sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b2ce38656fd1b4a2f32728025a7e2ddc51c49fd509fa464a25a538be94b6841c | MATLAB | 9,136 | 250 |
function [lfp, events, group, sex, age, channels_by_layer_csd, remove_chans_csd] = pre_CSD_by_speed(animal,filter, region, mins, maxs)
%make data for CSD
%get lfp for best row of 21 channels
%find channel assignments for each layer, bad channels
%to be removed for group analysis
%events = theta trough times
... |
363340851d2f2bff5eda5caeefdc5e808394f45b2bc1bd22254e1f367a342f7b | MATLAB | 9,167 | 320 | 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
%% ======================= compare... |
918df83d74aae62f71a8cf498846d068ec0883d5757f1c8b63920902250a946c | MATLAB | 9,167 | 242 | % std_detachplots() - Given a figure with subplots and several lines per axis, will add a callback to
% each axis specified in the 'figtitles' input. The callback consist in a figure with all the detached
% individuals lines.
%
% Usage:
% >> std_detachplots('','','data',data 'figtitles', alltitlestmp,'sbtitles',sb... |
10474955f2eee9b29557d6afc5527710f67f7251a7b44d58e1b59beb10bc0e43 | MATLAB | 9,169 | 223 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% demo_wave_model_simulation.m
%%%
%%% MATLAB script to demonstrate how to simulate the wave model on a
%%% cortical surface. In particular, the script demonstrates how to
%%% (1) simulate resting-state activity and
%%% (2) simulate evoked ac... |
9cc425c60f865c2120a7d65c80ce986271199466476220e15ff366c0cb31b206 | MATLAB | 9,176 | 146 | %% ETLAS2 Dual-Echo pCASL Summary Statistics
% Aggregate calibrated-BOLD metrics (CBF, BOLD, CMRO2, n) per subject in visual ROI
p = "/mnt/projects/ETLAS2/data/derivatives/dual_echo_pcasl/";
overview = readtable('/mnt/projects/ETLAS2/data/subjects_overview_dual_echo_pcasl.xlsx', "TextType", "string", "EmptyFieldRule"... |
502a5b1f068c5538a0bbcae5fd136a71dff7d524eee98862e639b4ea625e94d5 | MATLAB | 9,179 | 261 | %% LaBGAScore_atlas_binary_mask_from_atlas.m
%
%
% *USAGE*
%
% This script creates a binary mask by combining regions from one or more
% atlases, and automatically saves the fmri_mask_image, and .nii versions
% of it in maskdir of your dataset
%
% There are options to save the original atlas object created by
% select_... |
0993015f6ffc63f9a5849d844f52b78d15b8b16716f5e239f129573e9dd30318 | MATLAB | 9,186 | 129 | % Step 1: Create a main analysis folder <basedir> and navigate there
% -------------------------------------------------------------------------
% Run:
a_set_up_new_analysis_folder_and_scripts % Creates local folders and copies in relevant scripts
% Step 2: Edit these files in you local analysis folder an... |
52d432f673d561c2e12dda8426913c1dddf396e63cf8a1e314aae7a6ab0b8fb6 | MATLAB | 9,187 | 268 | function varargout=ami_thomas(varargin)
% [tau,ami]=AMI_Thomas(x,L)
% inputs: x - time series, vertically orientedtrc files selected by user
% L - Maximum lag to calculate AMI until
% outputs: tau - first true minimum of the AMI vs lag plot
% AMI - a vertically oriented vector containing valu... |
2b5fde60540ce21258dc48573d52ad7696cc389bb64dcf84943397acd526a808 | MATLAB | 9,188 | 235 | function varargout = segment_ar_gui(varargin)
% SEGMENT_AR_GUI MATLAB code for segment_ar_gui.fig
% SEGMENT_AR_GUI, by itself, creates a new SEGMENT_AR_GUI or raises the existing
% singleton*.
%
% H = SEGMENT_AR_GUI returns the handle to a new SEGMENT_AR_GUI or the handle to
% the existing singleton... |
5dc3623515d66f4608dcbfa190d6763e4021c4cddf675243a8d965c75f102c46 | MATLAB | 9,196 | 218 | function [positionDecodingGLM_gaussian] = bz_positionDecodingGLM_gauss(varargin)
% USAGE
% [] = bz_positionDecodingGLM_gauss()
%
% INPUTS
%
% spikes
%
% behavior
%
% lfp
%
% smoothingRange
%
% plotting - cell UID to plot
%
% saveMat
%
% OUTPUTS
%
% positionDecodingGLM_gaussian cellinfo stru... |
3373d006e7474a4448cc30659a1b0a23316ef49890c454e5d3db2f289bbffda8 | MATLAB | 9,201 | 285 | function [ixes,R,p]=ea_leoo_significance(XYZV)
% clear NAN vars:
XYZV(isnan(XYZV(:,4)),:)=[];
% setup randomization:
maxiter=1001;
csize=nan(maxiter,size(XYZV,1));
dimen=length(XYZV);
for iter=1:maxiter
dat=XYZV;
if iter>1
dat(:,4)=dat(randperm(length(dat)),4);
end
% generate predicted co... |
2987f24c4c2d7196669755ebc654558c9fc30e0c602fb2c7cdc7cb7b72eecc0f | MATLAB | 9,207 | 283 | function [ixes,R,p]=ea_leoo_significance(XYZV)
% clear NAN vars:
XYZV(isnan(XYZV(:,4)),:)=[];
% setup randomization:
maxiter=1001;
csize=nan(maxiter,size(XYZV,1));
dimen=length(XYZV);
for iter=1:maxiter
dat=XYZV;
if iter>1
dat(:,4)=dat(randperm(length(dat)),4);
end
% generate predicted co... |
1768c2d235920e9493e75b935a011d04158719129be2ea044e495ba2a2617ecb | MATLAB | 9,208 | 247 | function [n_cnt,con_mat,pval]=ea_NBSstats(varargin)
%NBSstats Computes network components among edges that survive a primary
%test statistic threshold. Assigns a corrected p-value to each component
%using permuted data that has been supplied as part of the structure STATS.
%
% [N_CNT,CON_MAT,PVAL]=NBSstats(ST... |
5e718a1ad01f5a9422734fff95c9a5c6828c17169264cb9f87d1aef7caa04948 | MATLAB | 9,208 | 226 | % pop_newcrossf() - Return estimates and plots of event-related spectral coherence
%
% Usage:
% >> pop_newcrossf(EEG, typeproc, num1, num2, tlimits,cycles,
% 'key1',value1,'key2',value2, ... );
% Inputs:
% INEEG - Input EEG dataset
% typeproc - Type of proces... |
44845b3facd16e23917719f320ffcce5b732df8823fb4919d9866a9065a91655 | MATLAB | 9,213 | 201 | % icadefs() - function to read in a set of EEGLAB system-wide (i.e. lab-wide)
% or working directory-wide constants and preferences. Change the
% way these are defined in the master icadefs.m file (usually
% in dir eeglab/functions/sigprocfunc) or make a custom copy of
% ... |
0ce42cd577bb397c331bb94bbe6bbec7300ddf01751d1b55e4a0d6a8ba4ade84 | MATLAB | 9,218 | 210 | function ea_convert_ossdbs_axons(options,settings,side,prob_PAM,resultfig,outputPaths,source_i)
% Prepare Lead-DBS BIDS format fiber activations.
% By Butenko and Li, konstantinmgtu@gmail.com
arguments
options % Lead-DBS options for electrode reconstruction and stimulation
settings % par... |
efffe663609f7d9fe3a07f9f5e72c21304fd5d001526f3ff6357564aecf0db82 | MATLAB | 9,219 | 300 | %% Description errorb(x,y,varargin)
% errorb(Y,E) plots Y and draws an error bar at each element of Y. The
% error bar is a distance of E(i) above and below the curve so that each
% bar is symmetric and 2*E(i) long.
% If Y and E are a matrices, errob groups the bars produced by the elements
% in each row and plots the ... |
c20fe2adc81d74f843b13657c899e69be9a279d2ffbafaf3ca8196df9dafbbe1 | MATLAB | 9,223 | 260 | function [Y, Z] = FilterM(b, a, X, Z, Dim, Reverse)
% FilterM - Fast C-Mex filter
% [Y, Z] = FilterM(b, a, X, Z, Dim, Reverse)
% INPUT:
% b, a: Filter parameters as DOUBLE vectors. If the vectors have different
% lengths, the shorter one is padded with zeros.
% X: Signal as DOUBLE or SINGLE vector or array.
% ... |
b7b58a5d6b21fefac2b90e79dbdcde694ce11677de4333ae42f7ae217ea17059 | MATLAB | 9,228 | 261 | % 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 computationa... |
1dbbaade19d4bdbda1c3ece9013a2909c527f118d24a061c9f4c135c11622b5c | MATLAB | 9,232 | 296 | function cs_fmri_conseed_seed_matrix(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')... |
8ef5a89efcfe611598a946d119ec2cabc88725c93b367038758d103d12d85e72 | MATLAB | 9,240 | 222 | %% Perform a voxel-wise t-test
%
% In this example we perform a second level analysis on first level
% statistical parametric maps. Specifically we use a t-test to obtain an
% ordinary least squares estimate for the group level parameter.
%
% The example uses the emotion regulation data provided with
% CANlab_Core_Too... |
24f16193758d50332a247de9b2b5f45613f807bf1fafff06a69d4c30bc3dd1aa | MATLAB | 9,244 | 292 | function layout = prepare_layout_NIRx(probe_file, montage_name, varargin)
%FNIRSPOWER.HELPERS.PREPARE_LAYOUT_NIRX
% Prepare and optionally save a 2D FieldTrip layout from NIRx probe data.
%
% Usage:
% layout_dense = fnirspower.helpers.prepare_layout_NIRx( ...
% probe_file, 'dense');
%
% Required inputs:... |
98d4d2a2d320b115a82944604af39de761b0a50010d1bfda072c8db599d17328 | MATLAB | 9,251 | 288 | function varargout = ea_spm_preproc_run(job)
% Segment a bunch of images
% FORMAT spm_preproc(job)
% job.channel(n).vols{m}
% job.channel(n).biasreg
% job.channel(n).biasfwhm
% job.channel(n).write
% job.tissue(k).tpm
% job.tissue(k).ngaus
% job.tissue(k).native
% job.tissue(k).warped
% job.warp.affreg
% job.warp.reg
%... |
5c5b2b6524cb4260e3ae39bf9883e86e71f5aee467e49e5a17ceed2aa372c364 | MATLAB | 9,256 | 276 |
% 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 comp... |
80c6b63b0b1f24e996f7542ae4a49d655de71292f0aa7094850b9542097ac31e | MATLAB | 9,264 | 304 | function turnDistribution = RadialMazeTurns(data,mode)
%RadialMazeTurns - Compute distribution of successive turn angles in radial maze.
%
% In order to detect stereotypic egocentric strategies that a rat could employ to
% solve a radial maze task, this function determines the distribution (over trials)
% of success... |
f9f9914196d80546a35cd2b39d08ddea9671ad5c88d039e6c9da45592f215ad2 | MATLAB | 9,269 | 223 | %% modeltype1 - simple stimulation of Izhikevich RS neuron
% Generates data for a simple Izhikevich regular spiking neuron. The neuron
% is stimulated with one of four types of stimuli.
%
% Syntax: [mV,spkTimes,memNoise,stim,modelParams] = modeltype1(varargin)
%
% Optional Input:
% modeltype1(..., 'ONvsOff', pulseSiz... |
1e485a684b001401c7807cccbab24bb5a3ba45ec28da833e360c686e1db0f005 | MATLAB | 9,274 | 216 | function [trl_dirs_corr, FOV, nodata] = NDK_Motion_Correction5D_savecat(fileexpnum, trialcat, zsplit)
% clear all
% zsplit = 0;
% trialcat = 1;
% % fileexpnum = SS02255_mar172023_f3e3 %thor expt #
%set headpath (and reset if in "extracted" output folder)
tic
headpath = pwd; %'/Volumes/Samsung_T5/2p rotaball/21D07/2107... |
6b5b50f26ff16a090f7f88c9fe09ca57fce99ee881cf2e7d0d6cbcbb8bf71eba | MATLAB | 9,279 | 209 | %%OLD COPY JUST IN CASE
function index=singleflyeventdetection(headpath,fileexpnum,version,saveex,picknew,savefigs)
%This is for doing every trial, plotting the colour, and the sum of
%detected events
%make another version that does the mean
if ~picknew
load('paperexample')
end
if version==2
cd('extracted2'... |
18d43ea8b6310c8c1cace46370d6c0010ca52d3c92f6cc2da7cd5c74f8728115 | MATLAB | 9,297 | 270 | function [cuts,allcontour]=ea_add_overlay(boundboxmm,cuts,tracor,options)
% This function overlays atlas data over 2d-slice views to be exported by
% LEAD-DBS. The function is called from ea_writeplanes.m
% __________________________________________________________________________________
% Copyright (C) 2014 Charite U... |
aef9f6d9b6169d5d24d59badcfd07260aa1b157f3a531d268b6c04afc0bcce2b | MATLAB | 9,297 | 231 | % F03_B.m
% Manuscript Fig 3b: spatial correspondence by ROI.
% Input tables are read from manuscript_figure_source_data/data/main_text_source_data.xlsx.
clear all
ROI={"Dorsal", "Lateral","Ventral"}
%% read dataTables
Fig3b=read_main_text_source_table("fig3b_points"); % includes all 5 seeds, averaged
Fig3b_noiseCeili... |
440ac7740886728a5613a3566e7ed92510388cf838a30d1dd72774a324856f28 | MATLAB | 9,328 | 280 | function [Matching,Cost] = Hungarian(Perf)
%
% [MATCHING,COST] = Hungarian_New(WEIGHTS)
%
% A function for finding a minimum edge weight matching given a MxN Edge
% weight matrix WEIGHTS using the Hungarian Algorithm.
%
% An edge weight of Inf indicates that the pair of vertices given by its
% position have no... |
27938187456f106b947a4fdd41ae142408ea380ca0693354369642a7f52449ca | MATLAB | 9,333 | 231 | function avm_viscous(nsteps, interval, seed, Npts, P0_value, KA_value, dt, tau_T1, L_thresh, v0_value, Dr_value, B)
% AVM_VISCOUS Run an Active Vertex Model (AVM) simulation of a confluent
% epithelial tissue with cell-cell viscous adhesion, on a flat (non-
% sheared) periodic box, and save the results to a .mat file.... |
15f8b7e14950816bd3e078acbe7f12e301276d53c05cb8a5389bd6453bbf4e71 | MATLAB | 9,345 | 221 | function [spindles, segments] = fun_spindle_features(segments, srate, freqs, doPlot)
% Calculate spindle features.
%
% Inputs:
%
% segments : cell matrix with EEG segments to analyze
%
% srate: The sampling rate of the data (in Hz)
%
% freqs: [low high] frequency boundaries for spindle characterization
%
% doPlot: Plot... |
b8b72b891279b857d69d6f050f143ca205180c0dd792873696ff2da257ecb6a2 | MATLAB | 9,351 | 321 | function varargout=sigstar(groups,stats,nosort)
% sigstar - Add significance stars to bar charts, boxplots, line charts, etc,
%
% H = sigstar(groups,stats,nsort)
%
% Purpose
% Add stars and lines highlighting significant differences between pairs of groups.
% The user specifies the groups a... |
789b7fe7a1cd1a8c829447251de4bd03c5ab602f51d1c87c1dc7578ebe5649de | MATLAB | 9,360 | 243 | % pop_eegfilt() - interactively filter EEG dataset data using eegfilt()
%
% Usage:
% >> EEGOUT = pop_eegfilt( EEG, locutoff, hicutoff, filtorder);
%
% Graphical interface:
% "Lower edge ..." - [edit box] Lower edge of the frequency pass band (Hz)
% Same as the 'locutoff' command line input.
% "Hi... |
376ea48eb3a194fba6f7dfaa9d5d27da6537aee7f31e4378abdb118d732cfdc7 | MATLAB | 9,362 | 215 | % pop_rejtrend() - Measure linear trends in EEG data; reject data epochs
% containing strong trends.
% Usage:
% >> pop_rejtrend( INEEG, typerej); % pop up an interactive window
% >> OUTEEG = pop_rejtrend( INEEG, typerej, elec_comp, ...
% winsize, maxslope, minR, superpose, reject,ca... |
ed04921ecf49b09f4d5a618b19036a4d7d8f6a952681bfb67e78771f36ad78ff | MATLAB | 9,364 | 258 |
%% Load stats
savefilenamedata = fullfile(resultsdir, 'svm_stats_results_contrasts.mat');
if ~exist(savefilenamedata, 'file')
disp('Run prep_3b_run_SVMs_on_contrasts_and_save with dosavesvmstats = true option to get SVM results.');
disp('No saved results file. Skipping this analysis.')
return
end
fprin... |
6b208cb27b71a8ed53e6d2b20affc3de310e3e8626e050a3dbfd3f7edaba898d | MATLAB | 9,383 | 289 | function [t,y]=chaos_library(S,t,IC,p)
% function chaos_library(S,t,IC,p)
% inputs - S, string name of chaotic attractor
% - t, time, either of the form [to,tf] or [to:f:tf]
% - IC, initial conditions
% - p, coefficients of the system of differential equations used.
% outputs - t, time
% ... |
8c6cb1f1f1d09572229e895e187e804e57060f9f7232fc421e1f85dfb46e35eb | MATLAB | 9,389 | 286 | %% Reweighted graphs in MatlabBGL
% Matlab sparse matrices only support non-zero values. Because the
% structure of the sparse matrix is used to infer the edges of an
% underlying graph this limitation prevents MatlabBGL from trivially
% addressing graphs with 0-weight edges.
%
% To fix this problem, codes that accept... |
f71a99c11736541dbe56b0361592a5ddbe7769571b116675922982a83a19305e | MATLAB | 9,390 | 236 | function affinefile = ea_ants_linear(varargin)
% Wrapper for ANTs linear registration
fixedimage = varargin{1};
movingimage = varargin{2};
outputimage = varargin{3};
if nargin >= 4
writeoutmat = varargin{4};
else
writeoutmat = 1;
end
if nargin >= 5
if isempty(varargin{5}) % [] or {} or ''
otherfi... |
3a45be8c8e85b6aa2b48d9cf5ec8006e872a6f71e9b1d54a57c8486813e3c081 | MATLAB | 9,395 | 195 | % pop_eegplot() - Visually inspect EEG data using a scrolling display.
% Perform rejection or marking for rejection of visually
% (and/or previously) selected data portions (i.e., stretches
% of continuous data or whole data epochs).
% Usage:
% >> pop_eegplot( EEG ) %... |
630b0ab1eabd51b3098ddffb894826f14f166a41b36ad84b0cc4a1ad93592f97 | MATLAB | 9,405 | 232 | %% =========================================================================
% 4. Plotting Configuration
% =========================================================================
% --- Selection Parameters (Adjust these values to slice the data) ---
% 1. Reference TSL for frequency sweeps (ms)
TSL_ref_value = ... |
9dea74396df240ce2b3b103d7bc4d751ed9eed16d5e672a126e6cd1d09b60553 | MATLAB | 9,407 | 286 | % Save NIFTI dataset. Support both *.nii and *.hdr/*.img file extension.
% If file extension is not provided, *.hdr/*.img will be used as default.
%
% Usage: save_nii(nii, filename, [old_RGB])
%
% nii.hdr - struct with NIFTI header fields (from load_nii.m or make_nii.m)
%
% nii.img - 3D (or 4D) matrix of NIFTI... |
2d34dfa3e2ab2aea8fce6e0e8c8fe4349271d147447ace6dbf9200f86dadafe3 | MATLAB | 9,410 | 261 | function data = TDTthresh(data, STREAM, varargin)
%TDTTHRESH TDT snippet extractor.
% data = TDTthresh(DATA, STREAM, 'parameter', value, ...), where DATA is
% the output of TDTbin2mat, STREAM is the name of the stream store to
% convert to snippets, and parameter value pairs define the snippet
% extracti... |
94ee901b1ba6444045fac9117c8f1e528de4ceeadf3a1f296ed5bc4379d8062d | MATLAB | 9,423 | 260 | function data = LoadBinary(filename,varargin)
%LoadBinary - Load data from a multiplexed binary file.
%
% Reading a subset of the data can be done in two different manners: either
% by specifying start time and duration (more intuitive), or by indicating
% the position and size of the subset in terms of number of s... |
27a9e8a2c34d4a27a4558e68ccbb60cef1118e40276fc9ee5461fb7a7b4a5bd7 | MATLAB | 9,432 | 301 | % gethelpvar() - convert a Matlab m-file help-message header
% into out variables
% Usage:
% >> [vartext, varnames] = gethelpvar( filein, varlist);
%
% Inputs:
% filein - input filename (with .m extension)
% varlist - optional list of variable to return. If absent
% retrun al... |
75d8e23e01b503713e732bf60dc827b92d413e8d56bab6bbc172dd3c0deb1b24 | MATLAB | 9,438 | 238 | function varargout = segment_property_viewer(varargin)
% SEGMENT_PROPERTY_VIEWER MATLAB code for segment_property_viewer.fig
% SEGMENT_PROPERTY_VIEWER, by itself, creates a new SEGMENT_PROPERTY_VIEWER or raises the existing
% singleton*.
%
% H = SEGMENT_PROPERTY_VIEWER returns the handle to a new SEGMENT... |
128c2d9778c4182c36f5d7acd91e711f150a7a22a9c78381efc9081b1f921e13 | MATLAB | 9,441 | 232 | function ea_preprocess_fmri(options)
directory=[options.root,options.patientname,filesep];
V=spm_vol([directory,options.prefs.rest]);
signallength=length(V);
%% run sequence of proxyfunctions (below):
ea_realign_fmri(signallength,options); % realign fMRI
% BIDS FIX: Check if segmentation already exists before runni... |
17ed297b5f8b5bbbd4c7cbbaa1de43a4e55fa3c46c5b36362e561442ac8cc12a | MATLAB | 9,442 | 298 | % Check for required DAT fields. Skip analysis and print warnings if missing.
% ---------------------------------------------------------------------
% List required fields in DAT, in cell array:
required_fields = {'conditions', 'colors', 'SIG_conditions'};
ok_to_run = plugin_check_required_fields(DAT, required_fields... |
556125d5c14748ed9ad5d03a6bd8da0258ac1dc9a316ad6c0edc5db8a5f68b32 | MATLAB | 9,443 | 297 | classdef Container < handle
%uix.mixin.Container Container mixin
%
% uix.mixin.Container is a mixin class used by containers to provide
% various properties and template methods.
% Copyright 2009-2016 The MathWorks, Inc.
% $Revision: 1358 $ $Date: 2016-09-14 11:34:17 +0100 (Wed, 14 Sep... |
39fe940bf240ad1c25b1edf84c69121fc22259b2811625373bc86ea36e2e760c | MATLAB | 9,446 | 220 | %% Step 4 Tiny Dancers: Group analyses for frequencies
clear
clc
% load all frequency data
cd('D:\TinyDancers_Movement\fieldtrip_velo\PM_PROC\Step2c_timefrequency\3m');
FileNames = {dir(['*_freq' '.mat']).name} ;
for k=1:1:length(FileNames)
load(FileNames{k})
avg_baseline_3m{k} = freq_baseline;
... |
f17d0f4d43156b5ed9b6a46040382ccfe9dac9aa4efd45a50bc71741f3af77d9 | MATLAB | 9,452 | 271 | function varargout=xwt(x,y,varargin)
%% Cross wavelet transform
% Creates a figure of cross wavelet power in units of
% normalized variance.
%
% USAGE: [Wxy,period,scale,coi,sig95]=xwt(x,y,[,settings])
%
% x & y: two time series
% Wxy: the cross wavelet transform of x against y
% period: a vector of "Fourier" ... |
d5620bce0f87a35a49e039c3da67f044a3f2e7589e95f445d86b4808cbf19a5a | MATLAB | 9,460 | 266 | % This is a standard data format spike times class for the CMB
classdef Spike
properties
i % index in root.b_ts aligned from more accurate spike times 'ts' below. not directly used by end user
i_lfp % cell array of indices in root.b_lfp(i).ts aligned from higher sampled spike t... |
9dbd19327e72e2d971c3a1774955d894d94b87939643792307d8e80e4e3cbd1e | MATLAB | 9,477 | 261 | function varargout = RegistrationWin(varargin)
% developed by Yiyi Yu, 2021 July
% Last Modified by GUIDE v2.5 27-Feb-2022 17:09:07
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
... |
f46ab27e9d4f612c0b7dd15d85da989c8e54dd256fb4a052b75cb4e98425f1c3 | MATLAB | 9,484 | 246 | function CFA_RunAllJob(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,files... |
3716d219b03025e9eddaebe0297c816e3d04375799af5ce1ce4dfac7ed2588e9 | MATLAB | 9,486 | 244 | function clWaveforms = getClusterWaveform(clusterID, dataDir, baseName)
%GETCLUSTERWAVEFORM reads the raw binary file and compiles the voltage
%traces for the given cluster (the cluster number should be the one
%assigned by Kilosort/Phy). The output is a cell (or a structure)
%containing the mean waveform and its stand... |
02055714310089c2b197ee27c2820a830587b7359ba340a83e30970566064633 | MATLAB | 9,488 | 218 | % ====================================
%% Help
% ====================================
%
% CBIG_train_MSHBM_Epilepsy
%
% This script trains the MS-HBM model on 34 drug-resistant epilepsy subjects
% from the National Institutes of Health (NIH) dataset.
% It generates individual FC profiles, estimates group
% priors, and ... |
ce3cf7232286b2f40d68d09745fcbd0de07895d96c73826932859d6fa3e3f74e | MATLAB | 9,503 | 289 | %%% Supplementary Figure 11
% Passive prediction-error GC cross-ratio temporal correlation matrices.
%
% Structure:
% 1) Load passive differential PE-GC results
% 2) Compute band/time-window averaged topographies
% 3) Compute cross-ratio Spearman correlation matrices
% 4) Plot SFigure 11A-B
% 5) Save one inde... |
43ad5fc8070187208e76d5fcfab34748c4f21c66cc810bdd2277dd338fc654a5 | MATLAB | 9,504 | 313 | % This functions computes the SNR based on adjacent frequency bins
%
% INPUTS
% PS input data (channels, frequecies, trials)
% freq second dimention values for the data (frequecies)
% OPTIONAL INPUTS:
% fband range of frequecies to use for the normalization (SNR)
% If not prove... |
ff216248f27eee11e8133058554d6e4ee3abb0dbd842d90e0a297434198e9103 | MATLAB | 9,507 | 226 |
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 a... |
958130100f386407acae909f499a2651474d9a6a1adbd08396031039a0090f8f | MATLAB | 9,520 | 353 | function test_examples
%% Code examples
msgid='matlab_bgl:test_examples';
% all_shortest_paths
load('../graphs/clr-26-1.mat');
all_shortest_paths(A);
all_shortest_paths(A,struct('algname','johnson'));
[D P]=all_shortest_paths(A,struct('algname','floyd_warshall'));
i=4; j=1; p=[]; while j~=0, p(end+1)=j; j=P(i,j); en... |
27e1660846d0ec207b04064736b2103527e6143109948d4f95f9a2d8f6e2a341 | MATLAB | 9,525 | 289 | function obj=stat_cornerhist(obj,varargin)
p=inputParser;
my_addParameter(p,'nbins',30);
my_addParameter(p,'edges',[]);
my_addParameter(p,'geom','overlaid_bar'); %line, bar, overlaid_bar, stacked_bar,stairs, point
my_addParameter(p,'normalization','count');
my_addParameter(p,'fill',[]); %edge,face,all,transparent
my_... |
93f5503285ee6fb6a2dd3e9f3c219f9e77adc4a77980e256659ebd456d74f8a2 | MATLAB | 9,529 | 108 | function risk_genes = risk_genes(disorder)
%
% Usage: risk_genes = risk_genes(disorder)
%
% Description
% Outputs names of GWAS-derived risk genes for a given disorder (author:
% @saratheriver)
%
% Inputs:
% disorder ({'adhd', 'asd', 'bipolar', 'depression', 'epilepsy',
% 'hippocampal_volume', 'ocd', 'schizop... |
54dbd15f68e54ae46a1481df0bd441c475696c0b7ad01b8de76c9bc0b5890677 | MATLAB | 9,533 | 221 | %% LaBGAScore_pet_preprocess_data.m
%
%
% *USAGE*
%
% Assumptions:
%
% Data organization:
% Data are transformed to nifti format and organized according to BIDS.
% You have to specify a main directory where al the folders of the
% subjects can be found.
% In the folder of each subject, there mig... |
51ed1e6ac634f6d0a3ea1deaad242aad3162055a7eca5034c322871bf179fef5 | MATLAB | 9,535 | 260 | function data = bz_LoadBinary(filename,varargin)
%bz_LoadBinary - Load data from a multiplexed binary file.
%
% Reading a subset of the data can be done in two different manners: either
% by specifying start time and duration (more intuitive), or by indicating
% the position and size of the subset in terms of numbe... |
f329781cc90eb10bdd33eb9503649e42e719b2adc9d931cf41a33fdb46012ad7 | MATLAB | 9,548 | 253 | function save(this,filename,encoding)
% Save GIfTI object in a GIfTI format file
% FORMAT save(this,filename,encoding)
% this - GIfTI object
% filename - name of GIfTI file to be created [Default: 'untitled.gii']
% encoding - optional argument to specify encoding format, among
% ASCII, Base64Binary, ... |
95a333b285fe2064260bfd375ee09363f6afcaff352ab75f63faf6bad4e9643d | MATLAB | 9,552 | 232 | function [scoreTot, frameIndexTot, meanScoreByFrmMat] = speckleFrameAnalyse(actinPropPerTimeInt, outPath, fieldName, plotType, splitNum, figName)
%SPECKLEFRAMEANALYSE plots speckle properties for each frame of all movie (i.e. kinetic scores, speckle speed, etc) in an actinPropPerTimeInt structure
%
%SYNOPSIS [scoreT... |
ccd62fc0b36df618408f2143655f32d40abac14af59676e9c9c42d09103d7466 | MATLAB | 9,554 | 277 | % eeg_pvaf() - Compute EEG.data 'percent variance accounted for' (pvaf) by specified components.
% Can omit specified components and channels from the computation. Can draw a plot
% of the scalp distribution of pvaf, or progressively compute the pvaf for comps
% 1:k, where k = 1... |
68c3797b701cb333ab4e328800e6d1ef23287b95850ee638db7e8f758de9378d | MATLAB | 9,578 | 243 | % 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... |
6e6de93b83be01c8748b76eccb666059fb33224c2871f0576f1926f9e224cfdb | MATLAB | 9,585 | 244 | function trackSEL = getTrackSEL(trackedFeatureInfo,segmentSEL)
%GETTRACKSEL outputs track start times, end times and lifetimes
%
%SYNOPSIS trackSEL = getTrackSEL(trackedFeatureInfo);
%
%INPUT trackedFeatureInfo: -- EITHER --
% Output of trackWithGapClosing:
% Matrix... |
5861213d0f78f8321bbe46a6590eafe6cf1f25b70ad8111ce9bf6bdac4ff52cb | MATLAB | 9,588 | 238 | % reref() - convert common reference EEG data to some other common reference
% or to average reference
% Usage:
% >> Dataout = reref(data); % convert all channels to average reference
% >> [Dataout Chanlocs] = reref(data, refchan, 'key', 'val');
% % convert data to new refere... |
8fdab057d3d7f29fe2c266c7a98a94eb8aec84689b34c2e29b8aaead6a6103b6 | MATLAB | 9,589 | 301 | function [x y pos trials map mapping] = getBehavEvents_linearTrack(pos,bins)
dbstop if error
scatter(pos(:,8),pos(:,10),'.')
% axis([-1 1 -1 1])
[x y]=ginput();
cx = x(end-1:end);
y = y(end-1:end);
dist(:,1)=fastrms(abs(pos(:,8)-x(1))+abs(pos(:,10)-y(1)),120);
dist(:,2)=fastrms(abs(pos(:,8)-x(2))+abs(pos(:,10)... |
7723fa1b89444015f188663be62dc277fc631d48c807ac7f3dbcca13f2e07686 | MATLAB | 9,611 | 239 | function varargout = ea_normsettings_spmnewseg(varargin)
% EA_NORMSETTINGS_SPMNEWSEG MATLAB code for ea_normsettings_spmnewseg.fig
% EA_NORMSETTINGS_SPMNEWSEG, by itself, creates a new EA_NORMSETTINGS_SPMNEWSEG or raises the existing
% singleton*.
%
% H = EA_NORMSETTINGS_SPMNEWSEG returns the handle to a... |
b95d712bd924d2aa493feced16a5ee6a661fc5766a0a0577cd0e1796bfb2d126 | MATLAB | 9,621 | 225 | % convertlocs() - Convert electrode locations between coordinate systems
% using the EEG.chanlocs structure.
%
% Usage: >> newchans = convertlocs( EEG, 'command');
%
% Input:
% chanlocs - An EEGLAB EEG dataset OR a EEG.chanlocs channel locations structure
% 'command' - ['cart2topo'|'sph2topo'|'sphb... |
56c4744c6eaae2ccec9751bffbd1ce2824db4e1c334d2f8efecd03c81bf5bb89 | MATLAB | 9,639 | 164 | function varargout=ea_normalize_spmdartel(options)
% This is a function that normalizes both a copy of transversal and coronal
% images into MNI-space. The goal was to make the procedure both robust and
% automatic, but still, it must be said that normalization results should
% be taken with much care because all recon... |
b8f1161db284e6b969d1005f7c57605658d7b0f8aa8e1f04cfd216762abe8f93 | MATLAB | 9,641 | 272 | function CFA_MakeRes_Clustercorrected_vlsm(C05,C05P,C05N,PmapDir,TmapDir,ZmapDir,THRESHOLD,VQ,Voxdir2out05)
[VP DP] = Dynamic_read_dir_NIFTI(PmapDir);
[VT DT] = Dynamic_read_dir_NIFTI(TmapDir);
[VZ DZ] = Dynamic_read_dir_NIFTI(ZmapDir);
[pth nam ext] = fileparts(TmapDir);
[pth znam ext] = fileparts(ZmapDir);
THR1P = ... |
b7da5de9143516f99ef3cdaef8a41e06d113469d18c6317997afe84a4796cbc3 | MATLAB | 9,649 | 260 | function [PhaseLockingData] = bz_PhaseModulation(varargin)
% USAGE
%[PhaseLockingData] = bz_PhaseModulation(varargin)
%
% INPUTS
% spikes -spike time cellinfo struct
%
% lfp -lfp struct with a single channel from bz_GetLFP()
%
% passband -frequency range for phase modulation [lowHz highHz] form
%
... |
13f3d4e8c31ae4ed73cde2fe53cdf17f2e7c71ecf19801bec4b4d1159ae61658 | MATLAB | 9,652 | 254 | % std_chantopo() - plot ERP/spectral/ERSP topoplot at a specific
% latency/frequency.
% Usage:
% >> std_chantopo( data, 'key', 'val', ...)
% Inputs:
% data - [cell array] mean data for each subject group and/or data
% condition. These arrays are usually returned by function
% ... |
7d095dff48b5ed4172fef16c2bf409a0093b0cbed3f2d597ba7775f67091f182 | MATLAB | 9,664 | 208 | % std_readpac() - read phase-amplitude correlation
%
% Usage:
% >> [STUDY, clustinfo] = std_readpac(STUDY, ALLEEG);
% >> [STUDY, clustinfo] = std_readpac(STUDY, ALLEEG, ...
% 'key', 'val');
% Inputs:
% STUDY - studyset structure containing some or all... |
83caf9d6d9ee2789df6bf247f43ddc14f9445e4186827773e39f1cc334cc2f94 | MATLAB | 9,670 | 207 | function homo_with_weight = CBIG_ArealMSHBM_parameters_validation(project_dir, ...
mesh, num_sess, num_clusters, subid, w, c, beta, method)
% homo_with_weight = CBIG_ArealMSHBM_parameters_validation(project_dir, ...
% mesh, num_sess, num_clusters, subid, w, c, beta, method)
%
% This script will estimate the indivi... |
72ace0a0825a7423269c5016cf5b24e7de89321f1838d4a35579924c7a1b7c61 | MATLAB | 9,681 | 222 | function [Conditions, Triggers] = getConditions(sessionDir, varargin)
% Supplement the Highspeed Table with the individual on- and offset times
% of each trigger class, i.e. reward, punishment, drumcontact
% Default option values:
options = inputParser;
addRequired(options,'sessionDir',@ischar);
addParameter(options,... |
45ca9c2bb6509b675ea31a0f081df92d906920c502d96a071b89bd2e10c0019d | MATLAB | 9,683 | 221 | function [out,motionInfo] = gbvs(img,param,prevMotionInfo)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% This computes the ... |
7647f7971fac3f315fca1f63817a39fabc486055b996c9680890ec3b3779c9f4 | MATLAB | 9,686 | 199 | % make_timewarp() - Select a subset of epochs containing a given event sequence, and return
% a matrix of latencies for time warping the selected epochs to a common
% timebase in newtimef(). Events in the given sequence may be further
% restricted to those with s... |
50d5d1731596df3da7c986b114db7458369f4bafdffa740df158fed11a2c7947 | MATLAB | 9,693 | 344 | % Example script that extracts apical areas, contact lengths and
% ms2 intensities for each cluster
close all
clear all
%% Set Parameters and Select Window Folder
cluster_name = 'Window1Cluster4';
WindowFolder = uigetdir;
cd(WindowFolder)
res = 3.3453;
Interval = 24.36223; % seconds
mkdir([cluster_name,'/Absolute']... |
f2c801f483eae126d754296cf164da704ad8a68168174f59f730bd146be896ee | MATLAB | 9,697 | 276 | function CBIG_ASDf_Plot400Schaefer19Subcor17Networks_419by419Input(corr_mat, scalelim, filename_prefix)
% CBIG_ASDf_Plot400Schaefer19Subcor17Networks_419by419Input(corr_mat, scalelim, filename_prefix)
%
% This function draws the 419x419 correlation matrix (400 cortical ROIs +
% 19 subcortical ROIs).
% Major networks ar... |
5ab022d066707d66cb8b843bebac2b6eda6c316ce6d59229e3bdb4765493bc97 | MATLAB | 9,700 | 312 |
function dkl = rgb2dkl(rgb)
sz = size(rgb);
im = shiftdim(rgb,2);
im = reshape(im,[3 prod(sz(1:2))]);
im = im';
im = rgb2dkl_v(im);
im = im';
im = reshape(im,[3 sz(1:2)]);
dkl = shiftdim(im,1);
function dkl = rgb2dkl_v(rgb)
% bunch of constants used for RGB -> DKL conversion:
lut_rgb = [
0.024935, 0.0076954,... |
f59ac043f2d70248b44ed0571824b733b8ca67d533854e01d9eeafd561088657 | MATLAB | 9,701 | 244 | function varargout = ea_nbs_advanced(varargin)
% EA_NBS_ADVANCED MATLAB code for ea_nbs_advanced.fig
% EA_NBS_ADVANCED, by itself, creates a new EA_NBS_ADVANCED or raises the existing
% singleton*.
%
% H = EA_NBS_ADVANCED returns the handle to a new EA_NBS_ADVANCED or the handle to
% the existing si... |
19d1282d11d038696164968924ee5f9ba6b60ecc2cc3279d257a26143c577c4c | MATLAB | 9,713 | 237 | function CBIG_pMFM_step8_gene_expression_analysis_desikan()
% This function is the wrapper to perform all the genetic analysis
%
% There is no input for this function as it can automatically get the
% output file from previous step.
% There is no output for this function as it will generate the output files
%
% Writte... |
7cc824c755dffc66ca71f56c62edcdab5d0fd1444686a028dd81ae7bbe9474ba | MATLAB | 9,718 | 281 | %%% Supplementary Figure 7A-D
ccc;
%% Settings
run("private\plotConfig.m");
monkeys = ["XX", "CC"];
alphaVal = 0.05;
windowStat = [0, 350]; % ms
T = 10e3; % ms
exampleCh.XX.AC = 38;
exampleCh.XX.PFC = 47;
colors.XX = {[35 71 153], [244 179 179], [240 133 25], [233 90 111], [230 33 41]};
colors.XX = cellfun(@(x) x ... |
dbb423a4b3cfb8c7f05aca77e17ec6076a145413abd538a4c69e4d90b4a5b254 | MATLAB | 9,742 | 292 | function smoothed = Smooth(data,smooth,varargin)
%Smooth - Smooth using a Gaussian kernel.
%
% USAGE
%
% smoothed = Smooth(data,smooth,<options>)
%
% data data to smooth
% smooth vertical and horizontal kernel sizes:
% - gaussian: standard deviations [Sv Sh] (optionally,
... |
729e1dd8d2be3887803f1458b560e26e7f88e331e20b81e0df9b4964bcb5c814 | MATLAB | 9,745 | 273 | function ellipse_t = fit_ellipse( x,y,plot_opt )
%
% fit_ellipse - finds the best fit to an ellipse for the given set of points.
%
% Format: ellipse_t = fit_ellipse( x,y,axis_handle )
%
% Input: x,y - a set of points in 2 column vectors. AT LEAST 5 points are needed !
% axis_handle - optional. a ... |
fe213fd79db7924e6b683f2cbbf9baf945d8687a459fb9e186d636f4cf4f2295 | MATLAB | 9,753 | 209 | function CBIG_MMLDA_mean_correlation_map_wrapper(out_dir)
% CBIG_MMLDA_mean_correlation_map_wrapper(out_dir)
%
% Wrapper function to get mean correlation map between mean top5 behavioral zscores and atrophy zscores.
%
% Input:
% - out_dir : output directory
%
% Example:
% CBIG_MMLDA_mean_correlation_map_wrapper(... |
f82ff7ef1eba79934959906c42704812777a5de2144619363861501ee3960dc6 | MATLAB | 9,754 | 237 | function CBIG_pMFM_step8_gene_expression_analysis_schaefer()
% This function is the wrapper to perform all the genetic analysis for
% Schaefer 100 parcellation
%
% There is no input for this function as it can automatically get the
% output file from previous step.
% There is no output for this function as it will gen... |
018126ae473b8e0feb64fcc15fb4476c4c257f59753bc3fc3e36439d54e743a2 | MATLAB | 9,782 | 266 | %This function is called within the CSD_bygroup function
%Loads and formats an animal's data for CSD analysis
%Determines best column of 21 linear channels on the 64 channel silicon
%probe (by finding which column has the fewest bad channels).
%Loads in LFP data + creates a time x channels matrix
%Loads c... |
e1c745320e3b357faf9ce84adabfff6bd002fc99f9827efad19a15660231334a | MATLAB | 9,784 | 214 | function settings = ea_segment_MRI(options, settings, outputPaths)
% Create segmentation into GM, WM, CSF either based on T1 or Atlas or just
% copy for templates/ when computing in Template space.
% By Butenko and Li, konstantinmgtu@gmail.com
arguments
options % Lead-DBS options for electrode reconstruction a... |
2ff34710020bb92dc634910b4849f20bc73fe40c12cc571dd714296834840141 | MATLAB | 9,801 | 253 | function save(this,filename,encoding)
% Save GIfTI object in a GIfTI format file
% FORMAT save(this,filename,encoding)
% this - GIfTI object
% filename - name of GIfTI file to be created [Default: 'untitled.gii']
% encoding - optional argument to specify encoding format, among
% ASCII, Base64Bi... |
1d8f61f7200b10adff93fcbddb0b1d9bc66e641ac2e19422bfd1d76d598e7345 | MATLAB | 9,802 | 275 | % 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... |
f40be3617d5fdfa1bd47ce5d532aa5a9d35d3a0cd11846ec79ddc28936ca5670 | MATLAB | 9,813 | 267 | function [obj] = ft_convert_units(obj, target, varargin)
% FT_CONVERT_UNITS changes the geometrical dimension to the specified SI unit.
% The units of the input object is determined from the structure field
% object.unit, or is estimated based on the spatial extend of the structure,
% e.g. a volume conduction model of... |
0ebdb5078fe58073e95bf91949233e6e7acdad594bf60baedc0ffd1a01da1b0f | MATLAB | 9,815 | 275 | function freezeColors(varargin)
% freezeColors Lock colors of plot, enabling multiple colormaps per figure. (v2.3)
%
% Problem: There is only one colormap per figure. This function provides
% an easy solution when plots using different colomaps are desired
% in the same figure.
%
% freezeColors freeze... |
05a3ef8d157195684f5eee626228329577027fec6d9fe5e1732a2d539403f7cf | MATLAB | 9,816 | 275 | function [PVAL,ADJ,NULL] = CBIG_ASDf_NBS_permSetInput(X,Y,THRESH,permSet,TAIL)
% [PVAL,ADJ,NULL]=CBIG_ASDf_NBS_permSetInput(X,Y,THRESH,permSet,TAIL)
%
% Modified from original NBS code from Andrew Zalesky.
% This function computes the network-based statistic (NBS) as described in [1].
%
% Input:
% - X:
% ... |
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