sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
400fa510b64a3f1c7898123659eaac5742a0d1a7da8dca36ce99b060a6dea554 | MATLAB | 7,761 | 257 | function [Bset,nB,mtr] = palm_shuftree(varargin)
% This is a wrapper for the palm_permtree.m and palm_fliptree.m
% that generates a sigle set of permutations. It can also generate
% only permutations with sign-flipping depending on the input
% arguments.
%
% Usage (style 1)
% [Bset,nB] = palm_shuftree(Ptree,nP0,CMC,EE,... |
076d7525a5e3bfff8d312eb36d68ff4901c18f6598f5b61628aa6bbc669ba407 | MATLAB | 7,765 | 226 | function nptype21_imro
% Build imro table for single shank NP 2.0 (probe type 21) for some useful
% patterns.
%
% Output is saved in the directory where this script is run.
%
% If a mulitple electrodes are mapped to the same channel, this program
% will not save the imro table.
% patternType = 0 for single ... |
7ec2dd925585d7549a849799554492b159f63f116f0e58e4ee41fc0a0a705e4f | MATLAB | 7,771 | 233 | function hp = superviolin(dat, varargin)
% Basic implementation of Violin SuperPlots in MATLAB
% Please cite the original work (Kenny & Schoen 2021 Molecular Biology of
% the Cell) when using the code for your work. Thank you.
% by Ingmar Schoen, RCSI (c) 2021
% I would like to gratefully acknowledge Jonas Ries for hel... |
2f08d7126efb4c9859d4e0e93b34484c95ae16022fb5107f44c94d4197dca817 | MATLAB | 7,772 | 226 | classdef MyvarHolder
% Class for arbitrary time series variables.
properties (SetAccess=private, Hidden)
p_var % Backup of the original variable, from the time of making the object
p_ts % Backup of the original timestamps, from the time o fmaking the object
checkRoot ... |
9d4772840bc3e46641e3cc1d03031a5bc306a3ba40ed98d8a50a5144307708dc | MATLAB | 7,784 | 226 | function [result] = bfopen(id, varargin)
% Open microscopy images using Bio-Formats.
%
% SYNOPSIS r = bfopen(id)
% r = bfopen(id, x, y, w, h)
%
% Input
% r - the reader object (e.g. the output bfGetReader)
%
% x - (Optional) A scalar giving the x-origin of the tile.
% Default: 1
%
% y - (Optional) ... |
4aac20c92a8c8958cf46ca32d5ca40beceb7ad5f5f6e6d2ddfe37683f0064358 | MATLAB | 7,789 | 257 | function [ws, warned] = ft_warning(varargin)
% FT_WARNING will throw a warning for every unique point in the
% stacktrace only, e.g. in a for-loop a warning is thrown only once.
%
% Use as one of the following
% ft_warning(string)
% ft_warning(id, string)
% Alternatively, you can use ft_warning using a timeout
% ... |
4060cacbb186bcb8a43b8a4f36fda27a741ec6c6bb5abdedda7584d1b7311a7e | MATLAB | 7,793 | 193 | function [tassmInl, flagInl, tassmInlFollower1Out, tassmInlFollower2Out] = ...
retainTassmInliers(tassmMaster, thresholds, tassmFollower1, tassmFollower2)
%RETAINTASSMINLIERS: search for and NaN out outliers in each column of tassm
%
%INPUT: tassmMaster : (array of n cells), each cell contains 3 cells:
% ... |
57d93e628592672e8ad9fee3864e689d008ccd3890d65f896c2aeaeacaba2b78 | MATLAB | 7,799 | 251 | function [fig1, fig2] = plotRepresentativeGraphs(inputFile, outputFolder, numTracks, offset, options)
% PLOREPRESENTATIVEGRAPHS Plot 3D displacement graphs for n cell tracks.
%
% INPUT:
%
% Required:
% inputFile: (char | string)
% Path to the AggregatedCSVResults.xlsx produced by
% aggregateTrackingResul... |
6b33126e129c9d4cccea35a1ad0b56d8f32ed0bdff2654a2131588ada915385a | MATLAB | 7,805 | 220 | %% Set the working directory
clear
cd('C:\Users\perre\Cardin-Higley Lab Dropbox\Quentin Perrenoud\Partage-QP\FigShare'); %<--------- change to local path
addpath(genpath(pwd))
chFigDir = 'Figures'; %<--------- relative path to output figure directory
%% Load data
db2Mat = xlsread('Input_Matrix.xlsx', 'C2:AJ25');... |
aa2e5a7a97bd5d0477c97c7d085d2c3ed4c9b25248fa828fe7dde4bde91d61ea | MATLAB | 7,807 | 198 | % =========================================================================
% Script: Simulation_study2_SNR.m
% Authors: Zijian Gao,Qianxue Shan,Weitian Chen
% Email: zijian.gao@link.cuhk.edu.hk
% Date: 2025-12-19
% Version: 1.0
%
% Copyright (c) 2025 Zijian Gao, Qianxue Shan, Wei... |
e83b15840bc303d7778b81d8b9f0584126b1f9493520b0dcff48ee6ee8700cf9 | MATLAB | 7,809 | 206 | %PRINT2EPS Prints figures to eps with improved line styles
%
% Examples:
% print2eps filename
% print2eps(filename, fig_handle)
% print2eps(filename, fig_handle, options)
%
% This function saves a figure as an eps file, with two improvements over
% MATLAB's print command. First, it improves the line styl... |
73a3198bb115de843d271d48b0708aa37764308c04748871ecae832f55f4d46d | MATLAB | 7,817 | 198 | function RegPara = reg_NoCrossStack(RegPara, handles, imageinfo, figuretitlename, fext, k, w, f_wait)
[userview, systemview] = memory;
% fprintf('Available memory')
disp(systemview.PhysicalMemory.Available)
Mem_max = systemview.PhysicalMemory.Available;
if handles.useGPU
Mem_max = min(systemview.PhysicalMemory.Avai... |
6650cd49a17cc167e27f12c5af260a6064ee1ff2d0581a47466e59545ecc467c | MATLAB | 7,824 | 217 | function [res, errStr]= mrstruct_to_nifti(mrStruct, fName, dataType)
% Convert mrStruct image/volume/series to NifTI compatible files
% FORMAT [res, errStr]= mrstruct_to_nifti(mrStruct, fName, dataType)
% ======
% This routine tries to convert mrStruct data to NifTI compatible files
% using SPM functions spm_type, spm... |
f478e711bb343194fdf3ae4ad34310e423a7f6b141c44c5288c80f7d0a162dd9 | MATLAB | 7,824 | 240 | function [fig] = colormap_roi_meta(mat, sorting, label, labelmeta, varargin)
% DESCRIPTION:
% Save matrix sorted by network label.
% USAGE
% colormap_roi(sorted_matrix, 2, roifile);
% colormap_roi(sorted_matrix, 2, roifile, -.075, .075,'cool',1,'fig title','graph.png')
% colormap_roi(un_sorted_matrix, 1, roifile, ''... |
fb0834744950b0cee556cdbfec04b86aa530189635dec1a302141b56e23ce036 | MATLAB | 7,830 | 255 | % Decode extra NIFTI header information into hdr.extra
%
% Usage: hdr = extra_nii_hdr(hdr)
%
% hdr can be obtained from load_nii_hdr
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function hdr = extra_nii_hdr(hdr)
switch hdr.dime.datatype
ca... |
1343638baf300ed469343f2ebabaf2ff5181ba4cff7cb93a470d9de29a801764 | MATLAB | 7,833 | 147 | function [specklePropPerTimeIntByBoxClass, specklePropPerTimeIntByBoxNoClass] = stratifySpeckleByBoxClass(actinPropPerTimeInterval, boxClass, boxClassCondition, speckleIdPerBox)
%STRATIFYSPECKLEBYBOXCLASS: split the actin speckle data into groups based on their box classification
%
%SYNOPSIS: [specklePropPerTimeIntByBo... |
06cf3a041c0889bc717c6c7912df706f8baa9acb621c0e3987ba814ec2512667 | MATLAB | 7,838 | 186 | function varargout = ea_atlaseditor(varargin)
% EA_ATLASEDITOR MATLAB code for ea_atlaseditor.fig
% EA_ATLASEDITOR, by itself, creates a new EA_ATLASEDITOR or raises the existing
% singleton*.
%
% H = EA_ATLASEDITOR returns the handle to a new EA_ATLASEDITOR or the handle to
% the existing singleton... |
b1c592fe4ef5a7274740ea983ff21d8f99771306998d42e37295c222d8efef76 | MATLAB | 7,849 | 236 |
% Version 26/06/2026
% Authors: Alessandro Petrini and Davide Pierangeli
% -------------------------------------------------------------------------
% This script is provided as a reference implementation of the experimental
% procedure described in the manuscript. It documents the acquisition logic
% and computation... |
d17f9bd0b282926bd7b91dc9a7d6bb9dd6b6b7d08fde8d7271879ba9dc3939fa | MATLAB | 7,850 | 178 | %
% This is a calling routine to test & check out the power spectrum &
% spectrogram routines for unequal segment lengths. In addition, use it
% to compare with Chronux routines when segments are of equal length.
%
clear all;
if 0
dir = 'G:\ravi\Chrowser\Pass~ Tioga_0e927741-9673-46e5-9050-ca1d7541bf22\'... |
94e644160de662adec0496fc342a123b5a40ef4b891b2f865752ea0d96a21159 | MATLAB | 7,852 | 194 | %% 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... |
a632728c9aa2ce58bd3b1104dc1e05ad900ce590845ba97e6463ea2975ca755d | MATLAB | 7,854 | 202 | function ea_busyaction(varargin)
% function displays or hides a spinning wheel on top right corner (default)
% of figure.
if isa(varargin{2}, 'matlab.ui.control.Image')
switch varargin{1}
case 'on'
varargin{2}.ImageSource = fullfile(ea_getearoot, 'icons', 'busy.gif');
varargin{2}.To... |
e5db8077b3c0aa4a97d17ee67aae6c4fd784dcf5313789f649c1265cc7f6a842 | MATLAB | 7,859 | 120 | % -------------------------------------------------------------------------
% SUBFUNCTION which detects artifacts by using a sliding window
% -------------------------------------------------------------------------
function [ autoart ] = artifact_sliding_threshold(cfgT, data_in)
numOfTrl = length(data_in.tria... |
06e2266b65b65ad3f9fa3b288c55d1e3a651200e7ed14d3c2f8ae9a4ef57c071 | MATLAB | 7,860 | 182 | ccc;
RAWDATAPATHs = dir("..\MAT Data\raw\**\7-10Freq Active\**\*.mat");
% Date filter
% other ISI
DATESTRs = {'cc20220908', 'cc20221019', ... % 700, 400
'xx20221017', 'xx20221018'}; % 400, 400
RAWDATAPATHs = RAWDATAPATHs(contains({RAWDATAPATHs.name}, DATESTRs));
MATNAMEs = {RAWDATAPATHs.name}';
AREAs = ... |
b9bcf327da5b8b6935ff01b89471c8259c9c1a22f25a600a5e2fcb29cbd4dc4e | MATLAB | 7,860 | 234 | function [rate_map, xdim, ydim, occupancy, no_occupancy] = RateMap(self, varargin)
% Returns matrix rate_map with x and y dimensions in vectors xs and ys.
%
% [rate_map, xs, ys] = root.plot_rate_map(cel, varargin)
%
% Plots spatial rate map for cell cel = [ tetrode, cell ]
%
%
% ARGUMENTS
% cel 1 x 2 vec... |
32fbd3952d705e2ee4a4ca973e9043299ea29da2afa920038e846e7b59b5604c | MATLAB | 7,871 | 211 | function [lfp] = bz_GetLFP(varargin)
% bz_GetLFP - Get local field potentials.
%
% Load local field potentials from disk. No longer dependent on
% FMAT/SetCurrentSession.
%
% USAGE
%
% [lfp] = bz_GetLFP(channels,<options>)
%
% INPUTS
%
% channels(required) -must be first input, numeric
% ... |
4b601749a3463de513fc824453aadb27a450f42118af97f83765f22979b7228a | MATLAB | 7,874 | 172 | function [Obj,modified] = SOFAupgradeConventions(Obj)
%SOFAcompatibility
% [Obj,modified] = SOFAupgradeConventions(Obj) upgrades the Obj to the next higher
% version if required. MODIFIED is 1 when an upgrade was required.
% In order to obtain the most recent version, SOFAupgradeConventions
% should be p... |
3c7cc7bbc60851c46491427f26ecd846096cf05dc7141af4f02d618d7614ebdc | MATLAB | 7,876 | 159 | %Example script that extracts areas for fold change analysis shown in
%Figure 5
% Inputs are MasterMatAreaABSOLUTE, MasterMatLengthBondABSOLUTE and
% IntensitiesPerFrameMatrix .mats obtained from GetSizeAndBondTables.m
close all
clear all
movie_number = '3';
window_number = '1';
window_size = 10;
if str2double(mov... |
4bba39fbd203dde52d0886c14c6eb14e31e17c69d0f49555282a828b7a691e71 | MATLAB | 7,879 | 216 | function [] = thetaSeqDecoder(spikes,lfp,behavior)
% USAGE
%
%
% INPUTS
%
% spikes cell array of spike times where each element is a neuron and
% each timestamp is represented in seconds
% positions Nx2 matrix of X and Y positions
% lfp
% behavior.events.trialInter... |
bb3eb98e4c2a2f5b9e05f3f968fd765f9f37bcba13bbff9cdf2e17d3141d4766 | MATLAB | 7,879 | 220 |
%% ======================= step 01-00 for disposal all data
% compute some basic maps
%% compute cosine similarity between CBF and Cell-body staining intensity (CCSI)
Data_PScs_bil = subfun_ProfileSimilarity(Data_scan_bil,Data_BBLP_bil);
Data_PScs_uni = subfun_ProfileSimilarity(Data_scan_uni,Data_BBLP_uni);
Data_PSc... |
ef230373855111ba0ffc1b982a7af7a84546ba3bd68ce2ba3b1e9408f2d58cfe | MATLAB | 7,882 | 208 | % eeg_epochformat() - Convert the epoch information of a dataset from struct
% to array or vice versa.
%
% Usage: >> [epochsout fields] = eeg_epochformat( epochs, 'format', fields, events );
%
% Input:
% epochs - epoch numerical or cell array or epoch structure
% format - ['struct'|'array... |
3e98e414a4f5731121dd65e10deb0b64442a1141f1986945b9730ad75ecf8308 | MATLAB | 7,885 | 202 | % pop_firpm() - Filter data using Parks-McClellan FIR filter
%
% Usage:
% >> [EEG, com, b] = pop_firpm(EEG); % pop-up window mode
% >> [EEG, com, b] = pop_firpm(EEG, 'key1', value1, 'key2', ...
% value2, 'keyn', valuen);
%
% Inputs:
% EEG - EEGLAB EEG structure
% 'fcutoff' -... |
ca22cebe13ad95587df40429ca72d745d5df931f7d10bfa8968e79f168251efa | MATLAB | 7,893 | 233 | %
% mergeNSxNEV(filename1, filename2)
%
% This function loads two NSx and NEV files and it will combine them
% together into one file. The resulting file will be saved as new NSx
% and NEV files onto the disk. To combine two NSx and NEV files into
% indivual NSx and NEV variables in MATLAB see combineNSxNEV... |
d19a47f820dfaf5b3a065acbbee29a814f1c2de2459617513ce1bd4e76117508 | MATLAB | 7,896 | 161 | % Copyright (C) 2010 - 2019, Sabass Lab
%
% 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 Free
% Software Foundation, either version 3 of the License, or (at your option)
% any later version. This program is distributed ... |
0013a95b978e6668d134af2c613d6e90c3b2d700fe98ff92c3ad32a404598238 | MATLAB | 7,898 | 239 | function hp = superviolin(dat, varargin)
% Basic implementation of Violin SuperPlots in MATLAB
% Please cite the original work (Kenny & Schoen 2021 Molecular Biology of
% the Cell) when using the code for your work. Thank you.
% by Ingmar Schoen, RCSI (c) 2021
% I would like to gratefully acknowledge Jonas Ries for hel... |
5e8228f17e23f28fae84a86a2a8598ef2f7fd62fb79166514fb6a7f0697edb30 | MATLAB | 7,898 | 174 | %% BUZCODE TUTORIAL: SPW-R (HPC), UP/DOWN, and State Event Detection
% SUMMARY:
% In this tutorial we outline the use of the buzcode repository to load a
% .lfp file and detect i) hippocampal sharpwave-ripples and ii) cortical UP/DOWN
% states. We then create a .evt file that can be read into neuroscope for
% si... |
f6642e00d27702336b819acfd46dc75b369ac51e5202d3ce2c5752f9651805fe | MATLAB | 7,908 | 163 | % 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... |
1526f171ccaa0693dfa251edf9fa3a5e38f9f8192ea5c6ea6fb9f0710a2f7e2b | MATLAB | 7,921 | 236 | % Runs a two-sample t-test for a set of signature responses, for each
% conditions. Also runs NPS subregions.
% Signatures, scaling, etc. are defined below.
% created by @lukasvo76 from h_group_differences.m, March 2021
%% USER OPTIONS
% -------------------------------------------------------------------------
mys... |
67962673df9380a95adea6459addea008a35368b50a5874298468a828ab4765b | MATLAB | 7,924 | 190 | classdef StepWaveform < DiscreteWaveform
%STEPWAVEFORM is derived from the DiscreteWaveform class and contains
%only the extra necessary properties to produce time stamps for
%triggering or anyother desired method.
properties (SetAccess = 'private')
Triggers
% Reminder: Size and val... |
249c86bc709948647d6533261f93d9b0e102d3071b311d513f1e3e321fa24135 | MATLAB | 7,925 | 232 | function handles = loadtrace(handles, dataID)
datafilepath = handles.datafilepath;
datafilename = handles.datafilename{dataID};
fprintf('Load data from: ' ); fprintf('%s\n', fullfile(datafilepath, datafilename));
variableinfo = who('-file', fullfile(datafilepath, datafilename));
variablename = handles.variablename;
im... |
6cc2a6cd46ead0f578a67c60a461b39d35a233e4d8c425e8175bafcdecf5e0f3 | MATLAB | 7,928 | 217 | % GICA BIDS App (tweaked from spm BIDS app file @ https://github.com/bids-apps/SPM/blob/master/spm_BIDS_App.m)
gica_inputs = evalin('base', 'gica_inputs');
%==========================================================================
%-BIDS App structure
%================================================================... |
5c8be8487c3d62c76314eeef33d46732694e0cdd54e1c2bb5e6e0a51157079cb | MATLAB | 7,929 | 199 | %% Load and explore a sample dataset
% This example shows how to load a pre-set example fMRI dataset into
% an fmri_data object.
%% General instructions
%
% Before you start, the CANlab_Core_Tools must be added to your path with
% subfolders. Otherwise, you will get errors.
%
% The script canlab_toolbox_setup can help... |
8a7caabe490cd954261cefd2ef1dbe78ac375673557d6dc4148bbfb2400fcd3f | MATLAB | 7,936 | 256 | function [WC,T] = LeG_autoElecs(app)
Img = app.CTImg;
MaxElecs = app.detect.maxelecs;
ElecRad = 2; % electrode radius in mm (standard intracranial)
XYZScale = app.XYZScale; % voxel scaling (used earlier; now mostly for info)
MRInfo = app.MRInfo;
ProjSurfRaw = app.Pr... |
552665ba2b09d542de91b29e2cc15617f8e1c090753fd3a83d910269bb064182 | MATLAB | 7,950 | 196 | function cs_dmri_conseed_map(connBaseFolder,connName,sfile,cmd,space,options)
useNativeSeed = options.prefs.lcm.struc.patienttracts.nativeseed;
for s=1:length(sfile)
if useNativeSeed
vatdir = [fileparts(sfile{s}),filesep];
copyfile(ea_niigz([ea_getearoot,'templates',filesep,'spacedefinitions',files... |
ce44e4719c8e73ed780806bbabf962aae9a99d706217a7b7cf260d474ef137bf | MATLAB | 7,950 | 207 | function violins = violinplot(data, cats, varargin)
%Violinplots plots violin plots of some data and categories
% VIOLINPLOT(DATA) plots a violin of a double vector DATA
%
% VIOLINPLOT(DATAMATRIX) plots violins for each column in
% DATAMATRIX.
%
% VIOLINPLOT(DATAMATRIX, CATEGORYNAMES) plots violins for each
% ... |
842ce05d7641b75277cbbc34a301b7b853ad26a811fcbe4d5a48dee3ebdac0bc | MATLAB | 7,958 | 152 | function mris_SD_pairwise_register(fixed_surface, moving_surface, output_surface, disp_iter)
% mris_SD_register(input_surface, moving_surface, output_surface, disp_iter)
% Example call:
% <When in the same directory as mris_SD_pairwise_register.m>
% mris_SD_pairwise_register('../../example_surfaces/OAS1_0001... |
7aee96214b32e6a9f13c76087baa3f2831ff9d4ed7dfb859e58585cf6d7fdd14 | MATLAB | 7,961 | 211 | %Adapted from bz_eventCSD from Buzsaki lab repository. Almost identical to
%what is used by AFR lab as well.
%LV 1/10/25
function [ csd, lfpAvg ] = bz_eventCSD_lv (lfp, events, animal, group, filter, csd_lyr_borders, region, varargin)
% [ CSD ] = bz_eventCSD (lfp, events, varargin)
% Calculates event-triggered (i.e. ... |
2e94eb0030a25bfa89ed5dea26bf7fab6d8aac6009d27c96240bf339d4bc0af7 | MATLAB | 7,965 | 185 | function results = pass_index( varargin )
% PASS_INDEX - Calcultes the pass index and plots
%
% Calculates the pass index for the data passed. This function uses the
% pass_index_parser to generate its input structure.
%
% RESULTS = PASS_INDEX_PARSER(POS_TS,POS,SPK_TS,LFP_TS,LFP_SIG)
% RESULTS = PASS_INDEX_PARSER(POS_T... |
c1aa32e66af993e9394d16722a81bdfa2938ef7f4f527d6b376f8923a21b792e | MATLAB | 7,973 | 252 | function fit = fit_meta_d_mcmc_regression(nR_S1, nR_S2, cov, mcmc_params, fncdf, fninv, name)
% HMeta-d for between-subjects regression on meta-d'/d'
% cov is a n x s matrix of covariates, where s=number of subjects, n=number
% of covariates
% See fit_meta_d_mcmc_group for full details
%
% Steve Fleming 2017
%
% 16.09... |
2e3976963bfba23566cf38b21083c569614deb19413b3286774432a36219b8b3 | MATLAB | 7,986 | 309 | 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 sample ... |
a78d889dce0a13cd49b8935a3021c186fe33b8d2ed7458b74ea110d64baf5bd2 | MATLAB | 7,996 | 237 | function [SourcesMat,SetsMat,TransMat] = PIDLattice(N)
%PIDLattice creates necessary lattice variables for PID calculations.
% [SourcesMat,SetsMat,TransMat] = PIDLattice(N) is a collection of
% variables that describe the partial information lattice. These
% variables depend on the number of X variables that are ... |
2f5f21126df9f68bcfb12456403779196b374343c8d450dc82ff8a53f83ec272 | MATLAB | 7,999 | 212 | % eeg_eegrej() - reject porition of continuous data in an EEGLAB
% dataset
%
% Usage:
% >> EEGOUT = eeg_eegrej( EEGIN, regions );
%
% Inputs:
% INEEG - input dataset
% regions - array of regions to suppress. number x [beg end] of
% regions. 'beg' and 'end' are expressed in... |
cc6f3bd39c19361a17b10ffdeab981a509a355ad2ec0d1f649573bf24091621b | MATLAB | 7,999 | 131 | function cpDiff = couplingdiffs(coupling, spindles, so, srate, samples)
% Summarize slow oscillation and spindle parameters separately for coupled
% and uncoupled events
%
% Required inputs:
%
% coupling: A structure containing coupling data (output of
% fun_so_spindle_coupling)
%
% spindles: A structure containing spi... |
bda4156d4a8647aafc2da32cf1846356a517cb3172cdad8b9df1336dc38c8a17 | MATLAB | 8,008 | 236 | function this = read_gifti_file_standalone(filename, this)
% Low level reader of GIfTI 1.0 files
% FORMAT this = read_gifti_file(filename, this)
% filename - XML GIfTI filename
% this - structure with fields 'metaData', 'label' and 'data'.
%_____________________________________________________________________... |
81d432654b15d516e496f2a23e22bd4eb865332ee9dee90b173c7ceb49113193 | MATLAB | 8,017 | 226 | function varargout = dirwalk(topPath, visitor, recursionLimit, varargin)
%DIRWALK Generate the file names in a directory tree by walking the tree
%
% Description:
% Function DIRWALK generates the file names in a directory tree by walking the tree
% top-down. For each directory in the tree rooted at directory ... |
bcf114448e62ae9c9bdaf5faa57c72d7e11efa347191cb197f1c17cc76ccd4e2 | MATLAB | 8,023 | 224 | function stackview(mr,hr,ftr,showfun)
if nargin == 3,
showfun = @imagesc;
end;
ds.img = mr;
ds.hr = hr;
ds.ftr = ftr;
set(datacursormode,'UpdateFcn',{@(x,y) labeldtips(x,y,ds)})
%f = figure('Position',[360,500,750,585]);
f = gcf;
clf;
h = uicontrol('Style','slider','String','Surf','Position',[0,0,... |
363507cae4b932790d4dafed22212716f09d5ab6ccd61e596a698c2b6dbb6bb9 | MATLAB | 8,031 | 214 | % eegfilt() - (high|low|band)-pass filter data using two-way least-squares
% FIR filtering. Optionally uses the window method instead of
% least-squares. Multiple data channels and epochs supported.
% Requires the MATLAB Signal Processing Toolbox.
% Usage:
% >> [smoothdata] = ... |
d00702f7591bfed71ff9b960c2ccfdcdd344aa07148ecdb3084ce4efd8cfef0d | MATLAB | 8,035 | 189 | function varargout = impexp_run_probstruct2nifti(cmd, varargin)
% Template function to implement callbacks for an cfg_exbranch. The calling
% syntax is
% varargout = impexp_run_probstruct2nifti(cmd, varargin)
% where cmd is one of
% 'run' - out = impexp_run_probstruct2nifti('run', job)
% Run a job, an... |
922676d52b7a9569c5312794743190eff5986d18ebe7e5a53d611ef07c4fc3d7 | MATLAB | 8,044 | 204 | % function run_stress_calculation(traction_data,savename,domainname,BC)
%RUN_STRESS_CALCULATION
%
% run_stress_calculation(traction_data,savename,domainname,BC)
%
% Compute monolayer stresses. This follows the procedure the following
% papers:
% Tambe et al, Nat Mater, 2011, 10:469-475
% Tambe et al, Plos One, 2013,... |
7702be6b997f014a819f80da10469895194823df4109be723b3e1c17cbffdbcf | MATLAB | 8,046 | 287 | function map = turbo(m)
% TURBO An improved rainbow colormap for visualization
% TURBO(M) returns an M-by-3 matrix containing a colormap.
%
% TURBO returns a colormap with the same number of colors as the current
% figure's colormap. If no figure exists, MATLAB uses the length of the
% default colormap.
%
% S... |
0a6663b17c5087b33f8a539fb5fc8f05d6a50dc7e2c4ca0f59cc74fba29c2fd2 | MATLAB | 8,052 | 229 | function [N,X,sp] = optimalHistogram(varargin)
% OPTIMALHISTOGRAM generates a histogram using the "optimal" number of bins
%
% This function was previously called histogram prior to R2014B
%
% If called with no output argument, optimalHistogram plots into the current axes
%
% SYNOPSIS [N,X,sp] = optimalHistogram... |
b008c93e9471d3f6ce080f9491fcaf861200ccc8471847ea06983e3af17f28d8 | MATLAB | 8,056 | 214 | function ConvertMountainsort2Neurosuite(basepath,basename)
% 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 and base... |
09d24d56ebc8ad38fa31dac8624e3f2bcdbb728e859bbc7d8cf17d2ccb6669d9 | MATLAB | 8,071 | 263 | % [kcMax,A0,kcGM,d0,d] = getDcorrSect(im,r,Ng,Na,figID)
% ---------------------------------------
%
% Estimate the image sectorial cut-off frequency based on decorrelation analysis
%
% Inputs:
% im 2D image to be analyzed
% r Fourier space sampling of the analysis (default: r = linspace(0,1,50)
% ... |
4eda755026ba9ee0a9c101d1089cb6c97e9931386a1a0c4fe72c62dafea62c87 | MATLAB | 8,071 | 163 | function hndl=plotci(obj,x,y,yci,draw_data,geom,dodge,width)
if nargin<7
dodge=0;
end
if nargin<8
width=0.5;
end
x=shiftdim(x)';
y=shiftdim(y)';
%Hackis... |
34f195319e2d40bd0d9e71f3705893cbf29778e0d88e931f5e3af85477914568 | MATLAB | 8,079 | 214 | function [xscl,y,zscl,y0, w,relt, dxmdz,err, wr] = ...
wregion(L,Lden,Lsd,d,v,vfrm,A,DAt,dense, R,K,y,y0,b, pars, wr)
% [xscl,y,zscl,y0, w,relt, dxmdz,err, wr] = wregion(L,Lden,Lsd,...
% d,v,vfrm,A,DAt,dense, R,K,y,y0,b, pars, wr)
%
% WREGION Implements Sturm-Zhang Wide-region Interior... |
28316dd02e4ca778f5cb5becb244b519a7a5ac9718087c866cc588e8ad96ac22 | MATLAB | 8,081 | 209 | function demoBrowser()
%demoBrowser: an example of using layouts to build a user interface
%
% demoBrowser() opens a simple GUI that allows several of MATLAB's
% built-in demos to be viewed. It aims to demonstrate how multiple
% layouts can be used to create a good-looking user interface that
% retains the corr... |
22b1d2fbe16c0611187c6bf5a5bbf82b36b81c31254c4080b8783b7bd97d7016 | MATLAB | 8,085 | 317 | function [out] = EgocentricRatemap(root, varargin)
% calculates the egocentric ratemap and returns structure containing all of
% the relevant information for plotting or statistical testing.
%
% Note: In order to simplify distribution we assume that the "root" object
% contains cleaned and epoched data only.
%% Setup... |
8ccf6b3ddec34e578084585831604da367a73e43052c50a21cd489d73bacff06 | MATLAB | 8,085 | 232 | function[vardecomp] = glmfit_multilevel_varexplained(X,Y,B,varargin)
% Variance decomposition for multi-level linear model
%
% USAGE: vardecomp = glmfit_multilevel_varexplained(b,XX,YY,varargin)
%
% B is the transposed vector of beta weights returned by glmfit_multilevel
% Default is B = stats.beta' obtained from work... |
fd391635a3996a1674437cdde9d229fd51e10749f178a09904661f66992347fd | MATLAB | 8,088 | 229 | function [N,X,sp] = optimalHistogram(varargin)
% OPTIMALHISTOGRAM generates a histogram using the "optimal" number of bins
%
% This function was previously called histogram prior to R2014B
%
% If called with no output argument, optimalHistogram plots into the current axes
%
% SYNOPSIS [N,X,sp] = optimalHistogram... |
ab7ed33e6aa0ece6c1f90ca761a1dd23a3a68f8bb6978f2f6320951de2f8f8c4 | MATLAB | 8,092 | 218 | function vatlist = ea_networkmapping_getvats(obj)
% Return list of VATs
numPatient = length(obj.allpatients);
vatlist = cell(numPatient*2,1);
[modlist,modType] = ea_genmodlist;
[~,ix] = ismember(obj.connectome,modlist);
if ~ix
ea_error('Something went wrong, connectome disappeared?');
end
modType = modType(ix);
m... |
24d7c1fbb98d51847e8e0a7eb64308029feeda4fb940fb36aaf21ececf741409 | MATLAB | 8,093 | 200 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_nii_hdr(fileprefix, machine)
fn = sprintf('%s.hdr',fileprefix);
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
hdr =... |
99f524c4ddba4964bc7988794934a0d6d492fbf7795077c14f77152b4468666b | MATLAB | 8,110 | 201 | function CBIG_MMLDA_example_wrapper(out_dir, queue)
% Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
CBIG_CODE_DIR = getenv('CBIG_CODE_DIR');
addpath([CBIG_CODE_DIR '/stable_projects/disorder_subtypes/Sun2019_ADJointFactors/step2_MMLDA'])
doc_dir = [CBIG... |
6df5ee9496a9ed29a6d5187a1d76bf64b247c6809b6ff6ec0d95cf62f2ee5594 | MATLAB | 8,123 | 283 | function varargout=ea_genvat_kuncel(varargin)
% This function generates a volume of activated tissue around for each
% electrode.
% Usage: VAT=ea_genvat(coords_mm,stimparams,options).
% ? stimparams is a struct variable with fields U (8*1 with voltage
% entries) and Im (8*1 with Impedance measurements).
%
% This functi... |
07d5b80e8d84024772c875e6ed4951e75a5e1c87651ad79ff5dac896c17218c7 | MATLAB | 8,131 | 267 | function cm_data=GyRd(m)
cm = [0.1020 0.1020 0.1020
0.1100 0.1100 0.1100
0.1180 0.1180 0.1180
0.1260 0.1260 0.1260
0.1340 0.1340 0.1340
0.1420 0.1420 0.1420
0.1500 0.1500 0.1500
0.1580 0.1580 0.1580
0.1660 0.1660 0.1660
0.1740 ... |
78a1d9b73821b86307d3da39ddf146de742d2bdde514d5d484b969bad46796a5 | MATLAB | 8,131 | 267 | function cm_data=GyBu(m)
cm = [0.1020 0.1020 0.1020
0.1100 0.1100 0.1100
0.1180 0.1180 0.1180
0.1260 0.1260 0.1260
0.1340 0.1340 0.1340
0.1420 0.1420 0.1420
0.1500 0.1500 0.1500
0.1580 0.1580 0.1580
0.1660 0.1660 0.1660
0.1740 ... |
cae4ae7c13592648f314ae87c5585954c79c3c1681f22920bd2136670802352f | MATLAB | 8,133 | 267 | function cm_data=Reds_r(m)
cm = [0.4039 0 0.0510
0.4141 0.0025 0.0529
0.4240 0.0051 0.0546
0.4338 0.0077 0.0562
0.4434 0.0104 0.0577
0.4528 0.0130 0.0591
0.4621 0.0156 0.0603
0.4712 0.0182 0.0615
0.4801 0.0207 0.0626
0.4888 ... |
f6dfee68f283ebd8a863677a410ff3d6004574729907483840a058228ccf4a86 | MATLAB | 8,134 | 267 | function cm_data=Blues_r(m)
cm = [0.0314 0.1882 0.4196
0.0307 0.1925 0.4276
0.0299 0.1967 0.4355
0.0292 0.2010 0.4432
0.0285 0.2052 0.4508
0.0277 0.2094 0.4582
0.0270 0.2135 0.4655
0.0263 0.2177 0.4727
0.0256 0.2219 0.4797
0.0249 ... |
5cd8895f027f64b9213c0ea822ed9f507cf0f1a76819a8d24b24f547ba6caaac | MATLAB | 8,137 | 243 | function Pset = palm_fliptree(Ptree,nP,cmc,idxout,maxP)
% Return a set of permutations from a permutation tree.
%
% Usage:
% Sset = palm_fliptree(Ptree,nS,cmc,idxout,maxS)
%
% Inputs:
% - Ptree : Tree with the dependence structure between
% observations, as generated by 'palm_tree'.
% - nS : Number of... |
f3a9bb22b4da4144b2dcbebe4e841488349e7a9d3623a7015553ff045dd4dbcc | MATLAB | 8,139 | 307 | function [x,fval,exitflag,output] = fminsearchbnd(fun,x0,LB,UB,options,varargin)
% FMINSEARCHBND: FMINSEARCH, but with bound constraints by transformation
% usage: x=FMINSEARCHBND(fun,x0)
% usage: x=FMINSEARCHBND(fun,x0,LB)
% usage: x=FMINSEARCHBND(fun,x0,LB,UB)
% usage: x=FMINSEARCHBND(fun,x0,LB,UB,options)
% usage: x... |
9ef986c5b2ebb9ff668145923200bad7a4d8fcb6c62e4870358be7414751f9fa | MATLAB | 8,142 | 239 | classdef (Abstract) audio < matlab.mixin.Copyable
%AUDIO Abstract superclass providing audio-related properties and methods.
%
% The IOSR.DSP.AUDIO superclass is an abstract class that defines
% audio-related properties and methods. As an abstract class, it cannot
% be instantiated.
%
% IOSR.DSP.AUDIO is a su... |
6cef202216962684a05cc8952020807e68a71737b10cafb9d8a969bfcb2c5b03 | MATLAB | 8,148 | 218 | function vatlist = ea_unified_nm_getvats(obj)
% Return list of VATs
numPatient = length(obj.allpatients);
vatlist = cell(numPatient*2,1);
[modlist,modType] = ea_genmodlist;
[~,ix] = ismember(obj.calcsettings.netmap_connectome,modlist);
if ~ix
ea_error('Something went wrong, connectome disappeared?');
end
modType ... |
56d25fbf09a4cf4ef38ae857a3292c0fa4e1a4e31ea1ffbe7278eeee9af70ee5 | MATLAB | 8,149 | 267 | function cm_data=GyRd_r(m)
cm = [0.1020 0.1020 0.1020
0.1100 0.1100 0.1100
0.1180 0.1180 0.1180
0.1260 0.1260 0.1260
0.1340 0.1340 0.1340
0.1420 0.1420 0.1420
0.1500 0.1500 0.1500
0.1580 0.1580 0.1580
0.1660 0.1660 0.1660
0.1740 ... |
cbd44caac13ef297172247c3781aea0bb4239f5ca7c5bd808d3143b70be4548e | MATLAB | 8,149 | 267 | function cm_data=GyBu_r(m)
cm = [0.1020 0.1020 0.1020
0.1100 0.1100 0.1100
0.1180 0.1180 0.1180
0.1260 0.1260 0.1260
0.1340 0.1340 0.1340
0.1420 0.1420 0.1420
0.1500 0.1500 0.1500
0.1580 0.1580 0.1580
0.1660 0.1660 0.1660
0.1740 ... |
bdc7f3a5e1283c44086e4c98040b7cc6e8e5f05024eb1032a3a894c30ff451ce | MATLAB | 8,154 | 217 | function dicm_save(img, fname, s)
% DICM_SAVE(img, dicomFileName, info_struct);
%
% Save img into dicom file, using tags stored in struct, as dicomwrite does.
% The img can have up to 4 dimensions, with 3rd typically RGB and 4th frames.
%
% Comparing to dicomwrite: Advantage 1: DICM_SAVE supports img with any Matlab
%... |
1521f7a588fdd39bd570745fd7c39ab2250b520dd84c0642bcb74378c2b5e83a | MATLAB | 8,156 | 243 | % KMEANS: K-means clustering of n points into k clusters so that the
% within-cluster sum of squares is minimized. Based on Algorithm
% AS136, which seeks a local optimum such that no movement of a
% point from one cluster to another will reduced the within-cluster
% sum of squares. Te... |
5a965a93c346c417e4209dd3c7b54cc5ffa5062b2608088b66df25e7504bafd3 | MATLAB | 8,162 | 344 | function [regParams,Bfit,ErrorStats]=ea_absor(A,B,varargin)
%ABSOR is a tool for finding the rotation -- and optionally also the
%scaling and translation -- that best maps one collection of point coordinates to
%another in a least squares sense. It is based on Horn's quaternion-based method. The
%function works for bo... |
705f429b051fab7da80eece520abb7b1b6a6fd71ccdbe1e164c0e672143f4acc | MATLAB | 8,180 | 245 | function [ A ] = PhiIDFullDiscrete(varargin)
%%PHIIDFULLDISCRETE Computes full PhiID decomposition of discrete input data
% using the MMI PhiID.
%
% A = PHIIDFULLDISCRETE(X, TAU), where X is a D-by-T data matrix of D
% dimensions for T timesteps, and TAU is an integer integration timescale,
% computes the PhiID d... |
61886d967cef3c30bc7163ae20348a822a1694c6c50fe5222f8804ef03a15055 | MATLAB | 8,191 | 208 | function varargout=ea_ft_gqi_yeh(options)
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn
if ischar(options) % return name of method.
varargout{1}='Generalized Q-Sampling (Yeh et al.... |
958f7bb530a713c207bcf85670505b1b033c7a333d0de7eef813a52e3f7995cd | MATLAB | 8,193 | 262 | % eeg_pv() - Compute EEG.data 'percent variance ' (pv) of the whole EEG data versus the projections
% of specified components.
% Can omit specified components and channels from the computation. Can draw a plot
% of the scalp distribution of pv, or progressively compute the pv ... |
bbbf81c4d3c41cce68288fd686b6f4bf1f629392fd4bbaada5f2a41940b296ae | MATLAB | 8,203 | 195 | function tests = testHeadless
%TESTHEADLESS Structural sweep: constructs that make the library unusable in CI.
%
% These are source-level tests, not numerical ones. They exist because the
% failure they catch is invisible to any test that calls a function inside
% try/catch -- MATLAB does not break into the debug... |
1cb9822aa65cfe938404d90d5b53826be3b7c8c6cc714d0adcc986d0943ee7df | MATLAB | 8,206 | 196 | % pop_studyerp() - create a simple design for ERP analysis
%
% Usage:
% >> [STUDY ALLEEG] = pop_studyerp; % pop up interface
%
% Outputs:
% STUDY - an EEGLAB STUDY set of loaded EEG structures
% ALLEEG - ALLEEG vector of one or more loaded EEG dataset structures
%
% Author: Arnaud Delorme, SCCN, ... |
71b068b85f3670baca3ea65e3db6ec9efbb292f25deb3e4f14a2c09978713da6 | MATLAB | 8,212 | 153 | % dipfitdefs() - default settings and filenames for dipolefitting
% to source in the ICA/ERP package functions.
% Insert local dir reference below.
%
% Note: Edit this file to change local directories under Unix and Windows
%
% Author: Robert Oostenveld, SMI/FCDC, Nijmegen 2003
% SMI, ... |
3ab076f5681c30eb29e742441ce8ae4862d164fa4c3a72815e91349469430d13 | MATLAB | 8,219 | 214 | function CFA_CheckNormROI
ansct = questdlg('CT mode','CT mode','yes','no','no');
ansWithT1 = questdlg('With T1 mode','With T1 mode','yes','no','no');
PG = uigetdir(pwd,'Check Data(after normalize)');
dir1 = [PG,filesep,'NormBG',filesep];
if ~isfolder(dir1)
dir1temp = uigetdir(pwd,'Please Select Normalized Backgrou... |
7b286947551b4c5be2b0efe8c72fb2fad726af7b348a6e7e6c58db07b594b795 | MATLAB | 8,228 | 236 | function baseline = CBIG_MMLDA_hypotest_independent_factors(k, N, betas, stats, output, CI_scale)
% baseline = CBIG_MMLDA_hypotest_independent_factors(k, N, betas, stats, output, CI_scale)
%
% This function will do omnibus and pairwise tests of k factors.
%
% Input:
% - k : number of factors
% - N ... |
87ffd35f388584a9d5c7a4b7c8905e987c1aad3a4192ff8ad3a40c087f3ae5dc | MATLAB | 8,229 | 183 | % eeg_rejmacro() - Internal EEGLAB macro for all pop_ functions that
% perform data rejection.
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
%
% See also: eeglab()
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, arno@salk.edu
%
% This program is free software; you can redistribute it ... |
b5f83781e5ab657d1d3e3a50701f03cb29dde33e8ed1162e7037acda4f9af417 | MATLAB | 8,232 | 200 | function R = LaBGAScore_check_display(varargin)
%
%
% *USAGE*
%
% Checks whether the display of the current session is big enough to
% produce good figures in a published HTML report, and says what to change
% if it is not.
%
% Why this exists: publish() captures figures from the screen, so the size
% and DPI of your X... |
14f580af66b8ec8a51b9e140dad3d0ffb7a6f349943d55a7ecfbd97d101924d4 | MATLAB | 8,234 | 212 |
function [output Greg] = dftregistration(buf1ft,buf2ft,usfac)
% function [output Greg] = dftregistration(buf1ft,buf2ft,usfac);
% Efficient subpixel image registration by crosscorrelation. This code
% gives the same precision as the FFT upsampled cross correlation in a
% small fraction of the computation time an... |
cf7fdcd4f2df19c39e123e60dccd41d0103ca3070d59a2072ee67a9dde272fd1 | MATLAB | 8,237 | 210 | function y = signals(kind, n, varargin)
%SIGNALS Deterministic test signals with known analytic answers.
%
% y = nonantest.signals(kind, n, ...) returns an n-by-1 column vector.
%
% Every generator here is implemented from scratch in base MATLAB and is
% deliberately INDEPENDENT of the NONAN library. Known-answer... |
6421d57c02beebb2a689e82029a7853292e78764e5136e61c46cd7e07a6d85ac | MATLAB | 8,238 | 193 | function [timeStamps, waveForms] = BlackrockNEVLoadingEngine(varargin)
%%
% Blackrock Microsystems NEV loading engine for MClust 3.0.
%
% Kian Torab
% support@blackrockmicro.com
% Blackrock Microsystems
%
% Version 1.3.0.0
%
% Version 1.4 by Saman Hagh Gooie - 13 October 2016
% - Modifed to work with the lates... |
ad0f1208f6372e499d353b8c5a87f758ab88daa6be6b7f9c1727c66d18bbf982 | MATLAB | 8,242 | 268 | function cmd =ea_ants_schoenecker(varargin)
% Wrapper for ANTs nonlinear registration
fixedimage=varargin{1};
movingimage=varargin{2};
outputimage=varargin{3};
if ischar(fixedimage)
fixedimage={fixedimage};
elseif ~iscell(fixedimage)
ea_error('Please supply variable fixedimage as either char or cellstring');
... |
a0b1b3f8a938387a9e92933b0727d050f6cf2279099be0fe456c7262fab2a0b5 | MATLAB | 8,244 | 236 | function this = read_gifti_file_standalone(filename, this)
% Low level reader of GIfTI 1.0 files
% FORMAT this = read_gifti_file(filename, this)
% filename - XML GIfTI filename
% this - structure with fields 'metaData', 'label' and 'data'.
%________________________________________________________________... |
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