sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1c69b950ca469ba0a1164b3aca3e27d313f17609fe9b05d80651f56f6c574bd2 | MATLAB | 7,330 | 212 | function [data] = fixdimord(data)
% FIXDIMORD ensures consistency between the dimord string and the axes
% that describe the data dimensions. The main purpose of this function
% is to ensure backward compatibility of all functions with data that has
% been processed by older FieldTrip versions.
%
% Use as
% [data] =... |
dc7e5a1e798ca17a4f49fce0619d5984c638ee80eefcc58d846dae63e190fa05 | MATLAB | 7,332 | 189 | function violins = violinplot(data, cats, varargin)
%Violinplots plots violin plots of some data and categories
% VIOLINPLOT(DATA) plots a violin of a double vector DATA
%
% VIOLINPLOT(DATAMATRIX) plots violins for each column in
% DATAMATRIX.
%
% VIOLINPLOT(DATAMATRIX, CATEGORYNAMES) plots violins for each
% ... |
67d6c2e9d91b76a18ac2de4359a4897def5cd69aee9cc66e6bed068d612938d3 | MATLAB | 7,334 | 182 | % GLM analysis
%
% This script computes a fixed-effects GLM for one or multiple runs within
% one session. The script is designed for paradigms with 2-4 experimental
% conditions. However, for more than 2 conditions, not all contrasts are
% computed:) Stimulus parameters are read from a spm12 compatible *.mat
% fil... |
66a378d4a67ca508de2c256971e92816604d7e4a18876528da5afc142c770483 | MATLAB | 7,335 | 162 | function h = plot_brain3D_patch(plotInfo)
% plots semi-transparent 3D brain model into existing axes
% plots colorcoded channels as circles
% highlights selected brain areas
% (c) Jiri, Apr17, Nov18
% based on previous function brain3D_model.m
if ~isfield(plotInfo, 'visible_axis'), plotInfo.visible_axis = true; end
i... |
86483a7a569e2cdeaaf357e9482aa644d1ae7f62dec92ca281f1475284028529 | MATLAB | 7,336 | 66 | function map = cividis(N)
% Perceptually uniform sequential colormap from MatPlotLib. Designed for colorblind.
%
% Copyright (c) 2017-2020 Stephen Cobeldick
%
%%% Syntax:
% map = cividis
% map = cividis(N)
%
% Colormap designed by Jamie R. Nuñez, Christopher R. Anderton, Ryan S. Renslow.
%
% Developed with considerat... |
b6f6c41408fba9d747d2d048204f3a8060ca39b32b051c65a94da89d64438d12 | MATLAB | 7,336 | 169 | % STD_CUSTOM - Returns custom measure for a dataset.
%
% Usage:
% >> [spec freqs] = std_custom(EEG, func, 'key', 'val', ...);
%
% Inputs:
% EEG - a loaded epoched EEG dataset structure
% func - a function handle that takes a data array as input
%
% Optional inputs:
% 'components' - [numeric vector]... |
e382e4b7b73a3e6c0d434af6b355d00debf978cb8ab9c73067d653e1b5cc70da | MATLAB | 7,337 | 192 | function overwriteFlag = overwritePrompt(userOptions, promptOptions)
%
% overwritePrompt is a function which prompts the user, either at the command
% line or (when it's implemented) via a GUI dialogue box. The user will be
% notified if they are liable to overwrite pre-existing data and will be given
% the options to... |
aad481bbf28b3a96c0e13b0dc393655c0b9a72039abe20dd2a083c241494e9d3 | MATLAB | 7,338 | 103 | function outstr = GE_dumpSeriesHeader(series)
%
% outstr = GE_dumpSeriesHeader(series)
%
% Writes the series header to strimg the outstr
%
% Souheil Inati
% Dartmouth College
% May 2000
% souheil.inati@dartmouth.edu
%
outstr = sprintf('se_suid: %s\n' , char(series.se_suid));
outstr = strcat(outstr, sprintf('se_... |
2d0ad7c505eebff370487904e266f6b5500746d7daeca62d5aadde4688fffc88 | MATLAB | 7,340 | 257 | function M = spherefactory(n, m, gpuflag)
% Returns a manifold struct to optimize over unit-norm vectors or matrices.
%
% function M = spherefactory(n)
% function M = spherefactory(n, m)
% function M = spherefactory(n, m, gpuflag)
%
% Manifold of n-by-m real matrices of unit Frobenius norm.
% By default, m = 1, which c... |
2c9cb50c194060783047dc0a5377f154f88aa9c1d3c86c2af2f11a1474154e69 | MATLAB | 7,358 | 230 | function coactPaper_figureS03()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=6;
fontsize=6;
close all
fh=initFig('width',18.6,'height',9,'font','Arial','fontsize',fontsize);
x=14;y=6;
panel_01(x,y,fontsize);
print(fh,sprintf('~/Dropbox/FearAnalyses/paper/figure/figS03_%s.pdf',datestr(now,'yyyym... |
761ed5f0f0db31cf9aca1e48cfe8dea9556bc71dc6951393aabee034eb8f7105 | MATLAB | 7,358 | 191 | function y_embed = BF_Embed(y,tau,m,justGiveMeParams,randomSeed,beVocal)
% BF_Embed Time-delay embedding
%
% Returns a time-delay embedding of the input time series into an m dimensional
% space at a time delay tau.
%
%---INPUTS:
% y, univariate scalar time series
%
% tau, time-delay. Can be a string, 'ac', 'mi', ...
... |
f0e7ecaf1523c8363a89bdb36b4397c400ba23f488053b331303a689e651b589 | MATLAB | 7,366 | 238 | function [] = Figure5(datadir, codedir)
%Figure5 - Value computations for motivation do not depend on state
% uncertainty
% datadir = directory of dataset
% codedir = director of code
%% Set up paths
s = pathsep;
pathStr = [s, path, s];
onPath = contains(pathStr,...
codedir, 'IgnoreCase', ispc);
if ~onPath ... |
da051e0329eccd943635d785b17915d0f26cf759d61c50360671008bb01b11aa | MATLAB | 7,368 | 163 | function [valueMean, slopeMean, interceptMean, fullProbeSubj, subj, useNum] = plotStability(expInfoAll,subjectsToInspect,probeInfo,colAni,fullProbeScan,varType,paramplt)
switch varType
case 'count'
qm = expInfoAll.unitCount';
yRng = [1 4000];
funcProbe = @sum;
... |
a139d0832be2f2526b3008b8c9c368a5d9a485e33a4cec99a0e29124fc1703e2 | MATLAB | 7,376 | 181 | % [p, observeddifference, effectsize] = permutationTest(sample1, sample2, permutations [, varargin])
%
% Permutation test (aka randomisation test), testing for a difference
% in means between two samples.
%
% In:
% sample1 - vector of measurements from one (experimental) sample
% sample2 - vect... |
4870a97860781ec8c7111cfb722d1e873f782d3359eb3cfd1aa0080e3cd5390f | MATLAB | 7,379 | 241 | function [ subject ] = nmri_regenerate_cleaned(subject, workmode, backup, params)
%[ subject ] = nmri_regenerate_cleaned(subject, workmode, backup, params)
%
% This function will re-generate the cleaned dataset with the information
% stored in the backup struct
% if this is not passed to the function, will try to loc... |
0c922d7696bfefe904a2e7a08680be6732027ba388d07cd7a454263f8c8c9825 | MATLAB | 7,381 | 179 | function varargout = tapas_physio_report_contrasts(varargin)
% This function reports all relevant F-contrast-maps for physIO-created regressors
% in a given GLM
%
% - Section plots on an anatomical overlay are created and saved as
% post-script file with one page for each contrasts
%
% - Input parameters are speci... |
10b21d53ce6eb1b61fa9b3ebde86f3fe2989f872f4b9311d534f9238bdc570d9 | MATLAB | 7,382 | 164 | %% h = sepia_handle_panel_unwrap_optimum_weights(hParent,h,position)
%
% Input
% --------------
% hParent : parent handle of this panel
% h : global structure contains all handles
% position : position of this panel
%
% Output
% --------------
% h : global structure contains all new a... |
52006667129d7828f942d731db63e648b6f7d5466301b7729cec508b3644e0c5 | MATLAB | 7,383 | 200 | function [mri, seg, hdr] = read_asa_mri(fn)
% READ_ASA_MRI reads an ASA format MRI file
%
% Use as
% [mri, seg, hdr] = read_asa_mri(filename)
%
% The raw image data is returned, together with the position of the
% external head markers in raw image coordinates.
%
% In the ASA default PAN (pre-auricular/nasion) coord... |
439f3595e197dc0a1c9561340b6d1429aec8fbe66b561cb00b41fd7ea9c30835 | MATLAB | 7,386 | 198 | function [cmd,cmd2]=surfing_suma_talairach(sumadirs,trgdir,varargin)
% Transform surfaces and volumes to Talairach space and average them
%
% SURFING_SUMA_TALAIRACH(SUMADIRS,TRGDIR,...)
%
% INPUTS:
% SUMADIRS cell with directories created by SUMA
% TRGDIR directory where to store averaged results
% ... ... |
2b06a24585cf53bd5d7cb5d6a336a303f473b78b8c1b2c28e825564b3d103c30 | MATLAB | 7,387 | 203 | function [J,h,func_evals,E,S,D]=jacobianext(func,x,varargin)
% JACOBIAN CALCULATION AS A ROMBERG EXTRAPOLATION
%
% evaluates the jacobian of a function func at point x using romberg
% extrapolation. It respects bounds. Further, the step size, no of
% evaluations, an estimate of the error size and n... |
d842298750667d8be6b14efa1f32431712fb6ecfa7221be232f6b6317c0e8d1a | MATLAB | 7,388 | 287 | function optim = tapas_quasinewton_optim(f, init, varargin)
% This function implements the quasi-Newton minimization algorithm
% introduced by Broyden, Fletcher, Goldfarb, and Shanno (BFGS).
%
% INPUT:
% f Function handle of the function to be optimised
% init The point at which to initialize... |
2a164f17657411818d56631cd56ef4922d6744bdc5762c46c7f93b96e0e46a1e | MATLAB | 7,389 | 212 | function create_onset_files(subj_id, session, mod_name, do_plot)
% _
% Create "names, onsets, durations" files for first-level fMRI analysis
% FORMAT create_onset_files(subj_id, session, mod_name, do_plot)
%
% subj_id - a string, subject ID (e.g. "EDY7")
% session - a string, session name (e.g. "visual")
% ... |
0a6ade5c25cdf00ae1822ddba6eac5db8e47b7e1139d51455722d1f43c059763 | MATLAB | 7,390 | 232 | function [err,ITout,ColMapout] = ScaleToMap (ITvect,ColMap,Opt)
%
% [err,Mout,ColMapout] = ScaleToMap (M,ColMap,Opt)
%
%Purpose:
% This function scales a matrix (or vector) to make it fit a
% colormap. It was originally deisgned to represent functional
% data onto 3D and 2D meshes, but it works for a lot of oth... |
dc4d254d30f5ef3f3ec5c742bd774c90c4ee48c3ea47b82ef44d8e516c804a9e | MATLAB | 7,399 | 181 | function shuffle_icaReacCCG_REMdur(basename)
[rootPath,sesName,~]=fileparts(basename);
fprintf('%s load files for %s\n',datestr(now),sesName);
load(fullfile(rootPath,'data',[sesName '-icaReac.mat']))
load(fullfile(rootPath,'data',[sesName '.sleepstate.states.mat']))
load(fullfile(rootPath,'data',[sesName '.sessions.ev... |
7ff7fdd18d008c35aa531063ccff86df5e334f4f68ad80ab0ef57ba6e6fbdc4e | MATLAB | 7,404 | 167 | %% jobTesting.m
% This function is a jobTesting.m file .
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, structural imaging) data files
% ... |
f114f7b22c9034ed54bdce968368400a9824d51e9430325fe30bca47777752e0 | MATLAB | 7,406 | 209 | function [cpulse, verbose] = tapas_physio_findpeaks_template_xcorr(...
c, pulseCleanedTemplate, cpulseSecondGuess, averageHeartRateInSamples, ...
verbose, varargin)
% Finds peaks of a time series via pre-determined template via maxima of
% matlab cross correlations (xcorr) via going backward from search startin... |
66130930a9aa0f5f2d4fc4a3522c40304b00da4b962258e78d535df0b62bb44e | MATLAB | 7,408 | 193 | % STD_LIMODESIGN - create LIMO design matrices for categorical and
% continuous variables.
%
% Usage:
% >> [catMat,contMat,description] = std_limosavedesignfiles(factors, trialinfo)
% >> [catMat,contMat,description] = std_limosavedesignfiles(factors, trialinfo, 'key', val)
%
% Inputs:
% factor... |
de1dc719d47e324d8b892ac792ffba2dbdd00206f27d270aeed9438a59b589e1 | MATLAB | 7,408 | 142 | %% Load data
data_path ='Y:\Alice\0012_NeuroGI\NeuroGI_ephys_data\2024-11_all_ex-vivo_experiments\20241115_ExVivo-08\';
load([data_path 'EV_08_dmap_02_dist.mat'], 'EV08dmap02')
load([data_path 'datafile0017.mat'], 'data')
%% Preproces data
reorder = (1:32:128)' + (0:31);
reorder = reorder(:);
yr = resa... |
d0b7434f6d332c1b2f93a4cd48c2e6d3d6b2823601f4bf8bbd51781ec3ec4425 | MATLAB | 7,412 | 273 | % Single-Step QSM with a Total Variation regularization with spatially variable fidelity and regularization weights.
% This uses ADMM to solve the functional.
%
% Last modified by Carlos Milovic in 2017.06.09
% bug fix: line 165 (KC, 2 March 2020)
%
function out = WH_nlTV_4sepia(params)
%
% input: params - structure wi... |
82f43020003bf8d4848b431f149d5d97c30426b694b6a4b7e65ce99271c3ee48 | MATLAB | 7,413 | 248 | function [err, ErrMessage, Rules] = HEAD_Rules (FieldNames)
%
% [err, ErrMessage, Rules] = HEAD_Rules (FieldNames)
%
%Purpose:
% Retrieve the rules for the different fields in AFNI
%
%
%Input Parameters:
% FieldNames is a ~ delirited list of N field names
%
%
%Output Parameters:
% err : 0 No Problem
% : 1... |
0332e3ef69bab156d4286436321131e6eac6ae87b0d1851c29812ff608c7a63b | MATLAB | 7,414 | 211 | function [C2,cfg] = mahal_iem_trialwise_xtime(dat,theta,cfg)
% [C2,cfg] = mahal_iem_trialwise_xtime(dat,theta,cfg)
% authors: M Stokes, E Spaak, N Myers
if nargin < 2
help mahal_iem_trialwise_xtime
error('missing input arguments!')
end
ntrl = size(dat,1); % number of timepoints
nsens ... |
79cbccb1c2a8d54f5666d17f092536fb3c2647490cdb712275b9941f16302ed3 | MATLAB | 7,415 | 213 | function SyntaxAnalysis_Callback(hObject, eventdata, handles)
[filename, filepath] = uigetfile({'*.mat;*.xlsx'},'Select Detection Files OR Exported Detections','MultiSelect', 'on',char(handles.data.settings.detectionfolder));
if isnumeric(filename); return; end
filename = cellstr(filename);
settings = inputdlg({'Max... |
5ddf9acac5276f4287521cfb527bd8cc9118f3599f82742c6e8e3cefe004faf2 | MATLAB | 7,417 | 238 | function fear_spkModulationShBase(basename,varargin)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
% basename='~/data/Fear/triple/oberon200325/oberon200325';
%%
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
%%
param.... |
87622560e33ac1fd327b9f450115c73cc42ff5ad9b4d3cdce263cdd54f78cd2d | MATLAB | 7,418 | 205 | %This simulator matches the benchmarking aim: you know the ground-truth directed matrix A,
% you pass Z and rate_smooth through your pairwise/multi-predictor
% linear models (with/without L1), and you score recovery (AUPRC/ROC,
% weight correlation, SHD).
% Get the current script name
scriptName = mfilename('fullpa... |
307476c15c7517f6f4f4b0c7f2ecbb906722f67c05880bfd0f73c695a3bc5511 | MATLAB | 7,420 | 208 | function varargout = bucn_txt(filename, hdr, begsample, endsample, chanindx)
% BUCN_TXT reads the txt files produced by the UCL-Birkbeck NIRS machines, also known
% as the NTS fNIRS system from Gowerlabs. See https://www.gowerlabs.co.uk/nts
%
% Use as
% hdr = bucn_txt(filename);
% dat = bucn_txt(filename, hdr, beg... |
9ffc7aa4623f128acc197050ab09389b74d85423deb3749e27609762835c6030 | MATLAB | 7,424 | 145 | function [signal,removed_channels] = clean_channels_nolocs(signal,min_corr,ignored_quantile,window_len,max_broken_time,linenoise_aware)
% Remove channels with abnormal data from a continuous data set.
% Signal = clean_channels_nolocs(Signal,MinCorrelation,IgnoredQuantile,WindowLength,MaxBrokenTime,LineNoiseAware)
%
% T... |
427def94edbd1878b6732e8ee20f41cbd13172fd88212e54119465ceaacb90cd | MATLAB | 7,427 | 214 | function run_permuttest2_examples
%RUN_PERMUTTEST2_EXAMPLES Run two-sample permutation t-test 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. Ea... |
50a9153208b49c3cdb70d8ea459720b3931d0a680b759cca9b524d66b45a207e | MATLAB | 7,428 | 192 | function settings = sd_config_settings(todo, varargin)
% SD_CONFIG_SETTINGS Initializes empty settings variable or fills one with defaults
%
% DESCRIPTION
% This function initializes or completes the settings variable that is used
% by the sd_display function to visualize NIfTI images.
%
% SYNTAX
% settings = sd_config... |
05013021d3840acc456ecb3e04b6ed5fe8e1f78878826c40b99f9ccf5aee445e | MATLAB | 7,431 | 206 | % ANOVA2RM_CELL - compute F-values in cell array using repeated measure
% ANOVA.
%
% Usage:
% >> [FC FR FI dfc dfr dfi] = anova2rm_cell( data );
%
% Inputs:
% data = data consisting of PAIRED arrays to be compared. The last
% dimension of the data array is used to compute A... |
35e685d382f4840e6a48ccec358e81260ea17168ffcaecf171d95a9cfa70421b | MATLAB | 7,431 | 158 | %% h = sepia_handle_panel_TotalField_ROMEO(hParent,h,position)
%
% Input
% --------------
% hParent : parent handle of this panel
% h : global structure contains all handles
% position : position of this panel
%
% Output
% --------------
% h : global structure contains all new and oth... |
89d20110899e000191b08a258f22e27c1ff06e2b0e961fb1ff65008b411a9160 | MATLAB | 7,438 | 235 | function [y,lambda,idx_struct,XK] = simulateGLM(c,stim,ops,trial_id)
%generate synthetic data from a glm model
%
%This is basically the core code from the gradient that calculates lambda
%but the spike times are kept in real time to capture the correct spike
%history filter response
%how many time-dependent covariate... |
a1606a8d19c47ae2e193d4b071995ce89a27ce91eef15fd9cbd8e78aa21de696 | MATLAB | 7,438 | 161 | % (C) Copyright 2019 bidspm developers
%% analyze decoding experiments/runs
clear;
clc;
bidspmDir=fullfile(fileparts(mfilename('fullpath')),'..', 'lib','bidspm');
addpath(fullfile(fileparts(mfilename('fullpath')),'..', 'lib','bidspm'))
bidspm();
bids_dir = fullfile(fileparts(mfilename('fullpath')),'..', '..','input... |
169685064fcbd0068aac72a467eefc7a52b6858cc3b6b6f4df47b46678b36117 | MATLAB | 7,439 | 233 | function hfig = tightfig(hfig)
% tightfig: Alters a figure so that it has the minimum size necessary to
% enclose all axes in the figure without excess space around them.
%
% Note that tightfig will expand the figure to completely encompass all
% axes if necessary. If any 3D axes are present which have been zoomed,
% ... |
c3dc1f64225c4552ae51e6685f7142a641b2c13803e8c781cb6d9087bd65c203 | MATLAB | 7,442 | 179 | % eeg_compare - compare EEG structures. Differences are shown on the command
% line.
% Usage:
% eeg_compare(EEG1, EEG2);
%
% Input:
% EEG1 - first EEGLAB structure
% EEG2 - second EEGLAB structure
%
% Author: Arnaud Delorme, 2020
%
% See also: EEGLAB, EEGPLOT, POP_REJEPOCH
% Copyright (C) 2020 Arnaud... |
e1b53532c4b4b0fdbfed44949a6833d92ab60f685cc00c3f0182072594c571d3 | MATLAB | 7,443 | 231 | %% Figure 3 Neuropixels
% A schematic
% B waveforms
% C rasters
% load your cells and full OFC.
% these take a while to load and might crash computers
datpath = 'C:\Users\mld9131\Documents\GitHub\Papers\MLD\Figure2\Data';
load(fullfile(datpath,'OFC-CPi_projection_neurons_non-Stimulated.mat'));
load(fullfile(datp... |
0f02f47246d0a4818327c3bee60854cedcedd8a1fc34b3974e221a4125e7da7f | MATLAB | 7,445 | 198 | function [cmd,cmd2]=surfing_suma_talairach(sumadirs,trgdir,varargin)
% Transform surfaces and volumes to Talairach space and average them
%
% SURFING_SUMA_TALAIRACH(SUMADIRS,TRGDIR,...)
%
% INPUTS:
% SUMADIRS cell with directories created by SUMA
% TRGDIR directory where to store averaged results
% ... ... |
6240a472590d2a042034475a27f9c008f580f6fb835c335da74232737dfb7133 | MATLAB | 7,445 | 218 | function [y,lambda,idx_struct,lambda_var] = simulateGLM_logNormal(c,c_cov,stim,ops,trial_id)
%generates synthetic data from a glm, but from lognormal dist
%output mean as from a log-normal distribution
%
%This is basically the core code from the gradient that calculates lambda
%but the spike times are kept in real time... |
b4bb1c3e444b41509de3024d2cbb654385452b742e3fef4bf704a82436383618 | MATLAB | 7,447 | 252 | function M = obliquefactory(n, m, transposed)
% Returns a manifold struct to optimize over matrices w/ unit-norm columns.
%
% function M = obliquefactory(n, m)
% function M = obliquefactory(n, m, transposed)
%
% Oblique manifold: deals with matrices of size n x m such that each column
% has unit 2-norm, i.e., is a poin... |
9e17519e9bd8cc27298bbf0d6150b6cae1599eedf67478d6d3bca0e0ae3984d8 | MATLAB | 7,450 | 261 | function [traj, infStates] = tapas_hgf_ar1(r, p, varargin)
% Calculates the trajectories of the agent's representations under the HGF
%
% This function can be called in two ways:
%
% (1) tapas_hgf_ar1(r, p)
%
% where r is the structure generated by tapas_fitModel and p is the parameter vector in native space;
%... |
357cf97d9424d16543bc4558b1fab9ea7882ab6a23db49c92063e70b2cf20b95 | MATLAB | 7,451 | 192 | function step4_aggregate_and_plot_zScore(metricNames, Nlist, saveFigs)
% AGGREGATE_AND_PLOT_ZSCORE Build aggregated_metrics.csv from simulations2/results/zScore
% and plot metrics vs sparsity grouped by snr_db and N.
if nargin<1 || isempty(metricNames), metricNames = {'auprc_pos','F1_at_match'}; end
if nargin<2 || is... |
9c8c5a3e46338ef8b93fb3cb8ce197e614696e5b2e131148574ce066e6a3467e | MATLAB | 7,451 | 276 | function DB = Meta_tables_of_variables(DB)
% Constructs some tables for each variable, saved in DB.TABLES, so that we can easily see the levels and numbers of points & contrasts for each variable
%
% DB = Meta_tables_of_variables(DB)
%
% - Must run Meta_Setup.m first
% - Assumes each study has one and only one unique t... |
119ff6b2cba2bcb9e140dad6901ccfe71c6933f831fbfa4897215e5272186879 | MATLAB | 7,460 | 238 | function savesurfpoly(v,f,holelist,regionlist,p0,p1,fname,forcebox)
%
% savesurfpoly(v,f,holelist,regionlist,p0,p1,fname)
%
% save a set of surfaces into poly format (for tetgen)
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2007/11/21
%
% input:
% v: input, surface node list, dimension (nn,3)
% i... |
78f7610bc0e17eadfafb9f5020eb53f9476c111a92171383c2ca3a668255e2b2 | MATLAB | 7,461 | 211 | % ADVDIFF_TASCDMD Benchmark TASC-DMD, Exact DMD, and fbDMD on the
% linear advection-diffusion equation with KNOWN eigenvalues.
%
% NOTE: This example is NOT included in the paper.
%
% Equation: u_t + U0*u_x = nu*u_xx
%
% Analytical eigenvalues: omega_n = -nu*k_n^2 - i*U0*k_n
% In the comple... |
e5105febc6b3f63a69958f4b7450af7d8dbbe74ac79b1836b364cba7a1f14fa1 | MATLAB | 7,467 | 222 | function [stat,p,stats,tbl,dist] = permuchi2(x,varargin)
%PERMUCHI2 Permutation-based Chi-square test of independence.
% STAT = PERMUCHI2(X) performs a permutation test of independence based
% on the Chi-square statistic for the contingency table X, and returns
% the test statistic. If X is a 3D matrix (Rows x C... |
edbadc9e2c966d6dd0fc9c6342b49ed75497a8d1d3adeb9f712570ebcd8faead | MATLAB | 7,468 | 158 | function support_func_plot_legend(figLegend,varargin)
%% ########################################################################
% - Add custom legend to the current figure -
% #########################################################################
% Add a custom legend to your current figure.
%
% [Note:] Overwrite... |
c52b6ba2abdb387f80ca71fa2ebe76d7708d51f4675494154c16d2d5e9deb2ba | MATLAB | 7,469 | 147 | % STD_MOVECOMP - Move ICA component(s) from one cluster to another.
%
% Usage:
% >> [STUDY] = std_movecomp(STUDY, ALLEEG, from_cluster, to_cluster, comps);
% Inputs:
% STUDY - STUDY structure comprising all or some of the EEG datasets in ALLEEG.
% ALLEEG - vector of EEG structures in the... |
f259b31ab9e2b1e2c5425dc908606af9036a5e998fb5ba5b2c1a261ff425b6c6 | MATLAB | 7,470 | 101 | function ex_hdr = GE_readHeaderExam(fid, byte_align)
%
% ex_hdr = GE_readHeaderExam(fid, byte_align)
%
% Loads the exam header from the file with filed id fid
% and returns it as a structure.
% if byte_align = 1 then 32-bit alignment (SGI, LX2 format)
% if byte_align = 0 then 16-bit alignment (Sun, 5.X format)
%
%
% So... |
066c179ace3381cea95975f265a599ed720c01b9c3c5a98e05fae113a83e6b4e | MATLAB | 7,472 | 208 | function BpRF_run_pRF_analysis(subj_id, session, mod_name, ana_name, avg, conf, voxels)
% _
% Estimate Voxel-Wise Population Receptive Field Model
% FORMAT BpRF_run_pRF_analysis(subj_id, session, mod_name, voxels)
%
% subj_id - a string, subject ID (e.g. "EDY7")
% session - a string, session name (e.g. "visu... |
beca1a39574ff3c4b4cb175ce0cdfaf70b4fa5e5c602eebcb22f37cfd9beeb85 | MATLAB | 7,481 | 207 | function singleCalcium_activity_PB_DenisH2B ( Hz )
% script that analyses ROIs for two channels at the same time, plotting them
% next to each other
% we will have one ROI for the green channel and two ROIs for the red
% channel, so each graph will be composed of three lines
% choose folder where data is stored
myFol... |
7734b8ce97c54297c538799a3ab95ece6a9f79fbcc0cd08f32e22a1d8aa0d821 | MATLAB | 7,488 | 220 | function varargout = openpose_keypoints(filename, hdr, begsample, endsample, chanindx)
% OPENPOSE_KEYPOINTS reads keypoints from a series of OpenPose JSON files
%
% Use as
% hdr = openpose_keypoints(filename);
% dat = openpose_keypoints(filename, hdr, begsample, endsample, chanindx);
% evt = openpose_keypoints(f... |
9000488764a892fe944d04030a0da62f69a53edeb95290355b1f81d1176f6074 | MATLAB | 7,493 | 160 | function [MRSCont] = osp_saveNII(MRSCont)
%% [MRSCont] = osp_saveNII(MRSCont)
% This function writes all processed MRS data to NIfTI-MRS files.
%
% One file is produced for unedited MRS data (PRESS, sLASER, etc.), four
% files are produced for MEGA-edited data (A, B, sum, difference), and
% seven files are... |
e222f8cf03e74392ca3d09e0e08eb24f2fc119fe7faa8677d24cd0589d0c1dd7 | MATLAB | 7,494 | 169 | %% unitTest.m
% This function performs a command line unit test based on the jobTesting.m file in the
% ci folder. All Osprey modules are tested in dependence of the
% included dataset. You can change the jobTesting.m file according to your desired
% needs. The results unittest class includes detailed informati... |
9578e90e4ee7a768e0d8ef8a3fc6b1a310dcabd3e6f99ae83f134bbf801b8645 | MATLAB | 7,501 | 169 | function signalSpectra(plotInfo)
% loads training sessions and computes specified signal type the PSD
% - FFT
% - STFT
% (c) Jiri, Feb14
% known "little bug": bad recording epochs get rejected first, then PSD (-> "jumps in data")
%% settings
if ~isfield(plotInfo, 'signalType')
plotInfo.signalType = 'EcogGrid';
en... |
a9e930fa6409c0491d1326603baaf4e03619ae8391e4f689b134100a7b089929 | MATLAB | 7,502 | 269 | function flag=vis_valuetype(value, valid, str);
% VIS_VALUETYPE Used for type checks in SOM Toolbox visualization routines
%
% flag = vis_valuetype(value, valid, str)
%
% Input and output arguments:
% value (varies) variable to be checked
% valid (cell array) size 1xN, cells are strings or vectors (see below)
... |
5cc37e078988703204a35e799e542d017f1e6ec881146e41cb057dd5618233f2 | MATLAB | 7,506 | 104 | function osp_updatecorrOvWindow(gui)
%% osp_updatecorrOvWindow
% This function updates the correlation overview tab.
%
%
% USAGE:
% osp_updatecorrOvWindow(gui);
%
% INPUT:
% gui = gui class containing all handles and the MRSCont
%
%
% AUTHORS:
% Dr. Helge Zoellner (Joh... |
e0f0b9bd4c7ef1acf5a54fda4d8bd32577ebe1e43689c6ce358fbcd85ff58754 | MATLAB | 7,507 | 226 | function outtable = cluster_chi2(clusters,fnames,DB)
% function outtable = cluster_chi2(clusters,field list (cell array of strings),DB)
%
% tor wager
% counts studies in each cluster
% warning: does not count separate CONTRASTS, just STUDIES.
% DB is a structure that contains all info from the database
%
% clusters is ... |
4a96cc282acac0732aeb2d2773a6f89e47a8bc9726870ef46141eba0bc8b26e6 | MATLAB | 7,510 | 176 | function [tbl,rm] = simple_mixed_anova(datamat, varargin)
% tbl = simple_mixed_anova(datamat, between_factors, within_factor_names,
% between_factor_names)
%
% Repeated-measures or mixed ANOVA with any number of factors.
%
% Function built on top of existing MATLAB functions in an attempt to
% simplify user inputs and... |
4428cb4cbd7580dfe24cef587d595c911a9587ff66ff90bd9b9be34cd566f110 | MATLAB | 7,512 | 178 | function this = MrImage_load_from_file(this, testCondition)
% Test loading from files for MrImage, in particular if additional
% parameters are given.
%
% Y = MrUnitTest()
% run(Y, MrImage_load_from_file)
%
% This is a method of class MrUnitTest.
%
% IN
%
% OUT
%
% EXAMPLE
% MrImage_load_from_file
%
% See also ... |
c1041f4e5f69bfd4074055d909d790a983c851dd19893e2ce9e1d5d46a625f29 | MATLAB | 7,515 | 235 | % MAPCORR - Find matching rows in two matrices and their corrs.
% Uses the Hungarian (default), VAM, or maxcorr assignment methods.
% (Follow with MATPERM to permute and sign x -> y).
%
% Finds correlation of maximum common subset of channels (using
% channel location fil... |
d62e5aad80b621cffb750be9aaba6909dfdfe3a60b29623a5d7f1fe6bfc25044 | MATLAB | 7,517 | 175 | % Script make_example_data
% Creates example data for uniQC-demos based on the ME-data in Heunis et al.
%
% make_example_data
%
% NOTE: This script has to be run only once, in order to prepare some
% example files for all uniqc-demos from a publicly available imaging
% dataset.
%
% INSTRUCTIONS:
% 1. Plea... |
0bca3e20fc081570576d9d1c392653eb6406b639522d77def9d9b49adaea9972 | MATLAB | 7,518 | 192 | function gitInfo = TS_AddGitInfo(whatDir,whatData)
% TS_AddGitInfo Appends the git information to the hctsa file
%
% Note that after computing, functions and results may change and thus not
% reflect the commit at the time of initailizing (or whenver this is run).
%
%---INPUTS:
% whatDir: the directory to look for a ... |
7816a7517eb2a326e1bc499ba3f9571c436dc63d46122967a59cb67ce1eec1e5 | MATLAB | 7,519 | 183 | % fit_OspreyMultiplex.m
% Georg Oeltzschner, Johns Hopkins University 2019.
%
% USAGE:
% [fitParams] = fit_OspreyMultiplex(dataToFit, resBasisSet, fitOpts);
%
% DESCRIPTION:
% This is the function describing the Osprey fitting model, which is
% performed with the resampled basis set resBasisSet on the data contained
%... |
c70aa076e8359e715be54e2921baaba6847aef08803e8fe03525ab10d38c7526 | MATLAB | 7,524 | 204 | function [coherogram,phase,t,f] = MTCoherogram(lfp1,lfp2,varargin)
%MTCoherogram - Compute LFP coherogram by multi-taper estimation.
%
% USAGE
%
% [coherogram,phase,t,f] = MTCoherogram(lfp1,lfp2,<options>)
%
% lfp1,lfp2 unfiltered LFP <a href="matlab:help samples">samples</a> (one channel each).
% <opti... |
93fc29151b9ef0261a12f60820aefaeed2ec9efe24db83e6ab7ddf6da4733a32 | MATLAB | 7,525 | 150 | function triggers = getTriggers_zeroSpeed(params)
% detects events of zero speed (pauses) as continuous data payches whose
% |velocity| < thr [std]
% pauses -> trials
% binned pauses -> classes
% (c) Jiri, Dec12
%% try to load the processed dataset
if ismember('triggers', who('-file', params.storage.cacheFile))
... |
d0d6631b83444ed5bf4246a543df91c87e06d8af55cf93ed728023a106ff2384 | MATLAB | 7,527 | 136 | function FCMap = TMSSeedFC(SeedDir,FCMaskDir,FCOutDir,AnalysisDir,subj,targetdepth)
if nargin<5
error(' Error using ==> at least 5 arguments wanted.');
elseif nargin==5
targetdepth = 0 % number of voxels, distance from cortical target to c4
elseif nargin>6
error('E... |
e9ee25f8e73912709366d8a7f80f63ba76c67d31456e1a9bbee19aed734684db | MATLAB | 7,534 | 163 | %% This document shows several examples of how to use nsd_mapdata.m.
% NIFTI files can be viewed in ITK-SNAP.
% MGZ files can be viewed using FreeSurfer's freeview.
%% Setup path
addpath(genpath('/home/adf/charesti/Documents/GitHub/nsdcode/matlab'))
%% Map T1 anatomical to EPI space
% Here we map the 0.8-mm T1 t... |
991867930bcaa62c764583e9158243a2c87d07cf95c27e4b028971f925912e94 | MATLAB | 7,539 | 198 | % coreg_siemens.m
% Georg Oeltzschner, Johns Hopkins University 2019.
%
% USAGE:
% [vol_mask] = coreg_siemens(in, vol_image, maskFile);
%
% DESCRIPTION:
% Creates a SPM volume containing a voxel mask with the same dimensions
% as the SPM volume containing a structural image. The voxel mask will be
% created with the... |
57b55f92cd7b41f81a42e5b10c68f0140f84ae88cf22c37d99c7d55f33a1019e | MATLAB | 7,540 | 233 | %Analysis of the pipette deflection from micropipette force spectroscopy
%experiments using a cross-correlation apporach.
%
%Code written by Matilda Backholm, 5.6.2018.
%
%NOTE:
%This code assumes that there is no force acting on the pipette in
%the first frame, i.e. that the pipette is in its equlibrium position
%def... |
7b9870dd0f255fdfbc737a5f858585bdeac49f5736f88a6af19ba993a5b595f3 | MATLAB | 7,548 | 204 | load bs_results.mat %for plotting cortex
load cm17.mat % colormap
load dk_labels.mat %DK atlas labels
%dataset to use
load Hippo_data_ASB_norm.mat % data table with clinical/demographic and PAC data
save_dir = './Cluster_test_results/Hippocampus/';
if ~exist(save_dir, 'dir')
mkdir(save_dir);
end
pa=["Amplitude", "... |
7847692b70ae585a20cbcc118d78a07838c985d33a882d2331f174e3d87edb70 | MATLAB | 7,551 | 218 | % figure2_tf_switch_calculate.m - Calculate TF power differences: Switch vs. Repeat
%
% This script analyzes time-frequency power differences between switch and
% repeat trials, revealing oscillatory correlates of priority switching.
%
% KEY ANALYSES:
% 1. Load time-frequency decomposed data for each subject
% 2. A... |
81754cdca96b4aae623e62a2d550e6ad1513054283e5634ddb3cafdc2317492b | MATLAB | 7,551 | 234 | function [ subject ] = nmri_determine_datatype( subject )
%[ subject ] = nmri_determine_datatype( subject )
% central script to determine datatype (EEG/MEG/...)
% layout (for Fieldtrip viz and ICA)
% montages (for eeg_score viewer)
% will also try to deal with invasive EEG data
% check the call
if (~exist('su... |
d34ca6efa02fb04d37fd55d8d413a4ba10d4131f271424b7981c7d856cebed92 | MATLAB | 7,552 | 190 | % SCHRODINGER_EQU_TASCDMD Benchmark TASC-DMD, Exact DMD, and fbDMD on
% the Nonlinear Schrödinger (NLS) equation.
%
% This script reproduces Figures 2a–2i of:
% [TASC DMD Paper — citation to be added after publication]
%
% Workflow:
% 1. Load NLS data (run generate_NLS_data.m... |
4321499b57b0ad837f13b7d87028fa360dc8ea21ad34cae8050d26c5c2aec4bb | MATLAB | 7,556 | 192 | function [data_clean, EEGartifacts, SENSAI_score, SENSAI_score_per_band, artifact_threshold_per_band] = ft_denoise_gedai(cfg, data)
% ft_denoise_gedai FieldTrip wrapper for the GEDAI plugin.
%
% Use:
% [data_clean, EEGartifacts, SENSAI_score, SENSAI_score_per_band, artifact_threshold_per_band] = ft_gedai(cfg, dat... |
396ecc330021df4e0ef89009d8de3529e6fd9c9e3a26125711c35d7c12031972 | MATLAB | 7,561 | 197 | function [ obj ] = vb_init( obj )
% Initialize posterior and auxiliary variabels for VB inversion of HUGE.
% Requires obj.dcm and obj.prior to be intialized.
%
% This is a protected method of the tapas_Huge class. It cannot be called
% from outside the class.
%
% Author: Yu Yao (yao@biomed.ee.ethz.ch)
% Copyright (C... |
07d816d88cb38a4d543171d154b6f3a9a61916cccaa036ea97e1ecb381fb49f8 | MATLAB | 7,562 | 186 | %% ============================================================
% Main raw trace analysis script
% ============================================================
clear all
close all
clc
%% ============================================================
% Set parameters and import data
% =============================... |
d202e4178dc0adda780347a83a710a7720e31295a2f9a8d5c7683aee49730e7a | MATLAB | 7,572 | 225 | function [h,p,stats] = TestSkewness(control,repeat,test,varargin)
%TestSkewness - Test if firing field skewness changes between two conditions.
%
% Current implementation only tests 1D environments.
%
% USAGE
%
% [h,p,cr,ca] = TestSkewness(control,repeat,test,<options>)
%
% control firing fields in cont... |
5d8cb23a71adfc91567b6421c632120a9a83a73c637bb1881571399eabe3f4da | MATLAB | 7,577 | 217 | %% BiExpFitModel.m
% This function contains a biexponential diffusion model
%
% lossFunction - calculates loss function for optimizer
% forwardJacobian - calculates the forward jacobian for optimizer
% forwardModel - converts parameter struct into model prediction
% x2pars - converts x vector ... |
bf618b892d81734f1c9a6ee85b762f77174d085c91acba1e97fceec16a501b3d | MATLAB | 7,581 | 281 | function hh = errorbar_h(varargin)
%ERRORBAR Error bar plot.
% ERRORBAR(X,Y,L,U) plots the graph of vector X vs. vector Y with
% error bars specified by the vectors L and U. L and U contain the
% lower and upper error ranges for each point in Y. Each error bar
% is L(i) + U(i) long and is drawn a distance of ... |
daa172d7662bc789c6f949da6e890c2948a92be8052fe70699fd4fac88372b40 | MATLAB | 7,581 | 235 | function ProcessData_Figure3(BestFitEarly, codedir, savedir)
%ProcessData_Figure3 - function to process data to generate Figure 3. Saves
% data in savedir to be accessed by PlotFigure3
% INPUTS:
% BestFitEarly - BestFit.mat file found at: Mah_CellReports_BehavorialData/FitAll_ITI_VanillaAlpha_First10/BestFit.mat
% fr... |
1a2227eda632808cd62143df99b519bcae0a5a1246d7d80612d6dc60ae78ac47 | MATLAB | 7,585 | 214 | function [trials,Ftrials] = volbin_all_cells(all_SU,goods,all_S,all_index,win,varargin)
%plot heatmats aligned to reward volume for all cells 5/10 and 40/80 binned
% input:
% all_SU - the data of all cells
% all_behEvents - data of all cells
% all_index - indexing of all cells
% win - [start,end] of window you want pl... |
76b4b40b456e82fad7aee6cd10e732c5c5634c82fab39ab254103c9521be27bf | MATLAB | 7,585 | 185 | function out = NL_DelayTime(y, maxDelay, past, randomSeed)
% NL_DelayTime Optimal delay time using the method of Parlitz and Wichard.
%
% Computed natively in MATLAB. TSTOOL's own 'delaytime' code
% (tstoolbox/@signal/delaytime.m, vendored in this repo under
% Toolboxes/OpenTSTOOL) turned out to be pure MATLAB itsel... |
d669b024d7de9e4b66f7cc4a680b95e2ab5fb759cae1635952d7e9aed1f633ff | MATLAB | 7,585 | 186 | %% ============================================================
% Main raw trace analysis script
% ============================================================
clear all
close all
clc
%% ============================================================
% Set parameters and import data
% =============================... |
f61c8532cc145ce66ffda90bb1d4bac1d93dadbbc4952b1dbe5e84ca419acf6c | MATLAB | 7,587 | 231 | function build_mmx(verbose)
% BUILD_MMX - compiles mmx() for different platforms and provides help
% regarding compilation.
%
% BUILD_MMX will try to compile, in this order, 3 different builds of mmx:
% mmx_mkl_single - linked to Intel's single-threaded MKL library (usually fastest)
% mmx_mkl_multi ... |
00681cc19a358dbb5a898d65b5e01821b1a92a4f9ce685797bd4530ec927920d | MATLAB | 7,591 | 204 | function runSearchlight(Searchlight,inFiles,outFiles,analysisName,rsaFunction,varargin)
% function runSearchlight(Searchlight,infiles,outfiles,rsaFunction,varargin)
% Main analysis engine for searchlight-based analysis
% The function deals with data loading from the infiles, concatinates the
% data to a nObservation x ... |
d96854afd77f88771368ad6e28170a7cb36124359cec43d7ad3c6e53ae1d5b17 | MATLAB | 7,595 | 205 | function runSearchlight_subspaceGener(Searchlight,inFiles,outFiles,rsaFunction,run,tempFilesDir,varargin)
% function runSearchlight(Searchlight,infiles,outfiles,rsaFunction,varargin)
% Main analysis engine for searchlight-based analysis
% The function deals with data loading from the infiles, concatinates the
% data t... |
39e591e4ca9fe3b634e62b77babfb7f83707b93627aa4e77fdb46b4ef11b97b1 | MATLAB | 7,598 | 233 | function [p, h, clusterinfo] = cluster_test(datobs, datrnd, tail, alpha,...
clusteralpha, clusterstat)
% CLUSTER_TEST performs a cluster-corrected test that datobs is higher/lower
% than the distribution as expected under the null hypothesis. The 'null'
% distribution should be pre-computed (manually or using CLUST... |
990d3a0d054c4ff015d63cba6e5549206ec12c79792424f05248f1ff439c78d1 | MATLAB | 7,598 | 170 | function trialsData = prepare2plotTrials(params, trials)
% arranges the 'trials' structure to trialsData structure used by plotTrials.m
% (c) Jiri, Nov16
if ~isfield(trials, 'get_pValsBase')
trials.get_pValsBase = true;
end
if ~isfield(trials, 'get_pVals')
trials.get_pVals = true;
end
if ~isfield(params, 'sav... |
a09de68ea0de5f60d1c7286bffb694915fd05a37a5dcf1c240a4b6c1485a8cd4 | MATLAB | 7,601 | 209 | function [adjMs, coords, channels, FisCell, FdenoisedIsCell, spksIsCell, spikeTimes, fs, Params, activityProperties] = suite2pToAdjm(suite2pFolder, Params, Info, oneFigureHandle)
%SUITE2PTOADJM Converts suite2p data to adjacency matrix
% Detailed explanation goes here
% Params = struct();
% Info = struct();
% adjMs... |
f15a952f4893064b72b7010a638e6dea82976df51f1ed19a9d1f7f3f8185ebf6 | MATLAB | 7,602 | 256 | function [f,p,ci,stats,tbl,dist] = permuanovan(x,group,varargin)
%PERMUANOVAN Permutation-based N-way ANOVA and rank ANOVA.
% F = PERMUANOVAN(X,GROUP) performs a permutation-based N-way analysis
% of variance (ANOVA) for comparing the means of data in matrix X, and
% returns the test statistics. X is an N-by-V m... |
19db8e9d3730c0b3112eb0f60f298e99a7ee8eedd96407610837df906daefe60 | MATLAB | 7,604 | 247 | function varargout = shadowplot(varargin)
% SHADOWPLOT Add a shadow to an existing surface or patch plot
%
% For some surface plots, it can be helpful to visualize the shadow (2D
% projection) of the surface. This can give a quick perspective on the
% data's variance.
%
% SHADOWPLOT PLANE Adds a shadow plot on th... |
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