Input:
% data (structure array of spike times with dimension channels/trials;
% ... |
753824419ad5fe106acccecd9a061e78af30a79640fdf6b3937bc5dc9fe98995 | MATLAB | 4,926 | 136 | %% RUN_PERMUTATION_TESTS
% The help file shows you how to run permutation tests for nonparametrical
% significance testing for correlational data
% More information can be found here: https://docs.google.com/document/d/e/2PACX-1vTPQTLiYvKNUBpVc3PlRHDyonNaVLu-IAyEqyD8-M3jqvhVTPwvDi8wKNOVthNc6BqGxrcefyqrJSET/pub
%
% by m... |
775c45d75635f8fa15550ed7cdc4848f9051796622610b86d0bdfff28c161ac9 | MATLAB | 4,927 | 231 | function rtf(plot_frq,flag_save)
close all
evalin('base','stop=0;');
%=========SET THE BASIC FIGURE=================
fig = figure('Position',[500,500,800,600],...
'NumberTitle','off',...
'Name','Scope',...
'doublebuffer','on',...
'HandleVisibility','on',...
'KeyPressFcn', @k... |
75ec0f88638690869fa02d58c262b4887b6a91c0e5dffae87ec4df92ba392f74 | MATLAB | 4,932 | 99 | function obj=geom_line(obj,varargin)
% geom_line Display data as lines
%
% This will add a layer that will display data as lines
% If the data is not properly grouped/ordered things can look weird.
p=inputParser;
my_addParameter(p,'dodge',0);
my_addParameter(p,'alpha',1);
parse(p,varargin{:});
obj.geom=vertcat(obj.ge... |
2870b6b219576f9cb1a956c854158aef525265f7dd6b6da235b92cd4688573f4 | MATLAB | 4,937 | 128 | function [ccg,ic] = chXcorr2(hc_L,hc_R,fs,varargin)
%CHXCORR2 Calculate cross-correlograms with a range of options.
%
% CCG = IOSR.AUDITORY.CHXCORR2(HC_L,HC_R,FS) cross-correlates the input
% 2-D matrices HC_L and HC_R over 10ms frame with a maximum lag of 1ms.
% It is assumed that the number of frequency channe... |
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