sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9cc7d29f06d2fa93fdb66c348413766a9627ff0bc12ddbba73d8f20b6d9525ec | MATLAB | 16,744 | 428 | function [data, powindx, hasrpt] = univariate2bivariate(data, inparam, outparam, dtype, varargin)
% UNIVARIATE2BIVARIATE is a helper function for FT_CONNECTIVITYANALYSIS
%
% Use as
% [data, powindx, hasrpt] = univariate2bivariate(data, inparam, outparam, dtype, ...)
% where
% data = FieldTrip structure acco... |
797daabb2db6287276da6cd265ce938e2b0c70d32364535249659c180ad6a495 | MATLAB | 16,747 | 428 | function [data, powindx, hasrpt] = univariate2bivariate(data, inparam, outparam, dtype, varargin)
% UNIVARIATE2BIVARIATE is a helper function for FT_CONNECTIVITYANALYSIS
%
% Use as
% [data, powindx, hasrpt] = univariate2bivariate(data, inparam, outparam, dtype, ...)
% where
% data = FieldTrip structure acco... |
10b6caa6a5885c27982cceaf0ed2cfd72e5b28a795f533062d3a41ebef9f4f90 | MATLAB | 16,787 | 542 | function [y,O,X,S] = filterAdjust(O)
% :Usage:
% ::
%
% [y,O,X,S] = filterAdjust(OPTIONS)
%
% :O:
%
% **O.y:**
% signal
%
% **O.HP:**
% high pass freq. cutoff
%
% **O.TR:**
% sampling rate in s
%
% **O.doHP:**
% [0 or 1] - do HP filter (spm), default is 0
%
% **O.doLP:**
% ... |
23a5d59d98f501b6838c3edbeb598744614025c099191ea0119b947939ae32e5 | MATLAB | 16,806 | 346 | function colocalization_statistics_module()
figure()
set(gcf,'name','Colocalization Statistics Module','NumberTitle','off','color','k','units','normalized','position',[0.25 0.2 0.5 0.6],'menubar','none','toolbar','figure')
global data listbox
uicontrol('style','pushbutton','units','normalized','position',[0,0.95,0.... |
3deb860ab13035734835c5aaf2ee1454d1f01e291f8c9059d4d2eaee934cf08a | MATLAB | 16,818 | 386 | function ps2pdf(varargin)
%PS2PDF Function to convert a PostScript(R) file to PDF using GhostScript(R)
%
% Converts a PostScript file into PDF. The resulting PDF file will contain
% one page for each page defined in the PostScript files, so a multi-page
% PostScript file, like those generated by using the '-append' ... |
5d8aa1ec3b295175f59c80f82cd518cc3e4f3b7ceaeb277affd40de0f49a11f1 | MATLAB | 16,821 | 410 | function [data] = femdata_stnd_TR(mesh,t,dt,varargin)
% FEMDATA_STND_TR Returns time-resolved photon fluence rate for the
% 'standard' FEM mesh in NIRFAST format.
% This function generates sparse matrices representing the FEM problem
% (the time-resolved 'mass' mastrices and sparse sources vectors). Then,
% it ... |
7bf69d0ca4e09ea15067289bdd17f53d9cb5dd63d5cdae076064434d20446b59 | MATLAB | 16,831 | 508 | function [pv,stat,df,all] = GLM_contrast(X,y,c,type,verbose,Xnames,Ynames,notest)
% computes classical p-values for any contrast applied onto GLM effects
% function [pv,stat,df] = GLM_contrast(X,y,c,type,verbose,Xnames,Ynames)
% In brief, this function uses classical tests of linear mixtures of
% effects, under the gen... |
016f965230521286d2cc108f0f2fc35ab6952c340067b4e1ec5ecb3b91861a15 | MATLAB | 16,850 | 191 |
% This file is from pmtk3.googlecode.com
% # This file contains reasonable default settings for various inference
% # algorithms in libDAI. Each non-empty line should either be a comment
% # (starting with #) or contain an alias definition in the format
% #
% # alias: name[key1=val1,key2=val2,...,keyn=valn]
% #
% ... |
0114c113b3b08fd9b2b0cf1b3ab06480b5e56242f3e87227b3988ee040280a2f | MATLAB | 16,889 | 470 | function split_dat(data_path,save_path, subject_order,varargin)
% split_dat for recordings of multiple animals from Intan RHX USB
% acquisition system. Assumes intan one data per data type format. Will
% split amplifer and aux by available ports by default.
% input:
% data_path: path to file location with intan dat... |
a4adb5b727a39cc87698511c46bd6bccbd872476237e59f0538055ae85ea14e5 | MATLAB | 16,930 | 435 | function [data] = ft_channelrepair(cfg, data)
% FT_CHANNELREPAIR repairs bad or missing channels in the data by replacing them with the
% plain average of of all neighbours, by a weighted average of all neighbours, by an
% interpolation based on a surface Laplacian, or by spherical spline interpolating (see
% Perrin e... |
1e5ee324696a2ce51b0064c9d3f880a4de88e46e43d050206e0749c02191cef1 | MATLAB | 16,931 | 465 | % HIFDE3X Hierarchical interpolative factorization for differential equations
% in 3D.
%
% This is essentially the same as HIFDE2X but extended to 3D, reducing first
% cells to faces by elimination, then faces to edges and, optionally, edges
% to points by skeletonization. Note that edge skeletonizat... |
a3c43a0d249031c633439c11ff8e22ccfad37d090c26fefd8ffe4c3c7459691e | MATLAB | 16,950 | 553 | function [ss,p,pwmd]=FscatJit2(identifiers, data, p, pwmd, varargin)
% Plots data as both jittered points and an error bar, in the
% order the identifiers are passed to it. It preserves whatever order
% was in the fbmm structure. Also includes the option to define the circle
% size or use a default. Also allows someo... |
6ce5470d374266b7e25b2bede945d8976ca880cc8a137e21ef336c9b72df40cb | MATLAB | 16,955 | 467 | function [hs] = ft_plot_mesh(mesh, varargin)
% FT_PLOT_MESH visualizes a surface or volumetric mesh, for example describing the
% realistic shape of the head. Surface meshes should be described by triangles and
% contain the fields "pos" and "tri". Volumetric meshes should be described with
% tetraheders or hexaheders... |
229d732367f8463c93fc5e1e43bcac1905344344f56634f1552549cc90acddc9 | MATLAB | 16,983 | 554 | function [ss,p,pwmd]=FscatJit2(identifiers, data, p, pwmd, varargin)
% Plots data as both jittered points and an error bar, in the
% order the identifiers are passed to it. It preserves whatever order
% was in the fbmm structure. Also includes the option to define the circle
% size or use a default. Also allows someo... |
3db213778be053c2d81b6b8ab48e7c21846dd55c3117c9dc6dbbbdd0945c59ed | MATLAB | 16,997 | 284 | %% muscle GCaMP 1P imaging
% This works with folder arrangement as in glue muscle imaging
subFolders = dir(pwd);
realSubFolders = subFolders([subFolders.isdir]');
realSubFolders = realSubFolders(3:end);
% remove unwanted folders like those containing movies or plots from the
% list of real data-containing subfo... |
0ee4b34cca2a29dff88fb155d429a69e123815d01fd80469fb1db545da4cd1b1 | MATLAB | 17,018 | 560 | //========================================================================
// GLFW 3.4 macOS - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <elmindreda@glfw.org>
//
// This software is provided ... |
302aee940987feb646aa8a1120cfda43eaccc9daf4cb105eb91779215f950278 | MATLAB | 17,019 | 448 | function out = seqIo( fName, action, varargin )
% Utilities for reading and writing seq files.
%
% A seq file is a series of concatentated image frames with a fixed size
% header. It is essentially the same as merging a directory of images into
% a single file. seq files are convenient for storing videos because: (1)
%... |
62e0b615a58f501fcfca23ceb52f097994e3cc5242a334281b70f15cb87c30e5 | MATLAB | 17,025 | 520 | function varargout = w_Montage(varargin)
% W_MONTAGE MATLAB code for w_Montage.fig
% W_MONTAGE, by itself, creates a new W_MONTAGE or raises the existing
% singleton*.
%
% H = W_MONTAGE returns the handle to a new W_MONTAGE or the handle to
% the existing singleton*.
%
% W_MONTAGE('CALLBACK',hO... |
cc800bfff6034f8732b8cf04e84023fa1d9ae0cdbfd41f61396400e55857a5cf | MATLAB | 17,025 | 461 | clear;
clc;
doSaveFig= 0;
doSaveGrandAvg= 0;
CodeDir= '..\';
addpath(CodeDir);
%% load estimate AM trajectory
fig_TF= 4;
nSProws= 5;
nSPcols= 5;
sp_ax_TF = get_axes(fig_TF, nSProws, nSPcols);
%% human plots: first column
verboseAxis= 1;
[dam_traj_Hz_human_NFvalid, all_pow_am_human, all_pow_am_human_NF, mu_pow_am_... |
e57745ee90c1988312288ab253b3476a2a1fa572daad9c648d32ce232f16f917 | MATLAB | 17,072 | 353 | function [log_odd] = extract_ground_truth_info_back_up_15_06(folders,option,method,shuffles,ripple_zscore_threshold,p_val_threshold)
% Input:
% Folders: Each Folder is data for a session
% method = 'linear' or 'wcorr' or 'spearman' or
% Output:
% log_odd: save the log odd - log(sum(probability of T1)/sum(probability ... |
acaf0f58bf07eb83369a3be7d90e4f6bf2ed1b49f3f61bfa36ee6e30f2320ddd | MATLAB | 17,076 | 512 | %% Josh Tenenbaum's Number Game
%
%%
% This file is from pmtk3.googlecode.com
function numbersGame
%%
first = 1; last = 100; %Range for the hypothesis space
hypFn = @mathHypothesesSmall;
priorFn = @mathPriorSmall;
likelihoodFn = @likelihood;
posteriorFn = @posterior;
postPredFn = ... |
6deb2c9db5e9e3079841a86313173f43b066ecf8b31296d16a99bb7718db8d98 | MATLAB | 17,088 | 469 | function [fH,figNames,Pk] = meg_channelsPeakSort(sessionDir,data,nChOI,p,passCh)
% MEG_SELECTCHANNELS(sessionDir)
%
% INPUTS
% sessionDir
% data
% matrix time x channel x trial
% channel selection method
% 1. ampMax: max(abs(amp))
% 2. promAvg: max prominence across two peaks
% 3. promMax: max prominence... |
253fee888d89c3df1643fdb266127fecfbd5c1562a00cae163e8d7abe64985dd | MATLAB | 17,103 | 506 | function [cfg] = ft_movieplotTFR(cfg, data)
% FT_MOVIEPLOTTFR makes a movie of the time-frequency representation of power or
% coherence.
%
% Use as
% ft_movieplotTFR(cfg, data)
% where the input data comes from FT_FREQANALYSIS or FT_FREQDESCRIPTIVES and the
% configuration is a structure that can contain
% cfg.pa... |
50385867d7184cf98fcc5bee1591fd7e6c6add7b7d30882ea61d1ff1ecc4bcf3 | MATLAB | 17,103 | 399 | function data = h_frameAnalysisPlot3(handles)
% global FV_img
[currentInd, handles, currentStruct, currentStructName] = h_getCurrendInd3(handles);
fig = findobj('Tag','h_imstack3Plot','Selected','on');
if isempty(fig)
fig = figure('Tag','h_imstack3Plot','ButtonDownFcn','h_selectCurrentPlot3','Selected','... |
434b06fc6b4bec3526e047da957818f66a77923df636b5abe18e07e49e748f33 | MATLAB | 17,111 | 499 | function [mri] = ft_read_mri(filename, varargin)
% FT_READ_MRI reads anatomical and functional MRI data from different file formats.
% The output data is structured in such a way that it is compatible with
% FT_DATATYPE_VOLUME.
%
% Use as
% [mri] = ft_read_mri(filename)
%
% Additional options should be specified in ... |
dbe611538aad462debbcf2aff3d48a202e573b19a323d6b45694db720ad57a3a | MATLAB | 17,112 | 322 | function plot_correlation_RUN_evolution(folders, method, option)
%methods: wcorr or spearman
switch option
case 'time'
bin_edges= 60*[[0:1:24-1]' [1:1:24]'];
num_bins = size(bin_edges,1);
case {'laps','cumulative_laps'}
num_laps = 20;
jump_laps = 1;
num_bins = floor(20/j... |
326ee9a021eddba4f0feb18b657a0b46f6bfbe73a01fc412c9fd237c4e31b784 | MATLAB | 17,117 | 472 | function [sens] = ft_read_sens(filename, varargin)
% FT_READ_SENS read sensor positions from various manufacturer specific files. See
% further down for the list of file types that are supported.
%
% Use as
% grad = ft_read_sens(filename, ...) % for gradiometers
% elec = ft_read_sens(filename, ...) % for electro... |
01da6f88d8c3686306c97491846b15c7c2f4b91369db9f1b477908fc01ccd0cf | MATLAB | 17,142 | 434 | function varargout = h_spineAnalysisGUI3(varargin)
% H_SPINEANALYSISGUI3 M-file for h_spineAnalysisGUI3.fig
% H_SPINEANALYSISGUI3, by itself, creates a new H_SPINEANALYSISGUI3 or raises the existing
% singleton*.
%
% H = H_SPINEANALYSISGUI3 returns the handle to a new H_SPINEANALYSISGUI3 or the hand... |
8258501d67e83fd9164960c423cc7ca9d92a6df2090c86f60d057ffecea730f9 | MATLAB | 17,155 | 393 | function [qrs_amp_raw,qrs_i_raw,delay]=pan_tompkin(ecg,fs,gr)
%% function [qrs_amp_raw,qrs_i_raw,delay]=pan_tompkin(ecg,fs)
% Complete implementation of Pan-Tompkins algorithm
%% Inputs
% ecg : raw ecg vector signal 1d signal
% fs : sampling frequency e.g. 200Hz, 400Hz and etc
% gr : flag to plot or not plot (set it ... |
6af7b96fb5d2dac040c2dedd8b92055801eca6c15e8c5ffaaf2c9e8c1674482b | MATLAB | 17,156 | 395 | function [h_f,h_a] = NdimSliderPlot(data,varargin)
% arguments
% data % An N-dimensional array of the values of the dependent variable.
% end
% arguments (Repeating)
% varargin % See parameters below.
% end
%% Parse optional Name,Value... |
8026e2cd67dfdc4a2b0b09a81572b6f2e7259c68194fb53dba2517953934057d | MATLAB | 17,183 | 458 | function varargout = Linear_settings(varargin)
% LINEAR_SETTINGS MATLAB code for Linear_settings.fig
% LINEAR_SETTINGS, by itself, creates a new LINEAR_SETTINGS or raises the existing
% singleton*.
%
% H = LINEAR_SETTINGS returns the handle to a new LINEAR_SETTINGS or the handle to
% the existing si... |
f7a07fd733b4a530638b10fabfca94851085e07c530bac15cd20a5d2a3c19ba4 | MATLAB | 17,190 | 444 | function M = fixedrankfactory_tucker_preconditioned(tensor_size, tensor_rank)
% Manifold of fixed multilinear rank tensors in Tucker format.
%
% function M = fixedrankfactory_tucker_preconditioned(tensor_size, tensor_rank)
%
% n1 = tensor_size(1);
% n2 = tensor_size(2);
% n3 = tensor_size(3);
% r1 = tensor_rank... |
9573c833d06f372a91cb95ab98d87258632bcd52f783db02ae4794225e2d48aa | MATLAB | 17,204 | 386 | function ps2pdf(varargin)
%PS2PDF Function to convert a PostScript(R) file to PDF using GhostScript(R)
%
% Converts a PostScript file into PDF. The resulting PDF file will contain
% one page for each page defined in the PostScript files, so a multi-page
% PostScript file, like those generated by using the '-app... |
644c040fe09af197a7b7898fff9b6994254395af8757c10b39cc2824f4292a61 | MATLAB | 17,205 | 435 | classdef tpsFitter < surfaceFitting.surfaceFitter
% Generate surface from a point cloud using thin plate spline fit
%
% The thin plate spline method fits a surface that behaves like a plate
% with some bending stiffness. This surface remains parametrized by
% coordinates xy on a plane, which we are ... |
60b9d8a9c32f9d69aab8cdc9ac15e499f7d9af331acf10448b37530026aa444d | MATLAB | 17,206 | 382 | function [obj] = TLgetROIs(obj, ...
left_AC_search_region_mask,right_AC_search_region_mask, ...
left_VC_search_region_mask,right_VC_search_region_mask, ...
Y_grayMatter_mask,Y_whiteMatter_mask,Y_CSF_mask,...
grayMatterMask_eroded,whiteMatterMask_eroded,csfMask_eroded, ...
interme... |
1478b1356f336b115322c44e076d973e20cca04654c878ea55ff2a6a5840a20e | MATLAB | 17,231 | 422 | function varargout = y_PALMSetting(varargin)
% Y_PALMSETTING MATLAB code for y_PALMSetting.fig
% Y_PALMSETTING, by itself, creates a new Y_PALMSETTING or raises the existing
% singleton*.
%
% H = Y_PALMSETTING returns the handle to a new Y_PALMSETTING or the handle to
% the existing singleton*.
%
% ... |
365f345f2ab6882177d134b4322a1f3ba0b5b6640526aea10d0611dd092a0b99 | MATLAB | 17,231 | 536 | function Answer=inputdlgcol(Prompt, Title, NumLines, DefAns,Resize,NumCols)
%INPUTDLGCOL Input dialog box.
% Answer = INPUTDLGCOL(Prompt) creates a modal dialog box that returns
% user input for multiple prompts in the cell array Answer. Prompt
% is a cell array containing the Prompt strings
%
% INPUTDLGCOL... |
838b386bc0cbab8d115299d2ee42c96394f4f9e8fa15f53c6dc07a2bd8912e23 | MATLAB | 17,246 | 513 | function TrioEEGBehMicrosaccades(fixResult, cuesToAnalyse)
% analyse microsaccades in the ready period and early target period.
% microsaccade density, ocular drift speed, FFT of movements in early and
% late period between ready cue and target onset.
%
% requires edft
%% load up
if ~exist('cuesToAnalyse','var') || ... |
4d437f6046a33b2c2e185a8f6148d463efb5a9f6ce8c54eedd5b8331deef482e | MATLAB | 17,247 | 426 | function [ ISIstats ] = bz_ISIStats( spikes,varargin )
%ISIstats = bz_ISIStats(spikes,varargin) calculates the statistics
%inter-spike intervals for the spiketimes in spikes.
%
% INPUTS
% spikes Structure with spikes.times and spikes.UID
%
% (options)
% 'ints' A structure with intervals... |
2ad24e216beeca644f2ece6eafafedd0f5abb711b20646d291d4eba8b4ca0dfb | MATLAB | 17,254 | 539 | function Answer=inputdlgcolZN(Prompt, Title, NumLines, DefAns,Resize,NumCols)
%INPUTDLGCOL Input dialog box.
% Answer = INPUTDLGCOL(Prompt) creates a modal dialog box that returns
% user input for multiple prompts in the cell array Answer. Prompt
% is a cell array containing the Prompt strings
%
% INPUTDLGC... |
d1fb7d864876f898e9ae819dad5e49da24ed5d7bc88fdcdf3403755fda3bcc32 | MATLAB | 17,257 | 438 | function [output] = ft_volumelookup(cfg, volume)
% FT_VOLUMELOOKUP can be used in to combine an anatomical or functional
% atlas with the source reconstruction results. You can use it for forward
% and reverse lookup.
%
% Given the region of interest (ROI) as anatomical or functional label, it
% looks up the locations... |
21e48ef52bf30257ad0ce2a3e88a0b77cf15ffc7c8bbcf1b96e5330ac49c14f9 | MATLAB | 17,294 | 433 | function [dipout] = beamformer_lcmv(dip, grad, headmodel, dat, Cy, varargin)
% BEAMFORMER_LCMV scans on pre-defined dipole locations with a single dipole
% and returns the beamformer spatial filter output for a dipole on every
% location. Dipole locations that are outside the head will return a
% NaN value.
%
% Use as... |
e7c47281221d73add38fb6d379de3548b1adbd509d54ed36c12cb50c81926cd0 | MATLAB | 17,298 | 372 | %% Before running this script - manual stages:
% 1. Compute ANOVA across all subjects with the five social scales conditions,
% to identify regions with scale sensitivity ("ANCOVA random effects analysis" dialog);
% Change threshold to q=0.01 (FDR-corrected); Save the results to a VMP file - "anova_results.vmp"
... |
c65b23890ee04e8cbccaac9970e95796b1adf0ca454738b5d16c4bb086e60d97 | MATLAB | 17,300 | 450 | %% Hub disruption
cmap = BrBG_cmap(8);cmap = cmap([6:8,3:-1:1],:);
refgroup = bins==4;
refgroupstr = 'YoungNC';
S = Scorr;
Pc = Pccorr;
Z = Zcorr;
S_ref = mean(S(refgroup,:));
Pc_ref = mean(Pc(refgroup,:));
Z_ref = mean(Z(refgroup,:));
%% Plot
[p_MC,HDI.slope,HDI.intercept,HDI.p,HDI.R2,HDI.slopeupper,HDI.slopelowe... |
9cb202711aa2e4f244c72b2289244b59698464801e919baf1ffbf47dda4e71ee | MATLAB | 17,304 | 401 | %% Sleep decode analysis of Shin et al., 2019
% exptSleepDecodePlotting.m
%
% Statistical analysis of the decoded events from the first sleep session
% of Shin et al., 2019
%% Set up
% Get data directory
userDir = char(java.lang.System.getProperty('user.home'));
if ispc; boxDir = 'Box';
elseif ismac; boxDir = ['Libr... |
314e92886555ff3a4d1e3a5e3365e871417633e516fa048258220a3f6f4fe1d5 | MATLAB | 17,320 | 435 | function linescanDiamAnalysis(fname,prefs)
%
%function to find the diameter of a vessel from a linescan
%this is less complex then for xyFWHM as the vessel is scanned in a
%straight (vertical) line, and there will be no branches
%will step through in 40ms windows and find mean intensity, then FWHM
%written Dec 20... |
aa3578c46bab8d662a5fecfbfaaa1d45e9a7cf20b4393a2f501e309252e70485 | MATLAB | 17,332 | 390 | function ensemble(segmentFilename, dataFilename, experimentName)
if isempty(dataFilename)
quit(2);
end
data = load(dataFilename);
shuffleRuns = 10000;
suffixes = [""];
if experimentName == "SDT"
suffixes = ["_A", "_N"];
end
for k=1:length(suffixes)
clear ensb_... |
33a8dc83e43005fbacfb4ecdb8edd1bd007ec52fb44af7e9ef19aea1c4854bf3 | MATLAB | 17,338 | 396 | % SYNTAX:
% EEG = RA_equaltrials_Beta001GH(EEG, eventCodeArray, minNumEp);
%
% INPUT:
%
% EEG - bin-based epoched dataset (artifact detection/correction already done)
% eventCodeArray - It's a 1xN cell array of event codes, where N is the number of
% "Confidence" responses (e.g. 5 respons... |
4bdc7869f1bbd3ff188b1a5d4e046e6933c22bb5f7171a232d720dd660ce7129 | MATLAB | 17,338 | 453 | %% OBSOLETE SEE HPOptim.m
%% Compile xv results over rounds
nE = 3135;
nH = 3252;
nPch = 39;
npts = 17;
xverrE = nan(nE,npts,nPch,0);
xverrH = nan(nH,npts,nPch,0);
pchsE = cell(0,nPch);
pchsH = cell(0,nPch);
xvresE = cell(nPch,0);
xvresH = cell(nPch,0);
[xverrE(:,:,:,end+1),pchsE(end+1,:),xvresE(:,end+1)] = HPOptim.l... |
95cce59a620be935a061cf4e47bb27b03ef8e8724a7d2195f9fb4931e5551542 | MATLAB | 17,348 | 362 | % Correlation script for nchannels vs DOPA
%% Generate csv files from PET data
% addpath C:\Code\wjn_toolbox-master
% addpath C:\Code\spm12
addpath(genpath('C:\Code\spm12'))
addpath(genpath('C:\Code\wjn_toolbox'))
addpath(genpath('C:\Code\leaddbs\leaddbs'))
% Read atlas parcellation
region_info = readtable('HCPex (Hu... |
a889728cf96c87a8ba865c022513477981cb64116f40e9badd02c1c7bacdfe85 | MATLAB | 17,395 | 457 | function CrossDecodeAnalysisActionBaseline(AllTrialData,Labels,TimeWindow,OutDir,Tag,varargin)
% Train on dim 1 to classify dim 2, test on how well it generalizes.
% e.g. train on nancy to diff bp, test how well bp diff'd in Tyson.
[~,PThresh] = Utilities.ProcVarargin(varargin,'PThresh','fdr');
% [~,NIter] = Uti... |
9431ae26ca829bb78729b00fa6c7dc5cce7e874ee4ca63b8195e0a68643b73c0 | MATLAB | 17,407 | 443 | function [Xloadings,Yloadings,Xscores,Yscores, ...
beta,pctVar,mse,stats, mse_byvar, Tnotnormal, pctVar_byVar] = plsregress_fullcode(X,Y,ncomp,varargin)
%PLSREGRESS Partial least squares regression.
% [XLOADINGS,YLOADINGS] = PLSREGRESS(X,Y,NCOMP) computes a partial least
% squares regression of ... |
ec6c3e69243caccab6c0ddf24d3a0083ad5d19c7b5f8ced9de39f8b9c17b40cd | MATLAB | 17,416 | 556 | function [mdlparams, xerr, errall] = gfFitSubunitGridModel(mdlparams, xvals, yy, opts,initialize)
%UNTITLED2 Summary of this function goes here
% Detailed explanation goes here
%==========================================================================
if nargin < 4
batchsize = 1000;
eta = 0.01;
beta1 = .... |
0a7f9b84dea41f8e965d71c97ca7a9af1bb0d77ea37762e329a1624653b6c5bf | MATLAB | 17,429 | 593 | function [R,Q,S,T,P_w] = MTEO_qrst(ecg,fs,gr)
%% ======== Delineates ECG based on MTEO Algorithm ============== %%
% Employs Multilevel Teager Energy Operator to delineate ECG. To see how
% MTEO is computed please see my paper and cite it if you are interested
% in using this code.
%%%%%
% Ref : H. Sedghamiz and D. San... |
7688f55762507a4e7169cc7fa3091fcfc8e9325f964966d1d908722d41eb8fe3 | MATLAB | 17,434 | 500 | function TSplotcdfs(varargin)
% Graphics helper function for TSapplystat.
% Plots cumulative distribution functions and labels them with subject
% and/or session, Trial and/or phase. Will plot multiple cdfs on single
% panels and multiple panels per figure. MUST BE CALLED BY TSAPPLYSTAT!!
%
% Syntax: TSapplystat('',... |
57c1d8e0ff31546f53eaf5c663db48a7a3deb3b12fc22bae3bad0204a961341c | MATLAB | 17,435 | 438 | function [ titlestr, settings, results] = computeMixingMatrix( dataview, settings )
% Computes and plots a mixing matrix based on a (k-NN) graph and a level
% and target variable. Both level and target variable should be categorical.
%
%
%
%<PRE>
% This file is part of dspace-core.
... |
f63a98085ae2924eeea287cabaf86d0bc7af3ac87ac4b10b49098ead6a20950a | MATLAB | 17,435 | 529 | function [stack, img_read] = tiffread2(filename, img_first, img_last)
% tiffread, version 2.4
%
% [stack, nbImages] = tiffread;
% [stack, nbImages] = tiffread(filename);
% [stack, nbImages] = tiffread(filename, imageIndex);
% [stack, nbImages] = tiffread(filename, firstImageIndex, lastImageIndex);
%
% Reads 8,16,32 bit... |
1173274e6927de020f01bde111a758e9ef683f7a3f51315ffb4f9fc636f5b79a | MATLAB | 17,462 | 475 | function json=savejson(rootname,obj,varargin)
%
% json=savejson(rootname,obj,filename)
% or
% json=savejson(rootname,obj,opt)
% json=savejson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a JSON (JavaScript
% Object Notation) string
%
% author: Qianqian Fa... |
05347fcfec81424b7e7a93d192d449399e85d2851b94121d9fe575625c6f489e | MATLAB | 17,490 | 518 | % [readframe,nframes,fid,headerinfo] = get_readframe_fcn(filename)
% get_readframe_fcn inputs the name of a video, opens this video, and creates a
% function that can be used for random access to frames in the video. it can
% input files of type fmf, sbfmf, and avi. if videoio is installed on your
% machine, then get_r... |
8ce429943386e94eccf9f6eae74e1d9ddeb4875f2f84f0bb1366834b86ddd5a7 | MATLAB | 17,500 | 541 | function Answer=inputdlgcol(Prompt, Title, NumLines, DefAns,Resize,NumCols)
%INPUTDLGCOL Input dialog box.
% Answer = INPUTDLGCOL(Prompt) creates a modal dialog box that returns
% user input for multiple prompts in the cell array Answer. Prompt
% is a cell array containing the Prompt strings.
%
% INPUTDLGCOL... |
c474aa83be0eaed058892eca960aa4918694f0517c6f8ff6a8b8564f9cc0d322 | MATLAB | 17,506 | 397 | function [data] = ft_steadystatesimulation(cfg)
% FT_STEADYSTATESIMULATION creates a simulated EEG/MEG dataset. This function
% allows to simulate the effect of several independent stimulus trains. These can
% be presented as a periodic sequence, or as single (or few) transient stimuli.
% This function creates a singl... |
2ecad3cdd665ff7b5f87aa5fa6a96ac07cdc292a4765786fbba7ff6c7c691bef | MATLAB | 17,507 | 397 | function [data] = ft_steadystatesimulation(cfg)
% FT_STEADYSTATESIMULATION creates a simulated EEG/MEG dataset. This function
% allows to simulate the effect of several independent stimulus trains. These can
% be presented as a periodic sequence, or as single (or few) transient stimuli.
% This function creates a singl... |
ecd72899f8b4a790074c5e6bea2f4fdf7be76363e2ef9198d503992cb367df43 | MATLAB | 17,520 | 449 | % fmrib_pas() - Remove pulse
% artifacts from EEG data collected inside an MRI machine.
%
% This program removes pulse artifacts from EEG data collected
% collected inside the MRI scanner. A choice of methods is available.
%
% The first choice is Optimal Basis Set [Niazy06].
% This method aligns all the pulse... |
7726cb858d636fe9106f06cc5b2b68fe8bbbf12dd67243825ba13b03c8ed1868 | MATLAB | 17,523 | 358 | classdef SuhMatch < handle
%%SuhMatch.Run is a wrapper for run_HiD_match and
% run_QfTree. It preprocesses csv input files
% to marshall the data and label arguments for both.
%
% The publication that introduces QfMatch is
% https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5818510/
%
... |
7c5da2ac8daed3ffb652e5ac7accee6681fa0a1ebc638c4bde3e6ef284b81f90 | MATLAB | 17,544 | 423 | %% computeSDO_populateSDOArray
% Given supplied point-process and time series data sets, compute the
% stochastic dynamic operator for every supplied combination.
%
% Hardfork update to actually pass in the xtDataCell and ppDataCell classes
% directly; making the evaluation more straightforward and function-calls
% cl... |
227a984abae5ebc23ebb7f1434de409936d90ebb7f3326ac775d0f5f0b493f81 | MATLAB | 17,566 | 442 | function mysavefig(fname, varargin)
% Usage: savefig(filename, fighdl, format, options)
%
% Saves a pdf, eps, png, jpeg, and/or tiff of the contents of the fighandle's (or current) figure.
% It saves an eps of the figure and the uses Ghostscript to convert to the other formats.
% The result is a cropped, clean pictur... |
8163d6f6972024b4f4c2f6a8687e89618f378fab4cc3c4326479217ec797fd26 | MATLAB | 17,577 | 523 | function data = loadjson(filename,varargin)
%
% data=loadjson(fname,opt)
% or
% data=loadjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (q.fang <at> neu.edu)
% created on 2011/09/09, including previous works from
%
% Ned... |
1854bc1606585f778ff4a3b2a7fb89d440602812e728eb5118460dd533925370 | MATLAB | 17,583 | 429 | function [out,fmethod,pmethod] = boney_segment_filenames(P,job)
%bonefilenames(P). Prepare output filenames and directories.
%
% [out,fmethod,pmethod] = boney_segment_filenames(P,job)
%
% P .. list of m-files
% job .. main job structure to include some parameters in the filename etc.
% out .. main output structur... |
2a357daef58a96235bec6047ddfacaa6e3fede1e8fbb18b499a89171e30d834b | MATLAB | 17,587 | 361 | % pipeline_PLSR_variability.m
% Sarah West
% 10/3/23
%% Initial Setup
% Put all needed paramters in a structure called "parameters", which you
% can then easily feed into your functions.
% Use correlations, Fisher transformed, mean removed within mice (mean
% removed for at least the cases when you aren't using mic... |
b54d601d713a8f977ebb8c77e238aa0f20c1d368fe4a72dc970ea6c75c40ba5a | MATLAB | 17,602 | 725 |
%% dfof range
%need to load data: contact lead author for data
%%
%dfof
% randChance=40/700;%0.571, 10%
% rate=nRuns(:,1)./nRuns(:,2)
%remove the one that the sccess rate is
i=find(nRuns(:,1)>1);
fields = cat(1, allDfofs{i});
for n=1:size(fields,1);
fields(n,:)=naninterp(fields(n,:));
end
% iUs... |
2f73088d29ede9f1af52bd34607a90b7b1c110c561b16f0680a3a73bf657b55e | MATLAB | 17,614 | 437 | function data_analysis_software()
clear global;clear;clc;
warning off
addpath(strcat(pwd,'\load_files'))
addpath(strcat(pwd,'\load_files\tiff'))
addpath(strcat(pwd,'\load_files\storm'))
addpath(strcat(pwd,'\load_files\tracks'))
addpath(strcat(pwd,'\load_files\image'))
addpath(strcat(pwd,'\loc_analysis'))
addpa... |
201eff679e3cd6454998e5d4d84da045b928baad1a5812c558d8a90ed1499e20 | MATLAB | 17,633 | 398 | function noise=FindNoise(data,posspikes,negspikes,fs,Settings,DoDisplay)
%Look through the data, using the parameters set in 'Settings', and return all noise indices.
%1. Use a sliding window to determine various metrics of the signal
%2. Compare metrics of interest to thresholds, and flag as noise if they exceed se... |
0c306a6c3193f669eeb447ccebef2cbbaad73affd2e1b148db295a531aea12a8 | MATLAB | 17,638 | 362 | function [QuaSOR_Image,QuaSOR_Image_TemporalColors,myPool]=QuaSOR_Map_Maker(myPool,GPU_Accelerate,...
QuaSOR_UpScaleFactor,QuaSOR_ImageHeight,QuaSOR_ImageWidth,...
All_Location_Coords,QuaSOR_Gaussian_Filter_Size,QuaSOR_Gaussian_Filter_Sigma,...
SpotNormalization,TemporalColorization,QuaSOR_Colormap,Verbo... |
a055316e56f9d6c76f7499a692e97100ce310180e4482f7f064dd272d6f7f4cf | MATLAB | 17,652 | 281 | clear EpisodeStruct EpisodeStructCurves
if ImagingInfo.FramesPerEpisode>500&&ImagingInfo.NumEpisodes>3
warning('I am going to save each episode sepearately to make loading easier...')
SplitEpisodeFiles=1;
fprintf('Processing Episodes...Separate, Bleach Corr, DeltaF....\n')
else
... |
3da6888939a6f7927fd584f775743b7464c7d962a080e05d372f1082e1082a64 | MATLAB | 17,662 | 369 | function ft_defaults
% FT_DEFAULTS (ending with "s") sets some general settings in the global variable
% ft_default (without the "s") and takes care of the required path settings. You can
% call this function in your startup.m script. This function is also called at the
% begin of all FieldTrip functions.
%
% The glob... |
c5786862c72a8f86363430e77aa71ee8388e04a2d865e72131112c0961a21856 | MATLAB | 17,675 | 438 | function [dipout] = beamformer_lcmv(dip, grad, headmodel, dat, Cy, varargin)
% BEAMFORMER_LCMV scans on pre-defined dipole locations with a single dipole
% and returns the beamformer spatial filter output for a dipole on every
% location. Dipole locations that are outside the head will return a
% NaN value.
%
% Use as... |
78861a7eda64520012017cdb820a5ae8af41111c5170857587a3da76199a0fac | MATLAB | 17,697 | 410 | function CBIG_MMLDA_visualize_factors(in_dir, out_dir, k, min_thresh, max_thresh, ...
mask, behavior_name, behavior_domain, mni_space)
% CBIG_MMLDA_visualize_factors(in_dir, out_dir, k, min_thresh, max_thresh, mask)
%
% This function will visualize atrophy maps and cognitive deficits of estimated factors.
% The at... |
c1f9296234a48c65ffb4664337e2eee2365bc8bb791a5fa8a4d064557e38ae70 | MATLAB | 17,724 | 685 | %%
load trnDataSH_Apr18.mat
%%
ci = load('cropInfo20180426.mat');
%% normalized shapes
mdl = struct('D',10,'d',2,'nfids',5);
n = height(tFinalReconciled);
nGT = height(tGT);
pLbl = nan(n,10,2); % n,coords,ivw
pLblN = nan(n,10,2);
pLblGT = nan(nGT,10,2);
pLblGTN = nan(nGT,10,2);
for ivw=1:2
bbvw = makeBBoxes(IFin... |
b7607d20f89f13fd41576d7510062310aa4cc1218e7d310950b864d344643820 | MATLAB | 17,729 | 370 | function [] = Twave_personalisation_POMs_ToRORd_IKs_not_converged(nb_models, celltype, stimAmp, stimulus_function_str, result_dir)
% Population of models generation for T-wave personalisation
% Adapted from scriptDemonstration_2_ParameterComparison.m:
%% Setting parameters
param_baseline.bcl = 8... |
5221959b6bb33df09b54c17207409cf1e34c0a0110ffff577583be21bbfbe823 | MATLAB | 17,739 | 512 | function img = meg_plotTime(sqdfile, analStr, rejectTrials, rejectChannels, p)
% MEG_PLOTTIME Plots: (1) concatenated trial time series, (2) trial time
% series averaged by channel, (3) fft
%
% MEG_PLOTTIME(sqdfile, analStr, rejectTrials, rejectChannels)
%
% sqdfile = 'datafile.sqd'
% analStr = 'string of analysis ... |
efb160b9aed0f93958ef1bbda383efddf7df0ef00c040c9b32ee3cca4067acd0 | MATLAB | 17,761 | 437 | % meg_fitAnticipatory1_freeFreq
% all trials (or single precue condition), free frequency
% November 2023 Karen
%% Settings
saveFigs = 1;
user = 'kantian'; % kantian (persona), karen (lab)
workingDir = sprintf('/Users/%s/Dropbox/github/ta-meg-analysis-model/model_anticipatory',user);
addpath(genpath(workingDir)) %... |
95bc105f2a32a8638abdbf297e37838e3156208a2818aba257b1d5c281b73c90 | MATLAB | 17,776 | 362 | function [] = ObservableAnalysis_3D(processedDataFName,meta)
warning('off','MATLAB:dispatcher:UnresolvedFunctionHandle')
warning('off','MATLAB:table:ModifiedAndSavedVarnames')
behaviorPath = meta.behaviorPath;
stimulusPath = meta.stimulusPath;
DLC_modelext = meta.DLC.model;
DLC_dataSubFold = meta.DLC.subFold;
... |
7b18430a5057be17523802dbc5012c31c0e34ffc0918043a6cacd7259c02dca6 | MATLAB | 17,783 | 363 | % pipeline_duration_place_concatenation.m
% Sarah West
% 6/12/23
%% Initial setup
% Put all needed paramters in a structure called "parameters", which you
% can then easily feed into your functions.
clear all;
% Output Directories
% Create the experiment name. This is used to name the output folder.
parameters.e... |
396b3d6427c41e11e31e4c6eb54556162ca71ece9debb8c4869c277b5fc9e1d9 | MATLAB | 17,791 | 496 | function [freq] = freq_wltconvol_lan(cfg,LAN, texto);
%
% Funcion de Fieldtrip 2009 adapatada para LAN
% FIX CEIL 04.04.2013
%
% FREQANALYSIS_WLTCONVOL performs time-frequency analysis on any time series trial data
% using the 'wavelet method' based on Morlet wavelets.
%
% Use as
% [freq] = freqanalysis(cf... |
4b7150a6fd04cb7f8502e221e1d10baa8f0277361ee2a8d7c4ae9bee6a9c8528 | MATLAB | 17,795 | 375 | function ft_defaults
% FT_DEFAULTS (ending with "s") sets some general settings in the global variable
% ft_default (without the "s") and takes care of the required path settings. You can
% call this function in your startup.m script. This function is also called at the
% begin of all FieldTrip functions.
%
% The glob... |
c961973a66681779807ac0cc9ae29078f6575ef4e05275a9e3b0655223797d06 | MATLAB | 17,800 | 612 |
clear
clc
% f = gcf;
% exportgraphics(f,'Fig1_Original.png','Resolution',600)
MotionData = load('MotionData.mat');
MusculoskeletalData = load('MusculoskeletalData.mat');
%% Motion Data
MotionData = MotionData.MotionData;
% Joint Angles
SHLa = MotionData.GenericCat.Angles.AngShou.Total*(pi/180);
ELBa = MotionData.G... |
e8f4c191580e21153a703b072b6fcdbbf77878c64771ce61a5797db883349137 | MATLAB | 17,818 | 474 | function mesh = prepare_mesh_hexahedral(cfg, mri)
% PREPARE_MESH_HEXAHEDRAL
%
% Configuration options for generating a regular 3-D grid
% cfg.tissue = cell with the names of the compartments that should be meshed
% cfg.resolution = desired resolution of the mesh (default = 1)
% cfg.shift
% cfg.background
%... |
d2273136633d6fdf8a1c544319d70b755ef22de32b3119cb5103c3be054b8ac6 | MATLAB | 17,855 | 417 | function varargout = h_frameAnalysisGUI3(varargin)
% H_FRAMEANALYSISGUI3 MATLAB code for h_frameAnalysisGUI3.fig
% H_FRAMEANALYSISGUI3, by itself, creates a new H_FRAMEANALYSISGUI3 or raises the existing
% singleton*.
%
% H = H_FRAMEANALYSISGUI3 returns the handle to a new H_FRAMEANALYSISGUI3 or the hand... |
3637d92e80bd72b6d06e77acf4ac778c61e26a7177305743a3e371f082a6dc04 | MATLAB | 17,864 | 616 | clear
clc
% f = gcf;
% exportgraphics(f,'Fig1_Original.png','Resolution',600)
MotionData = load('MotionData.mat');
MusculoskeletalData = load('MusculoskeletalData.mat');
%% Motion Data
MotionData = MotionData.MotionData;
% Joint Angles
SHLa = MotionData.GenericCat.Angles.AngShou.Total*(pi/180);
ELBa = MotionData.Ge... |
6a80ec42ed18eda6afff3317d49c57f5b701698051cb3128dd4f01eca3abb613 | MATLAB | 17,866 | 446 | %% SDO Matrix
% Data Class for dealing with the SDO matrices. For use with the SDO
% Analysis Toolkit.
%
% 1) sdoMat may be generated from 2 'pxtDataCell' classes
% 2) sdoMat may be generated fom the 'sdo' common data structure
% 3) sdoMat may be extracted from an 'sdoMultiMat' Class
% TODO: Further optimization, par... |
d3e93900f58849f6500838ea501be61c12a913fb3778ce35a786d166b9a6539f | MATLAB | 17,886 | 462 | function GLCM_TOP(varargin)
% GLCM on Three Orthogonal Planes (TOP)
[fileList,maskFiles,OPT,SPACE] = ParseParams(varargin);
tlboxDir = fileparts(mfilename('fullpath'));
currentDir = pwd;
MNIMaskVol = load_untouch_nii([tlboxDir '/data/T1_Mask.nii']);
maskMNI = MNIMaskVol.img>0;
% MaskVol = load_untouch_nii(maskFi... |
b2f5c1ab98f9a1e5e9a13f351c011320d56b69ee5049f48b03766baec0b0d6ef | MATLAB | 17,890 | 401 | function [channel] = channelselection_lan(channel, datachannel)
% CHANNELSELECTION for EEG and MEG labels
%
% This function translates the user-specified list of channels into channel
% labels as they occur in the data. This channel selection procedure can
% be used throughout fieldtrip.
%
% You can specify a mixture ... |
0eeee90eb9a1c998f208bcb636482e81c7517dd15f56e23e431ac5734dc626df | MATLAB | 17,894 | 269 | function get_distributions_tracks_replay(varargin)
available_controls= {'fixed_rate','fixed_spike_count','global_remapped','rate_remapped'};
available_scoring= {'wcorr','spearman'};
available_methods= {'TRACK_PAIRS','ONE_TRACK'};
p= inputParser;
addParameter(p,'scoring','wcorr',@(x) ismember(available_scoring,x));
ad... |
8c2fa3c3fa9491d1f1b1704935146a5ca54fbd341d98d1fd40b90e14e6cf0053 | MATLAB | 17,907 | 460 | function varargout = w_TransMat(varargin)
% W_TRANSMAT MATLAB code for w_TransMat.fig
% W_TRANSMAT, by itself, creates a new W_TRANSMAT or raises the existing
% singleton*.
%
% H = W_TRANSMAT returns the handle to a new W_TRANSMAT or the handle to
% the existing singleton*.
%
% W_TRANSMAT('CALL... |
e97d56c13ae568b16ac4ea32b5add7d056f8aeec7faa3138578d5fbd625fe2d9 | MATLAB | 17,917 | 382 | function [Error, Cfg]=DPABI_BIDS_Converter_run(Cfg,WorkingDir,SubjectListFile)
% FORMAT [Error, Cfg]=DPABI_BIDS_Converter_run(Cfg,WorkingDir,SubjectListFile)
% Cfg - the parameters for auto data processing.
% WorkingDir - Define the working directory to replace the one defined in Cfg
% SubjectListFile - Defi... |
f646f5f160321d93a2bcbdcb1fe45bad2c421e6500d98753231952c82bab5634 | MATLAB | 17,917 | 395 | function CBIG_gwMRF_regenerate_Schaefer2018_parcellations(output_dir)
% CBIG_gwMRF_regenerate_Schaefer2018_parcellations(output_dir)
%
% This function uses current Schaefer2018 parcellation to regenerate new
% version of Schaefer2018 parcellation under given folder.
%
% In our previous versions (v0.8.1-Schaefer2018_... |
62b05111ee834d0eedc91adaeacace464ebafd0209287f1cb9895415c0641594 | MATLAB | 17,923 | 441 | function varargout = print( varargin )
%PRINT Print figure or model. Save to disk as image or MATLAB file.
% SYNTAX:
% print
% PRINT alone sends the current figure to your current printer.
% The size and position of the printed output depends on the figure's
% PaperPositi... |
895a52dee8e503be4bcf7d38255a77efd47f7f029ad3bfd8d498abd88ef38a14 | MATLAB | 17,928 | 614 | clear
clc
% f = gcf;
% exportgraphics(f,'Fig1_Original.png','Resolution',600)
MotionData = load('MotionData.mat');
MusculoskeletalData = load('MusculoskeletalData.mat');
%% Motion Data
MotionData = MotionData.MotionData;
% Joint Angles
SHLa = MotionData.GenericCat.Angles.AngShou.Total*(pi/180);
ELBa = MotionData.Ge... |
a3782e3f5d4ab74b23d25ef6bdcd201cd19dbc4d974b519dd5320fe29ae46498 | MATLAB | 17,965 | 623 |
clear
clc
% f = gcf;
% exportgraphics(f,'Fig1_Original.png','Resolution',600)
MotionData = load('MotionData.mat');
MusculoskeletalData = load('MusculoskeletalData.mat');
%% Motion Data
MotionData = MotionData.MotionData;
% Joint Angles
SHLa = MotionData.GenericCat.Angles.AngShou.Total*(pi/180);
ELBa = MotionData.G... |
024b438f7c5c967d369c91fea98e667ac8108fd636ed41c67287a568f8afea6e | MATLAB | 17,972 | 512 | function [p_sub,o_sub,p_group,o_group] = VBA_MFX(y,u,f_fname,g_fname,dim,options,priors_group, options_group)
% VB treatment of mixed-effects analysis
% function [posterior,out] = VBA_MFX(y,u,f_fname,g_fname,dim,options)
% This function approaches model inversion from an empirical Bayes
% perspective, whereby within-su... |
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