sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
8db024c0077b4c75574258504d166c2a1542201c744316b2f267a75e3187d3e3 | MATLAB | 2,569 | 65 | %%% Figure 1 - Percept maps
addpath("HelperFunctions")
load(fullfile(DataPath, 'SurveyMainData_Processed.mat'))
export_path = fullfile(DataPath, 'Figure1_Intro');
SetFont('Arial', 9)
SubjectIDs = {'BCI02', 'CRS02', 'CRS07'};
subj_str = {'C1', 'P2', 'P3'};
[pbt_regions, dbt_regions] = GetHandSegments();
%% Get implant ... |
fe7f5d8166c6310723f7011cceaddb09a99f1a636d7186634062147b1ca240ba | MATLAB | 2,569 | 64 | function model = plotMCmatlabGeom(model)
% Displays
% Geometry cuboid
% Media optical, thermal and fluorescence properties
%
% Requires
% NdimSliderPlot.m
%
%%%%%
% Copyright 2017, 2018 by Dominik Marti and Anders K. Hansen, DTU Fotonik
% This function was inspired by lookmcxyz.m of the mcxyz... |
347572a0b1c1ceb18cfebc0173962439d64b294c79eb563a36047a366afa0f7c | MATLAB | 2,570 | 61 | function ts_denoised = meg_environmental_denoising_new(ts, opt)
% This function uses the timeseries of the three MEG non-physiological
% channels to denoise the physiological channels.
%
% ts_denoised = meg_environmental_denoising(ts, opts)
%
% INPUTS:
% ts MEG timeseries (number of timepoint... |
306124f3ec03933884ecf9a76d958f4381517a6ce3abd44c5787927825e55441 | MATLAB | 2,571 | 69 | function str = VBA_summaryMFX(out)
% writes a summary string from output of VBA_MFX model inversion
% function str = VBA_summaryMFX(out)
% IN:
% - out: the 'out' structure of VBA_MFX inversion routine
% OUT:
% - str: a cell array of strings, which summarize the VBA inversion
str{1} = sprintf(['Date: ',datestr(out.... |
e0268c56423ff2d2d71be843b5b8138c9935f7949c8a2bfb0e1063be5c49728f | MATLAB | 2,571 | 86 | function [mask sz] = mkMasksRadial(imSize,windows,verbose)
%
%-----------------------------------------
% mask = mkMasksRadial(imSize,windows)
%
% generates a family of radial window functions
% that tile evenly in angle and log eccentricity
%
% imSize: size of image (2-vector)
% windows: structure containing window p... |
e7cf1470831280268c55468260b0aab602b91db23866185b353d318ace5b04dd | MATLAB | 2,571 | 70 | %{
Copyright (c) 2025 Axion BioSystems, Inc.
Contact: support@axion-biosystems.com
All Rights Reserved
%}
classdef StimulationChannels < Tag
%STIMULATIONCHANNELS File data that enumerates channels used in a
%stimulation
properties (GetAccess = private, Constant = true)
CurrentVersion = 0... |
40f573babd077cfd471810ba63bded2ba8ccc3ac624c5be5ffb62d1b77edb978 | MATLAB | 2,572 | 102 | function [d, pre, post, cycle, f, pred] = dfsPMTK(adj_mat, start, directed)
% DFS Perform a depth-first search of the graph starting from 'start'.
% [d, pre, post, cycle, f, pred] = dfs(adj_mat, start, directed)
%
% Input:
% adj_mat(i,j)=1 iff i is connected to j.
% start is the root vertex of the dfs tree; if [], all ... |
7eaaf8216e33f0dbccafcae9c4eaae55c46626a6812c7f1c10d32d92f0a9be2d | MATLAB | 2,574 | 84 | function CBIG_ABCD_proc_rs_qc(id,proc_dir,bbr_thr,maxFD_thr,length_thr,FD_th,DV_th)
%
% CBIG_ABCD_proc_rs_qc(id,proc_dir,bbr_thr,maxFD_thr,length_thr,FD_th,DV_th)
%
% This function reads some qc measures and then remove runs that failed qc from the bold list
%
% Inputs:
%
% - id:
% subject id
%
% - proc_dir:
% ... |
fa65fce43debe59d03af0d748a32b909d34fb4b9f9ffc0dacbf9ccfa090625ce | MATLAB | 2,576 | 68 | function [y,excl,rmsFd] = afxDenoising(y,subjectMasks,brainMask,rpFile,options)
% if >options.unsmoothed< is true, tissue signal will be extracted from
% unsmoothed data (y2), confound removal and filtering will be performed
% also for unsmoothed data
fprintf(' Denoising ...')
% calcula... |
53da11fd05e9b971e52a532a2761e9e4b05bf6429e3da0f65d28fcd1128e1192 | MATLAB | 2,577 | 85 | function [x,mx,sx] = standardise(x,dim,lim)
% X = STANDARDISE(X, DIM) computes the zscore of a matrix along dimension dim
% has similar functionality as the stats-toolbox's zscore function
% Copyright (C) 2009, Jan-Mathijs Schoffelen
%
% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip
% fo... |
4c7b5cbe70acf806ba9378958c7fb3c2d57d2b0a9344590b2d55d1c5dbe80574 | MATLAB | 2,578 | 112 | %% Interpolate some data using a joint Gaussian
% Based on p140 of "Introduction to Bayesian scientific computation"
% by Calvetti and Somersalo
% See also https://users.oden.utexas.edu/~tanbui/PublishedPapers/BayesianTutorial.pdf
function main()
demo(0.1)
demo(0.01)
end
function demo(priorVar)
setSeed(1);
n = 150;... |
cacb9be5e2357aa139449e1c6c8b6ad3adb5a7b8188df5d7bbc6ad7a84c905a7 | MATLAB | 2,578 | 53 |
ind = 1;
data = dir('/DATAPOOL/ERRORMONITORING/SEM_mri_data/P*');
%%
for i = 1:size(data,1)
data_func = dir([data(i).folder, '/', data(i).name, '/mri/SEM_', data(i).name, '/nifti/func/run*']);
fprintf(data(i).name);
for j = 1:size(data_func,1)
images = [data_func(j).folder, '/', data_... |
0c076efc3de5670cd027577c7797a659f4d3975b2f8a74aee32089000ac3a7a8 | MATLAB | 2,580 | 68 | function [ F, J ] = diffofgauss2dfun( params, xy)
%GAUSSIAN2DFUN evaluates modified gaussian with params at x
% Output:
% F: function value
% J: Jacobian of the parameters
%Written by Dimos.
%==========================================================================
%Unwrap inputs
%=====================... |
74dac547c4dd5d295fc9b2b8744178c182f315514c93af374b003e614a1e9544 | MATLAB | 2,580 | 95 | %% ------------------------------ Initialize ------------------------------
% include all functions
% clear all
% addpath(genpath('src'));
% parameters;
%
% name = 'P8_No28_Iba1-A647_DAPI_b1_h1_12'; % must be without tiff extension !
mkdir(['results/' name]);
%% ----------------------------- Load the BW mask ------... |
6b71ee239490082cb611eed31add306bc3565645718cf497b55a5b322ff26ad5 | MATLAB | 2,581 | 78 | function event = read_spmeeg_event(filename, varargin)
% read_spmeeg_event() - import evtns from SPM5 and SPM8 meeg datasets
%
% Usage:
% >> header = read_spmeeg_event(filename);
%
% Inputs:
% filename - [string] file name
%
% Outputs:
% event - FILEIO toolbox event structure
% ________________________________... |
a591db6291a8051542eb7190a0f37251f67638565be6705f711d59a17131f849 | MATLAB | 2,582 | 87 | %% smvgc_to_mvgc
%
% Average (integrate) frequency-domain causality over specified frequency range
%
% <matlab:open('smvgc_to_mvgc.m') code>
%
%% Syntax
%
% F = smvgc_to_mvgc(f,B)
%
%% Arguments
%
% See also <mvgchelp.html#4 Common variable names and data structures>.
%
% _input_
%
% f spectral (freque... |
d252864e67eef020c4cb4658bfdaa4ff2a5c3af267a9e3df7f07d3685e6ae218 | MATLAB | 2,582 | 68 | function [dat] = read_nihonkohden_m00(filename, begsample, endsample)
% READ_NIHONKOHDEN_M00 reads data Nihon Kohden EEG system and converts the
% floating point ASCII values to 16-bit signed integers from *.m00 file
% format. This function is an adaptation of convert_nkascii2mat.m written
% by Timothy Ellmore
%... |
3c27e10b0d8e961ae2b0ef5188a92c6b92e261f71d29cec857b44827d77835b8 | MATLAB | 2,583 | 84 | %% Water sprinkler network Example
%
% Make DAG
% C
% / \
% v v
% S R
% \/
% v
% W
%%
% This file is from pmtk3.googlecode.com
nvars = 4;
%% Create the dgm
ordered = true;
if ordered
[dgmJ, C, S, R, W] = mkSprinklerDgm('infEngine', 'jtree');
dgmV = mkSprinklerDgm('infEngine', 'varelim');
dgmE = ... |
e8c1ac818fcc40b64053a128d9f628624ab42cc126ef0fb66c658cbcbb3039cf | MATLAB | 2,583 | 95 | %% ------------------------------ Initialize ------------------------------
% include all functions
% clear all
% addpath(genpath('src'));
% parameters;
%
% name = 'P8_No28_Iba1-A647_DAPI_b1_h1_12'; % must be without tiff extension !
mkdir(['results/' name]);
%% ----------------------------- Load the BW mask ------... |
e7d8eed9a09f4f87aa2c003c2544ce583577556befb901156bb57106dfda3758 | MATLAB | 2,584 | 74 | % This is an electrode processor script: it imprints an arbitrary number
% of electrodes.
%
% Copyright SNM GCNP 2012-2024
elec_path = fullfile(dipole_folder,strcat(patno,'_',model_name,'_', ...
dipole_name,'_electrodes.mat'));
%% load BEM-FMM Engine
addpath(fullfile('... |
cf7f0c9c45e73799e9dc7d189a59696564e8f2a4e4a8ac7618adbc9e3ed10376 | MATLAB | 2,586 | 87 | function [p,out,hf] = doROC(xp,xn,displayWin)
% implements a ROC analysis on samples from alternative hypotheses
% function [p,out] = doROC(xp,xn)
% IN:
% - xp: values under the 'positive' hypothesis (H1)
% - xn: values under the 'negative' hypothesis (H0)
% OUT:
% - p: area under the ROC curve (probability of di... |
f6e31ed6c1e4e01a451d3e480230c007994cffedaa49ecaeadafdad34dd5afbc | MATLAB | 2,586 | 70 | function p = p_bt_median(w,w_boot,rng_seed,do_plot)
% for each voxel: test weight from regression with original data against the
% sampled null distribution of weights for this voxel
% sort the bootstrap distributions for all voxels' weights by their median,
% and choose voxels whose median value lies in either the s... |
1019523869980c113155cdf58adfdf052fc651cc447e844a0d8dbe748ff06a71 | MATLAB | 2,588 | 69 | %% Across time-point accuracy
load(fullfile(saveLoc, 'par_sess'))
load(fullfile(saveLoc, 'decoder_excl_SL'), 'excl', 'exclName', 'useN_dec', 'winCenter', 'winStart', 'winEnd')
for sess = 1 : 8
disp(num2str(sess))
par = par_sess{sess};
%% Load normalized activity for this session
... |
781ec1b783d60b78c27adb043c2bf1c67b3b002a2a5bf6b480256d2b03d9f695 | MATLAB | 2,588 | 150 |
if ~exist('calib_name')|~exist('format_image'),
data_calib;
return;
end;
check_directory;
if ~exist('n_ima'),
data_calib;
return;
end;
check_active_images;
images_read = active_images;
if exist('image_numbers'),
first_num = image_numbers(1);
end;
% Just to fix a minor bug:
if ~exist('first_num'... |
22483f9d3e28ade5a3d8f539122cea90ae8701bdc4d328fd2dd1e724f8a1e50c | MATLAB | 2,589 | 70 | % This script accurately computes and displays magnetic fields sampled on
% a cross-section (sagittal plane) via the FMM method with accurate
% neighbor integration
%
% Copyright SNM/WAW 2018-2024
%% Load/prepare data
planeABCD = [1 0 0 -1e-3*Xm]; %Analytical equation of the observation point plane for neighb... |
297bd6ace5a267f3276119d203ffdfa54be03e79ddcf06de9fb19d120b762346 | MATLAB | 2,589 | 69 | % This script accurately computes and displays magnetic fields sampled on
% a surface (coronal plane) via the FMM method with accurate
% neighbor triangle integration.
%
% Copyright SNM/WAW 2018-2024
%% Load/prepare data
planeABCD = [0 1 0 -1e-3*Ym]; %Analytical equation of the observation point plane for ne... |
4b94adf27a712090a41bbde82a6aeca6a901c3fad7f251c081c3d0f33cfaae49 | MATLAB | 2,589 | 88 | function M=movpwjph(N,Np,typesig);
%MOVPWJPH Influence of a jump of phase on the interferences of the pWVD.
% M=MOVPWJPH(N,Np,TYPESIG) generates the movie frames illustrating the
% influence of a jump of phase in different frequency modulations
% on the interference terms of the pseudo Wigner-Ville distribution.
%
%... |
3c170e8656cdc40e990a0fad1e9f3ffb4e2c0407057437a04135d9378b89a36b | MATLAB | 2,590 | 83 | function [nrm] = normals(pnt, tri, opt)
% NORMALS compute the surface normals of a triangular mesh
% for each triangle or for each vertex
%
% Use as
% [nrm] = normals(pnt, tri, opt)
% where opt is either 'vertex' (default) or 'triangle'.
%
% See also PCNORMALS, PROJECTTRI
% Copyright (C) 2002-2007, Robert Oostenvel... |
d625b04ae94f41139a32f362737519dcd5f2f0e1636ee784a888b36e675f2b2c | MATLAB | 2,590 | 57 | %% select subset of stimuli for practice, which will not be shown during the task
stimuli_all = load('/Volumes/LNDG/StateSwitch/B_paradigm/StateSwitchMR/C_Paradigm/StateSwitch/stimuli_corrJQK.mat');
stimuli_exp = load('/Volumes/LNDG/StateSwitch/B_paradigm/StateSwitchMR/C_Paradigm/StateSwitch/stimuliSelected.mat');
Cu... |
2620440e064d9cf6b648e62ec3349eb6c502f746fd1a3578b717789d8b75d9cc | MATLAB | 2,592 | 81 | function testPmtk3()
%% Minimal test that PMTK3 is correctly installed and working on your system
%
%% matlab Tools
% This file is from pmtk3.googlecode.com
%% Check that initPmtk3 was run
% It generates a file called 'isOctave.m' that is not preinstalled
fprintf('Checking initialization..........');
initPassed = ex... |
9952bc33e018595615195c39bba3e0b8ea825efe84ea379e5dd2f6ae378c9db9 | MATLAB | 2,592 | 90 | % create a channel map file
Nchannels = 32;
connected = true(Nchannels, 1);
chanMap = 1:Nchannels;
chanMap0ind = chanMap - 1;
% ycoords = [100,100,120,120,...
% 220, 220, 240, 240,...
% 340,340,360,360,...
% 460,460,480,480,...
% 580,580,600,600,...
% 700,700,720,720,...
% 820,820,840,840,.... |
5d992dc07b23a091568478bdef9745fcfeb54eb7f32462b3e14bc3d0a4e15b1a | MATLAB | 2,593 | 83 | function [tfr,t,f] = tfrpage(x,t,N,trace);
%TFRPAGE Page time-frequency distribution.
% [TFR,T,F]=TFRPAGE(X,T,N,TRACE) computes the Page distribution
% of a discrete-time signal X,
% or the cross Page representation between two signals.
%
% X : signal if auto-Page, or [X1,X2] if cross-Page.
% T : time instan... |
c69166fcdd80fb71941818924e232a0187aa169d14aefc40bd1cfdae300b98be | MATLAB | 2,593 | 87 | function [subj_ids, dzne_ids, mbm_nos, subj_info, tab_hdr] = read_subject_ids(subj_file, varargin)
% _
% Read Subject IDs and DZNE IDs from Excel or text file
%
% subj_file - an XLS or TXT file containing subject information
% property - (optional) property to select sub-set of subjects
% value - (opt... |
2d4c4d23a1329c831e3341c092292401bab8f2789bf9b8ddfc143537cfc56811 | MATLAB | 2,594 | 67 | %% Corr vs distance pooled
% linear fit
% [r_all,distance_all] = extract_variables ('corr_vs_dist','tot',resultsPath, 'r_all', 'distance_all',conditionType,conditionValue);
% r_all = cell2mat(r_all);
% distance_all = cell2mat(distance_all);
% mdl = fitlm(distance_all,r_all);
% figure
% subplot(231)
% plot(mdl);
% xlabe... |
f41dfbf3fe35e20e8d6e18ed8473c7e24e08463299aa65ee112f2a0ca82fb071 | MATLAB | 2,594 | 84 | classdef MovieManagerModel < handle
% State that backs the MovieManagerController view but is not
% itself graphical. Lives on the Labeler so it persists across
% MMC open/close cycles, and so batch code can mutate it without
% a controller present.
properties (Access=private)
showPathEnds_ = true
... |
f72812fde83703a1da06a872a3dacb475831966b7c205c4a665a1a70356fe2c1 | MATLAB | 2,594 | 75 | function CBIG_RF_make_cortexMask(template_sub_id, count_map, num_sub, output_dir)
% CBIG_RF_make_cortexMask(template_sub_id, count_map, num_sub, output_dir)
%
% This function creates loose cortical mask for a volumetric atlas,
% using surface-to-volume count maps
% The mask is created by thresholding the mapping by 15... |
0c6302f27fb279c5bbc7a114f3faaa88e5d9f5985ca3156a8d18f057c858a529 | MATLAB | 2,595 | 61 | % Demo for aggregate channel features object detector on Inria dataset.
%
% See also acfReadme.m
%
% Piotr's Computer Vision Matlab Toolbox Version 3.40
% Copyright 2014 Piotr Dollar. [pdollar-at-gmail.com]
% Licensed under the Simplified BSD License [see external/bsd.txt]
%% extract training and testing images ... |
e88711eb64f82f95458336a5ff8378cfbd57f218cb1dc235cc554017e61ef572 | MATLAB | 2,595 | 93 | function CBH = cbhandle(varargin)
%CBHANDLE Handle of current colorbar axes.
%
% SYNTAX:
% CBH = cbhandle;
% CBH = cbhandle(H);
%
% INPUT:
% H - Handles axes, figures or uipanels to look for colorbars.
% DEFAULT: gca (current axes)
%
% OUTPUT:
% CBH - Color bar handle(s).
%
% DESCRIPTI... |
7dd885fe7ca9402b961735a935ba46317b4796329e420592cf244ecd77c1fb15 | MATLAB | 2,596 | 50 | function [censoredVolumes,lpffdCensoredVolumes,lpfdvCensoredVolumes] = ...
getCensoredVolumesFromNifti(fileNameDataNifti,fileNameBrainMask3D, ...
MPs,LPF_FD_Threshold,DV_GEV_d)
% This is a wrapper for getCensoredVolumes that opens a nifti or cifti time
% series using niftiread. It is identical, e... |
2b7e8527bb541789f3607f31e6f1024bae87189e06b3b8eaf13a46275494f4ef | MATLAB | 2,597 | 69 | %% Across time-point accuracy
load(fullfile(saveLoc, 'par_sess'))
load(fullfile(par_sess{1}.saveLoc, 'decoder_excl_SL'), 'excl', 'exclName', 'useN_dec', 'winCenter', 'winStart', 'winEnd')
for sess = 1 : 8
disp(num2str(sess))
par = par_sess{sess};
% Load normalized activity for th... |
7a27d30f30bdffd3cb871ea5be88404620368acb78a65596880c777bc241db6a | MATLAB | 2,597 | 94 | function c = ttt(varargin)
%TTT Tensor mulitplication (tensor times tensor).
%
% TTT(X,Y) computes the outer product of tensors X and Y.
%
% TTT(X,Y,XDIMS,YDIMS) computes the contracted product of tensors
% X and Y in the dimensions specified by the row vectors XDIMS and
% YDIMS. The sizes of the dimensions... |
28aa4bb3650c3663dc8acd5afcc567cf458f85987eedd47543bbf1c6c201803d | MATLAB | 2,598 | 82 | function Draw_ROIs_on_Cortex(Anat,ROI)
%
% This function will draw ROI spheres on a model of the cortical surface.
% Anat is a structure that describes the anatomy.
% ROI is a structure that describes the regions of interest.
%
% Anat fields:
% CtxL mesh for left cortex. mesh includes 2 fields, nodes and
... |
5094d57908af04fe5a0d5da091d5d61ad5af386f501d7e4681243a5b1571a6b0 | MATLAB | 2,598 | 71 | function str = gencode_substruct(subs, name)
% GENCODE_SUBSTRUCT String representation of subscript structure.
% Generate MATLAB code equivalent to subscript structure subs. See help
% on SUBSTRUCT, SUBSASGN and SUBSREF for details how subscript structures
% are used.
%
% str = gencode_substruct(subs, name)
% Input a... |
8efb0a283c0bf339d164924830267a5af99b4674c10899eae6bb64ba0a5b1eea | MATLAB | 2,598 | 63 | classdef ChristoffelPatch < diffgeometry.TransformableCP
% TransformableCP that transforms like the affine connection
%---------------------------------------------------------------------
% license
%---------------------------------------------------------------------
% Copyright 2015 Idse... |
72781adabda8787f18f603e440eec90593ab08609a5c9cd3c7ab933454d1c08e | MATLAB | 2,599 | 64 | function selected_color = color_picker_2(object_type)
exponential_weight = 0.03;
sigma = 1/3;
% COLOR_PICKER assigns all colors to be plotted in a synthetic image.
% Each object should have a representative color, a distribution, or
% alternative data to support color selection.
if strcmp(object_type, "table_backgro... |
8e38c522e615f5df5a64046c3f8a335313eb735fd0f819f9c92d42352e03dbfc | MATLAB | 2,599 | 56 | function [I,T]=bspline_transform(O,I,Spacing,mode)
% Function bspline_transform, is a wrapper of the mex
% bspline_transform_2d_double and bspline_transform_3d mex functions
%
% [Iout,T] = bspline_transform(O,Iin,Spacing,mode)
%
% inputs,
% Iin : Input image.
% O : Transformation grid of control points
... |
a4904effd516d4dba3725506676142819bf4be775299eff09f899bfd127ce576 | MATLAB | 2,599 | 100 | function [ intersections, volumes, rr, k_coef, m_coef , Rsquared] = sholl( img_3d, name )
% function: Short description
%
% Extended description
% loading the parameters
parameters;
%% ------------------------- Finding center of the cell -------------------
% Central position [x,y, z]
% Just take c... |
3868cdf85169c1d65f74ada9a25a2f651022f5cffd0edd7e7fa7fc1c59906282 | MATLAB | 2,600 | 70 | % This script accurately computes and displays magnetic fields sampled on
% a cross-section (transverse plane) via the FMM method with accurate
% neighbor integration
%
% Copyright SNM/WAW 2018-2024
%% Load/prepare data
planeABCD = [0 0 1 -1e-3*Zm]; % Analytical equation of the observation point plane for ne... |
f48e4f13cfd0affaf40fabacb07cc72b39b7f2df238817078d4082dedcb49efc | MATLAB | 2,600 | 91 | function [ ampbins,phasebins,sig2powerskew,sig2prefangle,phaseamphist ] = PhaseAmpCouplingByAmp( sig1phase,sig1amp,sig2amp,numbins )
%PhaseAmpCouplingByAmp(sig1phase,sig1amp,sig2amp,ampbins,numphasebins)
%calculates phase amplitude coupling between the phase of signal 1 and the
%amplitude of signal 2, with respect to t... |
30839af075b74202ec0edbdca36c7257f8e3e178cce1b179c8d82f8decc187eb | MATLAB | 2,601 | 91 | function dgm = dgmTrainFullyObs(dgm, data, varargin)
%% Fit a dgm via mle/map given fully observed data
%
% See dgmTrain
%%
% This file is from pmtk3.googlecode.com
[clamped, localEv] = process_options(varargin , 'clamped', [], 'localev', []);
if ~isempty(localEv) && ndims(localEv) < 3 && dgm.nnodes > 1
localEv =... |
dde30a1b21bb0e2c7c1430c7f65c75a8c1b09c5da8c2312413cf5bff06ef8145 | MATLAB | 2,601 | 67 | % Relationship between columns in out.dataMat and out.dataMap or dataMat
% and DataMap and behavior
% Dot trials
par.idx = struct('dot_on' , 1, ...
'dot_off' , 2, ...
'saccade' , 3, ...
'dot_dir' , 4, ...
'dot_coh' , 5, ...
'sig_coh' , 6, ...
'se... |
66a8ab156d83f6a7da0d8bb0b7e9efa5e809a37f1007a5d4f538bb965d258423 | MATLAB | 2,602 | 99 | % 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,... |
4fa16375220d55e88670401c8b472ea1a30c1fc89e04ede4a998020432f585ea | MATLAB | 2,603 | 89 | function [] = graphVizIt(adj,labels,landscape,removeDisconnected)
% graphVizIt(adj,labels)
%
% Path to graphViz is hard-coded in this function
nNodes = length(adj);
if nargin < 2
for n = 1:nNodes
labels{n} = sprintf('%d',n);
end
end
if nargin < 3
landscape = 1;
end
if nargin < 4 |... |
bcd0301c67400ffde0c43f55d9d5289dee761e3131848460709ab1baa8be0c1c | MATLAB | 2,603 | 77 | %% Plot unigrams and bigrams of Darwin's "On the origin of species"
%
%%
% This file is from pmtk3.googlecode.com
loadData('ngramData'); % cotnains bigrams, ugrams, etc (use ngramMake to create this)
if(0) % Plot bigram frequencies
bigramFig = figure;
axes1 = axes('Parent',bigramFig,...
'YTickLabel',... |
3ec5f1962101e8d5093f3d4f61ce51212c2e81226c0aeb4c705e43487821139a | MATLAB | 2,604 | 97 | % _ _
% ___ _ __ __ _| |__ ___ ___ _ __| |_
% / __| '__/ _` | '_ \/ __|/ _ \| '__| __|
% | (__| | | (_| | |_) \__ \ (_) | | | |_
% \___|_| \__,_|_.__/|___/\___/|_| \__|
%
% moves plots when scroll wheel or scroll bar is moved
function scroll(self,src,event)
d = dbsta... |
eea0888f899fa40921ebe2a41342195e3613ee003885840768595f3215531f8a | MATLAB | 2,604 | 75 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%-- Main 3D Scanning Script
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if exist('calib_cam_proj_optim.mat')~=2,
error('The scanner calibration file does not exist. Make sure to go to the directory where the scanning images and the calibration file are located (folder scanning_exam... |
389f5724296be45412fc6ce2cbd7671de6618bd40caeddac206ea86742690cc1 | MATLAB | 2,605 | 100 | function [x] = VBA_spm_cat(x,d)
% Convert a cell array into a matrix - a compiled routine
% FORMAT [x] = spm_cat(x,d)
% x - cell array
% d - dimension over which to concatenate [default - both]
%__________________________________________________________________________
% Empty array elements are replaced by sparse zero... |
a7b260522e7f90a712100e3e8dd5ca9c7b05255aec407608fe045d53228d576c | MATLAB | 2,605 | 86 | %% Fit a student distribution as class conditional density to the bankruptcy data
%
% This file is from pmtk3.googlecode.com
function robustDiscrimAnalysisBankruptcyDemo()
setSeed(0);
bank = loadData('bankruptcy');
N = size(bank.data,1);
perm = randperm(N);
trainNdx = perm(1:round(0.5*N));
testNdx = setdiff(perm, ... |
84dca9c44d3dbe676188d8bff6c5ec7d32cba1336d01d3c00c4326f387153b38 | MATLAB | 2,606 | 58 | function [fout, insignal,gbatch] = mleGradSubunitGridModel(mdlparams, xvals, yy, ArgSubs, iuse,lambda,wd)
%UNTITLED2 Summary of this function goes here
% Detailed explanation goes here
if nargout <3
Rf = calcSubunitActivationAmplitudes(mdlparams, xvals(iuse, 1));
subacts = Rf .* ArgSubs(iuse, ... |
9788ffd653716389e8c38682fa05714095c95dd1c6095289727a703c8d3e6f8c | MATLAB | 2,607 | 87 | function errstring = consist(model, type, inputs, outputs)
%CONSIST Check that arguments are consistent.
%
% Description
%
% ERRSTRING = CONSIST(NET, TYPE, INPUTS) takes a network data structure
% NET together with a string TYPE containing the correct network type,
% a matrix INPUTS of input vectors and checks that the... |
d49fba351afdc2df0300afe4e95a27168fffd10012d6c89d95a0b67993c6206c | MATLAB | 2,607 | 91 | % Demo for distributed (locally multivariate) HRF
close all
clear variables
% Choose basic settings for simulations
TR = 3; % sampling time interval (in sec)
n_t = 60/TR; % number of time samples (over 40 sec)
deltat = 5e-2; % micro-time resolu... |
56ea9d9392d86fb13c0ab2aafde4ac32d39962d5018b32b256e3d0d0220d76b9 | MATLAB | 2,608 | 76 | %{
Copyright (c) 2025 Axion BioSystems, Inc.
Contact: support@axion-biosystems.com
All Rights Reserved
%}
classdef DateTime < matlab.mixin.CustomDisplay
properties (GetAccess = public, Constant = true)
Size = 14;
end
%DATETIME class representation of a date and time.
properties (Get... |
879c18bfd80d7861f1057a7fa4eb45ffaae20290dc532df62134de039cfdc58a | MATLAB | 2,609 | 93 | % prepare
load clab_example;
sa=prepare_sourceanalysis(clab_example);
% load functional data
load cs_example; % this a cross-spectrum at 10 Hz
[u s v]=svd(real(cs_example));field=u(:,2); % construct an example field for demo
%% viewing options
% fields
figure;showfield(field,sa.locs_2D);
% cross-spectra
figure; s... |
7e27446d73042424f6c9e242270abe1b60b0d1f21f9ae871f03d6c8945e57b9f | MATLAB | 2,611 | 97 | %%
% BSIZES = [1 2 4 8 16 32 64 128];
%
% for n=nets(:)',n=n{1};
% s.(n).t_overall = cell2mat(cat(1,s.(n).t_overall{:}));
% s.(n).t_pred = cellfun(@cell2mat,s.(n).t_pred,'uni',0);
% s.(n).t_read = cellfun(@cell2mat,s.(n).t_read,'uni',0);
% end
s = load('res20200210.mat');
nets = setdiff(fieldnames(s),'bsizes');... |
26fb848e2f7e54969ca127c3fe88d1e71902ead9b3696f82faea26d775b287c8 | MATLAB | 2,612 | 87 | function [p, tstat, df, stats] = stattest(data, test, settings)
% _
% Perform statistical test for measured data
%%% chi-square test for indepence %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmp(test,'chi2ind')
Y = data{1};
if nargin < 3 || isempty(settings)
settings.corr = 'yes';
else
... |
6267051f2cc5d2cc15d0737a066017c4568ad6a9720d97169278904fe9d86613 | MATLAB | 2,613 | 64 | function EWsig=McNemar_Figs3(dataOut,Bxname,IM,B,params)
% Plot network pairs meeting significance
if ~exist('B','var'),B=1;end
Pth=0.05./B;
PthMcN=0.05;
[NNidx,Tidx,TNidx]=IM2idx(IM);
Npairs=length(TNidx);
Nnets=max(IM.key(:,2));
NetKey=[[1:Nnets]',[1:Nnets]'];
%cMap=[1,1,1;0,0,0];
%% Significant stats... |
72eb2d3ab63e25450a0ac13803164c6230231c73632ad13e98564d6f1cccb94c | MATLAB | 2,615 | 92 | %% RSA fMRI-behavior script for:
%% The transformation of sensory to perceptual braille letter representations
%% in the visually deprived brain
% Marleen Haupt and Monika Graumann
% 22.02.2024
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% RDMs are located in output folder
% (as a default setting or... |
7941b7c69e4eee99d94335ddd733d86d88227dcacdec73317cac5aef039f62d2 | MATLAB | 2,615 | 78 | % Matlab version of the R function one_over_f
% https://rdrr.io/cran/primer/src/R/one_over_f.R
% #' Function to generate 1/f noise.
% #'
% #' Generates 1/f noise with a specified power or amplitude.
% #' @param gamma spectral power, numeric, where 0 generates a white noise time series, 2 generates reddened noise. Defa... |
b6226107497c063ceac4be0e82324b8f22bbd560642d54e526f4fd7b9d50e27f | MATLAB | 2,615 | 78 | function [sdims,vidx] = tt_dimscheck(dims,N,M)
%TT_DIMSCHECK Used to preprocess dimensions tensor dimensions.
%
% NEWDIMS = TT_DIMCHECK(DIMS,N) checks that the specified dimensions
% are valid for a tensor of order N. If DIMS is empty, then
% NEWDIMS=1:N. If DIMS is negative, then NEWDIMS is everything
% but th... |
c7f483df56d595cdf904f6bc7ee2469c3320741742e86826f04f97f4d3ef2d3b | MATLAB | 2,615 | 73 | function [H] = quaternion(q)
% QUATERNION returns the homogenous coordinate transformation matrix corresponding to
% a coordinate transformation described by 7 quaternion parameters.
%
% Use as
% [H] = quaternion(Q)
% where
% Q [q0, q1, q2, q3, q4, q5, q6] vector with parameters
% H corresponding hom... |
38e1cad61e661fa7fa160e972dd53feff24413e3faab787f19b485b2887e9ded | MATLAB | 2,616 | 104 | % Better Stitcher v 1.01, released 2021 0326
% An improved version of the wably stitcher done by YTW in YK lab
clear
close all
% Basic setting
Sorce_folder = 'E:\lab_member\HB\20210223_16_57_04_HB_HB408_3_16wk_WTctrl_AbdAorta_DRAQ5-488_Iba1-594_CD31-647_15x_1um_Rsht_Transfer'; % This one "refered" to be SSD
... |
af8cdc0809dfdcba7e5e33dc13bda0a2ba9a04d2be5b72ae4d19fab7955d482f | MATLAB | 2,616 | 73 | function [gamma2] = DTFsigtest(gamma2,gamma2_sig)
% DTFsigtest - perform significance test for the calculated DTF values.
%
% Usage: sig_gamma2 = DTFsigtest(gamma2,gamma2_sig)
%
% Input: gamma2 - the calculated DTF values (nchan x nchan x nfreq)
% gamma2_sig - the significance cut-off values (nchan x nc... |
0477377e4b29361f1d2bd2232b37f6850cb7ef21453c2c254cf92efab9632f36 | MATLAB | 2,617 | 65 | %{
Copyright (c) 2025 Axion BioSystems, Inc.
Contact: support@axion-biosystems.com
All Rights Reserved
%}
classdef StimulationWaveform < Tag
%STIMULATIONWAVEFORM Storage element for StimulationEventData, before it
%is linked to StimulationEvents
properties(GetAccess = private, Constant = true)
... |
0a5f77fffbde6c436452da4b1ab80a755d393cd8b3d38db9b3f996a5b47b3eaf | MATLAB | 2,617 | 54 | function [experiment,stable_cell_ids,stable_cells_new_ids]= get_stable_cells(folders,method)
% calculates place fields for first and second half of laps for each track
% cells that have peaks > 1Hz in both are kept, rest are discarded
% OUTPUT: indices fo stable cells, coded by experiment, session cell id, and generali... |
129292b1186108ec514f9385db694018d9b12ff299baf4fd9e4fe7a79114f366 | MATLAB | 2,617 | 84 | function [scalo,f,T,a,wt,wavescaled] = contwtgnmir(x,fmin,fmax,N,wave);
% [scalo,f,T,a,wt,wavescaled] = contwtgnmir(x,fmin,fmax,N,wave);
% Continuous wavelet transform of mirrored 1-D signals
% If x = [a b c e f] is the signal to analyzed, contwtmir.m runs contwt.m
% on the mirrored version XxX = [c b [a b c d e f] ... |
38c78309601efb83a35ba6a28ab558299fac1180d2801601571cc6053da0ff62 | MATLAB | 2,618 | 94 | %% Plot contours of penalty(w1) + penalty(w2), where penalty(w) = -log p(w)
% and p(w) = normalGamma(w | delta, c)
% PMTKauthor Francois Caron
% PMTKmodified Kevin Murphy
%%
% This file is from pmtk3.googlecode.com
function normalGammaPenaltyPlotDemo()
c = 1;
pas=0.01;
%[X,Y] = meshgrid(-1:pas:1,-1:pas:1.1);
range= [... |
acf0d93862e469591dae3d8c9c82e5f49d61aae72d7e47a1f46ea47b9c58fca6 | MATLAB | 2,618 | 66 | function [miss,roc,gt,dt] = acfTest( varargin )
% Test aggregate channel features object detector given ground truth.
%
% USAGE
% [miss,roc,gt,dt] = acfTest( pTest )
%
% INPUTS
% pTest - parameters (struct or name/value pairs)
% .name - ['REQ'] detector name
% .imgDir - ['REQ'] dir containing test images... |
23a6ee4267790091d3e0ad7f1dabc67ae3c6d9f9371f13407bc56348e8ea5ec0 | MATLAB | 2,619 | 116 | clear;
clc;
close all;
%%
hist_data = [];
n_subjects = 6;
srate = 400;
for isub = 1:6
load(['ze' num2str(isub) '_cho_method_ecog_rest_v1.mat']);
load([ 'ze' num2str(isub) '_brodmann.mat']);
% ch_pk_freq_prob = [];
start_time_ch = [];
start_time_tp = [];
... |
c7503462d1a499d9302e0359c8d7c0c5a356750928aa475c9e8b60a072e68fd6 | MATLAB | 2,619 | 66 | function [options,dim] = prepare_kToM(K,payoffTable,role,diluteP)
% specify input structures for k-ToM learning models
% function [inF,inG] = prepare_kToM(level,payoffTable)
% Note: k-ToM models can be extended with partial "forgetting" of the
% opponent's sophisitication level [see RecToMfunction.m].
% IN:
% - K: de... |
1b192aa8d7957e6c6b38d2335367a6faa228f81aa3cd517a32a953981912d0b0 | MATLAB | 2,620 | 84 | function refreshZipFiles(localSource, refreshList)
%% Refreh the contents of the individual zip files in each data or pmtkSupport folder
% If refreshList is not specified, do this for every data or pmtkSupport directory.
%
%% Inputs
% localSource - this is the full path to the local copy of the pmtkData or
% ... |
18a85649694b88b50f236a5c579f44f5ad6fd23134cb08a5b30b2483edff4b4b | MATLAB | 2,621 | 77 | % Purpose: Calculate network for each MS-HBM network
% Inputs: Hungarian-matched individual network parcellations
% Outputs: rh_labels and lh_labels containing overlap values for
% each network
%
% Written by M. Peterson, Nielsen Brain and Behavior Lab, under MIT License
% 2024
% To run:
% 1. Claim computing resourc... |
267e5706aedc481704e07f07ff6d4c29d9f19845008d95929774da4d5d309658 | MATLAB | 2,621 | 65 | loadParameters;
filename_centroidsORIG = fullfile(params.punctaSubvolumeDir,sprintf('%s_centroids+pixels.mat',params.FILE_BASENAME));
load(filename_centroidsORIG);
%% Load the number of puncta in each round and get an average
num_puncta_per_round = zeros(params.NUM_ROUNDS,1);
for rnd_idx = 1:params.NUM_ROUNDS
nu... |
8ca609f6b7066cf027ddf923cbb7467caa47d8f42bc4bbd39ed12dc309068b57 | MATLAB | 2,621 | 77 | function mesh = prepare_mesh_tetrahedral(cfg, mri)
% PREPARE_MESH_TETRAHEDRAL
%
% See also PREPARE_MESH_MANUAL, PREPARE_MESH_HEADSHAPE,
% PREPARE_MESH_HEXAHEDRAL, PREPARE_MESH_SEGMENTATION
% Copyrights (C) 2016, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the docume... |
c0a52cc281a157c20625ffaa760fdfd84a8c7e3c9fd26cbc48dfea0dc02339c1 | MATLAB | 2,622 | 79 | function [dat] = ft_preproc_hilbert(dat, option)
% FT_PREPROC_HILBERT computes the Hilbert transpose of the data and optionally
% performs post-processing on the complex representation, e.g. the absolute
% value of the Hilbert transform of a band-pass filtered signal corresponds
% with the amplitude envelope.
%
% Use ... |
ca46c27a9fdef58171d58a2e87a640f6a9380218ff696ad07b3728bf6736691f | MATLAB | 2,623 | 116 | clear;
clc;
close all;
%%
hist_data = [];
n_subjects = 6;
srate = 400;
for isub = 1:6
load(['ze' num2str(isub) '_cho_method_ecog_rest_v1.mat']);
load([ 'ze' num2str(isub) '_brodmann.mat']);
% ch_pk_freq_prob = [];
start_time_ch = [];
start_time_tp = [];
... |
bf159ae04a9e31f7a7a85b7c377070d528645c2e0ff1ff8a865430a53d8dcf8e | MATLAB | 2,624 | 116 | clear;
clc;
close all;
%%
hist_data = [];
n_subjects = 6;
srate = 400;
for isub = 1:6
load(['ze' num2str(isub) '_cho_method_ecog_rest_v1.mat']);
load([ 'ze' num2str(isub) '_brodmann.mat']);
% ch_pk_freq_prob = [];
start_time_ch = [];
start_time_tp = [];
... |
f84b6b149d394c83b0dd9aa8298351184654ecbbae861f945c0bedd1eaeb8584 | MATLAB | 2,624 | 90 | function tree = struct2xml(s,rootname)
%STRUCT2XML Convert structure to an XML tree object and specify its root name
% TREE = STRUCT2XML(S,ROOTNAME) converts the structure S into an XML
% representation TREE (an XMLTree object) with ROOTNAME as the root tag, if
% provided. Only conventional objects (char, double,... |
cf53ad63027c0710a638925a14f20ef43c56690bcc2149984a3ebfb2787e0b4b | MATLAB | 2,625 | 146 | function mean_d = erp_lan(LAN,roi,bl,ifplot,hh,st)
%
%
% erp_lan.m
% plotea erp por electrodo o grupos de electrodos (roi)
% roi = vector de electrodos
% bl = tiempos de linea de base [s s]
%
%
% v.0.0.3
% Pablo Billeke - Rodrigo Henriquez
% 2009
%
% 08.08.2010
% 16.04.2010
color =[{'blue'},{'red'},{'green'},{'yellow'... |
216b8d82074a3bfcfa9e32eb072e5564ee6ff434270437dcdb28bddafd7b7ee4 | MATLAB | 2,626 | 80 | classdef EgnorRecording < AudioRecording
methods (Static)
function canLoad = canLoadFromPath(filePath)
% See if the file's extension is .ch1, .ch2, etc.
[~, ~, fileExt] = fileparts(filePath);
canLoad = ~isempty(regexp(fileExt, '^\.ch[0-9]$', 'once'));
... |
3aeab83f41a1994e01d143cf9a340b54ad3fdc6ee44fcdc754d95739246bafca | MATLAB | 2,626 | 73 | function [microsaccades, msdx,msdy,stddev, maddev] = GetMicrosaccadesEK(EyeDeg, SAMPLING, VFAC, MINDUR, blink_data)
%% INPUTS
%EyeDeg is 2xN long matrix of gaze location data (in degrees, Left and
%Right eye are input separately
%SAMPLING is the hertz of the data. Ex: 1000 for 1000Hz
%VFAC is the constant ... |
92a65ea240b33faa0c03f115b6a8ba2d77ea59606a5325f297679c506f36f14b | MATLAB | 2,626 | 67 | function createLightTrigfromADC(p,rangeOFsubj)
%
% Version 1 Sonya Bells
% 2016 November
% Based on Mark L scripts
%
% INPUT FILES:
% - raw .ds (MEG 'RAW')
%
% OUTPUT FILES:
% - adjusts markerFile
%%% OUTPUTS %%%
% p.paths.fig_headmotion = @(id) [p.paths.output_dir(id),'headmotion.png'];
% determine which subjects ... |
a4185efaf5446965b3c957a7906155b2c3badec1df833fb3baf73833313a22d5 | MATLAB | 2,626 | 60 | function output = SOFAconvertCoordinates(input,input_type,output_type,input_unit,output_unit)
%SOFAconvertCoordinates
% output = SOFAconvertCoordinates(input,input_type,output_type,input_unit,
% output_unit), converts the specified coordinate variable to specified
% output_type and returns the results.
% SOFA AP... |
b7dc71a32146d1d610980ae5c6de75d70720cf97dd185065b206e1919f3bcbeb | MATLAB | 2,626 | 87 | %% ANOVAS for GAMMA data
DIRresults_anova = [DIRresults, '/anova'];
mkdir(DIRresults_anova);
% running multiple one-way ANOVAs on the words vs non vs noise data
% should be used after REMAP and HILBERT are done
for j = 1:length(good_chan)
chan = good_chan(j)
chan_words = squeeze(trials_aligned_word(:,:,ch... |
5b60efedb4fbb1be7c84a0b53af049bac3e9fb13024fe7750d1fd1b5867232fa | MATLAB | 2,627 | 76 | function [functionList, classList] = dependsOn(mfile, dirRoot)
% Find dependencies on a directory structure for a single file
%%
% This file is from pmtk3.googlecode.com
dependencies = depfunTB(mfile);
functionList = {};
classList = {};
for i=1:numel(dependencies)
try
fid = fopen(dependencies{i});
... |
805c01c871e5697b937f8d580af18f468728f76bb6fcc7818fd2b5c3f13494c7 | MATLAB | 2,627 | 83 | function [tfr,t,f] = tfrmh(x,t,N,trace);
%TFRMH Margenau-Hill time-frequency distribution.
% [TFR,T,F]=TFRMH(X,T,N,TRACE) computes the Margenau-Hill
% distribution of a discrete-time signal X,
% or the cross Margenau-Hill representation between two signals.
%
% X : signal if auto-MH, or [X1,X2] if cross-MH.
% T ... |
a75b4961436a959158f0430cde8f6689279acec0fe16b7293ae18ec2438efb56 | MATLAB | 2,628 | 86 | function [dat, ref] = ft_preproc_rereference(dat, refchan, method, handlenan)
% FT_PREPROC_REREFERENCE computes the average reference over all EEG channels
% or rereferences the data to the selected channels
%
% Use as
% [dat] = ft_preproc_rereference(dat, refchan, method, handlenan)
% where
% dat data matr... |
bcdda030cedf507ef0e78950ce1e77f61ae89cd961058c27366c0dcacc0de0f2 | MATLAB | 2,628 | 116 | % 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,... |
d0ae928b090529529c13780ee6077663201fcc409bda4e126b65697215b67f30 | MATLAB | 2,628 | 84 | function lan_master_gui_spks_auto(ts, clu)
figure
maxlag = 300;
choice = 1;
bin = 3;
uibg = uibuttongroup('units', 'norm', 'position', [.55 .0 .45 .08]);
uicontrol('style', 'radiobutton', 'string', 'c1',...
'units', 'norm', 'position', [.1 .1 .2 .5], 'parent', uibg);
uicontrol('style', 'radiobutton', 'string', 'c... |
2ac20621cbbca68e71551815d5e04161de4b5586332fbcf14ef5ce63191a7905 | MATLAB | 2,631 | 66 | function global_warpingTEMP(round_mov,keys_fixed,pos_fixed,FOVS,FOVS_per_fixed_fov_total,bigparams)
% In this function we know all the moving fovs that are implicated per
% fixed fov. So in this case, we calculate what the warp would be if they
% were directly overlaid. This means we can do the math on local, not
% gl... |
395a989cca2a5c7e3aa4d0d45ffe124812e522952e0cde559832b62ad0f66771 | MATLAB | 2,631 | 86 | function [stimulus, response, segment, timezero] = read_brainvision_vmrk(filename)
% READ_BRAINVISION_VMRK reads the markers and latencies
% it returns the stimulus/response code and latency in ms.
%
% Use as
% [stim, resp, segment, timezero] = read_brainvision_vmrk(filename)
%
% This function needs to read the hea... |
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