sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b2f570e61c25c314810b62301da5b8440d612ac4e5dfcc67a2255bec347421c9 | MATLAB | 5,131 | 147 | function statTestResult = condColocStatTest(saveRes)
%STATTESTRESULT takes compiled results from plotSaveConditionalColoc.m and do ranksum test on the results
%
%SYNOPSIS statTestResult = condColocStatTest(saveRes)
% Function does a ranksum test comparing each conditional colocalization
% measure to its corresponding... |
10b0d2201c8b957742e9b71446a85e3787371097ad93f31a57c0197a3b86a8af | MATLAB | 5,134 | 159 | function fit = fit_meta_d_mcmc_groupCorr(nR_S1, nR_S2, mcmc_params, fncdf, fninv, name)
% fit = fit_meta_d_mcmc_groupCorr(nR_S1_1, nR_S2_1, nR_S1_2, nR_S2_2, mcmc_params, fncdf, fninv)
%
% Estimates correlation coefficient between metacognitive effiency
% estimates between two domains. See fit_meta_d_mcmc_group for ful... |
c9c24f50dac25688268f54d70ef56e0e4ee91b6795a5c1f59dcc9e4a225ccb99 | MATLAB | 5,134 | 129 | function call_behresp(handles)
mainfig_pos = get(handles.mainfigure, 'Position');
clear trace_stamp_pool trace_num_all ttlabel_pool
for k = 1:length(handles.datafilename)
handles = loadtrace(handles, k);
framestamp = handles.framestamp{1};
stampinfo = handles.stampinfo{1};
if handles.plotRawdff == 0 && ... |
3b15389ebb499399e12f93befdeb6c5047f51746d6df21c72452db303c2e4a09 | MATLAB | 5,135 | 160 | function coeffs = nonneg_poly_coeffs( deg, trig, mm ) %#ok
%NONNEG_POLY_COEFFS Coefficients of nonnegative degree-n polynomials.
% NONNEG_POLY_COEFFS(DEG), where DEG is a nonnegative integer, creates a
% vector variable of length DEG+1 and treats its values as
% coefficients of a polynomial (in the same sense... |
d6809c8c296687fa9aed6e88037516b4fb9e88cad8c056609ae5890ff5443e1c | MATLAB | 5,135 | 148 | % Behavioral variables
% -------------------------------------------------------------------------
% unpack variables
names = DAT.BETWEENPERSON.between_subject_design.Properties.VariableNames;
for i = 1:length(names)
eval([names{i} ' = DAT.BETWEENPERSON.between_subject_design.' names{i} ';'])
end
disp(names)
% Gr... |
a472658c36afee0989a46a9be4d571b67792f6ad8aaa75b9044871d880206147 | MATLAB | 5,137 | 90 | %%*************************************************************************
%% parameters.m: set OPTIONS structure to specify default
%% parameters for sqlp.m
%%
%% OPTIONS.vers : version of direction to use.
%% 1 for HKM direction
%% 2 for NT direction
%... |
653025cfbd5f77a96455746c2ab5bf69c190abcb2c5280cc31d6b368c7c704cd | MATLAB | 5,138 | 101 | function [ft_struct,rejected_comps] = RFT_IClabel(ft_struct,eeglab_template_file,numComp,threshold)
%%% From a fieldtrip structure (with N trials), concatenates all trials,
%%% create an eeglab structure with this 'single concatenated trial',
%%% cleans the data with ASR, based on cutoff and windowlen ... |
8a2d34493a5279ee4e20a19b1242d6bfd8eb34f26aa2a913427b9fb3e24d264a | MATLAB | 5,138 | 140 | % std_substudy() - create a sub-STUDY set by removing datasets, conditions, groups, or
% subjects.
% Usage:
% >> [ STUDY ALLEEG ] = std_substudy(STUDY, ALLEEG, 'key', 'val', ...);
%
% Optional Inputs:
% STUDY - existing study structure.
% ALLEEG - vector of EEG da... |
8184b8378745f9437fe9fec359ed41c91c174c1061886d96b1b2062f04da4ddf | MATLAB | 5,139 | 164 | %% Load and display JSON file with study info, if we have it
plugin_display_study_info_json;
%% Load DAT structure with setup info
% ------------------------------------------------------------------------
savefilename = fullfile(resultsdir, 'image_names_and_setup.mat');
load(savefilename, 'DAT')
% For publish outpu... |
997a1abea0725e39e9daf55e5642b055349ec337ca26671bfd7808d4110538ef | MATLAB | 5,141 | 112 | function rqa_plot(data, rp, RESULTS, tau, dim, DIM, Zscore, Norm, radius, wrp, type)
scrsz = get(0,'ScreenSize');
f = figure('Position',[scrsz(3)/4 scrsz(4)/4 scrsz(3)/3 scrsz(4)/2]);tabgp = uitabgroup(f);
binary = uitab(tabgp,'Title','Binary');
heatmap = uitab(tabgp,'Title','Heatmap');
% Binary Plot (Tab 1)
a1 = axes... |
7bb129c368441aaeaa99ebec2d13236044781f19ff0462393954ab6d1676be69 | MATLAB | 5,142 | 123 | classdef LeG_parfor_wait < handle
%This class creates a waitbar or message when using for or parfor.
%Required Input:
%TotalMessage: N in "i = 1: N".
%Optional Inputs:
%'Waitbar': true of false (default). If true, this class creates a
% waitbar.
%'FileName': 'screen' or ... |
9597d020074fa6fdef9287d4b609e4381f54173c57a67aa5c64ee09ec6fcbcdf | MATLAB | 5,142 | 158 | function [ cellinfo,filename ] = bz_LoadCellinfo(basePath,cellinfoName,varargin)
%[ cellinfo,filename ] = bz_LoadCellinfo(basePath,cellinfoName) function for
%for loading cellinfo.mat files. cellinfo.mat files are saved as:
% datasetPath/baseName/baseName.cellinfoName.cellinfo.mat
%
%INPUT
% basePath
% cellinfoName... |
7fc30b87629d7427ca5233e8d7e8140742c143f869cfc41fe98ecec84dc2a1de | MATLAB | 5,143 | 105 | function [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpb(data,win,params,segave,fscorr)
% Multi-taper segmented spectrum for a univariate binned point process
%
% Usage:
%
% [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpb(data,win,params,segave,fscorr)
% Input:
% Note units have to be consistent. See chronux.m for more i... |
be429d4a0f90409728e96e68ac85edbbbc9d1832dec82aba7a5b41fcbdbd104e | MATLAB | 5,143 | 120 | function [likelihood, results, label, params, tau] = CBIG_hMRF_adapt_d(params, label, i, full_corr_mat,...
lh_mask, rh_mask, avg_mesh, tau, Neighborhood_lh, Neighborhood_rh, Neighborhood_lh_rh)
% [likelihood, results, label, params, tau] = CBIG_hMRF_adapt_d(params, label, i, full_corr_mat,...
% lh_mask, rh_mask, av... |
d2bf32e73c01d9db5acb4436e9e8fb70b9df97d9e5649c7383f03911877dc441 | MATLAB | 5,143 | 179 | %% figure S6
load('figure5_data')
%%
an_col = [30 58 205]/255;
aw_col = [229 32 21]/255;
% awake_color1_5 = [0.8272 0.3489 0.2865];
% anes_color1_5 = [0.1792 0.4769 0.7191];
norm_lim = [2.5*10^-3 3.17*10^-3];
x_lim = [0 360]; % Angle data range
%% A
% Define parameters
norm_... |
9bb8f0a60537aa2742ffa7f252b86804fa51ad491cdd8e9f6c66f9c01cc54969 | MATLAB | 5,145 | 161 | function [tau, curve, info] = ami_kde(x, L, opts)
%AMI_KDE Average mutual information versus lag, kernel density estimator.
% TAU = AMI_KDE(X,L) returns the lag of the first local minimum of the
% average mutual information of X with itself over lags 0:L, using Gaussian
% kernel density estimates of the marginal ... |
8ae5893f1a6b27ce15d9adc32e3439bc210ae0fb1f4e7437f5636ea79f0b3073 | MATLAB | 5,148 | 147 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
31fd88a1af2d7bac49fc46babfe02fd430dbbc3b381e251b822d5c131a0e82ec | MATLAB | 5,150 | 147 | function [dz,vdz,Adz]=two_group_test_spectrum(J1,J2,p,plt,f)
% function [dz,vdz,Adz]=two_group_test_spectrum(J1,J2,p)
% Test the null hypothesis (H0) that data sets J1, J2 in
% two conditions c1,c2 have equal population spectrum
%
% Usage:
% [dz,vdz,Adz]=two_sample_test_spectrum(J1,J2,p)
%
% Inputs:
% J1 tapered fou... |
64d097c742610795dfe1357d47d6b4959b58e56377f1eb8c2b06c3ad6855bc24 | MATLAB | 5,151 | 134 | %EPS2PDF Convert an eps file to pdf format using ghostscript
%
% Examples:
% eps2pdf source dest
% eps2pdf(source, dest, crop)
% eps2pdf(source, dest, crop, append)
% eps2pdf(source, dest, crop, append, gray)
% eps2pdf(source, dest, crop, append, gray, quality)
%
% This function converts an eps file... |
446af4e7e22c0737c775514c8ff83082b24996fc9415228ebabd7f5f309af4d0 | MATLAB | 5,152 | 89 | %% SimpleFieldSim3DViewElement - A panel that represents a View Element
% to configure a SimpleFieldSim3D Graphics Object
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicne
% 2013 - 2017
% mail@andreashusch.de, husch.andrea... |
eeba7c2f9c78248640ad062f356bcbc296c2d005a234b5bb523127e0cae26174 | MATLAB | 5,153 | 145 | function [a, cb] = plot_subcortical(data, varargin);
%
% Usage:
% [a, cb] = plot_subcortical(data, varargin);
%
% Description:
% Plot subcortical surface with lateral and medial views (authors: @saratheriver)
%
% Inputs:
% data (double array) - vector of data, size = [1 x v]. One value per
% subcortical... |
54d3339ac6bd9dfd6f1853a435aeba6ff1259fab1616dc96ac00c38d1677138c | MATLAB | 5,158 | 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',...
'Ke... |
e148c1e515a708005eee96bb63639818e2b79dbebf800343a72a60b3127629ac | MATLAB | 5,158 | 144 | function [dev devControl] =...
bz_peerPrediction(spikeTimes,winRange,extraPredictors,pairsToRun)
% INPUT
%
% spikeTimes - (M x N x D) matrix of spike times. M is the cell number,
% N is the trial number, and D is length of a trial in
% milliseconds
% winRange - vector tha... |
abea870acd7d06ffce225456ea2b4111c409412d7921e6cf6c0a57366a3ac24c | MATLAB | 5,161 | 157 | function y = base64encode(x, eol)
%BASE64ENCODE Perform base64 encoding on a string.
%
% BASE64ENCODE(STR, EOL) encode the given string STR. EOL is the line ending
% sequence to use; it is optional and defaults to '\n' (ASCII decimal 10).
% The returned encoded string is broken into lines of no more than 76
% ... |
49f360565302d4201b6351f3d9a7f4b6d3a7d59bd54ced80ae82f5d6866d96dc | MATLAB | 5,162 | 114 | function [leftpos rightpos leftM rightM] = getPFNbumps(allflies,trialtypes,flies,datatype)
% This function produces summary data structures for the left and right
% halves of the PB for PFN bump data.
% Be sure to clear the values of 'leftpos', 'rightpos, 'leftM', and 'rightM'
% before running the function.
%... |
87099925dc5bf08d239265939c53919207c809f8119b7cafb78e233294068297 | MATLAB | 5,162 | 162 | % compplot() - plot a data epoch and maps its scalp topography at a given time
%
% Usage: To plot the projection of an ICA component onto the scalp
% >> projdata = icaproj(data,weights,compindex);
%
% then >> compplot(projdata);
%
% else to plot an EEG epoch with a topoplot at one selected time point
% ... |
44a3f29d74c2ce6d334a54a87f047315d012096d0bf3371986358217e67b0c2e | MATLAB | 5,163 | 166 | %CCG - Compute multiple cross- and auto-correlograms
%
% USAGE
%
% [ccg,t] = CCG(times,groups,<options>)
%
% times times of all events
% NOTE: spiketimes in SECONDS.
% groups group IDs for each event in time list (should be
% integers 1:nGroups)
%
% alter... |
3de342832605e7169f46db79dca114c1af44aec3dc54cacf65e6d76320d62dc9 | MATLAB | 5,165 | 112 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
f3f2b946d132f57c158cf61df6f67169d52e79c67c3128843671597fae44c89c | MATLAB | 5,165 | 136 | function contact_perc_currents = ea_get_optimal_currents(N_contacts,stimfolder,side,plot_progress)
% check pam_optimizer results and return currents for the best solution
if side == 0
side_suffix = '_rh';
else
side_suffix = '_lh';
end
if isfile([stimfolder,filesep,'NB',side_suffix,filesep,'optim_iterations_C... |
62b26454e78cc25408d20541da29d51cffdd3c9a46af927fccd3d7773c13a704 | MATLAB | 5,168 | 155 | function [At,b,c,K]=fromsdpa(fname)
% readsdpa Reads SDP problem from sparse SDPA-formatted input file.
% [At,b,c,K] = readsdpa(fname) produces conic optimization problem
% data, as can be used by sedumi. "fname" contains a full pathname
% to the SDPA 4.10-formatted file. (SDPA is a stand-alone solver for
% ... |
7b438e3dfc74a4767ce87e53c3ab686d4bbf76f0d86bafc7f4b40a59cc6d6c77 | MATLAB | 5,170 | 172 | function [pos_ts,pos,lfp_ts,lfp_sig,spk_ts] = import_spiking_data(filepath, tetrode, unit)
% [pos_ts,pos,lfp_ts,lfp_sig,spk_ts] = import_spiking_data(filepath, tetrode, unit)
%
% Extracts behavioral, lfp and spiking data from filepath.
%
% Inputs:
% filepath: Full path to the directory for the target session
% tetr... |
c139d88610ba8ec3057f6f0b23fbb93b99a8f13dc467bf7ba9cb374e16e46bb5 | MATLAB | 5,171 | 95 | function [fid, hdr, cleanupObj] = write_nifti2_hdr(hdr, filename)
mydelete(filename); %avoid permission issues, and replace links with files instead of overwriting the pointed-to file
fid = fopen(filename, 'Wb'); %always write native-endian - capital W means fwrite() doesn't flush every call
if fid == -1
... |
7a7262ac036d101bebb3c87e13e94f450cd8ec87ed0919b57be261052398d752 | MATLAB | 5,172 | 176 | % THIS SCRIPT extracts region averages and local pattern expression in each
% parcel of the Spm Anatomy v22c 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 ac... |
314ad4f1ae7d87bb9de17ecb46da319fa76e0bc81d44713ae4282b2f86ed03a9 | MATLAB | 5,175 | 133 | %%***************************************************************
%% degeneracy: determine if an SDP problem is non-degenerate.
%%
%% [ddx,ddz,B1,B2,sig1,sig12] = degeneracy(blk,At,X,y,Z);
%%
%% Assume that strict complementarity holds:
%% for primal non-degeneracy, we need rank([B1 B2]) = m
%% for dual non-degeneracy,... |
458065d50f6a4bb4e324eb3acd8ea904e408f5b0175edf1c3edb5a3f5328e7a7 | MATLAB | 5,175 | 125 | % mainfolder0 = '/Users/yiyuan/OneDrive - University of Essex/PG Research/0A_Journal/202004_unknown Journal_Probability Score/1_Results/0_Final Results/Results_Main/';
% figurefolder = '/Users/yiyuan/OneDrive - University of Essex/PG Research/0A_Journal/202004_unknown Journal_Probability Score/1_Results/0_Final Results... |
88f8b0c2e6a3b34e8fba6bf36bd521a35d37a46a14b8375042390bc8a4a7f339 | MATLAB | 5,177 | 174 | % Digital circuit sizing example (GP)
% Boyd, Kim, Patil, and Horowitz, "Digital circuit optimization
% via geometric programming"
% Written for CVX by Almir Mutapcic 02/08/06
%
% Solves the problem of choosing gate scale factors x_i to give
% minimum ckt delay, subject to limits on the total area and power.
% Uses max... |
6087d016b0ad6cd76ba528bfb6eac03f630971805ed303cd807de6ced1575f5d | MATLAB | 5,178 | 105 | % ----------------------------------------------------------------------- %
% M U L T I P L E T E S T I N G %
% ----------------------------------------------------------------------- %
% Function 'fdr_BH' computes the Benjamini-Hochberg correction of the %
% False Disc... |
a40b1b1214859f862519bfe535f0b0d9c65694e28599284580229880056edd90 | MATLAB | 5,180 | 147 | % THIS SCRIPT RUNS BETWEEN-PERSON CONTRASTS
% Assuming that groups are concatenated into contrast image lists.
% Requires DAT.BETWEENPERSON.group field specifying group membership for
% each image.
% --------------------------------------------------------------------
%% Load stats
switch myscaling_svm_between
... |
4291c91d6b30fe8b8120e9a4df021e5aefab3a2162cf1f537b3fb7c7c4bcdbf3 | MATLAB | 5,182 | 151 | function [maps,stats] = SurveyFiringMapsAutoCorr(units,varargin)
%SurveyFiringMapsAutoCorr - Compute and plot autocorrelogram maps for all conditions.
%
% USAGE
%
% [maps,stats] = SurveyFiringMapsAutoCorr(units,<options>)
%
% units optional list of units, i.e. [electrode group, cluster]
% ... |
c31d62ac6c2803aa873aeb8e0612a6e7c2153ab887cff8565965d23d9fc9077d | MATLAB | 5,183 | 114 | function [SS,tau]=mtspectrum_of_spectrumc(data,win,tapers2spec,params)
% Multi-taper segmented, second spectrum (spectrum of the log spectrum) for a continuous process
% This routine computes the second spectrum by explicitly evaluating the
% Fourier transform (since the spectrum is symmetric in frequency, it uses
... |
a573ab38ceb6f07e4259fffc65dbb1e9e95b3792a9ebb864e892f2544fcd7a1b | MATLAB | 5,189 | 217 |
function [n weights fod] = csd(data,bDirs,HRdirs, Strue,lmax)
SHscheme = genSH(double(bDirs'),lmax);
SHschemeOUT = genSH(HRdirs',lmax);
SHscheme300 = genSH(HRdirs',lmax);
shhres = SH2RH(amp2SH(Strue,SHscheme));
%shhres/shhres(1)
[n weights fod] = csdeconv (shhres, data, SHscheme,SHscheme300);
function [ locm... |
fd99d36df96ed947210eb45688348359b998fedeae8b16df365d0309564fcfb3 | MATLAB | 5,189 | 95 | function [fid, hdr, cleanupObj] = write_nifti2_hdr(hdr, filename)
mydelete(filename); %avoid permission issues, and replace links with files instead of overwriting the pointed-to file
fid = fopen(filename, 'Wb'); %always write native-endian - capital W means fwrite() doesn't flush every call
if fid == -1
... |
1bc9ffcb037e9117e65a0e0f2a46346089e7f33323b6fa2bb6d586c30b95225c | MATLAB | 5,190 | 129 | function affinefile = ea_spm_coreg(options,moving,fixed,costfun,doreslice,otherfiles,writeoutmat,interp)
% Wrapper for SPM coregistration
%
% SPM modifies the header of the moving image when doing coregistration
% (for both "Estimate" and "Estimate & Reslice"). This wrapper here will
% only modify the header if 'doresl... |
64ef9a3763e08f1699e0da39c1d3781f9b866f92aa590e767f8f89916c550188 | MATLAB | 5,192 | 150 |
%To combine vessel diameter along pericytes across animals
allnames={
'Tser4954b_res_cfr.mat'
'Tser4954c_res_cfr.mat'
'Tser5199_res_cfr.mat'
'Tser5072_res_cfr.mat'
'Tser5215_res_cfr.mat'
};
groupname='stimAllTrials';
all_rr1a_microns=[];
all_rr1nSEM_microns=[];
all_rr1a_percent=[];
all_rr1nSEM_percent=[];
all_rr2a... |
9391c4ae37131609b2f9394a952eaf0e180a0d0531be1f3b3eeda1752e9a5d3d | MATLAB | 5,201 | 148 | % LC oscillator design (GP)
% Boyd, Kim, and Mohan, "Geometric programming and its
% applications to EDA Problems", (DATE Tutorial 2005), pp.102-113.
% Original code by S. Mohan
% Written for CVX by Almir Mutapcic 02/08/06
%
% Designs an LC oscillator consisting of a loop inductor, varactors
% for fine tuning, binary w... |
0cc9322210b9c77f27ee791723b072b30bfc307aae63d479a707ba28c9a000d2 | MATLAB | 5,203 | 91 | function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpb(data1,data2,win,params,segave,fscorr)
% Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting
% two univariate binned point processes into chunks
%
% Usage:
% [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpb... |
ffb089899e705b5b51ca6a7cc3cc147f4468dd1b9eac7b5604a5e6273b115cb1 | MATLAB | 5,212 | 152 | function varargout = loadxml(filename,varargin)
%LOADXML Load workspace variables from disk (XML file).
% LOADXML FILENAME retrieves all variables from a file given a full
% pathname or a MATLABPATH relative partial pathname (see PARTIALPATH).
% If FILENAME has no extension LOAD looks for FILENAME and FILENAME.... |
f4b5b5aa50c810f6cd48c8f6acb8787d7de8a31dab295464f01d29727dbad1df | MATLAB | 5,218 | 144 | function obj=stat_ellipse(obj,varargin)
%stat_ellipse() Create confidence ellipses around 2D groups of
% points
%
% Parameters:
% 'type': The default '95percentile' displays an ellipse that
% contains 95% of the points (assuming a bivariate normal
% distribution). The option 'ci' will first compute boostrapped
% 2D mea... |
8c651b906d22ef21891078a7026d153d08519b68724aa0f492cb248362f24592 | MATLAB | 5,221 | 126 | function [hObject, eventdata, handles] = ea_convertGUIDEArguments(app, event)
%CONVERTTOGUIDECALLBACKARGUMENTS Converts App Designer callback
%arguments to GUIDE-style callback arguments.
% [HOBJECT, EVENTDATA, HANDLES] = CONVERTTOGUIDECALLBACKARGUMENTS(APP, EVENT)
% is automatically added to the be... |
c196d86cab36d9015f01108ab3acf13cbf26dd86c12d61f6ddfed2d18680cac3 | MATLAB | 5,221 | 106 | 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;
Dvol = sum(D)';
Dvole = sum(D,2);
IgV = Para.IgP;
indexs = find(Dvole>=(size(D,2)*IgV/100));
Dmasked = zeros(V.dim);
Dmasked(indexs) = 1;
f... |
affb72b6bb5ca338f0c2d2ee59967ef31b27f81ea3a5aa97b28ba88d75caee2b | MATLAB | 5,222 | 117 | function CortElecs = ea_importcorticalels(options)
% Import Cortical Electrodes
% __________________________________________________________________________________
% Copyright (C) 2017 University of Pittsburgh (UPMC), Brain Modulation Lab
% Ari Kappel
% save info to struct
CortElecs.patientname = options.patientname... |
80355435cf10aeeed28d7784cdad7e06ddf4a65261f188ee1cb4f25e13663e2a | MATLAB | 5,224 | 148 | function [V, C, topo] = T1_edgeswap(V, C, topo, T1_edge_ID)
% T1_EDGESWAP Perform a T1 (neighbor-exchange) topological transition on
% a single edge (non-sheared PBC version).
%
% [V, C, topo] = T1_EDGESWAP(V, C, topo, T1_edge_ID) collapses the edge
% T1_edge_ID (connecting vertices u0 and v0, shared by cells c1 a... |
5ca5c158a0eecdf871bb70dd95f6f55ce5921486e95ee36e89f924867e9d2685 | MATLAB | 5,225 | 167 | % cart2topo() - convert xyz-cartesian channel coordinates
% to polar topoplot() coordinates. Input data
% are points on a sphere centered at (0,0,0)
% or at optional input 'center'. This function
% is now DEPRECATED! See Important warning below.
%
% Usage: >> [t... |
8bf1804d1875780ad4edeff9ceb043ea234e2e3ee7b3962047c116f5273d72d7 | MATLAB | 5,225 | 186 | function baseline = CBIG_hypoTest_3t(betas, stats)
% baseline = CBIG_hypoTest_3t(betas, stats)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
baseline = zeros(9, 3);
%% AD
fprintf('\n--------------------------------- AD ---------------------------------\n\n');
%... |
9e61629101b889b23e84374a8017f0d03974f628ebdfb92a9dfd64a46eafeafe | MATLAB | 5,228 | 76 | function [matlabbatch]=batch_job(b,s,scannr)
%-----------------------------------------------------------------------
% Job configuration created by cfg_util (rev $Rev: 4252 $)
%-----------------------------------------------------------------------
%%
matlabbatch{1}.spm.spatial.realignunwarp.data.scans = b(scannr).da... |
59edbf9eaaa6d37cb7e3a41f5a25a08775b7375d3056ef08cfaf0320b133d406 | MATLAB | 5,233 | 103 | function [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpt(data,win,params,segave,fscorr)
% Multi-taper segmented spectrum for a univariate binned point process
%
% Usage:
%
% [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpt(data,win,params,segave,fscorr)
% Input:
% Note units have to be consistent. See chronux.m for more informat... |
5c8d09b1b6a0d86595414e6f9467609c0ab58884b57b060ee8b963ea77899940 | MATLAB | 5,234 | 152 | % Minimize thermal noise power of an array with arbitrary 2-D geometry
% "Convex optimization examples" lecture notes (EE364) by S. Boyd
% "Antenna array pattern synthesis via convex optimization"
% by H. Lebret and S. Boyd
% (figures are generated)
%
% Designs an antenna array such that:
% - it has unit a sensitivity ... |
0f55113fd5e0822939bcdbef0ef17339c2665c310d07390d802697473ec49a6a | MATLAB | 5,236 | 122 | function [ys,yi]=surr_pseudo_periodic(y,tau,dim,rho)
% [ys,yi]=surr_pseudo_periodic(y,tau,dim,rho)
% inputs - y, time series
% - tau, time lag for phase space reconstruction
% - dim, embedding dimension for phase space reconstruction
% - rho, noise radius
% outputs - ys, surrogate time series
%... |
d9e2c652430320f9718809384b1be513d64819b00c73b73a66f8118e2026facb | MATLAB | 5,241 | 151 | function frequency = Frequency(timestamps,varargin)
%Frequency - Compute instantaneous frequency for a point process (e.g. a spike train).
%
% Compute instantaneous frequency either by smoothing the point process using a fixed
% or adaptive Gaussian kernel, or by simply taking the inverse of the interevent intervals.
... |
5b504cd31e0152eee9e62c2c19041adfd01564affb7d11e692a347b7bf85da26 | MATLAB | 5,244 | 164 | %% RUN_MEASUREMENT_PREDICTION_STEP
% Driver: resolve project paths, pick ROI(s), run measurement prediction,
% optionally plot.
import fnirspower.*
P = fnirspower.setup_paths();
%% Load head model, forward model, dmu_a information
montageName = 'dense';
% Files
mesh_mat = fullfile(P.icbm_mesh_di... |
c639b977623d9af321c6d3a933ec606aeac3aaf515d17cdf45f9309c1667d266 | MATLAB | 5,245 | 164 | function [curves,stats] = SurveyTuningCurves(units,varargin)
%SurveyTuningCurves - Compute and plot tuning curves for all subsessions.
%
% USAGE
%
% [curves,stats] = SurveyTuningCurves(units,<options>)
%
% units optional list of units, i.e. [electrode group, cluster]
% pairs; set clus... |
e62ea2d131d644370ce9a0b3ab3a2bfebf17ad400d08d13f1ddcd2ca3e27a871 | MATLAB | 5,246 | 99 | function [Fval,A,f,sig,sd] = ftestc(data,params,p,plt)
% computes the F-statistic for sine wave in locally-white noise (continuous data).
%
% [Fval,A,f,sig,sd] = ftestc(data,params,p,plt)
%
% Inputs:
% data (data in [N,C] i.e. time x channels/trials or a single
% vector) - required.
% params... |
4dade328fb314bb98f0c869f6eb8fbee20cdbbf420d7226e78578d312ec0ff16 | MATLAB | 5,248 | 103 | function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypb(data1,data2,params,fscorr)
% Multi-taper coherency,cross-spectrum and individual spectra - binned point process
%
% Usage:
%
% [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypb(data1,data2,params,fscorr)
% Input:
% data1 (in form samples x ... |
a3c20f5f1fa8826952041b9fb6e703b24f8ebbd1d8477ab60c4d395519d5037d | MATLAB | 5,248 | 150 | function oimg = loadtiff_old(path, sFrame, num2read)
% Copyright (c) 2012, YoonOh Tak
% All rights reserved.
% Modified by Eftychios Pnevmatikakis, 01/2017.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are
% met:
%
% ... |
d68ad7fa0aff9e93b785ae360772be5073198768366b52081b9eba24c3a33edf | MATLAB | 5,249 | 135 | 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 tre... |
30028b21c1c18814f3fb8796b1f630aaccc90f8901c1533b682fa7aa34407035 | MATLAB | 5,250 | 147 | function colorMtx = colors(nColors, backgroundCol, type)
% JF, get distinguishable color-blind friendly colors
% ------
% Inputs
% ------
% nColors: number of colors to return (default: 15)
% backgroundCol: background color ('w' for white, 'b' for black, default: 'w')
% type: colormap type ('standard', 'wang', 'ibm', '... |
d55ce030a23825880a8e5b48b00c252f9ed1da514ec26ce940e2532844315c47 | MATLAB | 5,254 | 126 | %% TITLE OF HELP FILE - e.g., HOW_DO_I_xxx...
% One-line description of what this help file shows.
%% General instructions
%
% Instructions for creating a file:
% -----------------------------------------------------------------------
%
% - Try to give a brief, but complete, description
% - Code blocks with %% will ap... |
262e4a2db9f21629a9874432b94e4c7f17debe8132c94245c12d2ad7d1812d9d | MATLAB | 5,255 | 166 | % Script that runs imposed perimeter model shown in Figure 6 for a specific
% parameter choice
% Adapted from Troost et al., 2023
%% RUN SCRIPT for SOP Weighted Lateral Inhibition Model
clear; close all; clc;
%% Model setup
model.ratio = 'rho';
model.zone = 'Gaussian-like proneural genes';
%% Simulation paramete... |
81c753975f9d7a9893eb87ae885fcd05903849beacff780e6a248a1a30c167bf | MATLAB | 5,255 | 186 | function baseline = CBIG_hypoTest_3t(betas, stats)
% baseline = CBIG_hypoTest_3t(betas, stats)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
baseline = zeros(9, 3);
%% AD
fprintf('\n--------------------------------- AD ---------------------------------\n\n');
%... |
bcf91b0fc8d2e3ca671373b99edd3ac7dac15b27c0d609d917f02ff874c349d9 | MATLAB | 5,255 | 139 | function S = preprocess(snirf_path, model, params)
%NIRSPROC.PREPROCESS Motion→OD→filters→badch→DPF→Hb + stim vector (modular).
% S = NIRSPROC.PREPROCESS(snirf_path, model, params)
%
% See also: nirsproc.load_trim_snirf, nirsproc.motion_to_od,
% nirsproc.poly_detrend_cols, nirsproc.attenuate_spikes,
... |
58b233a55efb3ea358557a72e08cfb20c5067990c8b5edc7e1b1d4646da5aec4 | MATLAB | 5,258 | 128 | function handles = call_autoshaftDendr(handles, ifGUIdraw, resetparameter, ifhold)
if nargin < 4
ifhold = 1;
end
if resetparameter
prompt = {'Enter shaft segment length:'};
dlgtitle = 'Input';
dims = [1 35];
definput = {num2str(handles.defaultPara.shaftlength)};
answer = inputdlg(prompt,dlgtitle... |
6b095ba40c169b2d82d9a8a731b8350b422202b8b5501e914e414c95d117eca9 | MATLAB | 5,258 | 131 | function varargout = ea_sfc_setthreshs(varargin)
% EA_SFC_SETTHRESHS MATLAB code for ea_sfc_setthreshs.fig
% EA_SFC_SETTHRESHS, by itself, creates a new EA_SFC_SETTHRESHS or raises the existing
% singleton*.
%
% H = EA_SFC_SETTHRESHS returns the handle to a new EA_SFC_SETTHRESHS or the handle to
% t... |
10f78f4bda3d0b757d888330845de124848b73bcb718e466781db993a185ee9c | MATLAB | 5,260 | 195 | function [redblue, red, blue] = CustomColormap( varargin)
% generate blue and red colormaps
%
% Syntax
% [redblue, red, blue] = CustomColormap();
% [redblue, red, blue] = CustomColormap( varargin);
%
% Input
% Optional Key-value pairs
% 'N', length of colormap, default 200
% 'r1', a value between 0 ... |
7392e0ce09014153518799be2240f4137b7183cf7447534bff794b2f88f4d835 | MATLAB | 5,262 | 150 | function condColocGeneralAnalysisMLMD(MLMD,ptOrBlob,varargin)
%CONDCOLOCGENERALANALYSIS run colocalization analysis images with three channels with segmented and/or detected objects
%
% Function will run conditional colocalization analysis for three punctate
% or non-punctate objects or a combination. It will make all ... |
07f7a984781900635b4a06d962e2b1c50cf7730c6b55f086074e61398947335f | MATLAB | 5,264 | 154 | function [firingMaps] = bz_firingMapAvg(positions,spikes,varargin)
% USAGE
% [firingMaps] = bz_firingMapAvg(positions,spikes,varargin)
% Calculates averaged firing map for a set of linear postions
%
% INPUTS
%
% spikes - buzcode format .cellinfo. struct with the following fields
% .times
% posit... |
0b810f2de8fccf642e35a497b439bda77b434ad9b3350b1b4d0514b3a885953d | MATLAB | 5,265 | 184 | function[s,t,E] = sta(data_spk,data_lfp,smp,plt,w,T,D,err)
% Spike Triggered Average
% Usage: [s,t,E] = sta(data_spk,data_lfp,smp,plt,w,T,D,err)
%
% Inputs
%
% Note that all times... |
49767866cc0c0f14f45c663426d0ed1d7098fe749b4ecb3d1d9ae9772d2e8320 | MATLAB | 5,265 | 148 | function condColocAnalysisPt2Pt2PtMLMD(MLMD,varargin)
%CONDCOLOCANALYSISPT2PT2PT run conditional colocalization analysis for 3 punctate objects.
%
%SYNOPSIS function condColocAnalysisPt2Pt2PtMLMD(MLMD,varargin)
%
% Function will run conditional colocalization analysis for three punctate
% objects and will make all per... |
c7b6a02b5ab7e4e96ced85667b84996900c216da9a51111c5fc6a223b9dfa620 | MATLAB | 5,268 | 173 | %%*********************************************************************
%% gpcomp: Compute tp=1/gp in Proposition 2 of the paper:
%%
%% R.M. Freund, F. Ordonez, and K.C. Toh,
%% Behavioral measures and their correlation with IPM iteration counts
%% on semi-definite programming problems,
%% Mathematical Programmin... |
44bde75ec709607e2f260abdf563ead99c16cb12f2830c8f0a07f08f0593369b | MATLAB | 5,273 | 149 | function [r]=ea_skipped_correlation(x,y,type)
% performs a robust correlation using pearson/spearman correlation on
% data cleaned up for bivariate outliers - that is after finding the
% central point in the distribution using the mid covariance determinant,
% orthogonal distances are computed to this point, and ... |
b7ab0276c238cf26570b56ec19eab9e5d9d29c24b20992b0b1acd20faa765ae8 | MATLAB | 5,273 | 113 | classdef CBIG_ASDf_unit_test < matlab.unittest.TestCase
% Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
methods (Test)
function test_short(testCase)
% create output folder
CBIG_CODE_DIR = getenv('CBIG_CODE_DIR');
... |
a6293b5cc6e6abe0529a09ffeca958c7ffa3c1564c26023d090e8f31131b23aa | MATLAB | 5,283 | 151 | % go to data folder
% cd(['D:\TinyDancers_Movement\DLC_output\velo_timeseries\']);
cd(['D:\TinyDancers_Movement\DLC_output\PM_postimeseries\']);
addpath('C:\Users\tnguyen\OneDrive - Fondazione Istituto Italiano Tecnologia\Documenti\MATLAB\toolboxes\fieldtrip-20220929');
ft_defaults;
% load names of all files
... |
7273a1e4d0b1c0c103fa791550f19d1096b46a54fd66c2379e0a8d839fafac87 | MATLAB | 5,285 | 139 | function ea_importfssegmentations(options)
if options.prefs.fs.subcorticalseg.thalamus
% thalamus
thaldict=getthalmap;
temp=ea_getleadtempdir;
system([options.prefs.fs.dir,filesep,'bin',filesep,...
'mri_convert',...
' ',ea_path_helper(fullfile(options.subj.freesurferDir,['sub-',option... |
67d83eaeb6fb55e0dfd2207588d1e53ce87d364db355d2e3eb8bff702e12803e | MATLAB | 5,290 | 190 | function [spikemat] = bz_SpktToSpkmat(spikes, varargin)
%spikemat = bz_SpktToSpkmat(spiketimes,<options>) takes a
% 1 x N_neurons cell array of spiketimes and converts into a t/dt x N spike
% matrix.
%
%INPUTS
% spikes a structure with fields spikes.times
% can also take a {Ncells} cell array of ... |
891d1059c869b00c2ae01b02dc0efa69e9c81113ccdb3607ccd6696e8465ef2a | MATLAB | 5,294 | 91 | function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpb(data1,data2,win,params,segave,fscorr)
% Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting
% two univariate binned point processes into chunks
%
% Usage:
% [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherency... |
dc021744a766338b9f4f25063d8af93a2e491556875907fdbe6dbce651e56a3e | MATLAB | 5,298 | 170 | function ea_ants_apply_transforms(varargin)
% Wrapper for antsApplyTransforms used for reapplying coregistration
% (linear registration) and normalization (non-linear registration)
ea_libs_helper;
options = varargin{1};
useinverse = 0;
if nargin == 1
input{1} = options.subj.coreg.anat.preop.(options.subj.Anchor... |
f5a1fd4b1558d0834f65392ee325beef52fec04122ac66d762441b0c70d9a3a2 | MATLAB | 5,302 | 150 | function NEV = rethresholdNSx(varargin)
% rethresholdNSx
%
% Opens a NEV file and rethresholds it. It outputs a NEV structure into
% MATLAB. This version currently does not save a new NEV file.
%
% All input arguments are optional. Input arguments must be in the
% following order:
%
% NSx: The data struct... |
5acb860c6c2290d75d1137e492dcceca6f8b48320cbd813342965ec295f26c9d | MATLAB | 5,304 | 164 | %CCG - Compute multiple cross- and auto-correlograms
%
% USAGE
%
% [ccg,t] = CCG(times,groups,<options>)
%
% times times of all events
% NOTE: spiketimes in SECONDS.
% groups group IDs for each event in time list (should be
% integers 1:nGroups)
%... |
e44bd3221418833eabf814ad7df656a1664d3c54ac1d5f0e862386c00ab7c928 | MATLAB | 5,306 | 188 | function [R,t,E] = psth(data,sig,plt,T,err,t)
% function to plot trial averaged rate smoothed by
% a Gaussian kernel - visual check on stationarity
% Usage: [R,t,E] = psth(data,sig,plt,T,err,t)
%
% Inputs:
% Note that all times h... |
7c5d18ec5534ef7ff6b3f06fcb0c31e3f3d88dc913d50ce3bd0ec4f0f127a362 | MATLAB | 5,307 | 160 | function y = base64encode(x, eol)
%BASE64ENCODE Perform base64 encoding on a string.
%
% BASE64ENCODE(STR, EOL) encode the given string STR. EOL is the line ending
% sequence to use; it is optional and defaults to '\n' (ASCII decimal 10).
% The returned encoded string is broken into lines of no more than 76
% ... |
ef477d550f50e8862030c2856425353cfde12f57e3465333bb3571e13ede56c2 | MATLAB | 5,308 | 111 | function spikes = ss_outliers(spikes, reps)
% SS_OUTLIERS K-means based outlier detection.
% SPIKES = SS_OUTLIERS(SPIKES) takes and returns a spike-sorting object
% SPIKES. It identifies likely outliers in the SPIKES.WAVEFORMS and moves
% them from the (initially M x N) SPIKES.WAVEFORMS matrix to a (P x N... |
51c6f6aa939d5bf779a8b276d2852ea082de645f3f38ab1d446da0a585335230 | MATLAB | 5,309 | 124 | %% Script for fitting the interblade distribution histogram with a Gaussian mixture model with six peaks
% version 1.1 (25/07/2025)
% written by Clement Verkest & Stefan G Lechner
% INPUT: requires the 'result' structure generated by 'MFX_PIEZO1_ALFA_01_main_script.m'
% function FitInterbladeDistrib... |
02a9f55c6a50268b225f7a4ed01c97e26977fb9515b32cfbe652574d48524573 | MATLAB | 5,310 | 145 | % slider() - add slider to a figure
%
% Usage:
% >> slider( handler, horiz, vert, horizmag, vertmag);
%
% Inputs:
% handler - figure handler (for the current figure, use gcf)
% horiz - [0|1] add a horizontal slider
% vert - [0|1] add a horizontal slider
% horizmag - magnify the width of the figure be... |
417b691d3ae480a97c1c3147c4a02308da08bf2135e033d0a6ea5cb2930b2a15 | MATLAB | 5,316 | 97 | function done = ea_coregpreopmr(options)
% Entry function to coregister pre-op MRI
done = 0;
% Set anchor image
anchor = options.subj.coreg.anat.preop.(options.subj.AnchorModality);
% Set moving and output image
preopImage = rmfield(options.subj.preproc.anat.preop, options.subj.AnchorModality);
coregImage = rmfield(... |
a67912e2aa04341dd0151c48175889b2ff16dcaf37fa4f3efc93b79aa56f5c73 | MATLAB | 5,317 | 158 | function [R_points, t_points, im_mask_reg, handles] =...
setupCross_SessionReg(handles, im_mask, withrotation, maskdir)
%%%% im_mask_reg is a transformed version of im_mask to match
%%%% im_current
im_current = handles.im_norm;
% ops.maxIter = 150;
% ops.tot = 10^-4;
% ops.distTh = [2, 50];
% ops.dispreg = 0;
%%%%... |
61d9bd1760ad4e6dacad36c3a4425bde24cbadc5bcba312496ca2421075199f1 | MATLAB | 5,318 | 157 | function y = base64encode(x, eol)
%BASE64ENCODE Perform base64 encoding on a string.
%
% BASE64ENCODE(STR, EOL) encode the given string STR. EOL is the line ending
% sequence to use; it is optional and defaults to '\n' (ASCII decimal 10).
% The returned encoded string is broken into lines of no more than 76... |
d6ad2ef70ddc91b735c9a1fdd9354ba8cbf93d4ca0347babe6ade337366ba187 | MATLAB | 5,318 | 142 | function [] = v2structDemo1()
% V2STRUCTDEMO1 is a demo function showing some examples for using the function V2STRUCT
%
%% Last update:
% 30.06.2011, Adi N.
%%
fprintf(['\nRunning demo function with examples for using the function vs2truct:\n',...
'Press any key between breaks.\n']);
pause()
fprintf(['\n... |
5656234fe288217422ca363da1784c82e3c91665d82c6c75b102db8987b57c3f | MATLAB | 5,319 | 161 | function [A, vA, vB, bb_rel] = crop_borders(A, bcol, padding, crop_amounts)
%CROP_BORDERS Crop the borders of an image or stack of images
%
% [B, vA, vB, bb_rel] = crop_borders(A, bcol, [padding])
%
%IN:
% A - HxWxCxN stack of images.
% bcol - Cx1 background colour vector.
% padding - scalar indicating ... |
f3a450a079005232f0afecb2e34dabcda691613d3fd2fb4a7d5c855b66284a3f | MATLAB | 5,319 | 117 | %% Step 1 Tiny Dancers: Load EEG and preprocess
% Steps are Bandpass filtering, Bad channel rejection, ASR,
% Automatic ICA, Bad channel rejection part 2 and interpolation, followed
% by rereferencing to the average
% Trinh Nov 22
%% initialise fieldtrip
clc
clear all
close all
addpath('D:/MUSICOM_EEG/EEG/... |
c5438901126930ef102d81acd029ded8b284016f7a36e73678dda2ce841bfec0 | MATLAB | 5,323 | 133 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% process_volume_gradients_eigenmodes.m
%%%
%%% MATLAB script to process volume gradients and eigenmodes from HCP data.
%%% In particular, the script demonstrates how to
%%% (1) calculate the z-scores of the gradients,
%%% (2) calculate the ... |
fe76a48ae2fb6a1b822540e16e0fdce17bf1a2e63ac64c802f86477c4f7a5bcc | MATLAB | 5,324 | 148 | %% Basic Image Visualization
%
% Using Basic Plot Methods (plot, orthviews, and montage) to Examine a Dataset
%
% Objects can have methods with intuitive names, some of which overlap
% with names of functions in Matlab or other toolboxes. fmri_data.plot()
% is one of these. When you call plot() and pass in an fmri_data... |
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