sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
06971ecf783a73bf722f2bca780a4907c609dea676306f1cfd8a3d952b11782e | MATLAB | 49,810 | 1,685 |
%% --- Plot cohort age & sex metrics
load stroke_lokalization_data.mat
figure(667)
clf
% --- Filter out people under 60 from "old stroke cohort"
idxs = find(StrokeCohort.Ages >= 60);
StrokeCohort60Plus = StrokeCohort.Ages(idxs);
% --- Put cohorts in vector
CohortAges = [YoungControlCohort.Ages'; OldControlCohort.... |
2e8094364d77eed9fc71720447a9519409854d26eecb1a824a6adcb90fd58b0d | MATLAB | 49,842 | 1,424 | function m2html(varargin)
%M2HTML - Documentation Generator for Matlab M-files and Toolboxes in HTML
% M2HTML by itself generates an HTML documentation of the Matlab M-files found
% in the direct subdirectories of the current directory. HTML files are
% written in a 'doc' directory (created if necessary). All the o... |
bfebf3ac452406e12a145e4a40dee1ef50bfb6592bec015b7a1b1e6bef7b1267 | MATLAB | 49,856 | 943 | clear all;
clc;
ForderName=['PAG/BadMood'];
foldapath=['Figure/PavFo4C4S_task/',ForderName];
allfolda=dir([foldapath,'/*.mat']);
for num_file=1:length(allfolda)
num_file
FileName=allfolda(num_file).name;
Final_FileName=FileName(1:length(FileName)-4);
if FileName(7)=='P'
FileName=FileName(1:fin... |
7b11d61e7d8338a35104e87a19fda8f7ca931b4da807430891a26794629daab7 | MATLAB | 50,429 | 964 | function [MRSCont] = OspreyProcess(MRSCont)
%% [MRSCont] = OspreyProcess(MRSCont)
% This function pre-processes MRS data from all major vendors.
% Data is read from the provided input filenames. It is shaped,
% preprocessed, aligned, etc. according to the type of sequence
% (un-edited data, MEGA-edited (ON/OFF)... |
5f27eb919b692a4165cc6507918bfeabb576fca17c5db62bc92f798b9a455aa1 | MATLAB | 50,483 | 1,283 | % ENVTOPO - Plot the envelope of a multichannel data epoch, plus envelopes and
% scalp maps of specified or largest-contributing components. If a 3-D
% input matrix, operates on the mean of the data epochs. Click on
% individual axes to examine them in detail. The black lines repr... |
c3f8bc81dd44e4d6d0b2e955c69298f4f273e2330000b8935475a8980871514a | MATLAB | 50,690 | 1,116 | function ok = hlp_trycompile(varargin)
% Try to auto-compile a set of binary files in a folder, and return the status.
% OK = hlp_trycompile(Options...)
%
% This function tries to ensure that a given set of functions or classes (specified by their
% MATLAB identifier), whose source files are assumed to be located in a ... |
ebf455e83ffc24735ebc9197a60c9b183cc677db4cffda72e3273fab93ecd6ad | MATLAB | 50,709 | 1,396 | %% BBT_SL
%
% Full title: BroadBand frequency Tagging & Statistical Learning of distractor location
% Author: Oscar Ferrante
%
%
% PARADIGM:
% This experiment consists in an additional singleton visual search task.
% Four (4) gabor patches are presented across four (4) locations. After a
% short presentation of ident... |
2dd6b75417f4db77fe25fbde574b5054a40e780c0514ea9ae9431ce1dead3358 | MATLAB | 50,859 | 542 | % This script is used to generate the phantom data to plot the distribution
% figures in the manuscript. The analysis is run as a Monte Carlo Simulation
% with a single signal representation overlayed with different noise reps
%
% USAGE:
% Phantom_Script_BiExp_Relax
%
% OUTPUTS:
% Distributions from Mon... |
11b0f6aefa7f0d513fce37f8e4812c6eae13060885126c68683c7e8b8eb225ee | MATLAB | 51,715 | 1,159 | function [MRSCont] = load_mrsi_data(MRSCont)
%[off_spec_no_lb,on_spec_no_lb] = load_mrsi_data(FileName, PathName,lb, spec_zfill, k_zfill, seq_type, water_filter, k_fft2_wat_ref, k_fft2_wat_ref_no_k_zfill, k_sort_b4_2dfft, wat_file)
%% [off_spec_no_lb,on_spec_no_lb] = load_mrsi_data(MRSCont)
% This functions load dat... |
2a20ae597afce9303e24dfdc929a56ef62606870f63b3600530d8ce9b0d6d0ca | MATLAB | 51,781 | 1,370 | %% %%%%%%%%%%%%%%%%%% EXPORT FILES
% notes:
% - you must run on stone to get the Dropbox to update! and might even need to touch the directory
% - for betas, we should run on surly (for speed).
% in fact, i need surly in order to write nocompression betas .mat
% - we are zeroing-out betas! and zeroing-out timeseries... |
f04d2f1b7ac7ffb17665b8bf341f4262a47be5a58b19d0223c43238f8bad07e5 | MATLAB | 52,010 | 1,602 | %$Release 4.0
% Copyright (c) Copyright 2004 - 2006 - The General Hospital Corporation and
% President and Fellows of Harvard University.
%
% All rights reserved.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
%
% *... |
dcdeeaa6873986d3d34b4fa857674915230297bf6ea4582f6a89a92bf74e55ba | MATLAB | 52,819 | 1,106 | function stats_p_r=compareRefRDM2candRDMs(refRDM, candRDMs, userOptions)
% GENERAL PURPOSE
% This function compares a reference RDM to multiple candidate RDMs. For
% example, the reference RDM could be a brain region's RDM and the
% candidate RDMs could be multiple computational models. Alternatively, the
% reference ... |
5c3363321ec9a7b3fee6dc506774dd690b1eff52bcd4f5bc5d490ce118a27574 | MATLAB | 53,069 | 1,214 | % BIDS_EXPORT - this function allows converting a collection of datasets to
% BIDS formated folders and files.
%
% Usage:
% bids_export(files, varargin)
%
% Input:
% files - Structure with the fields 'file','session' and 'run'.
% The field 'file' should be a cell array of strings
... |
c87a5a6cbce6b3e5cd598127591243f6f7c238c754984d2aa7cf70c6049e8320 | MATLAB | 53,661 | 1,553 | function varargout = spider_plot(P, varargin)
%spider_plot Create a spider or radar plot with individual axes.
%
% Syntax:
% spider_plot(P)
% spider_plot(P, Name, Value, ...)
% h = spider_plot(_)
%
% Documentation:
% Please refer to the MathWorks File Exchange or GitHub page for the
% detailed docum... |
eca75e69de6886290731baba357b0a5167e4fdafdd15062eef7af17b7873873a | MATLAB | 54,160 | 711 | function osp_iniFitWindow(gui)
%% osp_iniFitWindow
% This function creates the initial fitting window in the gui.
%
% USAGE:
% osp_iniFitWindow(gui);
%
% INPUT: gui = gui class containing all handles and the MRSCont
%
% OUTPUT: Changes in gui parameters and MRSCont are written into the
% ... |
33dd0718d818783e0c248f65571ab78c54aa6156b06be4a15e3d24360b2a42ee | MATLAB | 54,408 | 1,408 | close all; clear all; clc;
% Base settings
runtime = 360;
cuttime = 120;
dt = 1/3600; % 1sec = 1/3600 hour
t = 0;
Nx = 101; % 101 - 201
Ny = 101; % 101 - 201
px = 0;
qx = 1; % 1 - 2
py = 0;
qy = 1; % 1 - 2
dx = 0.01;
dy = 0.01;
Pprof = 5/6;
x = px : dx : qx;
y = py : dy : qy;
Tanon = 0; % TAN switch / activated:0 / d... |
1baacce2289389c622b6d6ee4878aa0d86226c6710caf9d72cc75810f54dea6b | MATLAB | 54,499 | 1,109 | % POP_IMPORTBIDS - Import BIDS format folder structure into an EEGLAB
% study.
% Usage:
% >> [STUDY ALLEEG] = pop_importbids(bidsfolder);
% >> [STUDY ALLEEG] = pop_importbids(bidsfolder, 'key', value);
%
% Inputs:
% bidsfolder - a loaded epoched EEG dataset structure.
% options are 'bidseve... |
e0cd90614f360c0c57208a442a5e87cb15dc55af04414040984c2ec74a1b2928 | MATLAB | 54,591 | 2,709 | function plotFromSourceData()
close all
fig_1c();
fig_3a();fig_3b();fig_3c();fig_3d();
fig_4b();fig_4c();fig_4d();fig_4e();fig_4f();fig_4g();fig_4h();
fig_5a();fig_5b();fig_5c();
fig_6c();fig_6d();fig_6e();fig_6f();fig_6g()
fig_7a();fig_7b();fig_7c();fig_7d();fig_7e();fig_7f();fig_7g();fig_7h();fig_7i();fig_7j();fig_7k... |
1144e3a412c20032f2c88a68477cab79f0c6b0c368f8b08736ea98256d596e91 | MATLAB | 55,304 | 1,346 | function out=mmpolar(varargin)
%MMPOLAR Polar Plot with Settable Properties.
% MMPOLAR(Theta,Rho) creates a polar coordinate plot using the angle Theta
% in RADIANS and radius in Rho. Rho can contain negative values.
% MMPOLAR(Theta,Rho,S) creates the plot using the line spec given by S. See
% the function PLOT fo... |
0706cffa56f65b5cb0e16295b73914e9e91b1acf785efd8c1fff83092f7255dc | MATLAB | 55,894 | 1,923 | //========================================================================
// GLFW 3.4 macOS - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2009-2019 Camilla Löwy <elmindreda@glfw.org>
//
// This software is provided 'as-is', without any express or implied
// ... |
726e659b53c3795193c4008d00ef658352a924e1a04cbc09411d2badf1dd81e6 | MATLAB | 56,637 | 1,693 | function coactPaper_figure08()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=5;
fontsize=6;
close all
fh=initFig('width',18.6,'height',15.5,'font','Arial','fontsize',fontsize);
x=17;y=3;
panel_01(x,y,fontsize);
panelLetter2(x-letGapX-10,y-letGapY+3,alphabet(1,labelCase),'fontSize',labelSize,'isBo... |
366bed2fde656706bd01cfcf354715f5f16eafe16ac641858a1f7e1e079d80d3 | MATLAB | 57,195 | 1,336 | %% ICC Values for Within Session Functional Connectivity and Brain Variability
%% ICC Calculation and Analysis (Figures 2, 3, 6)
% This file contains code to calculate within session ICC values (Part 1) and
% complete statistical analyses from figures 2, 3 and 6 (Part 2) from the paper. The
% code is meant to be run s... |
8cb643ae28685525729eeed35287ac2147ab3ff6660557100eff736eeb873b89 | MATLAB | 57,768 | 1,224 | % GEDAI() - This is the main function used to denoise EEG da12ta using
% generalized eigenvalue decomposition coupled with an EEG leadfield matrix
%
% GEDAI (Generalized Eigenvalue Deartifacting Instrument)
%
% Usage:
% Example 1: Using all default values (and no bad epoch rejection)
% >> [EEG] = GEDAI(EEG);
... |
3397469f992f06fc03426d28c0d9851ba2ff05b666d316f7af59a4b9cc5aaa87 | MATLAB | 58,027 | 866 | function [MRSCont] = OspreyOverview(MRSCont)
%% [MRSCont] = OspreyOverview(MRSCont)
% This function creates te data structre needed for the overview panel
% in the GUI. It sorts the data by groups and performs the needed
% statistics.
%
% USAGE:
% MRSCont = OspreyOverview(MRSCont);
%
% INPUTS:
% M... |
6ce4e62cdf42e5a1246da3e5ba886c55146e9c3131204260efc133e39f4980d9 | MATLAB | 58,106 | 1,138 | function plot_prediction_performance_across_epoch
close all
clear all
clc
% Plot prediction performance in each epoch by reduced-rank regression.
% Select a folder containing data.
folder_name = uigetdir;
cd(folder_name)
load('population_regression_control.mat')
load('population_regression_APP.mat')
% Stimulus.
% C... |
9734e7756e9909a96b32ea30337387e3fc4c4717a6e8968f1ae682c6ff3115dc | MATLAB | 58,423 | 1,712 | function [shape] = ft_read_headshape(filename, varargin)
% FT_READ_HEADSHAPE reads the fiducials and/or the measured headshape and/or meshes
% that describe headsurfaces, headmodels or cortical sheets from a variety of files
% (like CTF and Polhemus). The headshape and fiducials can for example be used for
% coregistr... |
f4048a8dd4c619756153177ca8fcc6d28bd4c348c349d1e3a01f156ed6da35be | MATLAB | 59,871 | 1,457 | % CROSSF - Returns estimates and plots event-related coherence (ERCOH)
% between two input data time series (X,Y). A lower panel (optionally)
% shows the coherence phase difference between the processes.
% In this panel, output by > crossf(X,Y,...);
% 90 degrees (orange) means X lea... |
e7da3100c1de7c1ab148ad00884363ad20ed960ce520dc11fc25e62b0d7fbfc2 | MATLAB | 59,921 | 975 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%% BREATHING FILTER DETECTION TASK ANALYSIS %%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% -------------------------------------------------------------------------
% Author: Olivi... |
064e00aceb29d79d1a4fd53135f22fbff7a5ffdeed9f87f42f57491400a2c481 | MATLAB | 60,480 | 1,254 | function [MRSCont] = OspreyQuantify(MRSCont)
%% [MRSCont] = OspreyQuantify(MRSCont)
% This function transforms the raw amplitude parameters determined during
% OspreyFit into quantitative estimates of metabolite levels.
%
% By default, OspreyQuantify will report tCr ratios for all metabolites.
% These values wi... |
87775097f711be10e51d66712f5c819a55da7475088da56fa93dc3c1ea98d740 | MATLAB | 60,499 | 1,151 | function stimActivityAnalysis(spikeData, Params, Info, figFolder, oneFigureHandle)
% Performs analysis of spike data relative to stimulation times
% INPUT
% -------
% spikeData : struct
% Params : struct
% Info : struct
% figFolder : path
% oneFigureHandle : matlab figure object
% Default blank duration i... |
f155c8d01c4fcafe3cfb820effb75b72d98a6d6c7ab07b36759f0446e8c501aa | MATLAB | 60,673 | 968 | % POP_CLUSTEDIT - graphic user interface (GUI)-based function with editing and plotting
% options for visualizing and manipulating an input STUDY structure.
% Only component measures (e.g., dipole locations, scalp maps, spectra,
% ERPs, ERSPs, ITCs) that have been compute... |
28d3bbdf2c6c9fc1d75a2b068b9ca298a284bba15467e5c5d5aee233279d5fd6 | MATLAB | 60,841 | 687 | function A0_RSA_one_subj_41to50(subj)
% % Add software, add DPABI before spm
if ismac
addpath(genpath(fullfile('..', 'DPABI_V8.1_240101')));
addpath(genpath(fullfile('..', 'REST_V1.8_130615')));
addpath(fullfile('..', 'spm'));
greymask_path = fullfile('..', 'DPABI_V8.1_240101', ... |
74421e60ad9355b3b3985ffd2dd593267898d0272af3cb4c20bf1f57cbeaf4d1 | MATLAB | 60,841 | 687 | function A0_RSA_one_subj_31to40(subj)
% % Add software, add DPABI before spm
if ismac
addpath(genpath(fullfile('..', 'DPABI_V8.1_240101')));
addpath(genpath(fullfile('..', 'REST_V1.8_130615')));
addpath(fullfile('..', 'spm'));
greymask_path = fullfile('..', 'DPABI_V8.1_240101', ... |
f4f0cbbb74a798655936614b63e1151b8071297b20d131d7ea2bc2628fc6f306 | MATLAB | 60,841 | 687 | function A0_RSA_one_subj_21to30(subj)
% % Add software, add DPABI before spm
if ismac
addpath(genpath(fullfile('..', 'DPABI_V8.1_240101')));
addpath(genpath(fullfile('..', 'REST_V1.8_130615')));
addpath(fullfile('..', 'spm'));
greymask_path = fullfile('..', 'DPABI_V8.1_240101', ... |
ed3809e4c9cd027519352d24612316430468810647868a7d2b9c57ded9a9879d | MATLAB | 60,892 | 988 | function plot_functional_connectivity_task_var_cell
close all
clear all
clc
% Plot functional connectivity between task-variable cells.
% Select a folder containing data.
folder_name = uigetdir;
cd(folder_name)
% Control.
load('activity_control.mat')
load('activity_iti_control.mat')
activity = activity_control;
acti... |
e462cb5cbe33f0fdb2273a911672cd26e8959c28bf9b18f09c5e3fa7d7662f9e | MATLAB | 61,147 | 1,526 |
%this is the code for producing the analysis and figures for the manuscript
%"Overcoming off-target optical stimulation-evoked cortical activity in the
%mouse brain in vivo"; Simon Weiler, Mateo Velez-Fort and Troy W. Margrie
%this uses only data obtained in the year 2024
%% DEPENDENCIES, PLEASE READ
%Please get t... |
612c230df1c28c80560afc73358038c53fff0aae228bf73561bdeaca2d1f4e9d | MATLAB | 61,685 | 1,852 | function cmapOut = BF_GetColorMap(whichMap,numGrads,cellOut,flipMe)
% BF_GetColorMap Colorbrewer colors for Matlab.
%
% Returns a nice set of colors to make a nice colormap using the color schemes
% from http://colorbrewer2.org/
%
% The online tool, colorbrewer2, is copyright Cynthia Brewer, Mark Harrower and
% The ... |
727204bcfdef2a19484d949ac73f9bff95516a964ef5b18a1f586d42e6d894bb | MATLAB | 61,691 | 1,187 | %% ICC Values for Functional Connectivity and Brain Variability Between Sessions
%% And Analysis of Longitudinal ICCs (Figure 4)
% This script calculates ICC values across longitudinal fMRI scans. % This script
% is meant to be run section by section in order and used AFTER running the
% testretest_ICC.m script.
%%... |
ac912f7e85e19df05e319668625f93aa6888aa3199122ae227242f1f99fb6597 | MATLAB | 61,713 | 1,425 | % dipplot() - Visualize EEG equivalent-dipole locations and orientations
% in the MNI average MRI head or in the BESA spherical head model.
% Usage:
% >> dipplot( sources, 'key', 'val', ...);
% >> [sources X Y Z XE YE ZE] = dipplot( sources, 'key', 'val', ...);
%
% Inputs:
% sources - structure arr... |
4c9efbaab518aea0774bc207a00faaac86d9bfe2a92054a007b7f79d209957f9 | MATLAB | 62,379 | 633 | function plot_example_neural_activity
close all
clear all
clc
% Plot_example neural activity.
% Select a folder containing data.
folder_name = uigetdir;
cd(folder_name)
load('activity_APP')
% Sampling frequency of Scanimage.
fs_image = 9.35211;
% ALM.
animal_num = 4;
session_num = 1;
region_num = 1;
cell_num = 4;
... |
4046a875c075a81f76b9c55ef7e74132ba8c43b1551fb3ea34610f4093b8b394 | MATLAB | 62,787 | 1,164 | % POP_CHANEDIT - Edit the channel locations structure of an EEGLAB dataset,
% EEG.chanlocs. For structure location and file formats,
% see >> help readlocs
%
% EEG.chanlocs. For structure location and file formats,
% see >> help readlocs
%
% Usage:... |
2660f539111b97a53752efbea7b0ef6605a103869aa76288307ab14ed4503fcf | MATLAB | 63,266 | 1,279 | clear all;
close all;
clc;
foldapath=['POP_Behavior/PavFo4C4S/ALL/PAG/BadMood'];
allfolda=dir([foldapath,'/*.mat']);
for num_file=1:length(allfolda)
AllFileName_raw=allfolda(num_file).name;
if ~isempty(find(AllFileName_raw(13:length(AllFileName_raw))=='A'))
AllFileName{num_file}=(AllFileName_raw(1:fi... |
119d6933db515e8d1d1113856a4988a7a2f155ba33b5900d313714caec86c9ea | MATLAB | 63,639 | 1,503 | % RUNICA - Perform Independent Component Analysis (ICA) decomposition
% of input data using the logistic infomax ICA algorithm of
% Bell & Sejnowski (1995) with the natural gradient feature
% of Amari, Cichocki & Yang, or optionally the extended-ICA
% algorithm of Lee, Gir... |
6bab1afb9832b429474f0a0f2085a4bca55643deddd50ac0acecca9ca8953f3a | MATLAB | 63,760 | 1,266 | function [MRSCont] = OspreyHTMLReport(MRSCont,kk)
%% [MRSCont] = OspreyHTMLReport(MRSCont,kk)
% This function creates a short HTML report of the processing and modeling
% and should be called at the end of the analysis.
%
% USAGE:
% MRSCont = OspreyHTMLReport(MRSCont,kk);
%
% INPUTS:
% MRSCont =... |
f319441423280bfd3754d988f4f1424b3c15fdfe717532c9da16fd1ddff833d7 | MATLAB | 64,172 | 1,727 | function [templates,correlations,weights,variance] = ActivityTemplates(spikes,varargin)
%ActivityTemplates - Compute assemblies activity and neurons contribution from PCA of spike trains and ICA.
%
% Computes the templates for the component activation analysis described in
% Peyrache et al (2009). Optionally, computes... |
2f14ae398c7216c2c0410ac8bffad1b9a0671fd9411377781717d62456340604 | MATLAB | 64,211 | 1,353 | clear all;
close all;
clc;
ForderName=['ALL/LHbnPAG'];
foldapath=['POP_Behavior/PavFo4C4S/',ForderName];
allfolda=dir([foldapath,'/*.mat']);
for num_file=1:length(allfolda)
AllFileName_raw=allfolda(num_file).name;
if ~isempty(find(AllFileName_raw(13:length(AllFileName_raw))=='A'))
AllFileName{num_fi... |
46749cc299e068a8efa4bddb7b6d32f6b655645a7fb6936f1d16438de80a12a1 | MATLAB | 64,451 | 1,467 | % NEWCROSSF - Returns estimates and plots event-related coherence (ERCOH)
% between two input data time series. A lower panel (optionally) shows
% the coherence phase difference between the processes. In this panel:
% In the plot output by > newcrossf(x,y,...);
% 90 degrees (orange)... |
7c42f7513342ac46ea68ed7b980e28f9027f2303673c81bf33788607c66ed20a | MATLAB | 65,326 | 1,548 | % RUNICA - Perform Independent Component Analysis (ICA) decomposition
% of input data using the logistic infomax ICA algorithm of
% Bell & Sejnowski (1995) with the natural gradient feature
% of Amari, Cichocki & Yang, or optionally the extended-ICA
% algorithm of Lee, Gir... |
0c1cff7ef138e91a3c4387153c49338bc95d5f0c7e602fa816e967fdc096c321 | MATLAB | 65,534 | 1,610 | % topoplot() - plot a topographic map of a scalp data field in a 2-D circular view
% (looking down at the top of the head) using interpolation on a fine
% cartesian grid. Can also show specified channnel location(s), or return
% an interpolated value at an arbitrary scalp locat... |
cc4175922d68892bd74ff56d70c43c17cc2af167fa1c1c2c7fbbb9d4b8147274 | MATLAB | 66,963 | 1,358 | classdef OperationsUnitTests < matlab.unittest.TestCase
% Known-answer and edge-case unit tests for individual Operations/*.m
% functions, run in isolation (no database, no full pipeline).
%
% Complements BasicPipelineTests.m, which only exercises the full
% TS_Compute pipeline end-to-end.
meth... |
d4842d2fe93944552830d8beca55e3d80aff319a1216a10af0d25fec91e73926 | MATLAB | 67,218 | 1,351 | %% Script to load and fit behavioural data from the Responsibility project experiments
%% General setup
clear; close all; clc
owd = pwd;
colors = niceColorsDark(3); % the colors for the 3 experimental conditions
fontSize = 20;
set(0,'defaultAxesFontSize',fontSize)
addpath('fittingUtilityFunction')
%% get datafiles
% ... |
c19d834030d0985d8709bdaa02004187d998e6ffebffaf32f8ec165cf03ae98c | MATLAB | 67,547 | 977 | function out = osp_plotModule(MRSCont, Module, kk, Index, which, metab, corr)
%% osp_plotModule
% Callback function on print figure button click.
%
%
% USAGE:
% osp_plotModule(MRSCont, Module, kk, which, metab, corr)
%
% INPUT: MRSCont = Osprey data container.
% Module = String for t... |
616af1676ac49c0c58818a89e2001c33844fd6cea75df416c29a1f56d3cb0afc | MATLAB | 68,118 | 1,439 | % EEG_CHECKSET - check the consistency of the fields of an EEG dataset
% Also: See EEG dataset structure field descriptions below.
%
% Usage: >> [EEGOUT,changes] = eeg_checkset(EEG); % perform all checks
% except 'makeur'
% >> [EEGOUT,changes]... |
15c6833f01bb2f60955008f76c20b6fae011a5a085178efcdff7d286f2d819c3 | MATLAB | 69,103 | 1,910 | function [data] = ft_checkdata(data, varargin)
% FT_CHECKDATA checks the input data of the main FieldTrip functions, e.g. whether the
% type of data structure corresponds with the required data. If necessary and possible,
% this function will adjust the data structure to the input requirements (e.g. change
% dimord, a... |
afa49404eb0009cde63265c4bf0dc69b80b61deaddd3940cb50d7da04f744850 | MATLAB | 69,665 | 1,685 | function physio = tapas_physio_cfg_matlabbatch
% This file needs to be in a sub-folder of spm/toolbox in order for the
% Batch Editor to recognize PhysIO as an SPM toolbox.
% Author: Lars Kasper
% Created: 2013-04-23
% Copyright (C) 2013-2018 TNU, Institute for Biomedical Engineering, University of Zurich and ETH Zuri... |
e102013b6d2851e6e81daa68a31cf7f8a295fa57a6a5554fc75e0667783d3988 | MATLAB | 69,719 | 1,385 | %% Script to load and fit behavioural data from the Responsibility project experiments
%% General setup
clear; close all; clc
owd = pwd;
colors = niceColorsDark(3); % the colors for the 3 experimental conditions
fontSize = 20;
set(0,'defaultAxesFontSize',fontSize)
addpath('fittingUtilityFunction')
%% get datafiles
% ... |
7ade2d4130781634ce75e7c8b45811d7fe0e0668f592f537598585683940ac83 | MATLAB | 70,009 | 1,198 | function out = osp_plotProcess(MRSCont, kk, which_spec,SubSpectraIndex,ExtraIndex,VoxelIndex, ppmmin, ppmmax)
%% out = osp_plotProcess(MRSCont, kk, which, ppmmin, ppmmax)
% Creates a figure showing processed data stored in an Osprey data container,
% ie in the raw fields. This function will display the *processed a... |
e217db007b171c3f9805011c603a1fbb1b55beed1f588aa8895e675f00aa3ab0 | MATLAB | 71,619 | 1,575 | function MEApipeline(InputParamsFilePath)
% Process data from MEA recordings of 2D and 3D neuronal cultures
% Created: RC Feord, May 2021
% Authors: T Sit, RC Feord, AWE Dunn, J Chabros and other members of the Synaptic and Network Development (SAND) Group
%% USER INPUT REQUIRED FOR THIS SECTION
% In this section all m... |
21f0eb08b6fc1acf642e1187feb5c76c5ae53bd6162f9489b366548570f83510 | MATLAB | 72,357 | 1,586 | function MEApipeline_parity(InputParamsFilePath)
% Process data from MEA recordings of 2D and 3D neuronal cultures
% Created: RC Feord, May 2021
% Authors: T Sit, RC Feord, AWE Dunn, J Chabros and other members of the Synaptic and Network Development (SAND) Group
%% USER INPUT REQUIRED FOR THIS SECTION
% In this sectio... |
879c2e82f89b2be8473b0a39664953eb07b4632bc71f3d34a1cdee108af1e11a | MATLAB | 72,611 | 1,632 | function quality_matrices = prepQtnirs(nirsFilePath,varargin)
% QT-NIRS is a Matlab-based tool for the quality assessment of fNIRS data.
% QT-NIRS can quantify the quality of an fNIRS recording in two different ways, by using a GUI or through a function call.
% Graphically, the QTNIRS GUI allows the user to locate a w... |
bb190e0b449218aa3cc1e14f12b691f4ce2cac99e464ef47160f0fa9795978c5 | MATLAB | 72,676 | 1,632 | function quality_matrices = pruneAdaptedQtnirs(dotNirsFilePath,varargin)
% QT-NIRS is a Matlab-based tool for the quality assessment of fNIRS data.
% QT-NIRS can quantify the quality of an fNIRS recording in two different ways, by using a GUI or through a function call.
% Graphically, the QTNIRS GUI allows the user to... |
af2042d8077126a3fbd361d5aab43432352ab505f9fdd6c7dc285e7d5d353da1 | MATLAB | 72,983 | 1,774 | function [dat] = ft_read_data(filename, varargin)
% FT_READ_DATA reads data from a variety of EEG, MEG and other time series data files
% and represents it in a common data-independent format. The supported formats are
% listed in the accompanying FT_READ_HEADER function.
%
% Use as
% dat = ft_read_data(filename, ..... |
75d07d0f55d769661f0f62049c6af8e0cec088a239e0bc03ac7fe37979149d4c | MATLAB | 73,698 | 1,635 | function MEApipeline_timingBenchmark_debug(InputParamsFilePath)
% Process data from MEA recordings of 2D and 3D neuronal cultures
% Created: RC Feord, May 2021
% Authors: T Sit, RC Feord, AWE Dunn, J Chabros and other members of the Synaptic and Network Development (SAND) Group
%% USER INPUT REQUIRED FOR THIS SECTION
%... |
43116b0ff8ce7ed4193e5152c2443de0ea68ed7fc1f9dc3f265ce08d41a940c7 | MATLAB | 74,466 | 1,525 | function varargout = WhiteMatter(varargin)
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @WhiteMatter_OpeningFcn, ...
'gui_OutputFcn', @Wh... |
0916b3560d26646e5564e512d830037d45f645b60c43bed849a3da270f661e8a | MATLAB | 76,554 | 1,583 | function [imageData, alpha] = export_fig(varargin) %#ok<*STRCL1>
%EXPORT_FIG Exports figures in a publication-quality format
%
% Examples:
% imageData = export_fig
% [imageData, alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... -c[<v... |
caf0ff1b239e3b33ca6f54de145a869821c59455e3930689920727c188a543cd | MATLAB | 76,559 | 1,433 | function filtData = filterData(params, rawData, filterTags, init_srate)
% given 'rawData' (samples x ch) and 'filterSettings' struct containing all
% relevant information about the filtering routine, filters the raw data
% and outputs as 'filtData'
% 'filterSettings' is a cell struct, may contain several filters follow... |
dec34ea321efb546fc54ee75f6218926748572661a3a3136070af2e2e7976773 | MATLAB | 78,440 | 1,942 | function out = spm_dicom_convert_osp(Headers,opts,RootDirectory,format,OutputDirectory,meta)
% Convert DICOM images into something that SPM can use (e.g. NIfTI)
% FORMAT out = spm_dicom_convert(Headers,opts,RootDirectory,format,OutputDirectory)
% Inputs:
% Headers - a cell array of DICOM headers from spm_dicom_hea... |
35e5b1fad07338bb6bab5d8724801fee7961bfb2383703140e1d835814edc4d0 | MATLAB | 79,145 | 1,724 | function MEApipeline_timingBenchmark(InputParamsFilePath)
% Process data from MEA recordings of 2D and 3D neuronal cultures
% Created: RC Feord, May 2021
% Authors: T Sit, RC Feord, AWE Dunn, J Chabros and other members of the Synaptic and Network Development (SAND) Group
%
% ===========================================... |
268fa6da1886264527a3258bb041cce65eab20b925d5e204deb5feae6b3bed8d | MATLAB | 80,099 | 985 | function plot_trial_averaged_neural_activity_delay_cells
close all
clear all
clc
% Plot trial-averaged activity of delay cells.
% Select a folder containing data.
folder_name = uigetdir;
cd(folder_name)
% Control.
load('activity_control.mat')
activity = activity_control;
clear activity_control
% Initialize.
for reg... |
f8507cae61cfdc9a534511b69fb66b5a5fecfda80d12f6bcbcdd8c9bda75cdc3 | MATLAB | 80,288 | 1,282 | clear all;
clc;
ForderName=['PAG/GoodMood'];
foldapath=['Figure/PavFo4C4S_task/',ForderName];
allfolda=dir([foldapath,'/*.mat']);
for num_file=1:length(allfolda)
num_file
FileName=allfolda(num_file).name;
Final_FileName=FileName(1:length(FileName)-4);
if FileName(7)=='P'
FileName=FileName(1:f... |
818134bae451961297d8656e32ed098a57bde90d5c09f1441751128a4408b19b | MATLAB | 80,876 | 1,504 | classdef CreateOspreyJob_app < matlab.apps.AppBase
% Properties that correspond to app components
properties (Access = public)
InteractiveOspreyjobfilegeneratorUIFigure matlab.ui.Figure
FWHMMM3coEditField matlab.ui.control.NumericEditField
FWHMMM3coLabel m... |
02d6c95fdbfce31d468992178ea3f867f77650e3b2978a68604af945c76c16a9 | MATLAB | 83,218 | 1,006 | function osp_onPrint( ~, ~ ,gui)
%% osp_onPrint
% Callback function on print figure button click.
%
%
% USAGE:
% osp_onPrint( ~, ~ ,gui);
%
% INPUT: gui = gui class containing all handles and the MRSCont
%
% OUTPUT: Changes in gui parameters and MRSCont are written into the
% g... |
0b82198e34979f0a711a0438286173543c3c178f174c23c475ab51a36b790ce3 | MATLAB | 85,130 | 1,436 | clear all;
clc;
ForderName=['PAG/BadMood'];
foldapath=['Figure/PavFo4C4S_task/',ForderName];
allfolda=dir([foldapath,'/*.mat']);
for num_file=1:length(allfolda)
num_file
FileName=allfolda(num_file).name;
Final_FileName=FileName(1:length(FileName)-4);
if FileName(7)=='P'
FileName=FileName(1:fi... |
1836f7ae66c30562e4f82b2dd02adadc9ce055e38b2a9f1e81f422c572311069 | MATLAB | 85,156 | 1,191 | function [k_sort_on, k_sort_on2, k_sort_off, k_sort_off2,....
on_spec_k_1, on_spec_k_2, off_spec_k_1, off_spec_k_2,track_all_p_thresh] = motion_correct_mrsi_full(k_sort_on, k_sort_on2, k_sort_off, k_sort_off2,....
on_spec_k_1, on_spec_k... |
2966ad81c0cbd4fb965b1c8d0a382c0376a40b4efc984c638ed675d2bb2d215b | MATLAB | 85,465 | 2,547 | function coactPaper_figureS19()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=6;
fontsize=6;
close all
fh=initFig('width',18.6,'height',16,'font','Arial','fontsize',fontsize);
x=10;y=5;
panel_01_02_03(x,y,fontsize);
panelLetter2(x-letGapX-2,y-letGapY+2,alphabet(1,labelCase),'fontSize',labelSize,'... |
1721e25f2c12a6fd56cdabb160921acbd448430d8326bb856ebb0ef25a8bbeaa | MATLAB | 85,523 | 1,857 | function [type] = ft_filetype(filename, desired, varargin)
% FT_FILETYPE determines the filetype of many EEG/MEG/MRI data files by
% looking at the name, extension and optionally (part of) its contents.
% It tries to determine the global type of file (which usually
% corresponds to the manufacturer, the recording syst... |
6df982883e2b31e78d24f7e79f118d41f3f966cd2d40645680ce5a737671f69f | MATLAB | 87,201 | 2,620 | function varargout = eeg_score(varargin)
% [data, subject]=eeg_score(cfg,data,subject)
%
% This script is both a EEG/MEG viewer and can be used to set events
% (e.g. "spikes") and do a trial-based rating for vigilance / sleep and
% techinal artifacts. It should be faster than ft_databrowser and somewhat
% more conventi... |
958ac47efa03155fc0ccbcc2b44718855a3e70de3f3286f95f138d11f0060868 | MATLAB | 87,280 | 1,539 | %% simplified version to upload
%% set directories
matlab_set_paths
close all
clear all
clc
IF_LOAD_PROC_DATA = 0;
IF_AVG_BY_ANIMAL = 1;
IF_PLOT_SESSIONS = 0;
if IF_AVG_BY_ANIMAL
IF_VIOLIN = 0;
IF_CONNECT_SCATTER = 1;
else
IF_VIOLIN = 1;
IF_CONNECT_SCATTER = 0;
end
dist_thresh = 5/10*80;... |
b3ca34dc738623b98208bdece156bd93e5b2f5c90d4eb6b08b788c106ccb557e | MATLAB | 87,796 | 2,168 | classdef spider_plot_class < matlab.graphics.chartcontainer.ChartContainer & ...
matlab.graphics.chartcontainer.mixin.Legend
%spider_plot_class Create a spider or radar plot with individual axes.
%
% Syntax:
% s = spider_plot_class(P)
% s = spider_plot_class(P, Name, Value, ...)
... |
c9d4fa21101a1150b2a0388e24091de25f1caa80bdedbbf1d2e6ffbfbaafaed1 | MATLAB | 93,403 | 2,186 | % EEGPLOTLEGACY - Scroll (horizontally and/or vertically) through multichannel data.
% Allows vertical scrolling through channels and manual marking
% and unmarking of data stretches or epochs for rejection.
% Usage:
% >> eegplotlegacy(data, 'key1', value1 ...); % use interface butto... |
48ca7c7ed643156440f7aa14cd5e65b58a54f71a98ca77262f933e1125311ee2 | MATLAB | 93,755 | 2,291 | function GroupAna
%GroupAna.m
%
%Purpose:
%
%
%
%Input Parameters:
%
%
%
%Output Parameters:
% err : 0 No Problem
% : 1 Problems
%
%
%
%Key Terms:
%
%More Info :
%
%
%
diary('diary'); % save all subsequent command window input and most of the resulting command window output to be appended
... |
15e62a7bb6171eac237852629642036637407a919c710997900cc7e5430c64e4 | MATLAB | 93,904 | 2,234 | classdef Sources2D < handle
% This class is a wrapper of Constrained NMF for standard 2D data. It
% Both CNMF and CNMF-E model can be used.
% Author: Pengcheng Zhou, Columbia University, 2017
% zhoupc1988@gmail.com
%% properties
properties
% spatial
A; ... |
c3fcf4984de159be7c9f06f696a51e92316e9dc642ff581d2a118aec57855fef | MATLAB | 94,057 | 3,804 | function label = ft_senslabel(type, varargin)
% FT_SENSLABEL returns a list of predefined sensor labels given the
% EEG or MEG system type which can be used to detect the type of data.
%
% Use as
% label = ft_senslabel(type)
%
% The input sensor array type can be any of the following
% 'ant128'
% 'biosemi64'
% 'bi... |
cf5571c3357206758b0d9dbda7340d2251b45d8b90918f0ade1457266d8671be | MATLAB | 94,215 | 2,212 | % EEGPLOT - Scroll (horizontally and/or vertically) through multichannel data.
% Allows vertical scrolling through channels and manual marking
% and unmarking of data stretches or epochs for rejection.
% Usage:
% >> eegplot(data, 'key1', value1 ...); % use interface buttons, etc.
%
%... |
b72fb3cd979b033308d6860117b4d1d67ad9555a06232f43654d8e1dc3f71fda | MATLAB | 95,370 | 2,149 | % NEWTIMEF - Return estimates and plots of mean event-related (log) spectral
% perturbation (ERSP) and inter-trial coherence (ITC) events across
% event-related trials (epochs) of a single input channel time series.
%
% * Also can compute and statistically compare transforms for two time
% ... |
47d6c6dce96928bee367e961984d89bbcf1c8f6ab439eb2761879ce120826669 | MATLAB | 99,489 | 2,072 | function [data] = read_besa_besa(filename, header, begsample, endsample, chanindx)
% READ_BESA_BESA reads data and header information from a BESA file
% See formatting document <a href="matlab:web(http://www.besa.de/downloads/file-formats/)">here</a>
%
% Use as
% [header] = read_besa_besa(filename);
% where
% fi... |
a9b06cff8bca8c9f337bdec3fd54b7976968a297512555137ab8c8755bdcba92 | MATLAB | 100,674 | 2,820 | function ripples = DetectSWR(Channels, varargin)
%DetectSWR - Detect Sharp Wave Ripple in epochs of continuous data.
%
% DetectSWR Detect Sharp Wave Ripple in epochs of continuous data. This
% code is designed for linear probes, with at least one shank
% that simultaneously records acro... |
1548371ff801690878ea57b3648364f2bfa4e3c38a5c3206a9d3628540a3589c | MATLAB | 106,808 | 1,969 | for init_project = 1
GH = '/Users/ttsigaras/Documents/GitHub'; % GitHub directory
homeDir = [GH '/InfantMicro'];
% directory of each participant's native microstructure profile csv
MPs_dir = [homeDir '/data/native_MPs'];
% directory of vertex-wise Von Economo parcel indices
... |
074a469b53d3b0329511e87f61e751c29d9f6ce9d60e36d5f301b6bba7ce833e | MATLAB | 112,227 | 2,689 | function [event] = ft_read_event(filename, varargin)
% FT_READ_EVENT reads all events from an EEG, MEG or other time series dataset and
% returns them in a common data-independent structure. The supported formats are
% listed in the accompanying FT_READ_HEADER function.
%
% Use as
% [event] = ft_read_event(filename,... |
f519d821c1114d7142034780423ab3714963398f5f3528612534ae200e9b5fba | MATLAB | 115,708 | 2,228 | function [imageData, alpha] = export_fig(varargin) %#ok<*STRCL1>
%EXPORT_FIG Exports figures in a publication-quality format
%
% Examples:
% imageData = export_fig
% [imageData, alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... |
5ce83aa69f6ed337d28eba54462a13700cc7444195272756553c643bd7ad729a | MATLAB | 117,124 | 606 | function natsort_test()
% Test function for NATSORT.
%
% (c) 2012-2024 Stephen Cobeldick
%
% See also NATSORT TESTFUN_NSX ARBSORT_TEST NATSORTFILES_TEST NATSORTROWS_TEST
fnh = @natsort;
chk = testfun_nsx(fnh);
%
try categorical(0); isc=true; catch; isc=false; warning('No categorical class.'), end %#ok<CTCH,W... |
9e01677dbae0aa39e23cb0b867f7f2b9111d14f20fb1a88fbb46d3984d5e2d1b | MATLAB | 120,502 | 2,274 | % eeglab() - Matlab graphic user interface environment for
% electrophysiological data analysis incorporating the ICA/EEG toolbox
% (Makeig et al.) developed at CNL / The Salk Institute, 1997-2001.
% Released 11/2002- as EEGLAB (Delorme, Makeig, et al.) at the Swartz Center
% for Computational Neuroscience,... |
a91ff20d18e5a4bd63f4caa35bbff9653c6a71700f0aeb2f8fc64aaa0a9d7d91 | MATLAB | 120,724 | 2,017 | function [k_sort_on, k_sort_on2, k_sort_off, k_sort_off2,....
on_spec_k_1, on_spec_k_2, off_spec_k_1, off_spec_k_2,...
k_ph_corr_on1, k_ph_corr_on2, k_ph_corr_off1, k_ph_corr_off2,...
on1_replace_track, off1_replace_track, on2_replace_track, ...
off2_replace_track, zero_replace_track, k_space_locs, corr... |
959e4d4fb3fe1e0b6c5aff17257b13be82ea822aee6690f57994988b62d5643c | MATLAB | 121,041 | 3,096 | function [hdr] = ft_read_header(filename, varargin)
% FT_READ_HEADER reads header information from a variety of EEG, MEG and other time
% series data files and represents the header information in a common
% data-independent structure. The supported formats are listed below.
%
% Use as
% hdr = ft_read_header(filenam... |
63c23397f42d69ea60342282aa724b162ef744fa725d8486aa5d6cdf1ceeb94e | MATLAB | 124,330 | 2,079 | function [k_sort_on, k_sort_on2, k_sort_off, k_sort_off2,....
on_spec_k_1, on_spec_k_2, off_spec_k_1, off_spec_k_2,...
k_ph_corr_on1, k_ph_corr_on2, k_ph_corr_off1, k_ph_corr_off2,...
on1_replace_track, off1_replace_track, on2_replace_track, ...
off2_replace_track, zero_replace_track, k_space_locs, corr... |
ca23d9a8c8b9286908dcb631b61664f63b52cdf8a0d73f6547d966e6711d717f | MATLAB | 127,163 | 423 | %% 400 EXAMPLES OF ASSEMBLY CONFIGURATIONS WITH 5 ASSEMBLIES IN A HONEYCOMB STRUCTURED TECTUM
%
% THE ASSEMBLIES WERE CREATED IN HONEYCOMB STRUCTURED TECTUM OF DEGREE 5
% FROM n = 26 POINTS DRAWN FROM A 2D-NORMAL DISTRIBUTION WITH STANDARD
% DEVIATION s UNIFORMLY IN sqrt([1.0 2.5])
%
% THE SIZE OF ASSEMBLIES IN TERM OF... |
7c1f5bf867e95201842135aa0c361b6716c6a0abf8415a725a1cb227f67d6820 | MATLAB | 128,593 | 5,161 |
% Panel is an alternative to Matlab's "subplot" function.
%
% INSTALLATION. To install panel, place the file "panel.m"
% on your Matlab path.
%
% DOCUMENTATION. Scan the introductory information in the
% folder "docs". Learn to use panel by working through the
% demonstration scripts in the folder "demo". Reference
... |
bfd80e400a6825ef6f7054211f5f9f8f1ad1f5968ef9ad9e3c24d1a095dd5885 | MATLAB | 141,342 | 3,503 | function varargout = nii_viewer(fname, varargin)
% Basic tool to visualize NIfTI images.
%
% NII_VIEWER('/data/subj2/fileName.nii.gz')
% NII_VIEWER('background.nii', 'overlay.nii')
% NII_VIEWER('background.nii', {'overlay1.nii' 'overlay2.nii'})
%
% If no input is provided, the viewer will load included MNI_2mm bra... |
fd351368c189eb7ced2b95cc4eebb096cc58c6ac7518254d0814767cebe94a43 | MATLAB | 141,460 | 2,080 | function [k_sort_on, k_sort_on2, k_sort_off, k_sort_off2,....
on_spec_k_1, on_spec_k_2, off_spec_k_1, off_spec_k_2,...
k_ph_corr_on1, k_ph_corr_on2, k_ph_corr_off1, k_ph_corr_off2,...
on1_replace_track, off1_replace_track, on2_replace_track, ...
off2_replace_track, zero_replace_track, k_space_locs, corr... |
204c2060da0b5d471315c7a4c5b64f7ce8b00dbd709aae6553b3906921b1e644 | MATLAB | 142,159 | 2,940 | function [handles,levels,parentIdx,listing] = findjobj(container,varargin)
%findjobj Find java objects contained within a specified java container or Matlab GUI handle
%
% Syntax:
% [handles, levels, parentIds, listing] = findjobj(container, 'PropName',PropValue(s), ...)
%
% Input parameters:
% container - option... |
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