sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9ef076052df82fb95a89c2d8ceba74d61ff6b0395cc3a924dc22e0c48dd2ecca | MATLAB | 3,050 | 88 | function outputImage = perform_binary_operation(this, otherImage, ...
functionHandle)
% Performs binary operation (i.e. 2 inputs) on this and a second image
% for given dimension and returns a new output image
%
% NOTE: If voxel dimensions of 2nd image do not match - or a scalar is
% given as 2nd argument - data in... |
0ac012bf29e8a3f7563a9da52fdc37fd486e98afac68e15f9a85fb59332c04fe | MATLAB | 3,051 | 100 | % Script demo_split_complex
% splits complex nD data in (n+1)D magn/phase or real/imag
%
% demo_split_complex
%
%
% See also
% Author: Saskia Bollmann & Lars Kasper
% Created: 2018-05-22
% Copyright (C) 2018 Institute for Biomedical Engineering
% University of Zurich and ETH Zurich
%
% This fi... |
47c8547e2c50a8fda8ac5ff57a6e4a11735821e29ac902f6447088fe5a698d53 | MATLAB | 3,051 | 64 | function varargout = binaryEPGP(hyper, covfunc, x, y, xstar)
% binaryEPGP - The Expectation Propagation approximation for binary Gaussian
% process classification. Two modes are possible: training or testing: if no
% test cases are supplied, then the approximate negative log marginal
% likelihood and its partial deriv... |
54604efb5e58a17e03f2a1004ed070f6a7ad583123f557be59ba184aba22b4dc | MATLAB | 3,051 | 71 | % STD_CHANINDS - look up channel indices in a STUDY
%
% Usage:
% >> inds = std_chaninds(STUDY, channames);
% >> inds = std_chaninds(EEG, channames);
% >> inds = std_chaninds(chanlocs, channames);
% Inputs:
% STUDY - studyset structure containing a changrp substructure.
% EEG ... |
5a848b3f878504970f4d944c824402c19c8d72528afc5d30988e01a16d5274f3 | MATLAB | 3,053 | 107 | function [x, V, VV, loglik] = kalman_filter(y, A, C, Q, R, init_x, init_V, varargin)
% Kalman filter.
% [x, V, VV, loglik] = kalman_filter(y, A, C, Q, R, init_x, init_V, ...)
%
% INPUTS:
% y(:,t) - the observation at time t
% A - the system matrix
% C - the observation matrix
% Q - the system covariance
% R - the o... |
8d623d8c24156dcbd5f66272a212c230c8b30b2fc58e494a1da3fe9d6bc1c070 | MATLAB | 3,053 | 113 | function doCoactAnalysis(rootDir,sessionList)
if ~exist('rootDir','var') || isempty(rootDir)
rootDir='~/data/Fear/triple';
end
if ~exist('sessionList','var') || isempty(sessionList)
sessionList={
'achel180320'
'booyah180430'
'chimay180612'
'duvel190505'
'estrella18... |
c1c30ebc11d8c22b724ee427ed428005c2d94ab8a09b49afa5d592f63da20b51 | MATLAB | 3,053 | 82 | function N = tangentspacefactory(M, x)
% Returns a manifold structure representing the tangent space to M at x.
%
% N = tangentspacefactory(M, x)
%
% N defines a (linear) manifold that is the tangent space to M at x. Points
% are represented as tangent vectors to M at x. Tangent vectors are also
% represented as tangen... |
face0942e34aa2b3b38499d0c607e752d69ed7a929ad32f3f670043feec35b9a | MATLAB | 3,054 | 107 | function sero_srr_plot_sampling_stats_v3(tr, b, w)
%% sero_srr_plot_sampling_stats_v3 Visualize TR & b-value sampling statistics
% sero_srr_plot_sampling_stats_v3(tr, w, b) makes a 3×2 figure showing:
% (1) shot×slice log-TR image
% (2) sampling density vs. slice (line plot)
% (3) TR distribution heatma... |
8cba7f1b8d718f2bed96d618a3da733f7ba5498294883ff8b3c3f41ca240efef | MATLAB | 3,055 | 84 | % Analyses of the EMPRISE data set
% by Joram Soch <soch@cbs.mpg.de>
clear
%%% Session EDY7-visual: BayespRF, 2023-09-11 #############################
% specify analysis
addpath(genpath('C:\spm\BayespRF\toolbox\'));
dirs = load('project_directories.mat');
subj_id = 'EDY7';
session = 'visual';
mod_name = 'pRF'... |
086c2bcbee0691abea26fc5389cf486d1e7041a6f0c26d2c88cb987dd628090c | MATLAB | 3,056 | 86 | function this = analyze_rois(this)
% Extracts specified rois (masks) from specified images, and computes statistics
%
% Y = MrSeries()
% Y.analyze_rois(inputs)
%
% This is a method of class MrSeries.
%
% IN
% .parameters.analyze_rois.
% nameInputImages Cell of strings or string with image na... |
0f8b61e915baee343d9e7aeca98b1f5ac1e13514d89d33f27dcb5d03b064008c | MATLAB | 3,056 | 88 | function labels = run_ICL(version, images, psds, autocorrs)
%% check inputs
if any(strcmpi(version, {[], 'default'}))
version = '';
elseif any(strcmpi(version, 'lite'))
version = '_lite';
elseif any(strcmpi(version, 'beta'))
version = '_beta';
else
error(['Invalid network version choice. '...
... |
923394b4289ad6b75a969fb4d0d0db55667cc8f66f4f2b10dc514dc08f94c66a | MATLAB | 3,056 | 118 | function S=reducesim(S,minLimit,partition,scatter,scatterLimit)
%function S=reducesim(S,minLimit)
% or
%function S=reducesim(S,minLimit,partition,scatter,scatterLimit)
%
%PURPOSE
%
%To reduce the number of lines that are drawn when the similarity
%matrix is visualized. That is, to set similarities below certain
%thres... |
3502d90418d9f256b8d55f945abef2bd672d2bc9d509cc00c13cf215c1260505 | MATLAB | 3,057 | 76 | % EEG_GLOBAL - declare global EEGLAB variables. These variables are
% used only as global by the main function EEGLAB,
% the function POP_REJMENU and the history EEGH function.
%
% Global variables:
% EEG - structure containing the current dataset
% ALLEEG - array o... |
77da623845bf36a29fb6f90dc6afd8b8fc98211b658c433b3882d21fdc25f6cd | MATLAB | 3,057 | 70 | % SCANFOLD - scan folder content
%
% Usage:
% >> [cellres textres] = scanfold(foldname);
% >> [cellres textres] = scanfold(foldname, ignorelist, maxdepth);
%
% Inputs:
% foldname - [string] name of the folder
% ignorelist - [cell] list of folders to ignore
% maxdepth - [integer] maximum folder depth... |
628c7238f8c0056979b18ebc65fd52460659d11c89147f08e0001b2a0135260d | MATLAB | 3,058 | 69 | function [Out] = GetPercentageCorrect(sn, nTrialsPerCondition)
%% Info
% This is a wrapper function that takes in the subject data and get the
% percentage of correct responses for each loudspeaker and spectrum type
% Input: 'sn' = subject data struct
% 'nTrialsPerCondition' = Number of trials per condition
%
... |
f02688fee6cd4b73833850760f402eb8a602531092e064a3986fe45ad6dd7baf | MATLAB | 3,058 | 76 | function [all_spikes, unique_idx, intersect_matrix] = mergeSpikes(spike_times, option)
% Merges spike times across detection methods.
% TIP: to get spike waveforms corresponding to the merged spike times call e.g.:
% [~, spikes] = alignPeaks(spike_times.all, filtered_trace, 25, 0, 1, 10, 10);
% Parameters
% ------... |
8280393e799a0ad1597685bed092d339c9ee6057b673fb01ffacbcd8fdfa14be | MATLAB | 3,059 | 107 | function hhh=tapas_uniqc_hline(y,in1,in2)
% function h=hline(y, linetype, label)
%
% Draws a horizontal line on the current axes at the location specified by 'y'. Optional arguments are
% 'linetype' (default is 'r:') and 'label', which applies a text label to the graph near the line. The
% label appears in the same ... |
fa72ecf72567aeb17ae240242ee83a0941f45f8d9ef5b235a8a5f9ebd123f19d | MATLAB | 3,059 | 104 | function cmd=surfing_suma_makespec(varargin)
% Makes a AFNI SUMA spec file and script to start SUMA
%
% SURFING_SUMA_MAKESPEC('aligndir',D,surfvolalfn',S,'icold',I)
%
% INPUTS:
% D Directory that contains surface files
% S Anatomical file (e.g. 's01_SurfVol_fix+orig')
% I MapIcosehedron number of s... |
f5f6dcf34fb19f84ea6ac15ecacdc68f54bf95576b66ff886dc861f67f16ab90 | MATLAB | 3,063 | 92 | function map = vega10(N)
% Colormap from MatPlotLib 2.0. For attractive plots using the ColorOrder.
%
%%% Syntax:
% map = vega10
% map = vega10(N)
%
% For MatPlotLib 2.0 improved colormaps were created for plot lines of
% categorical data. The new colormaps are introduced here:
% <http://matplotlib.org/2.0.0rc2/users... |
dd4f0077935fb9be195a7480994604ebd75bee87f25186fd54cd9516733a86e5 | MATLAB | 3,064 | 105 | function [posa,pos,vel] = fixPos2d(file,dSamp,mode)
%% take position info from whl file and preprocess it
if ~exist('dSamp','var')
dSamp = 1;
end
if isstr(file)
pos = importdata(file);
else
pos = file;
end
pos(pos == -1) = nan;
reject = 0;
if exist('mode','var') && mode
thresh = 1.1;
rad = pos(:,1... |
e63cbf4ba3ba89d038be20298dc73dcfa1068166602f32569214f34431418ed5 | MATLAB | 3,066 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {''};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-control01_task-YOURTASK_run-1';
matlabbatch{1}.spm.tools.physio.log_files.vendor ... |
f67e9f8cda85fefb243bf6e591029e8ce3ef58b2fbb73dfd4fee6c75b5b7d639 | MATLAB | 3,067 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {''};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-control01_task-YOURTASK_run-1';
matlabbatch{1}.spm.tools.physio.log_files.vendor ... |
0fcd7d29bbea48be252bf9aaf31a4882fdc6c247f65b50ae295bd3c5452e1126 | MATLAB | 3,068 | 67 | function varargout = covMatern(mode, par, d, varargin)
% Matern covariance function with nu = d/2 and isotropic distance measure. For
% d=1 the function is also known as the exponential covariance function or the
% Ornstein-Uhlenbeck covariance in 1d. The covariance function is:
%
% k(x,z) = f( sqrt(d)*r ) * exp(-s... |
482b15c0309b5ca1a6007e11154720604999a22fc8ab9ca06671fac979bf321c | MATLAB | 3,068 | 104 | function [commitID,git_lastcommit,options]=gitLastCommit(varargin)
% EXAMPLE USE WITH ARGUMENTS
%[git_lastcommit,options]= gitLastCommit() - assuming path to the repo
%where function is located, two levels up
%[git_lastcommit,options]= gitLastCommit(repo_path) - last commit of repo
%of the path repo_path
%[git_lastcomm... |
5a6c2abac7038123f29753e058b783250b88845b8077ec5d418c04e43d349bd0 | MATLAB | 3,068 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {''};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-control01_task-YOURTASK_run-1';
matlabbatch{1}.spm.tools.physio.log_files.vendor ... |
5c3d0504d282f8809ecfaf91f997efbb234f86b4288af88e33ebefe786f253f8 | MATLAB | 3,068 | 83 | function success = TS_InitiateParallel(doInitiate)
% Initiates a parallel session for hctsa
%
%---INPUT:
% doInitiate: = true for the first time you want to initialize all workers
%
%---OUTPUT:
% success = true if a matlabpool was successfully initiated (or if one already
% exists)
% --------------------... |
82f622b229719902e9c09859bfe5ca82cb440a7dbdc17963a4e01705f228e1ea | MATLAB | 3,068 | 98 | function [Wrr, Wrf] = gen_connectivity(params, options, rng_seed)
% GENERATE_CONNECTIVITY - Create network connectivity matrices
%
% H1 Line: Generate connection matrices for neural network
%
% Syntax:
% [Wrr, Wrf] = generate_connectivity(params, options, rng_seed)
%
% Description:
% Generates connectivity matrices... |
757d63db169d24d47faf972767cbdc2e182bcdb89adb9db02f62aa6e19168021 | MATLAB | 3,070 | 101 | function [fstamps_path,summary]=find_framestapms(h5orDCIMGpath,varargin)
%
% HELP
% Finding a frame stamp file just given a file location. If h5 file, it is expected to be found in a subfolder
% SYNTAX
%[fstamps_path,summary]= find_framestapms() - use 1 if no arguments are allowed
%[fstamps_path,summary]= find_framesta... |
0a1e9a5f1cc5ebeeae509e89199ae088b842cac84ad8137112c026e49fd3a3fe | MATLAB | 3,072 | 90 | function [lratio, distance] = GetLratio(units)
%Lratio - Determine the isolation quality of one or more clusters.
%
% Compute isolation distance,
%
% USAGE
%
% lratio = Lratio(units)
%
% units list of units to process (default = all clusters except
% 0 and 1)
%
% OUTPUT
%
% ... |
e52d20246b243f816d3e077d21e394ebdb27162a67048f2fbbf1d14e75350df8 | MATLAB | 3,072 | 79 | % Example to export joint EEG and Eye-tracking data (child mind)
% The data is included in this repository (on Github, maybe not on the
% plugin downloaded from EEGLAB).
%
% THIS PLUGIN REQUIRES THE INSTALLATION OF THE GAZEPOINT AND SMI EEGLAB PLUGINS
%
% Arnaud Delorme - December 2023
clear
data = [];
p =fileparts(... |
5263136d99064c57b287e3b77f1ca1b943f89c6c687dbb74206ca77c9ce68e60 | MATLAB | 3,073 | 130 | function meta_add_spheres_in_rois(DB, varargin)
% Add spheres to selected ROIs
%
% [p, mesh_struct] = brainstem_slices_3d;
% meta_add_spheres_in_rois(PLOTINFO{1}, 'brainstem');
% colormap gray
%
% DB must be a DB or PLOTINFO struct with these fields:
% - colors
% - xyz
% - condf
%
% (for table)
% - nums
% - descrip
% -... |
bbcb3dec920ae1c9a26c1e524119572952249b3bfc143991d66cadb78aafd59d | MATLAB | 3,073 | 89 |
% Runs GUI mode for MEA-NAP
% CreateStruct.Interpreter = 'tex';
% CreateStruct.WindowStyle = 'modal';
opts = struct();
opts.Default = 'Okay';
opts.Interpreter = 'tex';
helloBox = questdlg("\fontsize{20} Hello! Welcome to the MEA network analysis pipeline (MEA-NAP)!", ...
'Welcome!', 'Okay', opts);
clear helloBox
o... |
2cfb08dc5a02c21e11392bf3021a2906bba7e1f703f6366ef8305c6f5d26aaed | MATLAB | 3,074 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {''};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-control01_task-YOURTASK_run-1';
matlabbatch{1}.spm.tools.physio.log_files.vendor ... |
43332372517a43b5c0eb8baa8769a10ccaa464858e62a0610166efa984571f11 | MATLAB | 3,074 | 86 | % std_indvarmatch - match independent variable value in a list of values
%
% Usage:
% indices = std_indvarmatch(value, valuelist);
%
% Input:
% value - [string|real|cell] value to be matched
% valuelist - [cell array] cell array of string, numerical values or
% cell array
%
% Output:... |
4ac70b6b43c148cec2eaa8ff818fd532e88375c7698a3a194ee3d0d931778414 | MATLAB | 3,074 | 119 | classdef tmovemex < matlab.unittest.TestCase
properties
numLabs
end
properties (TestParameter)
device = {'cpu', 'gpu'}
end
methods (TestClassSetup)
function openParpool(test)
test.numLabs = 4 ;
if ~isempty(gcp('nocreate'))
delete(gcp) ;
end
cl = parcluster('local... |
128201febd35ab742c9b88050a4db3c986e68e962c108a40f994fd901f77aa87 | MATLAB | 3,075 | 103 | function info = GetCurrentSession(verbose)
%GetCurrentSession - Get information about current session.
%
% USAGE
%
% GetCurrentSession
% GetCurrentSession('verbose') % detailed output
%
% info = GetCurrentSession % return info (do not display)
% Copyright (C) 2008-2024 by Michaël Zugaro
%
% This program i... |
77dc248850ccfca5ec48679325bd2c324a2483fa60c065581b58d93358e21a1e | MATLAB | 3,075 | 120 | function coactPaper_figureS21()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=5;
fontsize=6;
fh=initFig('width',8.9,'height',4,'fontsize',fontsize)
x=26;
y=6;
panel_01(x,y,fontsize)
print(fh,sprintf('~/Dropbox/FearAnalyses/paper/figure/figS21_%s.pdf',datestr(now,'yyyymmdd')),'-dpdf','-painters','... |
7d889e5d5b9a735f281126fdbec1823251a95f66e694ac3332db8afc71fa9d19 | MATLAB | 3,075 | 96 | function [fit,cfg] = fit_MixtureModelShift(x,data,bias,cfg)
% [fit,cfg] = fit_MixtureModelShift(x,data,bias,cfg)
%
% fit mixture model by minimising MSE
if nargin < 4
cfg = struct;
end
if ~isfield(cfg,'fitmean')
cfg.fitmean = false;
end
if ~isfield(cfg,'offset')
if is... |
f3208b5a6a03b76293dec47bc6e6738a649ed7fbce6781de86312d6a26a7a571 | MATLAB | 3,075 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {''};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-control01_task-YOURTASK_run-1';
matlabbatch{1}.spm.tools.physio.log_files.vendor ... |
0d4a9322bf52626268b7ffd5f333597a3b0cc3f253e21d79b17cc3deb4f7ae94 | MATLAB | 3,076 | 88 | function this = MrDimInfo_load_from_file(this, testFile)
% Unit test for MrDimInfo Constructor from file
%
% Y = MrUnitTest()
% run(Y, 'MrDimInfo_load_from_file')
%
% This is a method of class MrUnitTest.
%
% IN
%
% OUT
%
% EXAMPLE
% MrDimInfo_load_from_file
%
% See also MrUnitTest
% Author: Saskia Bollmann
... |
f5d3d782e659e62808706f52356ed2d4d76fb713f46dd825868801ccc1eaa7a5 | MATLAB | 3,076 | 95 | function Calls = merge_boxes(AllBoxes, AllScores, AllClass, audio_info, merge_in_frequency, score_cuttoff, pad_calls)
%% Merge overlapping boxes
% Sort the boxes by start time
[AllBoxes,index] = sortrows(AllBoxes);
AllScores=AllScores(index);
AllClass=AllClass(index);
% Find all the boxes that overlap in time
OverBoxe... |
0d12e368749b336b7a7364424309b862d1bd5af76482500ebb68326704d2eb4e | MATLAB | 3,077 | 109 | function varargout = pdftops(cmd)
%PDFTOPS Calls a local pdftops executable with the input command
%
% Example:
% [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for future refere... |
11706840695d3a742e68a51944d8ba2122d84b67182c62b218211181a6edbfa9 | MATLAB | 3,077 | 98 | %io_writelcm.m
%Jamie Near, McGill University 2014.
%
% USAGE:
% RF=io_writelcm(in,outfile,te);
%
% DESCRIPTION:
% Takes MRS data in matlab structure format and writes it to a text file
% that can be read by LCModel.
%
% INPUTS:
% in = input data in matlab structure format.
% outfile = Desired filename of ou... |
4bdfe54a077c7d3ef8e47284d7359dc833af7d8390697f08e839febd0eee6e8d | MATLAB | 3,077 | 110 | % load in and visualize snapshots
load('../../ERCaSims/networks/WT/WT_circreg.mat')
NT = WTnetworks(1);
%% load snapshot data
resdir = '../test/';
%filename = [resdir 'testrecoveryWT.mesh.txt'];
filename = [resdir 'testspreadWT.mesh.txt'];
MSH = MeshObj(filename);
%snapfile = [resdir 'testrecoveryWT.snap.txt'];
snapf... |
6b1cc6211d67abefd1d7d4c3af63114f9d2a81d9425eb8b6decea5ad8d853d00 | MATLAB | 3,077 | 104 | function glm_nsdrestingstate(ppdir,ppdirname,designfile,hrfbasisfile,tr,glmdirname,hrfmanifoldfile)
glmdir = regexprep(ppdir,'ppdata',glmdirname);
mkdirquiet(glmdir);
%%%%% LOAD
% define
stimdur = 3;
% figure out runs
files0 = matchfiles(sprintf('%s/%s/run*.nii',ppdir,ppdirname));
assert(length(files0)==14);
files0... |
99eef752798dcc723778b64dd957ab2b81c20b20ba53676911d924c8ea5ac4cf | MATLAB | 3,077 | 85 | %% ===== PREDICTION + METRICS =====
close all; clc; clear all;
%% ===== USER: EDIT THESE PATHS =====
featuresMat = 'C:\YOUR\PATH\TO\ResNet-101\Resnet-101_features_test'; % contains variable "features"
mosMat = 'C:\YOUR\PATH\TO\Test_MOS_New'; % contains variable "MOS" (vector Nx1 or 1xN... |
ae5e81e622164f29f5455498a0814423fa543940845d115911913b355d12bae0 | MATLAB | 3,077 | 102 | function eval = clusteval(new,result,param)
v = result.cluster.v;
c = size(result.cluster.v,1);%c = param.c;
if exist('param.m')==1, m = param.m;else m = 2;end;
X=new.X;
[N,n] = size(X);
X1 = ones(N,1);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if isfield(result.clus... |
bd9d78a891cba60b860161b36bce5d0929d3844fe342eaab54bd31e98e5bc8be | MATLAB | 3,077 | 95 | function run_permuanova1_examples
%RUN_PERMUANOVA1_EXAMPLES Run one-way permutation ANOVA examples.
% Generates random data for 5 groups along the columns of X. Each group
% has a mean value of 0, except for the first group which has a mean
% value of 1. Each group has 30 observations. The group labels are
% r... |
58771912a9e225c407d6599e23682395adb869ae2ab9aa05193b4d85018f5e5d | MATLAB | 3,078 | 91 | % SEEMOVIE - see an EEG movie produced by EEGMOVIE
%
% Usage: >> seemovie(Movie,ntimes,Colormap)
%
% Inputs:
% Movie = Movie matrix returned by EEGMOVIE
% ntimes = Number of times to display {0 -> -10}
% If ntimes < 0, movie will play forward|backward
% Colormap = Color m... |
11ef1fce5033dc165373e1770f1dd8c967655ea2f4613c838f363e21a0db9f4e | MATLAB | 3,080 | 79 | function run_paper_examples
%RUN_PAPER_EXAMPLES Run arXiv paper examples.
% Generates random multivariate data for 2 "independent" samples X and Y.
% Each sample has 20 variables, each with a mean value of 0, except for
% the first 10 variables of Y which have a mean value of -1. Each
% variable has 30 observa... |
e3cc893dc72036623cce9c1d6c7cad4360c5168c9e96f6ebd386e78b10eba33c | MATLAB | 3,080 | 87 | textlabel = {'valence'};
plots = {'surface';'medial'};
filenames = {'emotrev4_posneg_t.txt'};
plotdims= [1 2];
conditions = { ...
% plot 1
'strcmp(valence,''asdf'') | strcmp(valence,''fdas'')' ...
'strcmp(colors,''yv'')' ...
'strcmp(colors,''wo'')' ...
'strcmp(cogdemand,''y'') | strcmp(cogdemand,''n'')'... |
44e1a47793ce1de843e7727c808e28724a39f716ab72e29de6fb783b8f0bb8bc | MATLAB | 3,081 | 119 | function [] = plotConnectivityProperties(adjM, e, lagval, maxSTTC, meanSTTC, ...
ND, NS, MEW, FN, Params, figFolder, oneFigureHandle)
%
% Plots connectivity properties given the adjacency matrix (adjM)
% Parameters
% ----------
% adjM : matrix
% adjacency matrix
% e : int
% index of the lagvals var... |
c7c07a92f1b65562407b00b7dcdea56785ca8c26c394e07fde3c470ab8694c17 | MATLAB | 3,081 | 101 | function [statlist, docinfo] = doxyread(filename)
%DOXYREAD Read a 'search.idx' file generated by DOXYGEN
% STATLIST = DOXYREAD(FILENAME) reads FILENAME (Doxygen search.idx
% format) and returns the list of keywords STATLIST as a cell array.
% [STATLIST, DOCINFO] = DOXYREAD(FILENAME) also returns a cell array
% con... |
2c8b1b89b9d0567f2589323fe4353e35c0ed969383d75a37a6b6a83332c06053 | MATLAB | 3,082 | 91 | function [] = plotBiasAnalysis(saveFigures)
% Plot results from bias analysis.
if nargin==0
saveFigures = true;
end
% get file paths
paths = addPaths();
analysisName = 'bias_analysis';
% Load results
file = fullfile(paths.outputs, analysisName, [analysisName, '_results.csv']);
if ~exist(file, 'file')
error('... |
7d4a2da700fe412692277be67f39384f59fc62ca0cd67c494a4ccb78c360d8f7 | MATLAB | 3,082 | 109 | function terms = strsplit(s, delimiter)
%STRSPLIT Splits a string into multiple terms
%
% terms = strsplit(s)
% splits the string s into multiple terms that are separated by
% white spaces (white spaces also include tab and newline).
%
% The extracted terms are returned in form of a cell array of
% ... |
4925a05352bdb062df846538d47dbe97a5b24945c31d77eaf37289d13af08016 | MATLAB | 3,083 | 90 | function l = IsExtremum(samples,varargin)
%IsExtremum - Identify local maxima or minima.
%
% Find the maxima (resp. minima) in a signal by smoothing the signal and then
% finding the points where the derivative goes from positive to negative (resp.
% from negative to positive).
%
% USAGE
%
% status = IsExtremum(sa... |
ee525e033ddec14f37846699c5a0bfe285b0a4b5121e1cc7cbd089d4bf62a219 | MATLAB | 3,084 | 89 | function filtered = FilterLFP(lfp,varargin)
%FilterLFP - Filter the local field potentials, e.g. in the theta band.
%
% Filter the local field potentials using a cheby2 filter.
%
% USAGE
%
% filtered = FilterLFP(lfp,<options>)
%
% lfp local field potentials <a href="matlab:help samples">samples</a>
%... |
a0c5279dfdbb00bf74a3289a56f2b723b63fb34f2da428f540c3951d5e5a7a01 | MATLAB | 3,085 | 92 | %reading the clinical and demographic data as well as the PAC values and preparing the table for statistical analysis
clinical = readtable(fullfile(main_path, '/Dataset/eLife91044_processeddata_scalarmetrics.xlsx'));
clinical.diagnosis = categorical(clinical.diagnosis);
clinical.ID = categorical(clinical.ID);
cl... |
baef2eef86076bbf1b481b220a5ce6914cd19748a28275476fe17ac2c79d69c9 | MATLAB | 3,086 | 88 | function MS = createMeshCylindrical3D(varargin)
% MeshStructure = createMesh3D(Nr, Ntheta, Nz, Radius, theta, height)
% MeshStructure = createMesh3D(facelocationR, facelocationTheta, facelocationZ)
% builds a uniform 3D mesh:
% Nx is the number of cells in x (horizontal) direction
% Ny is the number of cells in y (vert... |
4e426fc86fb1183381a9e0569b21cdb845f4ab8cd4b9128d57dd0012fc4dbe76 | MATLAB | 3,087 | 97 | classdef MrGlm < MrCopyData
% Class providing General Linear Model of fMRI data
% (for mass-univariate analysis, i.e. per-voxel regression)
%
%
% EXAMPLE
% MrGlm
%
% See also
% Author: Saskia Klein & Lars Kasper
% Created: 2014-07-08
% Copyright (C) 2014 Institute... |
d9b5448bcc3db3e1efed1b65997b0c534b8fdf023ade61698d58646e55f3347d | MATLAB | 3,089 | 90 | %This code will regress 3 TR (6.3 sec) lags of global components
%Author: Kim Kundert-Obando for questions please reach out to me at k.rogge.obando@gmail.com
%%
%load subjects and paths
subj= readtable('/data1/neurdylab/datasets/nki_rockland/vigilance_analysis/great_HR_sub_coded.txt', 'readvariablenames', 0);
save_pa... |
8461a7002f4f71269a3fbe265cfa1c4d0d0b5e8ce90812790207775b62b97b50 | MATLAB | 3,090 | 87 | function varargout=pt_continuousabove(data,baseline,abovethresh,mintime,maxtime,ignorepts)
% function varargout=continuousabove(data,baseline,abovethresh,mintime,maxtime,ignorepts);
%
% Finds periods in a linear trace that are above some baseline by some
% minimum amount (abovethresh) for between some minimum amount of... |
bdb7a66a4cf331f6e5c0cb08af24036604b9b728da565db6185dfb412e81fd97 | MATLAB | 3,090 | 100 | function [groupingResult, numGroup] = groupUnits(zscoreMatrix, options)
arguments
zscoreMatrix (:,:) double ;
options.numCluster = 8;
options.cutoffLimit = 50;
options.showGraph = false;
end
loadxkcd;
Z_ = linkage(zscoreMatrix, 'average', 'correlation');
unitClusterId = cluster(Z_, 'maxclust', option... |
911d8502b99a5ab1244cbeb8f15874bd156b0d2f189ea3228e8c5aefc16ddbdf | MATLAB | 3,091 | 85 | function M = dicom2transform(dcmheader)
% DICOM2TRANSFORM converts the DICOM header parameters into a 4x4 homogenous
% transformation matrix that maps voxel indices to the Patient Coordinate System.
% Note that voxel indices are to be counted starting from 1 (MATLAB and Fortran
% convention, not C/C++ and Python conve... |
c6cd88a34b955cc079a86f60b9fcdec5b597df745362d4c0072a300b58062f47 | MATLAB | 3,091 | 79 | function batchDetectStim(ExpName, Params, app)
%BATCHDETECTSTIM Summary of this function goes here
% Detailed explanation goes here
if Params.guiMode == 1
app.MEANAPStatusTextArea.Value = [app.MEANAPStatusTextArea.Value; ...
sprintf('Running stimulus detection')];
end
spikeDetectionFolder = fullfile(Params.ou... |
3cec472d0a56065b5ce8e7d281a6049a6639e1a3aa3523e0891c26ffa0f4f81f | MATLAB | 3,092 | 82 | function N = tangentspherefactory(M, x)
% Returns a manifold struct. for the sphere on the tangent space to M at x.
%
% N = tangentspherefactory(M, x)
%
% N defines a manifold that is the unit sphere on the tangent space to M
% at x. Points are represented as tangent vectors of unit norm. Tangent
% vectors are represen... |
8fac3df3b947f0505996008a8698a535064a5b73f459f49d33fb604399a229f1 | MATLAB | 3,092 | 86 | function poolSubjects_slicesActivity(params, groupInfo)
% plots brain slices (ax,cor,sag) & activations (ERP + freq.band + spectra)
% pools together subject processed by a given job
% settings (subjects, directory names, ...) are stored in 'params'
% (c) Jiri, Apr18
if params.plot_brainSlices.plot_slices
disp('Pl... |
98358f4852ccca713b8776d5c825f88c129c5f8b758a751d3a6d81d64270345f | MATLAB | 3,092 | 112 | function Decis = ErrEval (FuncName, ErrCode);
%
% Decis = ErrEval (FuncName, ErrCode);
%
%This function displays an error message based on ErrCode and
%returns 1 if it's a lethal error (Err_) , or 0 if it's
%an error or a warning (Wrn_)that does not require aborting a function
%
%
%ErrCode is a string made out of two p... |
4a25626ebf653c9f0dc99982905abd238b5f3aa5ad3cc13a9c9cc2caad2d2b3e | MATLAB | 3,093 | 119 | function [err] = writeSPMmat (matin, matout)
%
% [err] = writeSPMmat (matin, [matout]);
%
%Purpose:
% Write an ascii version of SPM's .mat files
% containing a 4x4 transformation matrix.
% The output of this function can be used
% with 3dWarp to create AFNI-formatted data from
% SPM datasets.
%
%Input Param... |
876d9c84a27ad1fab32a21771a23a3be875fddec1dec9c447e62b4ff7d279de4 | MATLAB | 3,094 | 82 | %{
a stand-alone script for MadMax stimulus processing of galvo traces
%}
%% prepare
matched_trials = preprocess.Sync * vis.Trial * vis.Condition & 'trial_idx between first_trial and last_trial';
%% all galvo scans for which there is a monet stimulus
madmax_keys = fetch(preprocess.Spikes*preprocess.SpikeMethod*prepro... |
f0bf63b3bc048a0104d080b68da8532b5e23104d1182d916dbc878a60f8d2c31 | MATLAB | 3,094 | 117 | function [WTOpt, WTMdl, BlkInf, Belief, Prior, Kappa] =...
BayesMdlOpt(params, ratTrial,...
noise_arg, gen_arg, noise_params)
%GenerateSynthData_Bayes - generates synthetic wait times
%for optimal Bayes model.
% Inputs:
% params - Parameter vector. [kappa_mi, kappa_hi, kappa_lo, D, lambda]
% kappa_mi, k... |
84c5f5dad8d093aa044864cabff60ce6b231d97fcacab223ce0c8465034349be | MATLAB | 3,095 | 73 | %% cluster based rois
% this script reads the .mat file and the base space image that you select
% manually to create rois
% this script uses spm and marsbar
% step 0:
% follow the methods here to manually find and save your clusters
% marsbar and som save a .mat file
% https://marsbar-toolbox.github.io/tutorial/defi... |
c6c24ca98d5151e3d69060aa6eba71606b9fbc2c6610e6bdf81c7a43f921cad4 | MATLAB | 3,095 | 77 | function [distVec,links,distVec0,numItems] = BF_DoLinkage(distMat,whatDistance,linkageMeth)
% BF_DoLinkage Process an input distance matrix for linkage clustering
% (including custom processing for absolute correlation distances)
%---INPUTS:
%
%
%---OUTPUTS:
% ----------------------------------------------------... |
b79980cc37f4120fe10b71b4f7341a459db9ee5dcd0e1b8a9107e520c1f17a44 | MATLAB | 3,097 | 102 | function M = skewsymmetricfactory(n, k)
% Returns a manifold struct to optimize over k skew-symmetric matrices of size n
%
% function M = skewsymmetricfactory(n)
% function M = skewsymmetricfactory(n, k)
%
% Returns M, a structure describing the Euclidean space of n-by-n
% skew-symmetric matrices equipped with the stan... |
42803d7727c847b01fb668bbeb004174b78d487a14b1ea9a1fa4a4db2e5defe6 | MATLAB | 3,099 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {''};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-control01_task-YOURTASK_run-1';
matlabbatch{1}.spm.tools.physio.log_files.vendor ... |
0030a37c4d17e1945193ef36a289566e6d4c0843eb440044b18175e43b9816fa | MATLAB | 3,100 | 73 | %% naj_postICAopt_master
% Comparing five differennt pipelines post ICA decomposition to find the
% otimal one for this dataset.
%
% preprocessing up to this point described by naj_neurCorrYoung_master
%
% this is the master script, calling all other scripts in the correct oder
%% preparation
% copy ICA decomposed dat... |
a274292b6511914d274d1910e00e2e0e0e15a9e2c34a3780e2f363634b46f708 | MATLAB | 3,100 | 80 | function calcProjMatContrastsSubj_forPalm_ShirleyPC(slName, n_sub, spm_path, data_path, util_path)
% save single subject contrusts of Tim's PCA projections analysis
addpath(genpath(spm_path));
addpath(genpath(util_path));
nFiles = 16;
smoothKernel = 6;
matFname = slName;
projMat = zeros(91,109,91,nFiles); % dims of ... |
29babfcfab11b057147cee9d2f0187e056b63ab0baa920e7b1d6bdb86ad8d6f4 | MATLAB | 3,101 | 95 | function [y, x] = tapas_dcm_euler_gen(DCM, Ep)
% [y, x] = tapas_dcm_euler_gen(DCM, Ep)
%
% Generates synthetic fMRI data under a given signal to noise ratio (SNR)
% with the fixed hemodynamic convolution kernel
%
% Input:
% DCM - model structure
% Ep - data-generating parameters
... |
6ddbb2b171fdd670cbb6eab4309ae22c65daf9c4507469667fbe02daabce6cf9 | MATLAB | 3,102 | 99 | % op_getLW.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [FWHM]=op_getLW(in,Refppmmin,Refppmmax,zpfactor);
%
% DESCRIPTION:
% Estimates the linewidth of a reference peak in the spectrum. By default,
% the reference peak is water, between 4.4 and 5.0 ppm. Two methods are
% used to estimate the linewidth: 1. F... |
836b65e70047f75aafbec59a0d2525fbcd4fdfdd2a20e85f666068da6adf1b14 | MATLAB | 3,103 | 96 | function derivative = Diff(samples,varargin)
%Diff - Differentiate.
%
% USAGE
%
% derivative = Diff(samples,<options>)
%
% samples <a href="matlab:help samples">samples</a> to differentiate
% <options> optional list of property-value pairs (see table below)
%
% ================================... |
89e58e34d86cd2b7af902462528ba231744370a6627c7d4d4011142c3280e325 | MATLAB | 3,103 | 92 | %% [chi] = Wrapper_QSM_QSMnet(localField,mask,matrixSize,voxelSize,algorParam, headerAndExtraData)
%
% Input
% --------------
% localField : local field map (tissue fields), in Hz
% mask : signal mask
% matrixSize : size of the input image
% voxelSize : spatial resolution of each dimension of the dat... |
0f39090f78cca56ca709340fd11908d84895848a4aa6817f6b15b4bced3f3073 | MATLAB | 3,104 | 74 | % STD_CLUSTMAXELEC - function to find the electrode with maximum absolute projection
% for each component of a cluster
% Usage:
% >> [eleclist, setlist, complist] = std_clustmaxelec(STUDY, ALLEEG, clustind);
%
% Inputs:
% STUDY - STUDY set structure containing (loaded) EEG dataset str... |
a66a0bdd2523ce545e0428dad5c535f193b6f2257632b97cd27b6a2d3c4a0dfb | MATLAB | 3,104 | 79 | %{
monet.Cos2Map (computed) # orientation tuning maps
-> monet.OriMap
-----
cos2_amp : longblob # dF/F at preferred direction
cos2_r2 : longblob # fraction of variance explained (after gaussinization)
cos2_fp : longblob # p-value of F-test (after gaussinization)
pref_ori : longblob # (radians) prefe... |
0579b7c5edc79f9ff9925c91baed576a097c4c0c4ab178683aa5984755e59286 | MATLAB | 3,105 | 94 | % This function which initialises a struct containing the preferences and
% details for a particular project; in this case the demo for the toolbox.
% It should be edited to taste before a project is run, and a new one
% created for each substantially different project (though the options
% struct will be saved each ti... |
6e65aa7a097e935a99c95ffa693364bed1f5b9909d53a19ef567cffa0674025d | MATLAB | 3,105 | 60 | % STD_ITCPLOT - Commandline function to plot cluster ITCs. Either displays mean cluster
% ITCs, or else all cluster component ITCs, plus the mean cluster ITC, in
% one figure per cluster and condition. ITCs can be visualized only if
% component ITCs were calculated and... |
943a6792101ca385d9bcf4afe91dc26790bea7a20d27bd3ba31b779948d78bc2 | MATLAB | 3,105 | 91 | function ft_write_sens(filename, sens, varargin)
% FT_WRITE_SENS writes electrode information to an external file for further processing in external software.
%
% Use as
% ft_write_sens(filename, sens, ...)
%
% The specified filename can already contain the filename extention,
% but that is not required since it will... |
f2ea0e4b3ef57f0e50449741a99009fe3ee7dda59ece0a945e640c5a091f9062 | MATLAB | 3,106 | 74 | % std_rmalldatafields - remove all data fields from STUDY (before saving
% it for instance.
%
% Usage:
% STUDY = std_rmalldatafields(STUDY, type);
%
% Input:
% STUDY - EEGLAB study structure
%
% Optional input:
% type - ['chan'|'clust'|'both'] remove from changrp channel loc... |
3cef1c432bb3656130b28e95efc51949957a5fb36179d9b23f5831454c5a57aa | MATLAB | 3,108 | 73 | %{
monet.CleanRF (computed) # cleaned up and normalized receptive fields
-> monet.RF
-----
clean_map : longblob # cleaned up receptive field map
%}
classdef CleanRF < dj.Relvar & dj.AutoPopulate
properties
popRel = pre.ExtractSpikes & monet.RF
end
methods(Access=protected)
function makeTuples(self, k... |
47cdb662e81fb2f37e5a206f81565720a42808df23337c1c6d70789738d6ba1d | MATLAB | 3,108 | 87 | function [recon,cmap]=sero_pulseq_coilCombineAdaptive(yn,rn,norm)
% function [recon,cmap]=sero_pulseq_coilCombineAdaptive(yn,rn,norm)
% This function is copied from:
% https://github.com/andyschwarzl/gpuNUFFT/blob/master/matlab/demo/utils/adapt_array_2d.m
% Reconstruction of array data and computation of coil sensiti... |
7b5444ed9bb9cd988b22836c85b6a5e758bd64ddbe3a4d0260e34b0fb0620dfe | MATLAB | 3,108 | 111 | %% [pSWI,dSWI,swi_phase] = swi(magn,phase,filterSize,thres,m)
%
% Input
% --------------
% magn : image that combines with phase contrast, can be 3D/4D
% phase : phase map (in rad)
% filterSize : window length of Hamming filter
% thres : threshold used to create positive/negative phase contr... |
0cdbd203bbd986782d6f3db146d2a69b3aa0ef2185e2bd02fe2f5317aaade61b | MATLAB | 3,109 | 79 | function significance_distribution_check_v2(events,adjM,repNum,tail,method,downSample,lag,fs,genotype,bins)
% H Smith, Cambridge, 2021
% Show changes in thresholding as number of repeats increases
% Produces figure as described in significance_distribution_plots
% INPUTS:
% events = binary matrix of spikes/neu... |
197155c64e19050c7686dcf60bff568cd5dfe0b249142029573ea92c36e873e4 | MATLAB | 3,110 | 97 | %% load the fitted EC50 matrix
load(fullfile('.', 'results', 'MLEFit.mat'));
cMatrix = cMatrixMLE;
load(fullfile('.', 'data', 'doseResponseData.mat'));
%% Plot figure 3B
% order for visualize
ORNOrder = [19,21,3,6,8,14,10,16,9,7,11,4,12,13,1,2,20,5,17,15,18];
odorOrder = [19,33,12,32,27,15,14,7,8,9,6,22,24,31,30,29,1... |
1ca43ee5ed6070ea15ed0f259aeca6aa0b9514070958bc02c6b78e372602a902 | MATLAB | 3,110 | 101 | classdef toolsGetLargestCCTest < matlab.unittest.TestCase
%TOOLSGETLARGESTCCTEST Unit tests for petraToCT.tools.getLargestCC.
%
% DESCRIPTION:
% Verifies that getLargestCC retains the requested number of
% largest connected components in 2D and 3D binary images, and
% handles edge ca... |
55dd6392a5f95d7a40e5d155d7c638cbae4b93c1a6c4809e82f727941a04bb41 | MATLAB | 3,110 | 112 | % load in and visualize snapshots
load('../../ERCaSims/networks/WT/WT_circreg.mat')
NT = WTnetworks(1);
%% load snapshot data
resdir = '../test/';
%filename = [resdir 'testrecoveryWT.mesh.txt'];
filename = [resdir 'testspreadLin.mesh.txt'];
MSH = MeshObj(filename);
%snapfile = [resdir 'testrecoveryWT.snap.txt'];
snap... |
ba191331b445ea6d996dfa4c4f324b0865a956e5f9af7db95e65c5373eaf7938 | MATLAB | 3,110 | 83 | function [H] = quaternion(q)
% QUATERNION returns the homogenous coordinate transformation matrix corresponding to
% a coordinate transformation described by 7 quaternion parameters.
%
% Use as
% [H] = quaternion(Q)
% where
% Q [q0, q1, q2, q3, q4, q5, q6] vector with parameters
% H corresponding hom... |
1f36956e782694d171e92b503179556705f2e3ffb64d490bf0b80aff5215fa45 | MATLAB | 3,111 | 81 | function net = cnn_mnist_init(varargin)
% CNN_MNIST_LENET Initialize a CNN similar for MNIST
opts.batchNormalization = true ;
opts.networkType = 'simplenn' ;
opts = vl_argparse(opts, varargin) ;
rng('default');
rng(0) ;
f=1/100 ;
net.layers = {} ;
net.layers{end+1} = struct('type', 'conv', ...
... |
549e0235c4468e98179eebd7266de6c75457be853a4bc8c5835fcc6e22778f88 | MATLAB | 3,111 | 121 | classdef AffineGridGenerator < dagnn.Layer
%DAGNN.AFFINEGRIDGENERATIOR Generate an affine grid for bilinear resampling
% This layer maps 1 x 1 x 6 x N affine transforms to 2 x Ho x Wo x N
% sampling grids compatible with dagnn.BlilinearSampler.
% (c) 2016 Ankush Gupta
properties
Ho = 0;
Wo = 0;
end
... |
93c6bdaa8fb6880942cef9caf2865e6e1296ba52ce6c653481b94f53bdcfd78a | MATLAB | 3,111 | 90 | close all
clear all
load('Z:\BCI\Data\NDNF_Opto\NDNF_06\062424_NDNF_06\Baseline\baselineMask_2.mat')
dband = 80;
dband2 = 40;
frames_tmp = sbxgrabframe('Z:\Scanbox\Data\NDNF\NDNF_06\062424_NDNF_06\062424_NDNF_06_000_006\062424_NDNF_06_000_006', 1, 24000);
frames_tmp = squeeze(frames_tmp); frames_pl1 = frames_tmp(:,:, ... |
40b4632e093259443824a71539af9f3cc05e37cd3bb9494dcd99454b4bfeb4d9 | MATLAB | 3,112 | 97 | function m = Monochrome(color,n,varargin)
%Monochrome - Monochrome colormap (from white to a given color).
%
% USAGE
%
% m = Monochrome(color,n,<options>)
%
% color optional target color (default = black)
% n optional number of rows in output matrix (default = 100)
% <options> o... |
edf3195cf1fa784d1dba631ce852a3c0a2627b75d9d7bdfcf28f452bb1b9cb6a | MATLAB | 3,112 | 65 | function emptyImage = create_empty_image(this, varargin)
% Creates all-zeroes image with
%
% Y = MrImage()
% Y.create_empty_image(varargin)
%
% This is a method of class MrImage.
%
% IN
%
% varargin 'ParameterName', 'ParameterValue'-pairs for the following
% properties:
%
% Paramet... |
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