sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a4a742ce6ac2b2ae56e75cad8fa8c7ac1d5f88a6e4f4811e9b0e489d71525d75 | MATLAB | 3,644 | 190 | function RT = rt_read_ev2(cfg)
% v.0.0.1.1
% <*LAN)<|
%
%
%
% cfg.filename = 'nombredearchivo.ev2'
% cfg.ref =[]
% cfg.refl =
% cfg.delim = [est, resp,resp,resp;
% est, resp,resp,-99] %% matriz con estimulos
% y respuestas para ... |
874719eea66b804b60a2ff653f390ea92d6adf0e59805c9c76cf65394365d8d9 | MATLAB | 3,646 | 106 | % PlotStridePosition.m
% Sarah West
% 7/21/23
function [parameters] = PlotStridePosition(parameters)
x = parameters.x;
y = parameters.y;
resampleLength = parameters.resampleLength;
MessageToUser('Resampling ', parameters);
% Put strides of different instances together on same level
x_togeth... |
8b072629fb82d3e07d33a3ea9118b9b9e8ee76a73a7a9456c578906f99e76684 | MATLAB | 3,646 | 106 | % This code loads Results and looks at the peak frequency and determines
% SOZ at seizure onset of dominant frequency
% Abbas Sohrabpour
% 19/3/2018
close all; clear all;clc
bad_chan = [];
cd('../Grid Location and Defined Parameters')
load('UnconstCentLFD.mat')
[~, Num_Dip] = size(K);
K([bad... |
94df5ec7a074c2f56a2c73f8929d61de0367cd7783842fe681da0c8b4312f09c | MATLAB | 3,646 | 125 | function t = timeit(f)
% Measure time required to run a function
% T = TIMEIT(F) measures the time (in seconds) required to run
% F, which is a function handle.
%
% If nargout(F) is 0, TIMEIT calls F with no output arguments,
% like this:
%
% F()
%
% If nargout(F) is nonzero, TIMEIT calls F with a si... |
b70bd5b28285b14f5d8a9c913268de78179a017f1a74c87b6dc79dcba7f1a82f | MATLAB | 3,646 | 109 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
function pot_latency = bs_prepro_loop2(isubject, icondition, srmr_nr, is_min)
%% get potential latency
%% set variables
subject_id = sprintf('sub-%03i', isubject);
analysis_path = [getenv('ANADIR') subject_id '/bs/prepro/'];
save_path = [getenv('BSDIR') subject_id '/'];
... |
2f2486c82decbb09d74e12715c3b198ed04dcc07af1c9b5dc6e98fe464690d2b | MATLAB | 3,647 | 114 | function varargout = sccn_xdf(filename, hdr, begsample, endsample, chanindx)
% This is a wrapper to the reading function from the XDF MATLAB toolbox.
%
% Use as
% hdr = sccn_xdf(filename);
% dat = sccn_xdf(filename, hdr, begsample, endsample, chanindx);
% evt = sccn_xdf(filename, hdr);
%
% See also FT_FILETYPE, ... |
6e6e651106bce3dfb1ff84e266ea03338c470478af18a10913127249657a8bd7 | MATLAB | 3,647 | 132 | function [y,yidx] = weighted_prctile(x,p,w,dim,issorted)
% y = weighted_prctile(x,p,w,dim,issorted)
% similar to MATLAB's prctile, but takes weights
if ~isvector(p) || numel(p) == 0
error('stats:prctile:BadPercents', ...
'P must be a scalar or a non-empty vector.');
elseif any(p < 0 | p > 100) || ~isreal... |
6f3b9ad017e6d90c5c9cfae3ca60403be460db627ad4a0f7555fc31fa734ceb1 | MATLAB | 3,647 | 114 | function ax = animate_template_func(input_file_name,output_file_name)
% input_file_name -> for example, the name of the .mat input file containing the trajectory
% output_file_name -> true, false, or the name of the output video file
%
% you function plott goes inside the record_frame function below
mouse_track =... |
602a96e3b630864fb43a6ea1c4ea562e3641c2db1c2e5552f8f65697e8d19855 | MATLAB | 3,648 | 105 | function completionReport(yamlfile)
%Use a YAML file to load the parameters for a large experiment
yamlspecs = ReadYaml(yamlfile);
%The YAML files might have extra quotes so remove them
BASENAME = strrep(yamlspecs.basename,'''','');
NUM_FOVS = prod(yamlspecs.montage_size);
if isfield(yamlspecs,'reg_type')
REG_TYPE... |
fc23aa730b4b97465bc731e8050d6942bdef0b28d5c53eed3c2bb01da455a038 | MATLAB | 3,648 | 108 | function grating = buildColorGrating(pixelsPerDegree, sizeDegrees, ...
spatialFrequency, tiltInDegrees, phase, michelsonContrast, ...
squareWave, colorOption, redWeight, greenWeight)
% function grating = buildColorGrating(pixelsPerDegree, ...
% spatialFrequency, tiltInDegrees, phase, michelsonContrast, ...... |
5388fce91294f90da3f5d5ec1aba9c60839c49f3c0b0fa0d946c43cab2f230b0 | MATLAB | 3,649 | 112 | function [F,sE,sC] = VBA_spm_log_evidence(varargin)
% Return the log-evidence of a reduced model (under Laplace approximation)
% FORMAT [F,sE,sC] = spm_log_evidence(qE,qC,pE,pC,rE,rC)
% FORMAT [F,sE,sC] = spm_log_evidence(qE,qC,pE,pC,priorfun,varargin)
% FORMAT [F,sE,sC] = spm_log_evidence(qE,qC,pE,pC)
%
% qE,qC - p... |
be4d139b87fded98d0d414f8e1f05801c59cad5896567102baf5f239de0366ce | MATLAB | 3,649 | 84 | function [estimated_position,log_odds]=calculate_log_odds(spikes,place_fields,bin_size, track, opposite_track, shuffles)
% Input
% - spikes: where spikes(:,1)
% - bins: are time bin for spike count and decoding
% -
% By Daniel Bendor and Masahiro Takigawa 2023
common_good_cells=intersect(place_fields.track(track).s... |
03a985d6acf5e07b922ab0076562c0b18e2d49b9e8b1ed3ec606819b360e14d1 | MATLAB | 3,651 | 75 | function h_resetZoomBox3(handles, syncFlag)
global h_img3;
if ~exist('syncFlag','var')||isempty(syncFlag)
syncFlag = 1;
end
[currentInd, handles, currentStruct, currentStructName] = h_getCurrendInd3(handles);
[x_lim,y_lim,z_lim] = h_getLimits3(handles);
horizontal = get(handles.moveHorizontal,'Valu... |
edb0e2d8c14c7c86e1a5e7a1d14d19f993c7f621f0983c38cc78f7a1d1da206f | MATLAB | 3,651 | 143 | clear all
close all
clc
% Use this script to generate a figure similar to Figure 5C (lower panel) of:
%Luna, R., Li, J., Bauer, R., & van Leeuwen, C. (2023). Retinal waves in adaptive
%rewiring networks orchestrate convergence and divergence in the visual system.
%Network Neuroscience
cd '..\scripts\Outpu... |
a43b1d611f558491f46545e67a8983b7b78775bffb23e40a063ad3edc716326c | MATLAB | 3,652 | 114 | function [F2,po2] = VBA_SavageDickey(po1,pr1,F1,dim1,pr2)
% computes the free energy and posterior moments of a reduced model
% function [F2,po2] = VBA_SavageDickey(po1,pr1,F1,dim1,pr2)
% This function computes the approximate log model evidence and posterior
% density of a 'reduced' model, which is defined with respec... |
269b9128238b960b9c2448feb41a9523fc00a73ef1f19879186f4f53c90b7643 | MATLAB | 3,653 | 151 | function M = spheresymmetricfactory(n)
% Returns a manifold struct to optimize over unit-norm symmetric matrices.
%
% function M = spheresymmetricfactory(n)
%
% Manifold of n-by-n real symmetric matrices of unit Frobenius norm.
% The metric is such that the sphere is a Riemannian submanifold of the
% space of nx... |
32a57019c3d6466b95093b191c36d04e1aafea9c1bd7a825f241473f9e6033c1 | MATLAB | 3,653 | 118 | function H=w_PlotNode(Vector, ElementLabel, ...
HigherOrderNetworkIndex, HigherOrderNetworkLabel,...
ColorMap)
LineWidth=2;
LineColor=[0, 0, 0];
NumNode=size(Vector, 1);
if ~isempty(HigherOrderNetworkIndex) && NumNode~=size(HigherOrderNetworkIndex, 1)
errordlg('Invalid Length of HigherOrderNetworkIndex')... |
4610d9ba91d7aaa48cc60ab74b7f3f846309de5f2a505698b58f4b4e9c78a59e | MATLAB | 3,653 | 101 | % This script shows how to process and manipulate loaded datasources and
% how to call dataspace module-functions on them.
%
% The same exact procedures apply to programatically loaded datasources (not involving the GUI).
%
%
%
%<PRE>
% This file is part of dspace-core.
%
... |
8c1a493445a2fdb7d4cbcd0034c880318195dfa24b252d988cd20538bdf5f05a | MATLAB | 3,654 | 70 | function CBIG_AuthorTopicEM_GenerateDataFromText(text_data_path, ...
data_dir, gibbs_data_file_name, em_data_file_name, brain_mask1mm, ...
brain_mask2mm, binary_smooth_kernel_rad)
% CBIG_AuthorTopicEM_GenerateDataFromText(text_data_path, ...
% data_dir, gibbs_data_file_name, em_data_file_name, brain_mask1mm, ... |
71232bf06934db48cc87f47d7780a81a10d48282893b4d27f8b3c9c24b06f809 | MATLAB | 3,656 | 107 | % Demo code for multiple subplots of estimation plots. Original toolbox
% written by Adam Claridge-Chang's Lab
%
% Liangyu Tao June 10, 2019. Can now do multiple subplots
clear;close all
addpath(genpath(pwd))
% load data
load fisheriris
% create an extra category (to be used for the pair wise multiple
% comparison p... |
9e923bd37315105ed4c0581fd069dfea5023b3d54124eaa4e6ee3f8dd1a64e5a | MATLAB | 3,656 | 104 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
function esg_prepro_loop3(subject, conditions, srmr_nr)
%% set variables
subject_id = sprintf('sub-%03i', subject);
analysis_path = [getenv('ANADIR') subject_id '/esg/prepro/'];
save_path = [getenv('ESGDIR') subject_id '/'];
if ~exist(save_path, 'dir'), mkdir(save_path); ... |
f8381e13525dae9325bc3f84412660bb757b2cf8b205c1f12ef9688a67048d7c | MATLAB | 3,657 | 79 | fov = zeros(d1,d2);
figure
% Plot position of interneurons, pyramidal cells and assembly members
for assemblyCounter = 1:size(assemblies.CellCl,1)
assemblies.cellsInAssembly = assemblies.C0{1,assemblyCounter};
%assemblyN = ['assembly' num2str(assemblyCounter)];
if size(assemblies.CellCl,1) > 1 && size(assem... |
4fe52782cbfd25328f170315e7bbf816bde15e9f3b60eec2f2b14b226eb57c2c | MATLAB | 3,659 | 88 | function bbs = acfDetect( I, detector, fileName )
% Run aggregate channel features object detector on given image(s).
%
% The input 'I' can either be a single image (or filename) or a cell array
% of images (or filenames). In the first case, the return is a set of bbs
% where each row has the format [x y w h score] and... |
17c5c53173a897e1c34fce4286775b4406a7e6509041735bf8e259adcd44c920 | MATLAB | 3,660 | 98 | %timing irregularities
location = 'L1'; %'L1' 'laptop'
scanType = 'all frames'; % 'all frames' 'irregularity frames'
%% Plot timing
switch scanType
case 'all frames'
timeScanNames = {'stimulusSeq' 'targetSeq' 'targetPosSeq' 'trigSeq' 'keyCodeSeq' 'soundSeq'};
switch location
case 'lapt... |
7e708ef46bde476221d01059bbbff82107595c0228c65a168fab2f07112a9077 | MATLAB | 3,664 | 104 | %% Screen SDOs (struct) for significance
% Simple utility to screen the 'sdo' struct for particular spike-triggered
% SDOs which are demonstrate significance on at least SIG_THRESH tests.
%
% PREREQUISITE:
% computeSDO.testStatSig()
%
% INPUT:
% sdo - structure, as generated by computeSDO
% SIG_THRESH:
% ... |
0e0a7634fa4d6dcb5b3146dc446c457c0ecff8092979c4c15c957fdfc973a8d0 | MATLAB | 3,665 | 116 | function [U]=l3dpartdirect(nsource,source,ifcharge,charge,ifdipole,dipstr,dipvec,ifpot,iffld,ntarg,targ,ifpottarg,iffldtarg)
%LFMM3DPARTDIRECT Laplace interactions in R^3, direct evaluation.
%
% Laplace FMM in R^3: evaluate all pairwise particle
% interactions (ignoring self-interactions) and interactions with targs.
%... |
801e9839e1d145d3264a1fb2ff70eb518a019b783c3e4f4c0595f1dd8e0c55df | MATLAB | 3,667 | 136 | function M = complexcirclefactory(n)
% Returns a manifold struct to optimize over unit-modulus complex numbers.
%
% function M = complexcirclefactory()
% function M = complexcirclefactory(n)
%
% Description of vectors z in C^n (complex) such that each component z(i)
% has unit modulus. The manifold structure is ... |
88b99b44a31a1a786b064330ac55f2c8bac3e82fec5b65408954e5295f92bcee | MATLAB | 3,667 | 87 | function [M] = smoothModel(M, smoothrad, origin, mult)
%SMOOTHMODEL Smooth a brain model.
%
% For every vertex vx of a given model M, this function finds all the
% vertices vxd for which distance(vxd, vx) < smoothrad; from these vertices
% vxd, only those vertices vxd2 that are far enough from the origin ... |
d4ab33fe3c86079d50a2dee0948aca9aa8459296c83df0ab43dd1cffbd5e967b | MATLAB | 3,667 | 166 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
495b1be64f38e5aad3a0eb23da3fdb51c8662ece5be09d040e4a47119e5d4fa9 | MATLAB | 3,669 | 102 | function[region, region_lap, initiation_id, cell_id] = grab_samples(analysis_out, samples, measure, grab_lap, range)
session_names = fieldnames(samples);
initiation_id = {};
region_lap = {};
norm_region_lap = {};
idx = 1;
id = [];
for session = 1: length(session_names)
num_rois = length(samples.(session_names... |
66c125c1fb00780eb0c45e53eafd712a7539a83c699af4fe39ca93d8b0247091 | MATLAB | 3,669 | 110 |
% Kernel PCA toy example for k(x,y)=exp(-||x-y||^2/rbf_var), cf. Fig. 4 in
% @article{SchSmoMue98,
% author = "B.~{Sch\"olkopf} and A.~Smola and K.-R.~{M\"uller}",
% title = "Nonlinear component analysis as a kernel Eigenvalue problem",
% journal = {Neural Computation},
% volume = 10,
% iss... |
290a7fe9d53523ad0c5adac12c9248e7d85f04d16275d8c6f7931599660d182c | MATLAB | 3,670 | 65 | function [censoredVolumes,lpffdCensoredVolumes,lpfdvCensoredVolumes] ...
= getCensoredVolumes(timeSeries,brainMask,MPs,TR,LPF_FD_Threshold,DV_GEV_d)
% This function returns a boolean (logical) vector of censored volumes
% using combined LPF-FD and GEV-DV based volume censoring, given a time
% series ... |
3ea896da497697b9ae39dd92b173f5fb99fd20e84b60ecfd8e3669702deb06e9 | MATLAB | 3,670 | 90 | function s = fromcoco(cocos,varargin)
% s = fromcoco(cocos,...)
% Create a Labels structure for one movie from input cocos struct.
% If the coco structure contains information about which movies were
% used to create labels, then this will create a Labels structure
% from data corresponding only to movie imov... |
8fa558fe0f6d2aa09c538e956b9907fd8ab470cbf5a2364205104f18a1042d3a | MATLAB | 3,670 | 165 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
6a398457ed2c6c0e66a67929184f850f0651479d7ea1cbd4c99830c42a60e5b6 | MATLAB | 3,672 | 119 | %TTENSOR Class for Tucker tensors (decomposed).
%
%TTENSOR Methods:
% disp - Command window display of a ttensor.
% display - Command window display of a ttensor.
% double - Convert ttensor to double array.
% end - Last index of indexing expression for ttensor.
% full - Convert a ttensor ... |
22bcb0b5b207ab544b1465cd7cb9730ddc7eecc609098779c6e8e9f0bcd6dce0 | MATLAB | 3,674 | 65 | function correlational_analysis2_rmoutlier
%%The within and across task correlation code
subjects=[];
data_info='/gpfs51/dors2/gpc/JamesBooth/JBooth-Lab/BDL/jinwang/PlausGram_9-10/scripts/5mvpa/data_info.txt';
if isempty(subjects)
M=readtable(data_info);
subjects=M.participant_id;
end
root='/gpfs51/dors2/gpc/Ja... |
dad297b051cff8208eed739295c11d2ec5d7ca14a660a396fdf12cdeda7fb792 | MATLAB | 3,674 | 144 | % dummy susceptibility analysis
% this demo evaluates suscpetibility analyses in the following input-output
% scenario:
% o = P1*u1 + P2*(u1+u2) + u3*(P3+P4) + u4*P5 + P6.
% In other words:
% - u1 flows through two parallel branches: u1 --[P1 P2 ]--> o
% - u2 flows through one branch: u2 --[ P2 ... |
40c3ad20428d15560ae42b271d8683c250ee73600d8ca22e96ebe16ec41c5a02 | MATLAB | 3,675 | 115 | function LoadIntan(datDir, varargin)
% Used to load Intan data files in the "all-channels-in-one-file" format
% Will save select channels in .hsd (version 4) format
% hard-coded parameters
bytesPerSample = 2;
saveChan = {'C-108'};
% ECog = C-108
saveChan = {'S23_E04'};
% default parameter settings
timeRange = [0 In... |
690d44adcd563a14bd1f5c8196715785b5092cff088a4ef845bf1797ccaa4b39 | MATLAB | 3,680 | 155 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
a8b2a6284ea9279b99ff97906488368049cbabf84938c2c9636e2d92d43eaae3 | MATLAB | 3,680 | 73 | function [tps3dwarp_max_run_jobs,tps3dwarp_max_pool_size] = concurrency_size_in_TPS3DWarping(cond)
loadParameters;
num_rounds = params.NUM_ROUNDS - 1;
if ~isfield(params,'TPS3DWARP_MAX_RUN_JOBS')
round_list = 1:params.NUM_ROUNDS;
round_list(params.REFERENCE_ROUND_WARP) = [];
avr_n... |
746817e68473824febd9363248c6d46526809e0e34721670e109cda3f7ff5fa1 | MATLAB | 3,685 | 117 | function meg_msFigs_ITPCbyITI_TS
% function meg_msFigs_ITPCbyITI_TS
% load groupITPC_ITI
%% Figure settings
titleVis = 0; % if title vis off, then will plot for appropriate manuscript size
showN = 0; % show n = X annotation
figFormat = 'svg'; % svg
annotateMean = 0;
annotateStats = 1;
saveFigs = 1;
cueLevel = {... |
7717468dea0cefd8d32a1b83647642874c7ef36c5dafaebce33e1889e6fef7ee | MATLAB | 3,685 | 86 | function [EEGperiods] = DS_getEEGperiods(EEG,PARAM)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Extract EEG periods of a certain sleep stage label
%
% Part of detect_spindles toolbox:
%
% Authors: Stephane Sockeel, PhD, University of Montreal
% Stuart Fogel, PhD, Universi... |
3076a548e90c8288bed4c852eaae3ba748035ea41f945e0cfac70b6f5bedf235 | MATLAB | 3,686 | 112 | function [elec] = read_bioimage_mgrid(mgridfile)
% READ_BIOIMAGE_MGRID reads BioImage Suite *.mgrid files and converts them
% into a FieldTrip-compatible elec datatype structure with electrode
% positions in xyz coordinates (equals voxel coordinates in mm)
%
% Use as
% elec = read_bioimage_mgrid(filename)
% where th... |
91f463ab5aa0753619d5e461988c28691851efcb31a13dd0d425a1ea3f2eb319 | MATLAB | 3,686 | 99 | % Source-target evaluations on the unit sphere, Laplace kernel.
%
% This example computes the interactions between random source and target points
% on the unit sphere via the Laplace kernel. The associated matrix is
% rectangular and real.
%
% This demo does the following in order:
%
% - compress the matrix
% - ch... |
cbe28765c4e7b7f557e4a824d9cba40ad09e3d8100121e799e78b6bbc389a5ca | MATLAB | 3,686 | 110 | %% SAT - app_input::
%% concatenateFile
% Name: Phone Kyaw
% Date: 09/19/2024
% Description: Transferring multiple XT/PP files into one single concatenated file
% If input as 1, it will create "xt.csv"
% If input as 2, it will create "pp.csv"
% Parameter: file_type - Ac... |
f03e733aca362a257f194759541dadcc4e5bc8aac3dae3ee2348b36f79cab9a1 | MATLAB | 3,686 | 119 | function [W, varargout] = jacobian_stnd_BLT(mesh, varargin)
% Same format as femdata_stnd_BLT
%
% Part of NIRFAST package.
% S. Wojtkiewicz and H. Dehghani 2018
%% check in/out
narginchk(1,3);
nargoutchk(0,2);
%% get optional inputs, handle variable input
% default
solver = get_solver;
OPTIONS = solver_option... |
4015f16c5a334efda02967b6821e7b7939520bbcfd5151758a30780cba254a4a | MATLAB | 3,687 | 88 | % Compute the within-area shared dimensionality, by performing Factor
% Analysis to get the shared covariance matrix, and then assessing
% dimensionality (1) through the participation ratio measure, and (2) by
% determining how many dimensions are needed to explain >95% of the shared
% variability.
% INPUTS:
% data ... |
8ab6304b42a1d0ded8876f502935db51cd0cb857f3721a39ccea41392598be9f | MATLAB | 3,687 | 117 | function [proj] = elproj(pos, method)
% ELPROJ makes a azimuthal projection of a 3D electrode cloud
% on a plane tangent to the sphere fitted through the electrodes
% the projection is along the z-axis
%
% [proj] = elproj([x, y, z], 'method');
%
% Method should be one of these:
% 'gnomic'
% 'stereographic'
... |
b1801f9a70193194086dffbb6ecfd90683d8cf01209d4ab979fb15c3a4e87e25 | MATLAB | 3,687 | 118 |
%%% Scope: Calculating participation coefficient and within-module degree z-score
%%% Author: Jonas A. Thiele
%%% Date: 18.07.2023
%%% Uses functions from the Brain Connectivity Toolbox from:
%%% Complex network measures of brain connectivity: Uses and interpretations
%%% Rubinov M, Sporns O (2010) Neur... |
e5977e1d505c7a95588aa1cebb5c6b92895ee5e804906b1d28f9f038610d9410 | MATLAB | 3,687 | 101 | % registration_across_days.m
% Sarah West
% 8/23/21
% Modified from SCA_manual_masking.m, just the registration across days
% parts
function []=registration_across_days(parameters)
% Assign parameters their original names
dir_exper = parameters.dir_exper;
mice_all = parameters.mice_all;
transfor... |
f8d587a6ccfd29a329522ee47159883d663c75bedb8db07d1039e396c902aba1 | MATLAB | 3,687 | 117 | function [proj] = elproj(pos, method)
% ELPROJ makes a azimuthal projection of a 3D electrode cloud
% on a plane tangent to the sphere fitted through the electrodes
% the projection is along the z-axis
%
% [proj] = elproj([x, y, z], 'method');
%
% Method should be one of these:
% 'gnomic'
% 'stereographic'
... |
99ae9662a4ef1e97bd3679f0f92a972d5b7af9b6661b20f21601179c8286f760 | MATLAB | 3,688 | 115 | function model = depnetFit(X, varargin)
%% Fit structure of a dependency network
%
% Input:
% X is an N*D matrix of binary (0/1) or {1,2}
% Optional args
% 'method' - {'ARD', 'MI', 'L1CV', 'L1MB'}
% maxFanIn - only used by MI
%
% Output:
% model.G(s,t) = 1 if s depends on t (sparse)
% model.W(s,t) is some measure of th... |
1e0494d79e071641d8b1e02d2a0b61548f3bf698665cdd0a249008a18973b052 | MATLAB | 3,690 | 82 | function results = EstimateStmFromPhotocurrent(params)
% The EstimateStmFromPhotocurrent function inverts the photoreceptor model to
% estimate the stimulus that would cause a given photoreceptor output. This is
% achieved by using the impulse responses and model parameters to
% reverse-engineer the stimulus from the p... |
840792391ae79dbadef3175fa16011b1756a631472015a67f7ab07f2450b5d8e | MATLAB | 3,691 | 88 | function varargout = jbm_patchTemplate(varargin)
% JBM_PATCHTEMPLATE M-file for jbm_patchTemplate.fig
% JBM_PATCHTEMPLATE, by itself, creates a new JBM_PATCHTEMPLATE or raises the existing
% singleton*.
%
% H = JBM_PATCHTEMPLATE returns the handle to a new JBM_PATCHTEMPLATE or the handle to
% ... |
65ce50b6e8ae6762c094f5e3b2e9fd893b8932d46ea2bf5206092cc8decfd44e | MATLAB | 3,693 | 121 | function CorrMatrix(spkDat, varargin)
clustList = setdiff(unique(spkDat.id), 0);
clustListIn = clustList;
timeRange = [0 Inf];
plotRange = [-100 100];
binWidth = 1;
showAuto = false;
nSamp = 1000;
for i = 1:2:length(varargin)
switch lower(varargin{i})
case 'nSamp'
nSampTarget = varargin{i+1}; ... |
7a4a4ebb146905d73413fd6bfd61d400717bf0ef38bded6e247da9fb6fb79cc9 | MATLAB | 3,693 | 102 | function [dat] = read_nex_data(filename, hdr, begsample, endsample, chanindx)
% READ_NEX_DATA for Plexon *.nex file
%
% Use as
% [dat] = read_nex_data(filename, hdr, begsample, endsample, chanindx)
%
% See also READ_NEX_HEADER, READ_NEX_EVENT
% Copyright (C) 2007, Robert Oostenveld
%
% This file is part of FieldTri... |
d2bde500ccac7615f87aac78c505759a88db9a443f9c64ea9fa3b11af9a4b408 | MATLAB | 3,694 | 161 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
1c0ca5beff482fd24b2a0a7bbfce2c4196270edb3012048d4e08ea8ad1c1b71d | MATLAB | 3,695 | 130 | function [estimates,posterior,out] = SEM_analysis0(Y,A,B,C,flag)
% structural equation modelling (bayesian stats)
% FORMAT: function [estimates,posterior,out] = SEM_analysis0(Y,A,B,C)
% This function assumes a GLM of the following form:
% Y' = A*Y' + sum_i B{i}*Y(i)*Y' + C + e
% where e are normal iid residuals.
% IN:
... |
fb16a32c318f4a535e59f156bb1a7e694eb04c0de8f63516ad9f81a34a4e0400 | MATLAB | 3,695 | 68 | % IntgradFgradG_tet4_CPU carries out a spatial convolution of gradients of
% fields within a FEM mesh. This function runs on parallel on the CPU
% threads and is parallelized over the data pairs undergoing the
% convolution.
%
% SYNTAX:
% [J_BORN] = IntgradFgradG_tet4_CPU(MESH,DATA_1,DATA_2)
% [J_BORN] = Intgra... |
df5db52d4d22441c0a13875f2a1f7fe6cb0b362b861a09a44eb63cf9ff48ca15 | MATLAB | 3,696 | 166 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
68c63b92c8b70c08daaeec93c27ca28db4d4daa33a3c7f7d8bd2911155cc1bbf | MATLAB | 3,697 | 105 | %-----------------------------------------------------------------------------------------
% Plot odor decoding performance per recording session
%
% Kehl et al. 2024 (DOI:XX)
% Single-Neuron Representations of Odors in the Human Brain
% Figure 2e
% Author: Marcel Kehl
% License: MIT License
%-----------------------... |
80930fcd9732ed2d89b71fa9888a0887bcbf846cf3e7c424471920222a88ad63 | MATLAB | 3,697 | 82 | function TSsequencer(arg1,arg2)
% This function is called by the timer. It calls the DailyAnalysis function
% for each experiment in ActiveExperiments.
Dr = cd;
clear global Experiment
load('ActiveExperiments.mat') % This is a cell array created and updated by
% TSstartsession. It has one row of cells for e... |
b2310fbf59018ccc0f15b3105d9b6438bd19c7f21c215f4f7843b825cc6331bd | MATLAB | 3,697 | 116 |
%% THIS WORKS ONLY FO 2x2 MATRICES!
%% 1) X1
figure('Position', [50, 50, 700, 450]);
% X1: A1 e A3
neuron_index1 = 1 ; % A1
neuron_index2 = 3 ; % A3
% estrai indici e calcola matrice
cluster_indices = [ find(som_clusters == neuron_index1) ; find(som_clusters == neuron_index2) ];
cluster_matrices = connect... |
80f0e64ebcea211e7ab6074115a5b5689b304f6d95fbc6057653c3cfca0c86ac | MATLAB | 3,698 | 117 | function nRuns = rd_segmentSqd(fileName)
%
% function nRuns = rd_segmentSqd(fileName)
%
% Chunk data into smaller segments. Segments data between runs, based on
% triggers.
%
% Rachel Denison
% September 2014
%% setup
% file in
% exptDir = '/Local/Users/denison/Data/TAPilot/MEG';
% sessionDir = 'R0890_20140806';
% da... |
d3a1ffafc9d7d92440a19d0308c67a3e840f4f345a47c1369ddee4e46f7d920d | MATLAB | 3,698 | 117 | % read_eeglabevent() - import EEGLAB dataset events
%
% Usage:
% >> event = read_eeglabevent(filename, ...);
%
% Inputs:
% filename - [string] file name
%
% Optional inputs:
% 'header' - FILEIO structure header
%
% Outputs:
% event - FILEIO toolbox event structure
%
% Author: Arnaud Delorme, SCCN, INC, ... |
5b613d9a48cd17e97f226e81e25c31a4ada3013b9fec9ebbfdfdbbe605ef789b | MATLAB | 3,699 | 96 | % RestoreSources.m
% Sarah West
% 3/30/22
% Plots all the sources you removed with the RemoveArtifacts.m code and lets
% you restore some that you might have removed by accident.
function [parameters] = RestoreSources(parameters)
% Inputs:
% sources -- a 3D matrix (pixels, pixels, source #) of all the sources you dr... |
25778d04f2b909fde53d5fd2db9fe73a06da672fea4827431b62681745c9f74f | MATLAB | 3,701 | 96 | function [EEG,com] = pop_PAA(EEG)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% EEGlab GUI for Period Amplitude Analysis (PAA) on EEGlab data to
% detect and measure slow waves.
%
% Copyright, Sleep Well. https://www.sleepwellpsg.com
%
% Method adpated from:
%
% Feinberg et al, 1978.... |
4809e9608059c51e767e17c9e16cf4eead7ce610af4bc957869d531ac03fb65e | MATLAB | 3,701 | 105 | % Second-kind integral equation on the unit square, Laplace single-layer.
%
% This is the same as IE_SQUARE2 but using HIFIE2X.
%
% Inputs (defaults are used if not provided or set empty):
%
% - N: number of discretization points in each dimension (default: N = 128)
% - OCC: tree occupancy parameter (default: OCC =... |
d82db4fd8d913a1f65c4d54b367c102d723028da621bc0684770948518fa8f5f | MATLAB | 3,701 | 117 | function [scalo,f,T,a,wt,wavescaled] = contwtgn(x,fmin,fmax,N,wave);
% CONTWTGN [scalo,f,T,a,wt,wavescaled] = contwtgn(x,fmin,fmax,N,wave)
% computes a continuous wavelet transform.
%
% Input:
% x signal (in time) to be analyzed
% [fmin,fmax] respectively lower and upper frequency bounds of
% ... |
ee7ff4dda1db7ee708156021c747c8eb08d9e00d5d6bbfe121b0ea952e10cedd | MATLAB | 3,701 | 97 | function lrstats = lme_LR(lrmlfull,lrmlred,q)
% lrstats = lme_LR(lrmlfull,lrmlred,q)
%
% Likelihood ratio test for the random effects. It can be used to test if a
% model with q+1 random effects is significantly better than a model with q
% random effects.
%
% Input
% lrmlfull: Maximum value for the restricted log-like... |
6345ca109ed1893344f45ad20337943e4a107b35dcc65f78847cd43f9fbcceb9 | MATLAB | 3,703 | 169 | % chunks data into segements
% ignores data that is smaller than the chunk size
%
% usage
% data = crabsort.analysis.chunk(data)
% data = crabsort.analysis.chunk(data, neurons)
% data = crabsort.analysis.chunk(data, neurons, ChunkSize)
% data = crabsort.analysis.chunk(data, neurons, ChunkSize, dt)
%
function cdata = ... |
7c405abc1b3495471d910360b3f115f865d37ec2faa2488f04d149b997b6dbdd | MATLAB | 3,704 | 151 | function [pls_repro,splitflag]=split_half_PLS_TestTrain(x,y,n_con,numsplits,null_flag)
%[pls_repro,cca_repro,splitflag]=split_half_PLS_TestTrain(x,y,n_con,numsplits,null_flag)
%n_con= number of conditions
%numsplits: number of split half samples
%null_flag: save distributions 1=true default=0
%
% Uses a test-train loop... |
a7ba53d789982c6c80670138a84b5c9ac62ae0157948ecc7f29f824f77c93970 | MATLAB | 3,704 | 122 | % Tot pyr
figure
[data] = extract_variables ('pair_corr','tot',resultsPath, 'pyr');
for recCounter = 1:size(data,2)
data_mdn(recCounter) = median(data{recCounter});
end
data1 = data_mdn(contains(layer,'deep'));
data2 = data_mdn(contains(layer,'sup'));
subplot(331)
arrange_boxplot(data1,data2)
title('Whole recording... |
c94529f5f297bad5d26c4ada08fd4199d5162474e18baa6083eb1c63e7a29d12 | MATLAB | 3,704 | 154 |
function [verbose,verboseI,debug,doPlot,maxFunEvals,maxIter,tolFun,tolX,method,...
corrections,c1,c2,LS_init,LS,cgSolve,qnUpdate,cgUpdate,initialHessType,...
HessianModify,Fref,useComplex,numDiff,LS_saveHessianComp,...
DerivativeCheck,Damped,HvFunc,bbType,cycle,...
HessianIter,outputFcn,useMex,use... |
2688a860c92a1285a658c18e58774582342302fb6a97bbbfb87d11a3c4eab976 | MATLAB | 3,705 | 126 | function data = fixsampleinfo(data)
% FIXSAMPLEINFO checks for the existence of a sampleinfo field in the
% provided data structure. If present, nothing is done; if absent,
% fixsampleinfo attempts to reconstruct a sampleinfo based on either an
% trl-matrix present in the cfg-tree, or by just assuming the trials are
%... |
2a022f3adc7c0c177d43c01d9ca463ccb5801040572794262aca3d6d7d3796e1 | MATLAB | 3,707 | 117 | function meg_Fig5c_TE_byPrecue_mdlFit_freq_bar
% function meg_manuscriptFigs_TE_byPrecue_mdlFit_freq_bar
% Plot model fits (linear+periodic) free frequency by precue (All trials,
% precue T1, precue T2)
% Plots Fig 5c
%% Load data
filename = 'figData/ModelFit_freeFreq_session.mat';
load(filename)
%% Figure settings... |
dbf9767c34322a2d2b1b8ef65a87d78dad97e6e40ff3750199042fcfe42d7818 | MATLAB | 3,707 | 1 | function [ SUCCESS , ExperimentID, SubjectID, Phase, Box, MatlabStartDate,...
Duration, TSdata, Notes, Weight, Program, FileReportedUnits ]...
= TSload2ColAndHeader (filename,delimiter)
%
% Assumptions:
% File is tab delimited
% Dlm file forms a 2 column matrix
% First 12 rows are various session fields w... |
f8686ff2d6cdb77e67a89aa6af98401027396bf58c1eb709ff7414d68142e031 | MATLAB | 3,707 | 85 | function [s, cfg] = ft_statfun_diff_itc(cfg, dat, design)
% FT_STATFUN_DIFF_ITC computes the difference in the inter-trial coherence between
% two conditions. The input data for this test should consist of complex-values
% spectral estimates, e.g. computed using FT_FREQANALYSIS with method=mtmfft, wavelet
% or mtmconv... |
e7d206e2d145475d36b83a66cae3177c0e524fc4e96bc3e316ab7ff6cb478630 | MATLAB | 3,708 | 122 | function [] = measurementErrorPruned(F,mask)
mask = double(mask);
nanMask(mask==0) = NaN;
nanMask = cat(3,mask,mask);
sizeImg = size(F);
F = F.*nanMask;%Ignore transform vectors that map from parts of specimen with no features
n = 0;
Freshaped = NaN(size(F,1)*size(F,2),4);
for i = 1:size(F,1);
for j = 1:size(F,... |
1a62f8715218a2bd25b1f5cfec23e9ec7922a454619994b9d7bbe720a2753ed6 | MATLAB | 3,709 | 121 | function meg_manuscriptFigs_sessionPhaseConsistency
% Polar plot of the fitted phase difference by precue
% Session 1 v Session 2
% Mean phase difference ± 1 SEM
%
% thetaregion requires Matlab R2024a or above
%% Load data
user = 'kantian';
% Model fit data
filename = sprintf('/Users/%s/Dropbox/github/ta-meg-ana... |
9c74b6b2accdbd9f646be81dd428faa77f6c36c0b492d07594b2dd30f249d557 | MATLAB | 3,709 | 160 | function newmatrix = wlAux_splitEvMatrixByBand(oldmatrix, bandlist)
% function newmatrix = wlAux_splitEvMatrixByBand(oldmatrix, bandlist)
%
% This function sorts an event matrix's events into a new set of frequency
% bands. Old per-band lists are merged and repartitioned. Event matrix format
% is described in EVMATRIX... |
d9de743f437f99919f3ed0cac532c504946ea051352d354404da29771f87d47b | MATLAB | 3,709 | 97 | function[slope,intercept,pvalue,IJ,slopevar,intervar] = SSMMDIJ(datasource,datatarget,indexsource,indextarget,itertime)
%% The only difference from subsamplingMMD.m is IJ in output that records information needed for calculating IJ variance.
slope = 0;
intercept = 0;
%% This step determines the subsample size.
tmp = t... |
b1d65df6fbf2e39a7becd17e2babef9a1bf71e5c9bf505ddf8e5877d9b870a16 | MATLAB | 3,714 | 99 | %function [xml, rxml] = LoadXml(FileBase)
%
% loads the xml file using xmltools (have to have it in the path)
% rxml returns it's original layout - very messy structure but contains all
% the xml file contents.
% xml - is the ouput structure which is backwards compatible to LoadPar
% output, so you can use it instead .... |
42160aab34acc6d117ffa1719b6e2d8e8c3177abc8d3fbffd45d91a4118d5782 | MATLAB | 3,715 | 116 | % Hypothesis 3: STA
% Perhaps this is the 'change' of state? (i.e. spike-effects);
%_______________________________________
% Copyright (C) 2024 Trevor S. Smith
% Drexel University College of Medicine
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Pub... |
a77861692284a1d49b402586578cae5add1f046cdeb670c9927a3b620a685088 | MATLAB | 3,715 | 106 | function [mvar] = ft_datatype_mvar(mvar, varargin)
% FT_DATATYPE_MVAR describes the FieldTrip MATLAB structure for multi-variate
% autoregressive model data.
%
% The mvar datatype represents multivariate model estimates in the time- or
% in the frequency-domain. This is usually obtained from FT_MVARANALYSIS,
% optiona... |
a9369fd5d42c57929f16da575e11d9168207deec0f061bae2f69050759c2f299 | MATLAB | 3,715 | 169 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
c769c9bff690fee745c13a9b7159069514f023e9f5105bf3206fd2060f471ab7 | MATLAB | 3,715 | 105 | function ft_test_compare(varargin)
% FT_TEST_COMPARE
% Copyright (C) 2017, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General ... |
d833ae866ff00e200f5af4013e61f3c5e834f8d91ae8b4f1e005ac9fd9f4d18b | MATLAB | 3,716 | 153 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
0d0294e2e48dc2f3dc719856dd9eb11f87b2ced2fdc28ac89e6aff021d2c9c43 | MATLAB | 3,720 | 105 | % Description:
% This script initiates a full biophysical model for a specified type of photoreceptor.
% It generates the photoreceptor's response to a small, or dim, stimulus.
% This response is then used to fit a linear model of the photoreceptor,
% and to extract the coefficients for the linear model of the photorec... |
83b91483d50b28efb6f4bf39d19d0ea486a324b957878a684428f4148be04950 | MATLAB | 3,720 | 96 | function M = GeoMedian(X, Precision)
% M = GeoMedian(X, Precision)
%
% Calculate the geometric median: the point that minimizes sum of
% Euclidean distances to all points. size(X) = [n, d, ...], where n is
% the number of data points, d is the number of components for each point
% and any additional arr... |
eb5696c20151a2d46a4a9abb96f595adb2c0783824e9620f4c83fb7677232775 | MATLAB | 3,720 | 94 | function [spectrum, freqoi] = ft_specest_neuvar(dat, time, varargin)
% FT_SPECEST_NEUVAR computes a time-domain estimation of overall signal
% power, having compensated for the 1/f distribution of spectral content.
%
% Use as
% [spectrum,ntaper,freqoi] = ft_specest_neuvar(dat,time...)
% where
% dat = matri... |
3dbae1d320dc92f6cf17f9db4f8238169d2b244565da3d21cce76baa28e3939c | MATLAB | 3,721 | 126 | function [] = sam_svl2spm_command_smd(mrilist, svllist, num)
% sam_svl2spm_command(mrilist, svllist, num)
% mrilist(ii).names contains full path to mri
% svllist(ii).names contains full path of each svl file to be normalized
% If there is more than one svl file per mri they should be organized into
% an mXn matrix whe... |
3f5f601b0818fd1ccb9dceaa2b07405faed054b29bbd515d733da8d95e7279f3 | MATLAB | 3,721 | 122 | function [magn] = read_ctf_sens(filename)
% READ_CTF_SENS reads MEG sensor information from CTF configuration file
%
% magn = read_ctf_sens(filename)
%
% where the returned structure meg has the fields
% magn.pnt position first coil
% magn.ori orientation first coil
% magn.pnt2 position second coil
% m... |
571f9b57a05bdfba403c86df1379f80f4348c7ccfd86ac7a24c3f059da13e5ea | MATLAB | 3,721 | 114 | function [datout, tim, Fnew] = ft_preproc_resample(dat, Fold, Fnew, method)
% FT_PREPROC_RESAMPLE resamples all channels in the data matrix
%
% Use as
% dat = ft_preproc_resample(dat, Fold, Fnew, method)
% where
% dat = matrix with the input data (Nchans X Nsamples)
% Fold = scalar, original sampling freque... |
abced38ad89e199860cbf8f10311420d0d4b5fb4f5533a3300d3095399fa4e8d | MATLAB | 3,721 | 112 | function [newbnd] = mesh2edge(bnd)
% MESH2EDGE finds the edge lines from a triangulated mesh or the edge
% surfaces from a tetrahedral or hexahedral mesh. An edge is defined as an
% element that does not border any other element. This also implies that a
% closed triangulated surface has no edges.
%
% Use as
% [edge... |
4cde3aa5e8b731215f23c6b4bf3befb0ed4785e6de126c52fb5cc4391a9aaf48 | MATLAB | 3,722 | 96 | function [ALLEEG] = PAA_batch()
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Build EEG structure from multiple EEG datasets to batch run PAA
%
% Contact: sfogel@uottawa.ca
%
% Date: May 6, 2020
%
% Citation: Ray, L.B., Sockeel, S., Soon, M., Bore, A., Myhr, A.,
% Stoja... |
bbe913c5e8d7479b5cf3397dbc258c9b5aa3b560a97dce387000dabb3c9576b8 | MATLAB | 3,722 | 66 | function [Data, VoxelSize, Header] = y_ReadRPI(FileName, VolumeIndex)
%function [Data, VoxelSize, Header] = y_ReadRPI(FileName, VolumeIndex)
% Read NIfTI image in RPI orientation -- for NIfTI files without rotation in affine matrix!!!
% Will call y_Read.m, which does not adjust orientation.
% --------------------------... |
3fcdaf3044e4ddc3f3a11a1e8bc743d8953062a1d0f856298ca8ce7f41ef496c | MATLAB | 3,723 | 106 | % Plot SVM Performance
%----------------------------------------
% Description:
% This function visualizes the SVM performance for AI-optimized non-invasive
% brain stimulation dosing and treatment response prediction for major depression.
% It provides plots for ROC curves, AUC comparisons, and confusion matrices.
%
... |
d845ad54cb7ec9a22718cba63e29adb86b13f8bb16234d9eb0b630dc6176fdf4 | MATLAB | 3,723 | 114 | function [datout, tim, Fnew] = ft_preproc_resample(dat, Fold, Fnew, method)
% FT_PREPROC_RESAMPLE resamples all channels in the data matrix
%
% Use as
% dat = ft_preproc_resample(dat, Fold, Fnew, method)
% where
% dat = matrix with the input data (Nchans X Nsamples)
% Fold = scalar, original sampling freque... |
78e412c1938475c021a7e282b26b22f185d0b78ecc6c4509c8dbe4f43cd8e366 | MATLAB | 3,725 | 1 | function [ SUCCESS , ExperimentID, SubjectID, Phase, Box, MatlabStartDate, Duration, TSdata, Notes, Weight, Program, FileReportedUnits ] = TSloadstdxls ( filename )
%
% Assumptions:
% File is readable by Matlab's xlsread command
% Data are in 1st & 2nd cols of the spreadsheet
% First 12 rows are various session f... |
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