sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3e5439d996d333a0f518d3d3e1be8c0e3a7d530baa1993940b58e31bc7670400 | MATLAB | 10,043 | 156 | function info = process_Training( subjectName, subjectID, scanNum, currentRun )
% (c) Coraline Rinn Iordan 09/2017, 10/2017, 02/2018, 04/2018
%
% This version normalizes w.r.t. the initial 30 TR countdown in the run
% Each run has 316 TRs total ; used: 310 TRs ( = number of NIFTI files exported )
if nargin < 4, error(... |
64574dd21cdcceb80c9fb19a5e7a1322823a2a91df4f3999effa445c152b1313 | MATLAB | 10,051 | 257 | % 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 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
78ee9dfd443d8f0ba85c64d674a00dac3f932442993c0bcafe84aa2c4bd5bada | MATLAB | 10,057 | 182 | function replay_firing_stats= get_firing_stats_replay(folders,method)
% calculates firing distributions during replay for cells included in
% rate_remapping analysis for each epoch
% if epochs are added in remapping struct, need to update this code as well
% distributions returned: time between first and last spike in ... |
a68cc10e1c1ff32097745bebb2efc578c71eb14b7380cbf0be9be08138de93ed | MATLAB | 10,058 | 266 | function [im_hatch,colorlist] = applyhatch_pluscolor(h,patterns,CvBW,Hinvert,colorlist, ...
dpi,hatchsc,lw)
%APPLYHATCH_PLUSCOLOR Apply hatched patterns to a figure in BW or Color
% APPLYHATCH_PLUSCOLOR(H,PATTERNS) creates a new figure from the figure H by
% replaci... |
e82469188c230395ed5d76b75501cf325c9b4cb288de6803dff2b1a118f920c4 | MATLAB | 10,059 | 164 | function varargout = processArgs(args,varargin)
% Similar to process_options but allows both positional and named arguments
%
% This function also provides optional enforcement of required inputs, and
% optional type checking. Argument names, if used, must start with the '-'
% character and not precede any positio... |
2d2cc59a6ed366a15a9d0db611199e8b48c19a14f44c3acee19650727cb61ea2 | MATLAB | 10,060 | 253 | function varargout = DPARSF_FieldMap(varargin)
% DPARSF_FIELDMAP MATLAB code for DPARSF_FieldMap.fig
% DPARSF_FIELDMAP, by itself, creates a new DPARSF_FIELDMAP or raises the existing
% singleton*.
%
% H = DPARSF_FIELDMAP returns the handle to a new DPARSF_FIELDMAP or the handle to
% the existing si... |
7c0e1cf01442674945ca6725d3db7bfd324b380ebdfca257e93e7335111e209b | MATLAB | 10,062 | 294 | function [out1,out2,out3] = ginput(arg1)
%GINPUT Graphical input from mouse.
% [X,Y] = GINPUT(N) gets N points from the current axes and returns
% the X- and Y-coordinates in length N vectors X and Y. The cursor
% can be positioned using a mouse. Data points are entered by pressing
% a mouse button or any key... |
08bcbdad4eda4cf820f9af1ec2ccff32b6abd44077769111a74306cf43c3c1e2 | MATLAB | 10,066 | 315 | %% Overview
%
% Here we summarise the results of the HMM inference and compute the
% task-evoked GLM statistics
config = utils.get_studydetails;
% Define colours to use in state plots
set1_cols = utils.set1_cols;
% Define sample rate
sample_rate = 250;
%% Load in results from envelope data
% Meta data
method = 'en... |
b19de26abb188a0c1b448b89065329df6ddd0dde13e215d8575ac28cdb3dbf89 | MATLAB | 10,067 | 316 | function [fh,axh,lh] = plotPlotStruct(axh, pStruct, lineSet, widthSet, symbolSet, colorSet, plotArgs, errArgs, axisArgs, legendArgs, labelArgs, titleArgs)
if (nargin < 1) || isempty(axh)
fh=figure;
axes;
axh = gca;
else
fh = axh.Parent;
end
if ((nargin < 3) || (isempty(li... |
242a3eb3b45186325b62d0885722a8b70f8f2927c2b24c5835cf54fb5a804316 | MATLAB | 10,071 | 279 | function [xbest, fbest, info, options] = pso(problem, x, options)
% Particle swarm optimization (PSO) for derivative-free minimization.
%
% function [x, cost, info, options] = pso(problem)
% function [x, cost, info, options] = pso(problem, x0)
% function [x, cost, info, options] = pso(problem, x0, options)
% func... |
ba313ef3f7906dd3d7ad6132b3172b934437f8c6566ebbeba530ba1dc73f4d34 | MATLAB | 10,074 | 263 |
numClusters = som_dim(1)^2 ;
% Inizializzare una matrice per memorizzare le differenze medie per ogni neurone
differences = zeros(Nregions, Nregions, numClusters);
% Calcolare la matrice di connettività media per ciascun neurone (cluster)
mean_matrices = zeros(Nregions, Nregions, numClusters);
for k = 1:numC... |
47e62b800b5a9e92071ba25f34d6fa563ff20e1bcd0a8ae5bf735ef6c906c47e | MATLAB | 10,091 | 247 | % TODO make function?
% function [outstruct] = EyeMem_expdesign(phase)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% experimental design (start)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% % TEST SETTINGS: 1 runs, 30 trials study, 60 test. 70 minutes
% stim_category = {'naturals2'}; % 'fractals','landscapes','naturals1','natura... |
5c096cee6c6c6cf4d91b5c8a8d8e481975bf598277d716401db5f6f2d8889adf | MATLAB | 10,094 | 303 | function varargout = ginput_ZN(varargin)
%GINPUT Graphical input from mouse.
% [X,Y] = GINPUT(N) gets N points from the current axes and returns
% the X- and Y-coordinates in length N vectors X and Y. The cursor
% can be positioned using a mouse. Data points are entered by pressing
% a mouse button or any key... |
a0763747fb0c6aa069996c01e1c3954bb2179c043899f8e50d766192e9c8baa9 | MATLAB | 10,101 | 283 | function [mri, hdr, cpersist] = read_ctf_mri4(filename)
% READ_CTF_MRI reads header and imnage data from CTF format MRI file
%
% [mri, hdr] = read_ctf_mri(filename)
%
% See also READ_CTF_MEG4, READ_CTF_RES4
% Copyright (C) 2008 Ivar Clemens
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for... |
03ec981894d0bed5b49a53402f0efe97526099e52fbc82befa2e87887810e700 | MATLAB | 10,103 | 165 | function sPPI_and_gPPI_without_deconv_FIR(stat_path,exp_folder,N,N_ROIs,q_level,ground_truth)
% ========================================================================
% Ruslan Masharipov, October, 2023
% email: ruslan.s.masharipov@gmail.com
% ========================================================================
... |
088ca60f6d5d741ae2fccbfc6cfbbae5cf6ed25628dbbbfa35bdbfdb8729915e | MATLAB | 10,104 | 171 | %% muscle GCaMP imaging
% This only works with speicific folder,subfolder arrangement as in
% selected_60-30_powdered_ACR1
subFolders = dir(pwd);
realSubFolders = subFolders([subFolders.isdir]');
realSubFolders = realSubFolders(~startsWith({realSubFolders.name},{'movies'}));
realSubFolders = realSubFolders(~sta... |
c0045a4eb55338b4d252c52c98d230c2ade5af9499b930d99cc1831c11a7b833 | MATLAB | 10,107 | 318 | function [posterior,out] = VBA_groupBMC(L,options)
% VB algorithm for group-level Bayesian Model Comparison
% function [posterior,out] = VBA_groupBMC(L,options)
% IN:
% - L: Kxn array of log-model evidences (K models; n subjects)
% - options: a structure containing the following fields:
% .priors: this variab... |
73b250026733b93f9cec4a3bb80b26b1d1edc6f32792db0562148af615466eb5 | MATLAB | 10,112 | 364 | function stats = rm_anova(x, s, f)
%
% REPEATED MEASURES ANOVA
% REQUIRES STATS TOOLBOX, otherwise can use 'mycombnk' (ask Anne)
%
% Usage:
% >> stats = rm_anova(x, s, f);
% x = 1xN vector with data values
% s = 1xN vector with subject numbers, or the factor to repeat
% meas... |
ee4af474833bda7de425eabc61eac288c42a19130c5323a08e2f2907724515b9 | MATLAB | 10,112 | 334 | function F = srskelf_hybrid(A,x,occ,rank_or_tol,pxyfun,opts)
% SRSKELF_HYBRID Strong recursive skeletonization factorization with
% hybrid admissibility (symmetric positive definite only).
%
% F = SRSKELF_HYBRID(A,X,OCC,RANK_OR_TOL,PXYFUN) produces a
% factorization F of the interaction matrix A on the points ... |
372063d9fdc3c127e3e55a923db505b0d7a09f1b77ce70373d9bb84f209b2f30 | MATLAB | 10,115 | 187 | function shuffled_track = global_remapped_run_shuffles(shuffle_choice,analysis_type,num_shuffles,decoded_replay_events,place_fields_BAYESIAN,BAYSESIAN_NORMALIZED_ACROSS_TRACKS)
% computes shuffles on replay events
% shuffle_choice- determines what type of shuffles will be performed, entered as a string
%
% analysis typ... |
2ae2a427bee0a2262d01a37332b6dfed8b58aaa61fa054988c21a0d51cef18c4 | MATLAB | 10,118 | 176 | function y_ResultsOrganizer(WorkingDir,SubjectID,OutputDir)
% FORMAT y_ResultsOrganizer(WorkingDir,SubjectID,OutputDir)
% Input:
% WorkingDir - the directory contains processed data
% SubjectID - the list of subject IDs for organize. n by 1 cell
% OutputDir - the directory for saving results
% Output:
% ... |
98ec95b4ddccc81a57cec6064bf7bec3001153c412c0c7105a7a627ce3706b2b | MATLAB | 10,126 | 253 | function hText = xticklabel_rotate(XTick,rot,varargin)
%hText = xticklabel_rotate(XTick,rot,XTickLabel,varargin) Rotate XTickLabel
%
% Syntax: xticklabel_rotate
%
% Input:
% {opt} XTick - vector array of XTick positions & values (numeric)
% uses current XTick values o... |
0dbeb5733859b53303d093a1a6ca9ff9c72e6bd1e5a6d503823e1128a9e2176e | MATLAB | 10,127 | 227 | % MATLAB code provided by Seyed Mohammad Ali Rahmati
% Affiliation: Biomechanics and Motor Control Lab, Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA.
%
% Description:
% This m-file generates initial morphological parameters for 9 muscle
% groups, incluing a and phi
% It includes range... |
4ed0ae333104fa8fc510eb0dd60abfa53ee5329e637db4187165af9a57a83683 | MATLAB | 10,127 | 311 | %% CellHCat ("Cellwise Horizonal Concatenation")
% Macro to perform universal horizontal concatenation of array elements across a cell (dim 2)
% assumes that the 1st dimension is constant across all rows; tranpose if
% this assumption is violated.
%
%
% Potential Inputs and Behaviors:
% ---------------
% 1xN cell arr... |
c506ef6d18f40831156c282d593ae0312adda60175b18c617ee3be882d85a02c | MATLAB | 10,136 | 254 | function [Final_Spikes] = FP_SPIKECOUNT(DF_DEBLEACHED,Threshold, Ts,Fs, Hold_Constant, ZERO_RULE)
%% By David Estrin & David Barker for the Barker Laboratory
% Code is written for ____ et al., 2020
% The purpose of this code is to take debleached calcium signal previously
% calculated in FP_DEBBLEACHED.m function a... |
8e65fd50c90cc20c1ef4c44169ca68bee8aeceac1add8749de731dbca5a2b546 | MATLAB | 10,137 | 302 | %epa_4points Analyzes responses using 4 points per participant
%
% This script analyzes data from the endogenously driven
% pro/antisaccade task. It uses results generated by epa_win_pc, which
% computes, for each participant and each experiment, the probability
% of a correct pro or a correct anti choice for all ... |
48f4b0b74046a0dab66fb9e02722cea4bffa1ebf3a4f6c04f28cc3ae2f403fe4 | MATLAB | 10,144 | 221 | function [u,r,GAMMA,g] = GNblock_ur(u,r,nt,dt,par,tag_str)
%% Created by Xinan Chen in Dec 2021
%% This function is the main function to optimize on the velocity field u and time-space dependent relative source r
%%
if nargin < 6
tag_str = '';
end
[Gamma,Gamma1,Gamma2,Gamma3] = get_Gamma(par.drho0... |
0d572e1252084aa72e24eee19c9c66a9860f6c16684080a5f49d501e2e2b8e55 | MATLAB | 10,148 | 232 |
% Written by: Tianyin Xu
% Edited by: Qiuting Wen, Adam Wright
% Last modified: 20241007 -- AMW
% Inputs:
% fMRI_path -- the scans path -- this path must include the following
% files:
% - SSS_mask_fmri.nii.gz (Transformed SSS MNI atlas into fMRI space)
% - R2mean_100trial_wholeBrain.nii.gz (generated from alig... |
1716c8b9443d5378931fafe9333dc313e027a00c88a5956127e167147bf5c945 | MATLAB | 10,151 | 309 | %SPTENSOR Class for sparse tensors.
%
%SPTENSOR Methods:
% and - Logical AND (&) for sptensors.
% collapse - Collapse sparse tensor along specified dimensions.
% contract - Contract sparse tensor along two dimensions (array trace).
% ctranspose - is not defined for sparse tensors.
% disp - Co... |
0366f1e395b484af10625146e1c2eb449b75bbdbf485bb61f45bf667030b8343 | MATLAB | 10,161 | 264 |
% demo_flickering_gratings
% add repository path to MATLAB path
addpath(genpath('..\subunit_grid_model'))
%%
% set experiment folder
expfolder = '20220301_60MEA_marmoset_left_s1';
% load data from selected experiment
expdata = load(fullfile('..\subunit_grid_model', expfolder, 'expdata.mat'));
% grating flicker... |
166c4df4af36d13ad36f25f0a2e3f114e6a14cc21ffde87284e0649e81b3a22f | MATLAB | 10,162 | 240 | % create_mice_all_randomMotorizedTreadmill.m
% Sarah West
% 11/30/21
% Creates and saves the lists of data you'll use for the given experiement
% (mouse names and days of data collected).
% Each row of the structure is a different mouse.
%% Parameters for directories
clear all;
experiment_name='Random Motorized ... |
ffce0991d01e04fe43eb99cb67601557548170b30b45b0f15d7eebc364081546 | MATLAB | 10,162 | 210 | % Writes all features of the ImageJ (IJ) binary roi file format (*.roi) as specified by ij.io.RoiDecoder.
% matlabpathcoors - an ordered list of coordinate pairs that describe a single ROI boundary. Coordinates assumed to be (y,x) order (where y is vertical image axis and x horizontal image axis) and follow the Ma... |
b1fcd661f2bc28c0ed285c4306997cd688a4becd76d1de6de712b4070db53c1d | MATLAB | 10,168 | 287 | function [mri, hdr, cpersist] = read_ctf_mri4(filename)
% READ_CTF_MRI reads header and imnage data from CTF format MRI file
%
% [mri, hdr] = read_ctf_mri(filename)
%
% See also READ_CTF_MEG4, READ_CTF_RES4
% Copyright (C) 2008 Ivar Clemens
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for... |
fd0848bc5674938e889fb18c5a644ab3a634fbe404983adab8881e55edde8401 | MATLAB | 10,169 | 193 | %% Create manuscript table
% _________________________________________________________________________
%
% Robert Dahnke & Polona Kalc
% Structural Brain Mapping Group (https://neuro-jena.github.io)
% Departments of Neurology and Psychiatry
% Jena University Hospital
% __________________________________________________... |
d3c8b39fb7d68c9c8c6ccf063a0d9fda54a82de49d252568f8a39632c37df4c9 | MATLAB | 10,172 | 278 | %% Plot cortical sources for NeVRo study
% Project the spatial patterns from SSD, CSP, and SPoC into source space
% by using eLORETA.
%
% Launch this script from top level of the NeVRo repository.
% BEFORE RUNNING:
% - Download the "New York Head" Leadfield from https://www.parralab.org/nyhead/
% - make sure the file... |
b7523ca70721a5a89d2181d33b7af0b8d4966cb89139db9626a4d6b0b0f8cb2b | MATLAB | 10,175 | 290 | function [data] = ft_datatype_raw(data, varargin)
% FT_DATATYPE_RAW describes the FieldTrip MATLAB structure for raw data
%
% The raw datatype represents sensor-level time-domain data typically
% obtained after calling FT_DEFINETRIAL and FT_PREPROCESSING. It contains
% one or multiple segments of data, each represente... |
aac77793f7ecd8c322831b1794a100f5c6f60d431dcbbbabaab968c70c21f3b8 | MATLAB | 10,184 | 205 | function y_MixedEffectsAnalysis_Image(DependentDir,OutputName,MaskFile,CovariateDirs,OtherCovariates, PALMSettings)
% y_MixedEffectsAnalysis_Image(DependentDir,BetweenSubjectFactor,WithinSubjectFactor,OutputName,MaskFile,CovariateDirs,OtherCovariates)
% Perform mixed effect analysis: one between subject factor, one wit... |
db57779d56721fa793d4d1127fa4b269660b024cbcac46027a0d962753b2dd38 | MATLAB | 10,195 | 390 | % Copyright (c) 2008 INRIA - Asclepios Project. All rights reserved.
function [A,h]=loadinr(name,slice)
%Load INR format image
% [A,H] = LOADINR(NAME,SLICE)
% Input arguments:
% NAME filename
% SLICE slice numbers, optional, [first slice ,last slice]
%
% Output arguments:
% A im... |
37fe66f4bfd5d66ac80c09e3d3084f610bc8da2b55182dd6983a1a6addea90e2 | MATLAB | 10,196 | 260 | function [p_Brain, F_Brain, Header] = y_CWAS(DataUpDir, SubID, AResultFilename, AMaskFilename, Regressor, iter, IsNeedDetrend, Band, TR)
% [p_Brain, F_Brain, Header] = y_CWAS(DataUpDir, SubID, AResultFilename, AMaskFilename, Regressor, iter, IsNeedDetrend, Band, TR)
% Perform CWAS
% Input:
% DataUpDir The direct... |
b7e21f16a8bafa8038e559f4f6cc07ac698607f4f5e9020afcfe7b87d36663cf | MATLAB | 10,197 | 394 | function [varargout] = eig_geap(A,B,varargin)
%EIG_GEAP Shifted power method for generalized tensor eigenproblem.
%
% [LAMBDA,X] = EIG_GEAP(A,B) finds an eigenvalue (LAMBDA) and eigenvector
% (X) for the real tensor A and the positive definite tensor B such that
% Ax^{m-1} = lambda * Bx^{m-1}.
%
% [LAMBDA,X] =... |
87a27fddc7a479c2b13307cdc101a18a32c77961aa308429f93cd35eb80cedcc | MATLAB | 10,208 | 274 | %% Multiplying tensors
%% Tensor times vector (ttv for tensor)
% Compute a tensor times a vector (or vectors) in one (or more) modes.
rand('state',0);
X = tenrand([5,3,4,2]); %<-- Create a dense tensor.
A = rand(5,1); B = rand(3,1); C = rand(4,1); D = rand(2,1); %<-- Some vectors.
%%
Y = ttv(X, A, 1) %<-- X times A in... |
86313cf4a3138532a72f4e469a890542e3143eb4def34c8e9bb9baec993ff206 | MATLAB | 10,212 | 370 | %% All trials ERPAC
addpath([DIRscript, '/PAC']);
addpath([DIRscript, '/ERPAC']);
DIRspectro=[DIRresults, '/ERPAC/'];
mkdir(DIRspectro)
[PAC_value, PAC_z, PAC_sig] = erpac_corr(LFPRawAll(good_chan(26),:), DecFS, ...
task_data(:,3), [-100 900], 2, 8, 70, 190, 100);
figure
subplot(3,1,1)
plot(PAC_value)
xlabel('T... |
6394ad0ccfaefa917ae08acb406a9321774de726cb438b284b24da74eff516ea | MATLAB | 10,227 | 366 | classdef TreeNode < handle
% Seems to be a general handle class for representing a rooted tree, where
% each node can have some data associated with it. -- ALT, 2025-02-04
properties
Data
Children % vector of TreeNodes
end
methods
function obj = TreeNode(dat,isjsonstruct,varargin)
... |
9bc6d378704febc3a5de6709dfa26ea3677888603698024a41d5bd503812f869 | MATLAB | 10,228 | 166 | function sPPI_and_gPPI_without_deconv_no_centering_FIR(stat_path,exp_folder,N,N_ROIs,q_level,ground_truth)
% ========================================================================
% Ruslan Masharipov, July, 2024
% email: ruslan.s.masharipov@gmail.com
% ================================================================... |
34e3d4fee72fd61f011689494cc217ad9ffb870b9f47fd68bff91b9a2174bf69 | MATLAB | 10,231 | 255 | function CrossDecodeAnalysisAction(AllTrialData,Labels,DecodeLabels,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] ... |
8b46f5d86c4ad96d7d8f7f4c84415e2abbb17bd88c5579faf168bce061955f4a | MATLAB | 10,233 | 283 | function [x, cost, info, options] = neldermead(problem, x, options)
% Nelder Mead optimization algorithm for derivative-free minimization.
%
% function [x, cost, info, options] = neldermead(problem)
% function [x, cost, info, options] = neldermead(problem, x0)
% function [x, cost, info, options] = neldermead(probl... |
5721161515c7ee19576b40664ea3ad91c91065aea8d3266b829d8637ed686657 | MATLAB | 10,242 | 355 | % LIP single-trial decision variable analyses
%% General setting
% Always need to run this section
global mLoc
mLoc = 'My\code\location\m-files';
cd(mLoc)
dat_path = 'My\data\location\single trial_data';
global saveLoc
saveLoc = fullfile(dat_path, 'All Sessions');
if exist(saveLoc) == 0
mkdir(save... |
c0a11100366ff855c7cfdebd23cc815dc355cf133b14d36f39d8f76319b089e1 | MATLAB | 10,242 | 328 | % MediatedModeration
clc; clear all; close all;
timelock = 'readyBS';
load(sprintf('TrioEEGAnalyseByTrials_%s.mat',timelock), 'meanAmplTrials','meanAmplTrialsPost');
%%
load('TrioEEGBehAnalysis.mat','trialTab');
%%
trialTab.erp1 = col(meanAmplTrials(:,:,:,:,30,:)); % early ERP -Cz
trialTab.erp2 = col(meanAmplTrialsPos... |
1a443b6f9dde74daa56044c35640091643056be28d75e8fb38c6a81a842628a7 | MATLAB | 10,246 | 359 | function [C,Ceq] = Constraint_Function (xopt)
NineMuscleMorphParaInitial = load('NineMuscleMorphParaInitial.mat');
NineMuscleMorphParaInitial = NineMuscleMorphParaInitial.NineMuscleMorphParaInitial;
G = 8; % Muscle Group Number (G = 1 to 9)
x0(1) = NineMuscleMorphParaInitial{G, 1}.MorphologicalParameters.a1;
x0(2)... |
7a67a866f264f44e7156104136a392b38803c2e13a924fc982aa53c8def7806b | MATLAB | 10,247 | 362 | function [C,Ceq] = Constraint_Function (xopt)
NineMuscleMorphParaInitial = load('NineMuscleMorphParaInitial.mat');
NineMuscleMorphParaInitial = NineMuscleMorphParaInitial.NineMuscleMorphParaInitial;
G = 1; % Muscle Group Number (G = 1 to 9)
x0(1) = NineMuscleMorphParaInitial{G, 1}.MorphologicalParameters.a1;
x0(2)... |
e7436bdf261e4663206646a9fc704a7633d8741281b338c770523bf3996a7e1d | MATLAB | 10,247 | 293 | function [ output_args ] = PlotSingleUnitERAs(AllTrialData,PlotConds,Phases,TimeWindows,OutDir,varargin)
%PLOTSINGLEUNITERAS Plots ERAs for specified units and conditions.
% Units: Matrix of unit IDs (e.g. ASF). All by default
% PlotConds: Cell array containing subselection criteria use for
% extracting s... |
7b290673a32c72e8e1f7592a76b8a639b8db5d663c58bd060a68b8544ab0f54e | MATLAB | 10,249 | 247 | function [acc, loss] = CBIG_KRR_innerloop_cv_allparams( test_fold, sub_fold, num_inner_folds, ...
data_dir, y_resid_stem, with_bias, ker_param, lambda_set, threshold_set, metric )
% [acc, acc_concat] = CBIG_KRR_innerloop_cv_allparams( test_fold, num_inner_folds, ...
% outdir, y_resid, ker_param, lambda_set, th... |
ba3ea76e40f37b9deba393deee1584774225b66eaf657036041318350a3c5f85 | MATLAB | 10,253 | 293 | function [ output_args ] = PlotSingleUnitERAsAction(AllTrialData,PlotConds,Phases,TimeWindows,OutDir,varargin)
%PLOTSINGLEUNITERAS Plots ERAs for specified units and conditions.
% Units: Matrix of unit IDs (e.g. ASF). All by default
% PlotConds: Cell array containing subselection criteria use for
% extrac... |
067b319bf70a9398a90bbc7ddadde6ddc46fe4944b9cd85ffea4799f3a9b092a | MATLAB | 10,259 | 290 | function [dipout] = beamformer_sam(dip, sens, headmodel, dat, all_cov, varargin)
% BEAMFORMER_SAM scans on pre-defined dipole locations with a single
% dipole and returns the CTF Synthetic Aperture Magnetometry (SAM)
% beamformer estimates. location. Dipole locations that are outside
% the head will return a NaN value... |
5070b655c9add4028e0a0a094288c375e00d583e16f37de579b8a068d6b39f17 | MATLAB | 10,263 | 286 | function ConvertKilosort2Neurosuite_KSW(rez)
% Converts KiloSort templates 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 basename.xml.
%
% In... |
9153471d5068ff2f075add20f1d1e438d8eed82c609a21e6f868c0715d925e45 | MATLAB | 10,263 | 209 | function [cfg, artifact] = ft_artifact_tms(cfg, data)
% FT_ARTIFACT_TMS reads the data segments of interest from file and identifies artefacts in
% EEG recordings that were done during TMS stimulation.
%
% Use as
% [cfg, artifact] = ft_artifact_tms(cfg)
% with the configuration options
% cfg.dataset = string w... |
3f0bdda9d79af6477651f566b1f4e71f6d15d0e08f62bec446132b6eff715d00 | MATLAB | 10,267 | 211 | % This is performed through the BrainVoyager 20.6 scripting platform, along with NeuroElf v1.1
% (after running the preprocessing pipeline script)
%
% Each subject directory should contain VMR (anatomical) and FMR (functional) files
% In addition, you need to copy the relevant PRT (experiment protocol) files to the... |
aee9783f6ae724e4608450f068ee929d2bce47ca26b9c39e2c360362e0806ba9 | MATLAB | 10,271 | 276 | function [fet clu spktimes wav]= ConvertKlusta2Matlab(shank,basepath,...
basename,wvformExtract,saveFiles,numCores,keepMUA)
% USAGE
%
% [fet clu spktimes wav]= ConvertKlusta2Matlab(shank,basepath,basename,wvformExtract,saveFiles,numCores)
%
% INPUTS
%
% shank - the shank number (as a number, not text) equalling the... |
7d0e3d1cba9ac3518a05eabfe2e0480c80ece3ef141bdfd93e6c44eed31b644b | MATLAB | 10,278 | 227 | function h_getCurrentImg3(handles)
global h_img3
% tic
[redData, greenData, blueData] = h_getZFilteredData(handles);%this has to be done before below because it may change h_img3;
% toc
[currentInd, handles, currentStruct, currentStructName] = h_getCurrendInd3(handles);
siz = currentStruct.image.data.size;
cur... |
3aa9008b8011c0ec389582368e568ee748b3943dcee631c91edc3dd3e7514bd1 | MATLAB | 10,285 | 225 | function [beh, behMap, behView] = reformBehav(par, dd)
% reformBehav reformat behavioral indicators per trial into structures for
% different trial types
% Inputs
% par = structure defining file locations and a few additional
% paprameters
% dd = structure including behavioral indicators per... |
ab7b4d43bf31e83509bb95347d95c7ff6e353a50c46e010485e5923b4ea478fc | MATLAB | 10,286 | 294 | % HIFIE2_BASE Dispatch for HIFIE2 and HIFIE2X.
function F = hifie2_base(A,x,occ,rank_or_tol,idfun,pxyfun,opts)
% set default parameters
if nargin < 6, pxyfun = []; end
if nargin < 7, opts = []; end
if ~isfield(opts,'lvlmax'), opts.lvlmax = Inf; end
if ~isfield(opts,'ext'), opts.ext = []; end
if ~isfield(... |
8acbf418ccd777ad0ae99ebc980db923a15b6d1dd1c2ae3f6af8e7309ee1a8e2 | MATLAB | 10,290 | 277 | % RSKEL Recursive skeletonization.
%
% The recursive skeletonization algorithm approximates a hierarchically rank-
% structured matrix A as a multilevel low-rank perturbation A = D + U*S*V',
% where D is a block diagonal submatrix of A, U and V are block diagonal and
% rectangular, and S is a submatrix of ... |
3969933f3d2a55d99f5bd6af7acc285c02a1ab5048959414ce3e4e4999f85dc4 | MATLAB | 10,296 | 366 | % Field Trip-related test scripts - Synthetic FT data - Calculation
%
%
% Includes.
% FIXME - Assume init has already been called.
%
%
% Get event results for the "chosen" threshold values.
disp('-- Selecting event lists with chosen thresholds.');
detectft_mag_selected = detectft_mag{1};
detectft_freq_selected... |
b67f7f6c6ca53c614ad9695ea2578d09c8cccb72ec22c5ad359c02d697e6cd3f | MATLAB | 10,299 | 278 | %__________________________________________________________________________
% violin.m - Simple violin plot using matlab default kernel density estimation
%
% Updates:
% v2: extended for accepting also cells of different length
% v3:
% - changed varargin to parameter - value list
% - specification of x-ax... |
d6ec50799c2cfbc860e88fc78b0364d19d0a892b7d9a550d0a84bbb22e58c3a0 | MATLAB | 10,303 | 288 | function [scd] = ft_scalpcurrentdensity(cfg, data)
% FT_SCALPCURRENTDENSITY computes an estimate of the SCD using the
% second-order derivative (the surface Laplacian) of the EEG potential
% distribution
%
% The relation between the surface Laplacian and the SCD is explained
% in more detail on http://tinyurl.com/ptov... |
29f8dce0b01f581a05905efe90e60efa59eb9c20acdb4cfdef13ae5c30672f34 | MATLAB | 10,304 | 322 | classdef ViewConfig
properties (Constant)
GAMMA_CORRECT_CMAP_LEN = 256;
end
% A ViewConfig is essentially the .View substructure of a project
% configuration. It contains:
% * FigurePos
% * XLim, YLim (if present => .X/YLimMode='manual', otherwise 'auto')
% * XDir, YDir
% * CLim
% * Gamma co... |
023bfe5007d506bc27ea77d6ed24e27f52bd3e0974d81a24691ec9be5f21e0d1 | MATLAB | 10,306 | 235 | function TSimporteventcodes(filename,inter)
% TSIMPORTEVENTCODES Imports event codes to the Experiment from a textfile.
% TSimporteventcodes(filename) imports codes from an ascii textfile. This
% can be a file made with TSexporteventcodes or made in a text editor.
% This codeset will overwrite whatever codes were... |
7e24f0ffd51017c4f5182908b0d7fb855d0b901b5178027bb7e76338efac4ca8 | MATLAB | 10,307 | 266 | function [J,data] = jacobian_DCS(mesh,tau_DCS,varargin)
% JACOBIAN_DCS Calculates spatial distributions of sensitivity of
% normalized autocorrelation registerd on the mesh boundary (detector) to
% changes of flow per mesh node.
%
% SYNTAX:
% [J,DATA] = JACOBIAN_DCS(MESH,TAU_DCS)
% [J,DATA] = JACOBIAN_DCS(MESH,TA... |
511abe490e6dc1b1c12ff260734f7c259f8426d5410d337d7362e04e815a2643 | MATLAB | 10,310 | 258 | classdef planarEdgeDetector < surfaceDetection.planarDetector
% planarDetector Extract a surface point cloud from a planar data stack
%
% As opposed to other detectors, the detected surface is
% represented not only by a PointCloud object but also by an image
% surfaceMatrix, containing z values for... |
6157eb2fbd502b7c245d039a787676756984b221baa02292a3d66c74fa18110b | MATLAB | 10,312 | 308 | function [specslope,spec] = bz_PowerSpectrumSlope(lfp,winsize,dt,varargin)
%[specslope,spec] = bz_PowerSpectrumSlope(lfp,winsize,dt) calculates the
%slope of the power spectrum, a metric of cortical state and E/I balance
%see Gao, Peterson, Voytek 2016; Waston, Ding, Buzsaki 2017
%
%INPUTS
% lfp a buzcode-fo... |
a9e15cf284d1aa96abc846edca086bf7da6cd8b1277a03a8f39f87caa4d1341e | MATLAB | 10,312 | 227 | function varargout = DPABIFiber(varargin)
% DPABIFIBER MATLAB code for DPABIFiber.fig
% DPABIFIBER, by itself, creates a new DPABIFIBER or raises the existing
% singleton*.
%
% H = DPABIFIBER returns the handle to a new DPABIFIBER or the handle to
% the existing singleton*.
%
% DPABIFIB... |
1c7d3f8c1ee0f4d4fcb9ca0b2f1326ea195b0a6ba04c589bbc40da143a91eb47 | MATLAB | 10,314 | 306 | function save_mesh(mesh,fn)
% SAVE_MESH Saves a FEM mesh in NIRFAST format into ASCII files.
%
% SYNTAX:
% SAVE_MESH(MESH,FN)
% SAVE_MESH(FN,MESH)
%
% SAVE_MESH(MESH,FN) Saves the MESH structure of FEM mesh in NIRFAST
% format into MATLAB *.mat file or ASCII files.
% FN - the root filename of the mesh (with no... |
80560d6b94eaa8cca642f0c948b3c16790428270888dcb8abaabd1e5e485926b | MATLAB | 10,329 | 319 | function demo_designOptimization ()
% // VBA toolbox //////////////////////////////////////////////////////////
%
% [posterior, out] = demo_designOptimization ()
% demo of off-line and online design optimisation
%
% This demo simulates a psychophysics paradigm similar to a signal
% detection task, whereby the detection... |
94e7f1c2be4d1d3278f616f4432fa2dd0dfcec0cd51a0c70acfb28621a3c7b67 | MATLAB | 10,332 | 209 | function [cfg, artifact] = ft_artifact_tms(cfg, data)
% FT_ARTIFACT_TMS reads the data segments of interest from file and identifies artefacts in
% EEG recordings that were done during TMS stimulation.
%
% Use as
% [cfg, artifact] = ft_artifact_tms(cfg)
% with the configuration options
% cfg.dataset = string w... |
1aa41871885841712ffcc0864b9bcb82f001f6f7e671a6175c51562072ec2cf9 | MATLAB | 10,335 | 301 | function [type, dimord] = ft_datatype(data, desired)
% FT_DATATYPE determines the type of data represented in a FieldTrip data
% structure and returns a string with raw, freq, timelock source, comp,
% spike, source, volume, dip, montage, event.
%
% Use as
% [type, dimord] = ft_datatype(data)
% [status] = ft_... |
233d80d521e56f1d02694f411e9601bfd0803972efe9f69d78d8760bd91c9507 | MATLAB | 10,338 | 196 | %% Create manuscript-revision table
% _________________________________________________________________________
%
% Robert Dahnke & Polona Kalc
% Structural Brain Mapping Group (https://neuro-jena.github.io)
% Departments of Neurology and Psychiatry
% Jena University Hospital
% _________________________________________... |
31643be981e8441a9cc543aeb2848372e7825d263360f51d5533d47c6e57075b | MATLAB | 10,338 | 310 | 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: 1602 $ $Date: 2018-05-01 10:23:15 +0100 (Tue,... |
1765cb5abb94b44300ede2b9effdf5420e8fe9bc283c02c821cf45d56e1f6f3b | MATLAB | 10,345 | 262 | function [event] = read_trigger(filename, varargin)
% READ_TRIGGER extracts the events from a continuous trigger channel
% This function is a helper function to read_event and can be used for all
% dataformats that have one or multiple continuously sampled TTL channels
% in the data.
%
% This is a helper function for ... |
95a0555e47b1887b647bdd8c6f75d12fd63576e50c9f8d225b6ab112f9a380e8 | MATLAB | 10,358 | 441 | function GLAN = erp_stata_group(GLAN,cfg)
%
% REALIZA ESTADISTICA NOPARAMETRICA A ERP
%
% cfg.
% subject = [{}{}{};{}{}{}]
% comp = 1; % INDEX OF THE CONDITION TO COMPARED , ONLY TWO!!!
% alpha =0.05;
% s ='d'; OR ='i' % RELATIONSHEAP TO THE SAMPLES 'i'NDEPENDENT OR 'd'EPENDET
% bl =[ 0 0.4]; % BASELINE
% ... |
5649d364f6b66de8b2ac1677ed6c79744737c5f144cf20b9df57b3d4de0b6ce7 | MATLAB | 10,359 | 324 | function PlotClusters_AM(spkDat, clustList, varargin)
% convert waveform data from int16 to double-precision floating point
spkDat.waves = double(spkDat.waves);
maxScale = Inf;
refWave = [];
sameScale = false;
showMean = true;
convertToVolt = true;
quantiles = [];
minIsi = 1; % in milliseconds
nSampTarget = 500;
rate... |
37b4c301ce936cb82657d2403b14c03433098b9ace53d619425081d7bb9eaf6f | MATLAB | 10,360 | 199 | %Step 3 of CBIG Kong2019 Brain Parc Pipeline
%
%To run: 1. Open Matlab using salloc (ex: `salloc --mem-per-cpu 6G --time 2:00:00 --x11`)
% 2. source your config file containing the $CBIG_CODE_DIR variable
% 3. `cd` to the $CBIG_CODE_DIR/stable_projects/brain_parcellation/Kong2019_MSHBM/step3... folder
% 4. `cp` thi... |
30beffca1e6a2e05e5cb107620aab96a6005ac81e80cf65eec086bcd2cb60f7f | MATLAB | 10,361 | 352 | function lan_setref_micromed(LAN)
% <*LAN)<] toolbox
% v.0.0.3
%
% Pablo Billeke
% Francisco Zamorano
% 09.10.2012
% 06.09.2012
% 03.09.2012
% 31.08.2012
global nameLAN
global h
global ref
global h2
global ifview
global ifsmp_cr
%global LAN
nameLAN = inputname(1);
ifview = 2;
ifsmp_cr = false;
%LAN ... |
aef07145a76c649fb14c684c012fc3ff759b0366c636822cfe75bcf75cb7fc28 | MATLAB | 10,367 | 288 | % 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 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
648481044544ef7d68c23212282a3b8d6d0d164bc10bc5cb0b5602e646742c2f | MATLAB | 10,370 | 289 | function [outputs] = OEvent_Neymotin_v1(signal, srate, plot_on_off)
outputs = [];
minimum_cycles = 2;
%%
% [psd,f] = pwelch(signal,[],srate/2,1:srate/2,srate);
%
% figure();
% plot(f,log10(psd));
% xlim([0 40]);
%%
% cycles = 1;
% freq = 6;
% [ filtered_data ] = wavelet_single_freq_filtering_v2(signal, srate, freq,... |
1516e2e82cf8e68dd1192231970d07a9922eee8307d99e6faf21627a82cee43b | MATLAB | 10,371 | 249 | function [filePathNetwork,filePathRegion,filePathLabel,filePathLink] = CircosDataOrganize(workingDir,CircosStruct)
% FORMAT [filePathNetwork,filePathRegion,filePathLabel,filePathLink] = CircosDataOrganize(workingDir,CircosStruct)
% Data organization for Circos plot via the format of txt
%
% Input:
% workingDir - work... |
862eb0f1ca324dd640187048abc5a6d8a24a6b6461fba892cfa3ee27a066ddda | MATLAB | 10,381 | 226 |
function [parameters] = DatasetPrep(parameters)
MessageToUser('Prepping ' , parameters);
% Find the location & value of the comparison iterator in
% parameters.values
iterator_location = find(cellfun(@strcmp, parameters.keywords, repmat({'comparison_iterator'}, size(parameters.keywords))));
comp... |
79689ea2e2c5f7561b1ab19f7668429a93b1868e3bcf114dc07370ba9da7d690 | MATLAB | 10,382 | 294 | function varargout = optimize_mesh_gui(varargin)
% OPTIMIZE_MESH_GUI MATLAB code for optimize_mesh_gui.fig
% OPTIMIZE_MESH_GUI by itself, creates a new OPTIMIZE_MESH_GUI or raises the
% existing singleton*.
%
% H = OPTIMIZE_MESH_GUI returns the handle to a new OPTIMIZE_MESH_GUI or the handle to
% th... |
7d330702e622555420212c69950b507cca89cfd5c010aa33fd2380494a0fd0b2 | MATLAB | 10,389 | 262 | function [] = plot_ground_truth_subtract_global_remapped(folders,method,option)
total_number{1}(1:3) = 0;
total_number{2}(1:3) = 0;
for nfolder = 1:5
for nshuffle = 1:2
cd(folders{nfolder})
if nshuffle == 2
cd 100_global_remapped_shuffles
number_of_global_... |
d7a78e75f185adf3ba05efae93a0dc5209a7037fe7a98b94667797d3fb536dc2 | MATLAB | 10,412 | 367 | function show_vc_tri(vc,points,para);
% plots volume conductor/cortex as surfaces
% eventually plus sources/dipoles
% usage show_vc_tri(vc,points,para);
%
%
% vc is a structure with two fields:
% vc.tri is Nx3 matrix of integers where each
% column denotes the indices of three points
% forming a ... |
0554ebf47d0702fbd994b62f416c846f7d0f0f97f12f0e10a8af1a2fa5aa4c13 | MATLAB | 10,414 | 318 | function [ CF ] = Cost_Function (xopt)
NineMuscleMorphParaInitial = load('NineMuscleMorphParaInitial.mat');
NineMuscleMorphParaInitial = NineMuscleMorphParaInitial.NineMuscleMorphParaInitial;
G = 7; % Muscle Group Number (G = 1 to 9)
x0(1) = NineMuscleMorphParaInitial{G, 1}.MorphologicalParameters.OW.a1OW;
x0(2) = N... |
14a25a9ce2edbd0e210585fbfb28861571cadb80f5625ab4c088b3896e662293 | MATLAB | 10,420 | 308 | % Rough estimates for principal point and focal length:
fg = [1009.661057548567 1009.706970843858 ]';
cg = [ 1031.688786545889 1288.395050759215]';
kg = [-0.054285891395760 -0.026812583950935 0 0]';
%fg = [ 139.77712 139.61650 ]';
%cg = [ 319.62550 258.16616 ]';
%kg = [ 0.02859 -0.01812 0.00839 -0.00182... |
fc767034c3bb61ae5ee7d5102018db9cbcc4dd2f80faac64934718b2fb83c869 | MATLAB | 10,425 | 257 | function seizureInfo = getSeizureTimingInfo_EP(seizurePath, seizureCell, params)
% This function reads a seizure's mat file and extracts information about
% the baseline times, seizure times, postictal times, recovery times, and
% control times. It also extracts information about lick and click times.
% INPUTS:
% - ... |
881e4cfd349b9cad36cef11557234d270c95a4b2f07ca793cb94a8090a2a1b55 | MATLAB | 10,429 | 337 | function fieldtrip2fiff(filename, data)
% FIELDTRIP2FIFF saves a FieldTrip raw data structure as a fiff-file, allowing it
% to be further analyzed by the Neuromag/Elekta software, or in the MNE suite
% software.
%
% Use as
% fieldtrip2fiff(filename, data)
% where filename is the name of the output file, and data is ... |
75ec8e4f5537206371edb13dc5b5b6343b412fccfdcd2542123b656808971004 | MATLAB | 10,448 | 276 | % Address the basic question, when x is the salient category, what
% percentage of units are tuned to x.
function PlotAnalysisThroughTimeGroup(config,varargin)
[varargin,DateName] = Utilities.ProcVarargin(varargin,'DateName',[]);
if strcmp(mfilename,'') || nargin==0
opts=Analyze.Libet.Config_Basi... |
2ec540793e0f917b1531f35e9c166e0d04c927bfc3cb1fe7f7dbb4f388a3b5ed | MATLAB | 10,457 | 300 | function [type, dimord] = ft_datatype(data, desired)
% FT_DATATYPE determines the type of data represented in a FieldTrip data
% structure and returns a string with raw, freq, timelock source, comp,
% spike, source, volume, dip, montage, event.
%
% Use as
% [type, dimord] = ft_datatype(data)
% [status] = ft_... |
503b1192497eabc2ce37784bba0f9dc5c6e0781fed95b8f68067abba91039c6d | MATLAB | 10,458 | 328 | function mono_res = bz_MonoSynConvClick (spikeIDs,spiketimes,varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% INPUTS
%%%
%%% spikeIDs = Nx3 matrix. N = # spikes.
%%% col1 = shank ID, col2 = cluID on shanke, col3 = unit ID
%%%
%%% spikestimes = Nx1 matrix aligned with spikeIDs where each row is a
%%% time stamp ... |
7062c62817e227decfa74e5311ed63743f30bd05416f10bfdc0c839c65561d4a | MATLAB | 10,459 | 293 | function [varargout]=gscatter3(x,y,z,g,clr,mrksle,mrksze,mrkfclr,leg,legloc)
%------------------------------HELP START----------------------------------
% gscatter3 - 3D scatter plot by group
%
% Ussage:
% gscatter3(x,y,z,g);
% gscatter3(x,y,z,g,opt_param);
% opt_param - optional parameters such a... |
9f96ac04cfd644f54c07515487cca4607ff4a9b3bcedcc71908f8f9088edd99d | MATLAB | 10,465 | 207 | %% Code for additional analyses
%% creating and analysing randomised dataset
clear all
workingDir = 'P:\ground_truth_replay_analysis\Dropbo_data8';
cd(workingDir)
folders = {'2019-06-20_09-55-42' 'N-BLU_Day7_Ctrl-16x30_no_reexp' 'N-BLU_Day8_Ctrl-15-NoRest-15' 'Q-BLU_Day2_RateRemap' 'Q-BLU_Day3_RateRemap'...
'RAT1... |
8c7e75aaaba3483c0ce6f3b1ca8eb3b82af9fcf79f6084444604a09fd780ee7b | MATLAB | 10,467 | 269 | function [dataout] = ft_denoise_dssp(cfg, datain)
% FT_DENOISE_DSSP implements a dual signal subspace projection algorithm
% to suppress interference outside a predefined source region of
% interest. It is based on: Sekihara et al. J. Neural Eng. 2016 13(3), and
% Sekihara et al. J. Neural Eng. 2018 15(3).
%
% Use as
... |
11a3a4ad2d6adb815120421a78f154a1157682fcdbc0b492f4578b5954da90dd | MATLAB | 10,469 | 263 | function convertBinaryToSurface(fov_path,im2plot_path,subdir,subj,region,labelbase,outdir,max_ecc,dpp,inRetinalSpace,binary,force)
%{
This function takes in images of foveal location and some shape with
position relative to the fovea and converts them to surface space on the
subject's hemispheres. For this function, yo... |
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