sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1d2acc106804d2db92b11b382348a3dbdb29465c68a87058428fa065c535b7bc | MATLAB | 10,548 | 286 | function varargout = multiwaveplot(varargin)
%MULTIWAVEPLOT Stacked line plots from a matrix or vectors
%
% Multiwaveplot draws a series of stacked lines (one on top of the other)
% contained in the rows of an input 2-D matrix. Each line has a
% designated row on the plot; the first row is plotted at the bottom ... |
e3063513bcfb6d80b57f1c2190e92bf6f3ce6eafde7ebc41ef82515eab498b93 | MATLAB | 10,557 | 306 | function [FaceVertexCData,new_cmap,new_climits,orig_data_climits] = makeFaceVertexCData_old(vertices,faces,vertex_id,data,cmap,colorFaceBoundaries,colorUnknownGrey,climits)
% This script will plot the boundaries defined by some parcellation/ROIS on
% a surface projection. It can also alter the colormap so regions that... |
2c060a1244103e26a4fd215e60314b4749b3cf8b9475d14aca5b6c9ed33bd692 | MATLAB | 10,558 | 232 | classdef (Abstract, CaseInsensitiveProperties = true) statsPlot < ...
matlab.mixin.SetGet
%STATSPLOT An abstract superclass for classes that plot statistics
%
% As an abstract class, this class cannot be instantiated. It provides no
% public methods. The class is a super class for:
% - iosr.statistic... |
0e1a30032a18467eba047a40999dc2ecb208e14d81f88fe2637193d1950f7b11 | MATLAB | 10,571 | 263 | function dat=plotstrongestdir_save(avgfluor,redtemps,ROIs,Xpix,Ypix,framerate,maxvec)
%plot the data averaged for each ROI
%show the ROI?
fn=fieldnames(avgfluor);
[numROIs,triallength]=size(avgfluor.(fn{1}));
fig=figure('Position',[1 1 509 458]);
hold on;
subone=subplot(211);
subtwo=subplot(212);
fig2=figure('Position... |
fbd87fbb71e50a2e3eafb8f69197c598400121526fb35409f4aabbeac6dd9461 | MATLAB | 10,574 | 234 | function cmap=get_colormap(nc,nl,opts)
[temp_c , temp_l] = meshgrid(1:nc,1:nl);
color_ind = temp_c(:);
lightness_ind = temp_l(:);
if ischar(opts.map)
%Brewer colormaps from http://colorbrewer2.org
switch opts.map
case 'matlab'
cmap=lines();
cmap_nc = 8;
cmap_nl = 1... |
4bef8e3833d5c86665dfec6d07314c9e8e9628b5522a3c0827716617e07a13f4 | MATLAB | 10,575 | 227 | function [I,Ihat,cvs,val_struct]=ea_explorer_crossval(viz,tractset,strategy,iterations,posthoccorrect,customconfig)
if ~exist('customconfig','var')
customconfig=[];
end
switch tractset.multitractmode
case 'Split & Color By Group'
if ismember(strategy(1:6),{'Custom','Import'})
ea_error('Mul... |
c75b8cb6b4b8a3b56a26f070e20d9505024e10498f40dd0b8b116cdafa017020 | MATLAB | 10,576 | 227 | function [I,Ihat,cvs,val_struct]=ea_disctract_crossval(viz,tractset,strategy,iterations,posthoccorrect,customconfig)
if ~exist('customconfig','var')
customconfig=[];
end
switch tractset.multitractmode
case 'Split & Color By Group'
if ismember(strategy(1:6),{'Custom','Import'})
ea_error('Mu... |
96668611fc64b181d6727e157f47e44efa5bf67cebee8f657cbe33f62d3da497 | MATLAB | 10,587 | 322 | function stackview(hr,ftr,showfun)
if nargin == 2,
showfun = @imagesc;
end;
ds.maps = computeParameterMaps(ftr,1);
ds.img = ds.maps.vf;
ds.hr = hr;
ds.ftr = ftr;
set(datacursormode,'UpdateFcn',{@(x,y) labeldtips(x,y,ds)})
datacursormode on
%f = figure('Position',[360,500,750,585]);
f = gcf;
clf;
h =... |
1e07c634720e7df68b51a53d6d18969709cf817ca9c7a6a7cdb5303532eac3d9 | MATLAB | 10,593 | 271 | % pop_biosig() - import data files into EEGLAB using BIOSIG toolbox
%
% Usage:
% >> OUTEEG = pop_biosig; % pop up window
% >> OUTEEG = pop_biosig( filename, channels, type);
%
% Inputs:
% filename - [string] file name
%
% Optional inputs:
% 'channels' - [integer array] list of channel indices
% 'blockrange'... |
aa190a3f5f22fb0e6ae2c7369c56ae7e9873b668ea6a630054762cb82f6ebc61 | MATLAB | 10,607 | 357 | function baseline = CBIG_hypoTest_4t(betas, stats)
% baseline = CBIG_hypoTest_4t(betas, stats)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
baseline = zeros(18, 3);
%% AD
fprintf('\n----------------------------- AD -----------------------------\n');
fprintf('\... |
e14a42daf0dbf9418773786f288ef20aad9a6ebc0974a358316a8fe19cf2fc19 | MATLAB | 10,609 | 338 | %% a3_state_dependent_BGA_dynamics.m
%
% Goal:
% Characterize state-dependent BGA dynamics (UP vs DOWN)
% - Timecourses (onset-locked & response-locked)
% - Pre vs Post reversal (State × Period)
%
% Figures:
% Fig 2d : aIns timecourse (onset)
% Fig 2e : aIns State × Period
% Fig S3 : response-locked ... |
7649245d02c03438c33526364ed5202db497ef26187134e1e9de1e04afa02b39 | MATLAB | 10,613 | 336 | %% ===============================================================
% 03_state_dependent_BGA_dynamics.m
%
% Goal:
% Characterize state-dependent BGA dynamics (UP vs DOWN)
% - Timecourses (onset-locked & response-locked)
% - Pre vs Post reversal (State × Period)
%
% Figures:
% Fig 2d : aIns timecourse (onset)... |
a8992eb40b3d58fdec865d95846cdc5e152dda0f13ee45e801bde29d0af78a18 | MATLAB | 10,622 | 262 | clear;
load("data_folder/Egestive_priming_data.mat");
load("data_folder/btype.mat")
% Skip experiments 5, 6, 9
% Remove channel 141 for experiment 4
ch{4, 1}(141) = [];
ch{4, 2}(141) = [];
% Data processing code
animal = 1;
sigma = 0.05;
downsample_factor = 150; % 10 ms
spike_threshold = 0; % no threshold
protractio... |
ffa3673f59201b17eb5fad32f9ec2d9006c23bd2c2882ad82075b1ffed4c8cf7 | MATLAB | 10,622 | 327 | function [] = fig2u3d(ax, fname, imgtype, addaxes, varargin)
%FIG2U3D Convert figure to U3D file.
% FIG2U3D saves the current axes as a U3D file for inclusion as an
% interactive 3-dimensional figure within a PDF. Either LaTeX or Adobe
% Acrobat can be used to embed the U3D file in the PDF.
%
% A VWS fi... |
d9ed4c689e4b443714d8ffa982647a293a079ef1e96017eafcf8fcac366d3cff | MATLAB | 10,634 | 234 | % pop_firws() - Filter data using windowed sinc FIR filter
%
% Usage:
% >> [EEG, com, b] = pop_firws(EEG); % pop-up window mode
% >> [EEG, com, b] = pop_firws(EEG, 'key1', value1, 'key2', ...
% value2, 'keyn', valuen);
%
% Inputs:
% EEG - EEGLAB EEG structure
% 'fcutoff' - v... |
635bdf072b0c7911d69f591a0ce8e0f6feee65a816d821b391e09c7682e65adb | MATLAB | 10,637 | 297 |
function cm = magma(n, opt_interp)
% Colormap: magma
%-- Parse inputs ---------------------------------------------------------%
if ~exist('n', 'var'); n = []; end
if isempty(n)
f = get(groot,'CurrentFigure');
if isempty(f)
n = size(get(groot,'DefaultFigureColormap'),1);
else
n = size(f.Colormap,... |
a8d104264b2816ce6810b7c8f636ed3cfc006809bf77ea084d28470d89cf21c8 | MATLAB | 10,641 | 319 | function IDX = LaBGAScore_dep_build_index(varargin)
%
%
% *USAGE*
%
% Builds an index of every callable file (.m, .mex*, .p) under the given
% dependency roots, mapping each callable NAME to ALL of its candidate
% definitions. LaBGAScore_dep_map resolves identifiers against this index.
%
% The index exists because whic... |
f69ad886e28e5bea9fa64076f9f052cae6d845d6816b391cf0f6ed35abe7a8d5 | MATLAB | 10,649 | 282 | function self = LoadLFP(self, ind, varargin)
% Loads LFP data file into root.b_lfp property
%
% (1) Loads root.path_lfp(root.active_lfp)
% (2) Loads all root.path_lfp(indices) to current object
%
% So far, .mat files with lfp, lfp_ts fields can be imported. .ncs
% files can be imported. other methods
% can be added
%
%... |
6f282cde61581b85ef351de96f003826bd66572825122fe0881fb884cb58b204 | MATLAB | 10,655 | 280 | % subsasgn() - define index assignment for eegdata objects
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Nov. 2008
% Copyright (C) 2008 Arnaud Delorme, SCCN, INC, UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Fr... |
a7b45e7e2a8dd59ccf64f25da0e82e407c48b2905da574885f5c4f9658155482 | MATLAB | 10,661 | 357 | function baseline = CBIG_hypoTest_4t(betas, stats)
% baseline = CBIG_hypoTest_4t(betas, stats)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
baseline = zeros(18, 3);
%% AD
fprintf('\n----------------------------- AD -----------------------------\n');
fprintf('\... |
af69fd8fc53adce27ae38508b28fa0ad8c4638585ddae4f2b34f375914183bfa | MATLAB | 10,674 | 293 | %% Step 4 Tiny Dancers: Group analyses for autocorrelation
%% Load data
clear
clc
cd('D:\TinyDancers_Movement\fieldtrip_velo\AE_PROC\SD5\Step3_autocor\3m\');
respdata_mus=[];
respdata_freq=[];
FileNames = {dir(['*' '.mat']).name} ;
for k = 1:1:length(FileNames)
load(FileNames{k})
avg_baseline_3m{k... |
c7b9fbf9a0cea64f5c7bb2009391bd95b5bd07ac4353547f32039412c0a788b7 | MATLAB | 10,676 | 320 | % Find boundary of a cell layer in an image.
%
% This follows some of the recommendations by Treloar & Simpson, Plos One
% e67389, 2013
%
% The script first turns the image into a binary by finding locations in
% the image having gradients larger than a threshold value. Those locations
% are then dilated. Various oper... |
dc26077694c3ba78c26e7fe1c98754120e7e1406ee8e9723032fe50a10354b2d | MATLAB | 10,684 | 340 | function [ixes]=ea_centrality_significance(XYZV)
% clear NAN vars:
XYZV(isnan(XYZV(:,4)),:)=[];
% setup randomization:
ea_dispercent(0,'Permutation based statistics on strength centrality');
maxiter=5001;
csize=zeros(maxiter,size(XYZV,1));
for iter=1:maxiter
dat=XYZV;
if iter>1
dat(:,4)=dat(randpe... |
df688749e24078f109d21199ac4b5297ef69a5433f017152a9bb03f53efe5667 | MATLAB | 10,691 | 242 | % pop_rejchanspec() - reject artifacts channels in an EEG dataset using
% channel spectrum. The average spectrum for all selected
% is computed and a threshold is applied.
%
% Usage:
% >> pop_rejchanspec( INEEG ) % pop-up interative window mode
% >> [OUTEEG, indelec] = pop_rejchan... |
229901b6cad03975082b14828a148c6a5bfcf984e18b85ebf91952a0cf1279a5 | MATLAB | 10,715 | 179 | % pop_specparams() - Set plotting and statistics parameters for computing
% STUDY component spectra.
% Usage:
% >> STUDY = pop_specparams(STUDY, 'key', 'val');
%
% Inputs:
% STUDY - EEGLAB STUDY set
%
% Plot options:
% 'topofreq' - [real] Plot Spectrum scalp maps at one spec... |
7bd3aced4934d4b0a2b060968d51c88434245d674e597e526eb0be8e26b1fd8f | MATLAB | 10,732 | 248 | close all
% addpath ~/Documents/MATLAB/xml_io_tools/ (may need to add path to files)
my2Pscr1('TSeries-06132019-1507-4883/','do_load',{[1:1700],[1:2],[1]},'do_motc',[4 100 1 1 0],'do_motcref',[1 1],'do_keepraw');
%my2Pscr1('TSeries-05302019-1228-4772/','do_loadall','do_motc',[4 100 1 1 0],'do_motcref',[1 1],'do_keepr... |
d3cc26a10f76d54e78d12a1cc3dffafa0a6e482110fae8478e7045aa7744fe18 | MATLAB | 10,737 | 413 | function saveNSx(NSx,varargin)
%%
% Save an .NSx file from an NSx structure (gained by using openNSx)
% Works with file spec 2.3 and 3.0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Use: saveNSx(NSx,optionalinputarguments)
% NSx: The NSx data structure.
% All arguments belo... |
4d40ac7666cf4ecb7d850ba2998c654b18e607cad8a73a0aac2fff4332363f48 | MATLAB | 10,740 | 300 | function shim = cvx_sedumi( shim )
% CVX_SOLVER_SHIM SeDuMi interface for CVX.
% This procedure returns a 'shim': a structure containing the necessary
% information CVX needs to use this solver in its modeling framework.
global cvx___
if ~isempty( shim.solve ),
return
end
if isempty( shim.name ),
fname = ... |
46ecdd790da6a30a30f57ba4a303efe20cf526f6da102d2913072c3c9bbafe79 | MATLAB | 10,748 | 439 | % Main script with ODEs and solvers for dynamic perimeter model
% Adapted from Troost et al., 2023
function [yout,tout,params] = SOP_multicell_LI_adapted_DYNAMIC_perimeter_HillsNoRecovery(model,params,y0)
%% prepare
pp = genpath('functions');
addpath(pp)
% load defaults if absent
if(nargin < 2)
switch model.rat... |
5a97d9d4a885492d402e51aaf4cb8c61006ee58a36479eefc9a16d8e4f5745f9 | MATLAB | 10,759 | 361 | % The basic application of the 'reslice_nii.m' program is to perform
% any 3D affine transform defined by a NIfTI format image.
%
% In addition, the 'reslice_nii.m' program can also be applied to
% generate an isotropic image from either a NIfTI format image or
% an ANALYZE format image.
%
% The resliced NIfTI fi... |
71745730f29fbb65db30a65a83dd012de64e4e77baa51e810a1f342131ad7a3d | MATLAB | 10,775 | 273 | function [hObject, handles] = dan_plot_hypno(hObject, handles)
%%
% Authors: Dan Denis
% Date: 2021-07-14
%%
% How many stage files are loaded
f = fieldnames(handles.psg.stages);
f(cellfun(@isempty, regexp(f, 's\d', 'match'))) = [];
hypnoX = 1:1:length(handles.psg.stages.s1.stages);
%% Add lights out and light... |
ffa491b75898bece2fe99a2e76e12a843c21f1afa085baff8ea9ca18d876d60d | MATLAB | 10,777 | 372 | roimask_imagename = 'v4-topics-100_25_inhibition_response_control_pFgA_z_FDR_0.01.nii';
if ~exist(which(roimask_imagename), 'file')
try
roimask = gunzip([roimask_imagename '.gz']);
roimask_imagename = roimask{1};
catch
end
end
% this map is similar but with fewer unique regions:
%roimask_imagename... |
b1a47f78b30b66647a9ee86f7b0ff7431c54ec274e3fe0f68b8311d940678a8d | MATLAB | 10,784 | 254 | %% LaBGAScore_firstlevel_s3b_phMRI_signature_responses.m
%
%
% *USAGE*
%
% This scripts calculates signature response on every first-level condition
% (one per timebin per condition) and writes a summary table in long format
% for mixed model analysis in a statistical program of your choice.
%
% It also contains an op... |
ba2db574ce12a4cd629f75f982d9d36d64408e31ae7a3c666ebaad2efe55ffb2 | MATLAB | 10,806 | 130 | %-----------------------------------------------------------------------
% Job configuration created by cfg_util (rev $Rev: 313 $)
%-----------------------------------------------------------------------
matlabbatch{1}.menu_cfg{1}.menu_entry{1}.conf_files.type = 'cfg_files';
matlabbatch{1}.menu_cfg{1}.menu_entry{1}.con... |
0e48d8d51f6053fbe26f65869df36568b18237463bc7c0de7e62a99ee069b033 | MATLAB | 10,810 | 253 | %% NiftiyMod - Base class for all Nifti Objects. Wrapping the nifti Toolbox,
% rewritten no frills version of the more powerful NiftiModality Class
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicne
% 2016 - 2018
% mail@and... |
e931bf381ddb260d7a5120deed96d00122854967a5bc4c7a0993a9a89bc969bc | MATLAB | 10,812 | 309 | function [phasedistros,phasebins,phasestats,h] = PhaseModulation(spikes,lfp,passband,intervals,lfpfreq,method,plotting)
% USAGE
%[phasedistros,phasebins,phasestats,h] = bz_PhaseModulation(spikes,lfp,passband,intervals,lfpfreq,method,plotting)
%
%
% INPUTS
% spikes - spike train, in seconds, a population or a si... |
ffdb6424bec7e1445f21018b77ca80930698ea109b7405ed67f153617cf33e59 | MATLAB | 10,820 | 290 | % NOTE: the use of this script is being deprecated, as the option to run
% robust parcelwise second-level regression on conditions is now built into
% prep_3a_run_second_level_regression_and_save.m; please use that script
% instead of this one
% @lukasvo76, May 2022
% THIS SCRIPT RUNS BETWEEN-PERSON (2nd-level) Robust... |
af8f099affeca62197241a4b00630dd9dbea4f260d81da9e28b758cea597c913 | MATLAB | 10,823 | 316 | function CBIG_MMLDA_add_text_to_forest_plot(forest_plot, file_pvalue, out_dir, p_thresh, k, compare_factor_names)
% This function takes in the raw forest plot and p values, and add text to
% the forest plot, such as 'F2 - F1', 'Latter is worse'.
% The final figure will be saved in the same directory as out_dir, with a... |
500638d92b6daa3aed749d46d49215ea0f1da7c961971e9dcbc94dbcbf1a91a5 | MATLAB | 10,833 | 361 | function [subj_prob, avg_prob, roi_info] = compute_subject_ROI( ...
p, roi_def, varargin)
%FNIRSPOWER.MEASPRED.COMPUTE_SUBJECT_ROI
% Generate subject-specific spherical ROI maps on a brain mesh.
%
% For each subject and ROI:
% 1) Translate the nominal ROI center independently along x, y, and z.
% 2) Limi... |
eb352c2a0dc379f3b6e1aac61c3a6d34d8253e42ba51030d23ff5439a5acaad4 | MATLAB | 10,839 | 288 | % function run_reg_fourier_TFM
%RUN_REGULAR_FOURIER_TFM.M
%
% Compute tractions from substrate displacements.
%
% This script calls reg_fourier_TFM.m written by Yunfei Huang and Benedikt
% Sabass, and published as Sci. Rep., 2019, vol. 9, pp. 1?16.
% https://www.nature.com/articles/s41598-018-36896-x
% Optional: I... |
72b1b6e78a3b4dc2078865ec891b1bd86be77eaa3d00efe5bb393ac8fbf0355b | MATLAB | 10,856 | 333 | function AUC = quickCV_ENet(X,Y,C,opts)
% quickCV_ENet Leakage-free quick CV AUC estimate for Elastic Net.
%
% This helper function provides a *quick* (non-nested) cross-validated AUC
% estimate for Elastic Net models, intended specifically for high-repeat
% diagnostics inside:
% - permutation testing
% - bootstr... |
80212935588ef55546654d1cd7fcdfcb310981423ceb556d06f63a1347c96870 | MATLAB | 10,879 | 197 | % EEGLAB cross-platform compiling script
% should be run on a newly checked out EEGLAB version as
% some folder are temporarily modified
%
% Arnaud Delorme - August 3rd, 2009
% Copyright (C) 2009 Arnaud Delorme
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU Ge... |
943fc978102a18c92f3bc3c1463f1726599c0616dcd30771eac44c591b2b1015 | MATLAB | 10,887 | 262 | function [cpAll, cpMean] = fun_so_spindle_coupling(soData, ssData, chans, srate, soEvents, ssEvents, varargin)
% Slow oscillation-spindle coupling. Automatically detects coupling
% events on multi-channel data and returns index of coupled and uncoupled
% spindles as well as coupling parameters. Requires the circStats t... |
94eb4e366bb35e73230a4055b814ff436f09e0e800f580a5e4418fc2857cfbdd | MATLAB | 10,898 | 255 | %% Multi-level kernel density (MKDA) meta-analysis example: Agency database
% The starting point for coordinate-based meta-analysis (CBMA) is a text file
% with the information entered from published studies. In this example, the
% information is contained in the file "Agency_meta_analysis_database.txt"
% It is in th... |
8ab9ac006cb7d12dae94aed9b5a815cd647b07c194f9b543a8dbf5de6b2d39c3 | MATLAB | 10,905 | 396 | %% figure 5
load('figure5_data')
%%
an_col = [30 58 205]/255;
aw_col = [229 32 21]/255;
awake_color1_5 = [0.8272 0.3489 0.2865];
anes_color1_5 = [0.1792 0.4769 0.7191];
%% Figure 5B
% Define parameters
norm_lim = [2.5*10^-3 3.17*10^-3];
null_coloar = [0.5 0.5 0.5];
% Set de... |
4a8e2e4b642f1d6d01b8beae386ff4719ed1dbb9530c00745e8738e3f456ab48 | MATLAB | 10,907 | 332 |
function [maskBlobs,labels,maskBlobsVis] = segmentBlobs_locmax(image,...
thresholdMethod,methodValue,filterNoise,filterBackground,minSize,locMax,plotRes,mask)
%segmentBlobs_locmax segments blobs in 2Detection_IdxD images via various
%thresholding methods and use local maxima to catch the dim objects
%
%SYNOPSIS ... |
258a3bb94923c6ed344827b798bfb36be0096e3791ca415f48d22847c7f7528a | MATLAB | 10,916 | 326 | function varargout=ea_plot3t(varargin)
% PLOT3T Plots a (cylindrical) 3D line with a certain thickness.
%
% h = plot3t(x,y,z,r,'color',n);
%
% PLOT3T(x,y,z), where x, y and z are three vectors of the same length,
% plots a line in 3-space through the points whose coordinates are the
% elements of x, y and z. Wi... |
78bc208700f85b5f286e4732e05e608c288e45fb038b7805888b3a700273e7f2 | MATLAB | 10,919 | 243 | % pop_eegthresh() - reject artifacts by detecting outlier values. This has
% long been a standard method for selecting data to reject.
% Applied either for electrode data or component activations.
% Usage:
% >> pop_eegthresh( INEEG, typerej); % pop-up interactive window
% >> [E... |
9e1600330a73a2e8b6c44c8547000a9551c682b5a5644dd5757a7571431e811d | MATLAB | 10,924 | 334 | function AUC = quickCV_ENet_PR(X,Y,C,opts)
% quickCV_ENet_PR Leakage-free quick CV precision-recall AUC estimate for Elastic Net.
%
% This helper function provides a *quick* (non-nested) cross-validated AUC
% estimate for Elastic Net models, intended specifically for high-repeat
% diagnostics inside:
% - permutatio... |
6b885e447eb1cc6a5a17293f957e0dedd043641009e49fa1bb11d01ec4478f86 | MATLAB | 10,925 | 344 | classdef Divider < matlab.mixin.SetGet
%uix.Divider Draggable divider
%
% d = uix.Divider() creates a divider.
%
% d = uix.Divider(p1,v1,p2,v2,...) creates a divider and sets
% specified property p1 to value v1, etc.
% Copyright 2009-2016 The MathWorks, Inc.
% $Revision: 1436 ... |
1060a353f9abfff178eeae19b404648e1b6ea170d1966cd8a6962ce80f99d004 | MATLAB | 10,957 | 285 | % configure file for reading DWI data (Dicom, Bruker or other formats)
% DTI Configuration file
% BATCH system (Volkmar Glauche)
%
% File created by Susanne Schnell
function read_data = dti_cfg_read
% ---------------------------------------------------------------------
% dicom Input dicom file names
% --------------... |
6d81cd97e05b5f3035ef335deb94979f2a86b6857c4550a81a13b6fbd1e5bd49 | MATLAB | 10,964 | 319 | function [F,time,ID,U,taxa_data,time_data,ID_data,U_data,F_prime,X,magnitude]=...
import_data_and_construct_matrices(densities,total_biomass,perturbations,time,o_rescale_to_one,...
o_differentiation,specific_density,sample_indeces_to_remove);
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dy... |
7afb566d44da22304c878732e79f8010ce017ff088112b1d1f90cb43eaa3ec52 | MATLAB | 10,977 | 307 | % loadavg() - loading eeg average data file from Neuroscan into
% matlab.
% Usage:
% >> [signal, variance, chan_names, ...
% pnts, rate, xmin, xmax] = loadavg( filename, version );
% Input:
% filename - input Neuroscan .avg file
% version - [1 or 2] function version. Default... |
a791294a817051760e5b788118443d6c3b98a9f59c2d2a2db25ef117346388cb | MATLAB | 10,978 | 294 | function bz_fitPoissPlasticity(basepath, preID,postID,varargin)
% This function takes a pair of neurons and fits a Poisson GLM to account
% for long term monosynaptic coupling. This framework exploits a bin-by-bin baseline
% offset that reflects the postsynaptic spiking binned at a timescale
% slower than the fine time... |
988f6eb20777e16802926093192caedd89295d269c4b9d141ce2df6da9acd737 | MATLAB | 10,993 | 266 | function [A, bcol] = print2array(fig, res, renderer, gs_options)
%PRINT2ARRAY Exports a figure to an image array
%
% Examples:
% A = print2array
% A = print2array(figure_handle)
% A = print2array(figure_handle, resolution)
% A = print2array(figure_handle, resolution, renderer)
% A = print2array(figur... |
3c09f020508b9b30c875debb8e02ca3556c5cc3b3d1813de306b25313eb8a878 | MATLAB | 10,994 | 285 | % eegmovie() - Compile and view a Matlab movie.
% Uses scripts eegplotold() and topoplot().
% Use seemovie() to display the movie.
% Usage:
% >> [Movie,Colormap] = eegmovie(data,srate,elec_locs, 'key', val, ...);
%
% Or legacy call
% >> [Movie,Colormap] = eegmovie(data,srate,elec_locs,title,m... |
40a9950b43c79b5e8213b0c5f41c8e782eabfc3de7b01f3095de745eefba0f83 | MATLAB | 10,994 | 226 | classdef log_code_object < handle
% This helper object saves the code of files that have been run. It is useful for saving information about
% the exact code that was run so that one has a record of how particular results were generated. This object
% gives several different methods for saving code in different fil... |
c1fb6a6b235ef62310f4692eddcc83e8c0801f08904891dedabb089f790ab553 | MATLAB | 10,994 | 272 | function [input,pls_opts,save_opts] = myPLS_initialize(input,pls_opts,save_opts)
% This function sets up the defaults and checks the validity of inputs for myPLS_analysis
disp('... Initialization ...')
%% 1. Inputs
% Compatibility with X0 and Y0 inputs
if ~isfield(input,'brain_data') && isfield(input,'X0')
inp... |
fef6df7ef6ba83ef36de5eeb1dd6224cdc434be94167b1dc914bced7786abecd | MATLAB | 10,994 | 309 |
%% Thresholds are calulcated as 2SD above baseline
%% Extracting and Ploting sound evoked DF/F Data across time and individual neuron (MK)
% Requires NormCorrFissa extracted data (_tifFIleData.mat), cellOrder and Soundfile
% header in the workspace to work
% DF/F using mean F from 1 sec before each sound stimulai... |
3429f279aa1a0bc190155717c9003fed6e67e647cfe078897592490d06504967 | MATLAB | 11,010 | 287 | function CFA_RunAllJob2(SetUpPara,Template,Para)
Indir = SetUpPara.Indir;
Outdir = SetUpPara.Outdir;
filp = which('CFA_RunAllJob.m');
[pth,nam,ext] = fileparts(filp);
spmjobdir = [pth,filesep,'NormJobmat',filesep];
Atlasdir = [pth,filesep,'TemplateUsed',filesep];
voxelsize = SetUpPara.OutVsize;
BrainMaskdir = [pth,file... |
97f99a0bdf867f9cd0fcb5c24b6c4a78a4b0a5f145498c9689937c5d6abb5845 | MATLAB | 11,020 | 254 | % std_erpimage() - Compute ERP images and save them on disk.
%
% Usage:
% >> std_erpimage( EEG, 'key', 'val', ...);
%
% Inputs:
% EEG - a loaded epoched EEG dataset structure. May be an array
% of such structure containing several datasets.
%
% Optional inputs:
% 'components' - [numeric ... |
120ef8207fa9f1dea7950a36ce79fb95d2902afdcd1c197cfcad3c797c84dfe3 | MATLAB | 11,025 | 309 | function varargout = ea_sweetspotcontrol_hemi(varargin)
% EA_SWEETSPOTCONTROL_HEMI MATLAB code for ea_sweetspotcontrol_hemi.fig
% EA_SWEETSPOTCONTROL_HEMI, by itself, creates a new EA_SWEETSPOTCONTROL_HEMI or raises the existing
% singleton*.
%
% H = EA_SWEETSPOTCONTROL_HEMI returns the handle to a new E... |
ff61f0b3e1c5fabaf09f119c9ab6fefd1b84f3b231d3af29f5f95b495598c6cc | MATLAB | 11,031 | 362 | function cs_fmri_conseed_pmap(dfold,cname,sfile,cmd,writeoutsinglefiles,outputfolder,outputmask)
tic
% if ~isdeployed
% addpath(genpath('/autofs/cluster/nimlab/connectomes/software/lead_dbs'));
% addpath('/autofs/cluster/nimlab/connectomes/software/spm12');
% end
if ~exist('writeoutsinglefiles','var')
wr... |
8b3c5eff524e14954634533b90e005d484f22185a548938b467be0a477e056ee | MATLAB | 11,033 | 278 | %% ============================================================
% WT-only wrapper based on your original PrL SB code
%
% Purpose
% Run ONLY the WT mice with:
% - random 60% neuron selection
% - 50 repeats
%
% Output
% 1) PrL_SB_WTonly_struct_results_downsample60_repeat50.mat
% 2) PrL_SB_WTonly_detaile... |
055d103136ae6aea8acce1a0f8c4bb3d86a8076d8f8aef7d12ca24c56ed4032c | MATLAB | 11,035 | 371 | function y=processBiopacStruc(x,fs,fco,t0avg,dtt,po2cal,po2tr,refvar,skp)
% Usage ... y=processBiopacStruc(x,fs,fco,t0avg,dtt,po2cal,po2tr,refvar,skp)
%
% x- parseBiopac variable
% fs- sampling rate in Hz, fco- cutoff frequency in Hz, t0avg in time
% note: a second entry in fs will be the interpolated desired sa... |
2a695fd82496fdd2baec70f42d65c103121470af2d1948a9983e2e3389d67090 | MATLAB | 11,039 | 286 | function [varargout]=lye_r(X,Fs,tau,dim,varargin)
% [out]=lye_r(X,Fs,tau,dim)
% inputs - X, If this is a single dimentional array the code will use tau
% and dim to perform a phase space reconstruction. If this is
% a multidimentional array the phase space reconstruction will
% n... |
87ce38e2a10e4d9ac210c7ff196cd927e4a990fe607630716507d9c7b3c4164a | MATLAB | 11,064 | 307 | function DBExportGallery(name,query,varargin)
%DBExportGallery - Create figure gallery from current database.
%
% Select figures and create an HTML gallery (although not required, installing
% <a href="http://sites.google.com/site/oliverwoodford/software/export_fig">export_fig</a> will yield better PNG images).
%
% U... |
250b2baffd411885af3aed076f5e1f5ca8a2327482a0922d7f9a8e8733d8c630 | MATLAB | 11,069 | 237 | % Script to define all Inputs for PLS for Medical Image Processing Toolbox
%
% Parameters to be defined in this script are:
%
% - input : struct containing input data for the analysis
% - .X : N x M matrix, N is #subjects, M is #imaging variables
% - .Y : N x B matrix, B is #behav... |
4012658a145a9dc6f1d1293390e020b7c7dfc7004df8d17d079aa31ca1abf1c6 | MATLAB | 11,073 | 330 | function [] = run_model_fitting(SANDIinput)
% Main script to fit the SANDI model using Random
% Forest (RF) and/or multi-layers perceptron (MLP)
%
% Author:
% Dr. Marco Palombo
% Cardiff University Brain Research Imaging Centre (CUBRIC)
% Cardiff University, UK
% 8th December 2021
% Email: palombom@cardiff.ac.uk
mask... |
2dcf6e3f64a045ef6147529992c3f899bc3a906f00c2c3b4eca6db486553bf94 | MATLAB | 11,090 | 322 | function [h,stats] = CompareDistributions(group1,group2,varargin)
%CompareDistributions - Compare two N-dimensional distributions (e.g. prospective place fields).
%
% This non-parametric test determines in which dimensions two distributions are
% significantly different. For example, the two distributions could be
%... |
efcdeb8210883cc02787d9ff719d7cd61fe06efddb99ef308de0359ebf0b6e3d | MATLAB | 11,102 | 276 | %% Datasets used in CANlab tutorials
%
% Note: this report was generated from |canlab_help_2c_loading_datasets.m|
% in the repository <https://github.com/canlab/CANlab_help_examples>
%
%% The Neuroimaging_pattern_masks Github repository and website
%
% For these walkthroughs, we'll load several image datasets.
% Some ... |
24c85ef7fdc5e1ce6796c87cc0bade7ce2824a59e6f5bfd3b2aa80a7eb9186cd | MATLAB | 11,112 | 337 | function filteredTracks = filterDuplicateTracks(aggregatedTracks, options)
% FILTERDUPLICATETRACKS Detect and remove duplicate cell tracks from a
% compiled tracking table produced by compileResultsFromCSV.
%
% Two tracks are considered duplicates if, over their shared timepoints,
% their XY distance stays within XYTol... |
5b21315e8a55c0b53d6fe4e261d1476c9e6ff1b06a06cb4c97c6755874a22e81 | MATLAB | 11,131 | 333 | function stats = FieldPSP(stims,lfp,varargin)
%FieldPSP - Measure field EPSPs (waveforms, slope, amplitude) across time.
%
% Slope is determined as the maximum slope during the time window around stimulation.
% Amplitude is determined as the maximum amplitude during the same time window.
%
% USAGE
%
% stats = Fi... |
7b84b25cd904e8056674f15bbaf13190c853a7909f4621a76168174551817e4a | MATLAB | 11,138 | 233 | %% LaBGAScore_secondlevel_ooFmriDataObjML_example.m
%
%
% *USAGE*
%
% This is merely an example script to illustrate the object-oriented ML
% toolkit for fmri_data objects (and beyond), developed by Bogdan Petre
% @CANlab.
%
% This is a toolkit inspired by Python's scikit-learn, including more
% flexible options for al... |
5405b1f008c57f8737b23ac3e4d10e49abc48062340a50901bf6b12c896e46ea | MATLAB | 11,141 | 261 | %% LaBGAScore_firstlevel_s3c_phMRI_neurotransmitter_maps.m
%
%
% *USAGE*
%
% This scripts calculates cosine similarity with selected PET neurotransmitter maps
% (Hansen et al, Nature Neuroscience 2022) on every first-level beta
% (one per timebin per condition) and writes a summary table in long format
% for mixed mod... |
958840cfe96918d353ccfc77b8b179f86c862c3de86a5bb17de85036244d5a3c | MATLAB | 11,144 | 287 | function ConvertKlusta2Neurosuite(shank,basepath,basename,numCores)
% Converts .kwik/kwx files from Klusta into klusters-compatible
% fet,res,clu,spk files. Works on a single shank of a recording, assumes a
% 16bit .dat and an .xml file is present in "basepath" (home folder) and
% that they are named basename.dat... |
9cbd880219e5b322ee08d4b6a5827ea89fddfcae1aaa4b28bf7450dd0b6c2d86 | MATLAB | 11,158 | 229 | function tests = testSurrTheiler
%TESTSURRTHEILER Contract tests for Surr_Theiler.
%
% Each surrogate algorithm exists to hold one property of the data FIXED
% while destroying everything else. The test is therefore not "does it run"
% but "did the property it promised survive". The promises differ per
% algori... |
4c4d57985945d389f62ce787e83d7b3b4f7420da26f3c8dfe96a78c28bcc1f62 | MATLAB | 11,162 | 324 | function [ripples,sd,bad] = FindRipples(filtered,varargin)
%FindRipples - Find hippocampal ripples (100~200Hz oscillations).
%
% USAGE
%
% [ripples,stdev,noise] = FindRipples(filtered,<options>)
%
% Ripples are detected using the normalized squared signal (NSS) by
% thresholding the baseline, merging neighbo... |
ff6b356c70683ebe882fe3b8fec29777f003134d93be6a9123864ec466e6501a | MATLAB | 11,163 | 264 | % pop_biosig() - import data files into EEGLAB using BIOSIG toolbox
%
% Usage:
% >> OUTEEG = pop_biosig; % pop up window
% >> OUTEEG = pop_biosig( filename, channels, type);
%
% Inputs:
% filename - [string] file name
%
% Optional inputs:
% 'channels' - [integer array] list of channel indices
% 'blockrange'... |
07c28cbda163c1e5c25b014da4915f366fe5aa1235fe093e44f196d1cc5d59f5 | MATLAB | 11,169 | 244 | function ea_warp_parcellation(reference,options)
directory=[options.root,options.patientname,filesep];
% Regenerate the template or not
if isfield(options, 'overwriteapproved') && options.overwriteapproved
overwrite = 1;
else
overwrite = 0;
end
% BIDS FIX: Check if normalization has been run - if not, run SPM... |
83f66dafbaef230913c7ad74b02143e9bfc565ffa3bc4fff5fa13c9feb391b41 | MATLAB | 11,173 | 310 | function [ specvarcorr,specbyvar ] = bz_LFPSpecToExternalVar( LFP,extvar,varargin )
%[ specvarcorr,specbyvar] = bz_LFPSpecToExternalVar(LFP,extvar,<options>)
%calculates the relationship of the LFP spectrum to an external
%(e.g. behavioral) variable.
%Note: spectrogram are in units of dB (log(abs(spec)))
%
%INPUT
% ... |
31ab5445548f95f6b69cca0dcdf2228880c812051061bb91b12532a9a260c091 | MATLAB | 11,193 | 366 | function CFA_Checkandrun(H)
% function CFA_Checkandrun
pathss = which('CFA_Checkandrun.m');
[pth nam ext] = fileparts(pathss);
IOsetupdir = [pth,filesep,'IOparameter',filesep];
iosetup = dir('SetUpPara.mat');
if isempty(iosetup)
iosetup = dir([IOsetupdir,'SetUpPara.mat']);
if isempty(iosetup)
[fil pg] =... |
959009356aebe5a2ea983a77d8403e2a8091d1a6f82717e677362303520f7902 | MATLAB | 11,194 | 234 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
fd4ddf4d95fe170b4886c24026d87cc788fe6dd9de486193172822327be722ad | MATLAB | 11,195 | 206 | function cifti_write(cifti, filename, varargin)
%function cifti_write(cifti, filename, option pairs...)
% Write a cifti file.
%
% Specifying "..., 'keepmetadata', true" leaves the file-level metadata as-is:
% if false or not specified, the 'Provenance' metadata value is moved to
% 'Paren... |
17e72a5d570fbbb420e224e87dcb235a6421fcf83d139e74e0180cd916ca5554 | MATLAB | 11,198 | 256 | % std_stat() - compute statistics for ERP/spectral traces or ERSP/ITC images
% of a component or channel cluster in a STUDY.
% Usage:
% >> [pcond, pgroup, pinter, statscond, statsgroup, statsinter] = std_stat( data, 'key', 'val', ...)
% Inputs:
% data - [cell array] mean data for each subject g... |
94659d338926c719570ba00314a1d56cc4b1e469312b4aea47f046cecfc0ceeb | MATLAB | 11,211 | 287 | %Adapted from power_over_time
%goal: to see visualize the relationship between power and running speed
%across animals and groups
%to do - add steps to loop through windows to get LFP data and adjust
%channel-layer assignments for drift
%make sure speed value accounts for each animal's baseline
%add somethin... |
de0f42e430bddf4b620cfab3a34dce92c88e0254dfc9c1614fe86f1437d3870c | MATLAB | 11,240 | 253 | function [Cmn,Phimn,Smn,Smm,f,ConfC,PhiStd,Cerr] = coherencyc_unequal_length_trials( data, movingwin, params, sMarkers )
% This routine computes the average multi-taper coherence for a given set of unequal length segments. It is
% based on modifications to the Chronux routines. The segments are continuously structured... |
0199e8b269c98dee06f0559776f6f755480b708d7a65b5e1819179b46d7eda8c | MATLAB | 11,246 | 239 | function vw = videoWriter(url, varargin)
% videoWriter class constructor
% Creates a object that writes video files. We use a plugin
% architecture in the backend to do the actual writing. For example,
% on Windows, DirectShow will typically be used and on Linux, the
% ffmpeg library is often used.
%
% v... |
d049ba284154665c472bde923697209226528bbd6baba9a28c9e860994ee5468 | MATLAB | 11,264 | 263 | function harmonic_oscillatory_shear(strain_amp, nsteps, interval, seed, Npts, P0_value, KA_value, dt, ...
L_thresh, v0_value, Dr_value, omega, B, stress_only)
% HARMONIC_OSCILLATORY_SHEAR Run an Active Vertex Model (AVM) simulation
% of a confluent epithelial tissue with cell-cell viscous adhesion, under
% Lees-Ed... |
ec543eede11259788c8f6c1f8d3d0a34341b8817561728d4633db35323f73887 | MATLAB | 11,268 | 317 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
if ~contains(path, '/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
addpath(genpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab'));
end
%% ======================= step 1 ... |
944a2755e3c26f3608dedef94adc3e02846f1a9b83eb9f767e88ed5c8ebae4d0 | MATLAB | 11,271 | 215 | function [decompTrack] = decompoundCompTracks(compTrack)
%DECOMPOUNDCOMPTRACKS decompound (separate) all interacting segments of comptracks into separate tracks (ignore merge-split/MS)
%
%SYNOPSIS: [decompTrack] = decompoundCompTracks(compTrack)
%
%INPUT : compTrack : compound tracks structure (in alternative forma... |
8762e656a948aac0567e02f9af8080897ec74c922795964d244927a00a474a40 | MATLAB | 11,278 | 253 | %% DATA REQUIREMENTS
%
% To get started on applying topic models to your own corpus of text, there
% are various Matlab variables that need to be constructed. The exact format
% depends on which type of topic model you want to run. Below is a list of
% specification for the input that needs to be provided to each ... |
4c0c91a31049708d4ea7ebed4a45c11d16d47caa21db8b3751beeb17955bf996 | MATLAB | 11,280 | 315 | function out = catStruct(dim,structName,separator,string)
%CATSTRUCT catenates values from multilevel structures
%
% SYNOPSIS out = catStruct(dim,structName)
%
% INPUT dim : dimension along which you want the struct to be catenated
% structName : (string) full tree of the structure down to the fi... |
8332087b926e38c6a1f4b3b391cd018b45b49c61fa69c7d0567c06d3ef088f15 | MATLAB | 11,290 | 314 | function [ S, itypes ] = cvx_create_structure( varargin )
%CVX_CREATE_STRUCTURE Construct a basis for a structured matrix.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Parse the arguments, if needed %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
S = [];
itypes = {};
if iscell( varargin{1} ),
orig = varargin{1};
name = varargi... |
ccf72f1b83797695099b89c3a2c40d6722a810d538eedb503711137e38a95045 | MATLAB | 11,296 | 265 | % std_createclust() - dreate a new empty cluster. After creation, components
% may be (re)assigned to it using std_movecomp().
% Usage:
% >> [STUDY] = std_createclust(STUDY, ALLEEG, 'key', val);
% Inputs:
% STUDY - STUDY set comprising some or all of the EEG datasets in A... |
70cc748c581ec8af0b55787bb4ee68ebab65c65d12af9f29be5a30adb64233a6 | MATLAB | 11,307 | 315 | function p = pass_index_parser(varargin)
% PASS_INDEX_PARSER - Parses pass-index related inputs
%
% Parses pass index related inputs for pass_index and function that
% pass_index uses
%
% P = PASS_INDEX_PARSER(POS_TS,POS,SPK_TS)
% P = PASS_INDEX_PARSER(POS_TS,POS,SPK_TS,LFP_TS,LFP_SIG)
% P = PASS_INDEX_PARSER(POS_TS,P... |
9c549c0774b325388b0aac0ca45ceee7126e43348716225ffffeb4c86bdfa1cd | MATLAB | 11,315 | 319 | function varargout = InputMapping(varargin)
% Edit the above text to modify the response to help InputMapping
% Last Modified by GUIDE v2.5 13-Sep-2023 17:00:21
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singl... |
b195a3806ab88e8594818b0374ecec66f752d24a1d49dd27d3e6ce8a51d100c7 | MATLAB | 11,319 | 465 | function [C,T]=hungarian(A)
%HUNGARIAN Solve the Assignment problem using the Hungarian method.
%
%[C,T]=hungarian(A)
%A - a square cost matrix.
%C - the optimal assignment.
%T - the cost of the optimal assignment.
%s.t. T = trace(A(C,:)) is minimized over all possible assignments.
% Adapted from the FORTRAN IV code i... |
2dc92644f4bdeb20567c61ecffe0f4ca94628c960631688977e83aa74423d8c3 | MATLAB | 11,329 | 279 | % condstat() - accumulate surrogate data for comparing two data conditions
%
% Usage:
% >> [diffres, accres, res1, res2] = condstat(formula, naccu, alpha, ...
% bootside, condboot, arg1, arg2 ...);
%
% Inputs:
% formula - [string or cell array of strings] formula(s)... |
d9d17d5d8f58b1247bd60b478f866fc08e95f776ce43f414579d191babd74bcd | MATLAB | 11,330 | 366 | function sleepStats = fun_sleep_statistics(sleepstages, varargin)
% Calculate sleep statistics. Automatically generate sleep
% macroarchitecture information including time in bed, total sleep time,
% sleep onset latency etc, as well as time and % spent in each sleep stage.
%
% Required inputs:
%
% sleepstages: Either a... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.