sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a0abc9a3cb24cbf00e00d1af03f2474134e6aa6352884416c2b71abcf5573246 | MATLAB | 6,817 | 198 | function [out, commuteOrder] = osp_onOffClassifyHERMES(in, target,Order)
%% [outA, outB, outC, outD, commuteOrder] = osp_onOffClassifyHERMES(in, target,Order)
% This function decides how the four-provided HERMES/HERCULES sub-spectra are
% being edited. Currently, this function works for all combinations of
% HERM... |
4b92c69e0c46c8d3193961d4cf1d4969fcea3b8b95f817124ba098756ce671e8 | MATLAB | 6,819 | 220 | % COMPHEADS - plot multiple TOPOPLOT maps of ICA component topographies
%
% Usage:
% >> compheads(winv,'spline_file',compnos,'title',rowscols,labels,view)
%
% Inputs:
% winv - Inverse weight matrix = EEG scalp maps. Each column is a
% map; the rows correspond to the electrode positions
% ... |
5466f2e95f0115836c532bd83b3d96b411cefc0114bc4635dda9270787952f9c | MATLAB | 6,819 | 187 | function [cardiac_sess, respire_sess, mult_sess, ons_secs, order, verbose, ...
c_sample_phase, r_sample_phase] ...
= tapas_physio_create_retroicor_regressors(ons_secs, sqpar, order, verbose)
% calculation of regressors for physiological motion correction using RETROICOR (Glover, MRM, 2000)
%
% USAGE:
% [cardi... |
1743b89831b83fa8bc54a88512df64bc3d8b4865761f3dd083ab5d69049cee5f | MATLAB | 6,820 | 169 | function [ Sequenzen ] = DicomDatenLaden( folderraw )
%UNTITLED2 Summary of this function goes here
% Detailed explanation goes here
% folderraw: Angabe des letzten Ordners, in dem viele Subordner sind
% Beispiel: folderraw =
% 'C:\Users\LutzAn\UserData\BETTINA\TEST\BS167\DICOM\0000A628\AAC90853\AA80BB63';
Se... |
fdbd39a9efa976371ae809cdee2f5ba0369e4cc322087c8666bf6d056474a2ec | MATLAB | 6,822 | 161 | function TOL_fig_tolman1946(config,params,dat)
% TOL_fig_tolman1946, figure of Tolman et al.'s (1946) apparatus and design
% Figure 1 for: Duvelle and Grieves (2026) Tolman's Sunburst Maze 80
% years on: A meta-analysis reveals poor replicability and little evidence for
% shortcutting. European Journal of Neuroscienc... |
b0ea20631bc864446e168ab5d843fca267802ce7b7017e052844f4f78c66567a | MATLAB | 6,829 | 153 | function plot(staObject, cfg, varargin)
% Plot the contents of a McsCmosStaExplorerSource object.
%
% function plot(analogStream,cfg,varargin)
%
% Produces a time series plot for each identified unit in the object.
%
% INPUT:
%
% staObject - A McsCmosStaExplorerSource object
%
% cfg -... |
26c7eaf7391e4446e1ae0c051f8353e8af4f0e7ad77783991ed6a35394311848 | MATLAB | 6,834 | 206 | function xsol = radio_interferometric_calibration(N, K)
% Returns the gain matrices of N stations with K receivers.
%
% function xsol = radio_interferometric_calibration(N, K)
%
% N >= K is always assumed.
%
% The example considers calibration of an array of N stations.
% We simulate a system with N stations, each havi... |
3c10e42bad5e5c59034ff4eeaf071b2858f3e906787a6da80a959bb812260aa4 | MATLAB | 6,849 | 253 | function net = cnn_imagenet_init_inception(varargin)
% CNN_IMAGENET_INIT Initialize a standard CNN for ImageNet
opts.scale = 1 ;
opts.initBias = 0.1 ;
opts.weightDecay = 1 ;
opts.cudnnWorkspaceLimit = 1024*1024*1204 ; % 1GB
opts = vl_argparse(opts, varargin) ;
net = dagnn.DagNN() ;
net.meta.inputSize = [299 299 3 1... |
5290c33d0fd0068de693573cc9807582deaefa8a604e10d5650e1d9474c03246 | MATLAB | 6,851 | 252 | function OUT = whole_brain_ptask_givena(OUT,varargin)
% OUT = whole_brain_ptask_givena(OUT,verbose level, mask image or threshold value(for pa_overall) )
%
% OUT = whole_brain_ptask_givena(OUT,2,.001)
% OUT = whole_brain_ptask_givena(OUT,2,'Activation_thresholded.img')
% verbose flag
if length(varargin) > 0, vb = vara... |
289f1d808fc133b2aeb2f7ec6ff253b1d582f09b7d946b2d3fd468cd05129a94 | MATLAB | 6,855 | 203 | function out = HT_DistributionTest(x, theTest, theDistn, numBins)
% HT_DistributionTest Goodness of fit of a distribution fitted to a data vector.
%
% Fits a distribution to the data and then computes the test statistic of an
% appropriate goodness-of-fit test, as an effect size that quantifies the
% difference betwe... |
6e687be459ffc625bad93262abb1170558a3ac200933393924d982236c00ec9f | MATLAB | 6,856 | 193 | function [Ae, indice, Rp] = vca(R,varargin)
% Vertex Component Analysis
%
% [Ae, indice, Rp ]= vca(R,'Endmembers',p,'SNR',r,'verbose',v)
%
% ------- Input variables -------------
% R - matrix with dimensions L(channels) x N(pixels)
% each pixel is a linear mixture of p endmembers
% signatures R = M... |
b6e7c70e12949aaba925ab7cc464c1de7e95f766d992b3204e8003a76d92cb20 | MATLAB | 6,857 | 185 | function [est model] = baydiff(data,varargin),
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% estimates microstructural diffusion parameters by Bayesian estimation
% written by Marco Reisert, Medical Physics, University Hospital Freiburg
%
% [est model] = baydiff... |
629a2d2f83ea2cc24897545bdbf323c0e287158a20ea4a23fc5f7b3a188e4ebe | MATLAB | 6,858 | 120 | function plot_region_by_region_interactions_across_analyses
close all
clear all
clc
% Plot region-by-region interaction relationships across analyses.
% Select a folder containing data.
folder_name = uigetdir;
cd(folder_name)
load('functional_connectivity.mat')
load('trial_by_trial_correlation.mat')
load('regression... |
6f23fbb6d50e4f27a258fcd04ff83f15bbf7cbef6125c6dd2850f6835c098154 | MATLAB | 6,864 | 188 | % POP_SAVESTUDY - save a STUDY structure to a disk file
%
% Usage:
% >> STUDY = pop_savestudy( STUDY, EEG ); % pop up and interactive window
% >> STUDY = pop_savestudy( STUDY, EEG, 'key', 'val', ...); % no pop-up
%
% Inputs:
% STUDY - STUDY structure.
% EEG ... |
d74fafe305822a13b10f84dbf9a715f60b264c7498dcbc79d17b32ad0ba1dbd9 | MATLAB | 6,864 | 229 | function fear_reactFrzModShBase(basename,varargin)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
%%
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
%%
param.sesIdx=2;
param.nIte=500;
param.recalculate=false;
param=pars... |
1e70d0adf9ce46d7b28883846b58d2d03d8342ac414c1f7b91c37cd64e07bbff | MATLAB | 6,874 | 169 | function makeHeatMap(spikeMatrix,option,channels, fs)
% outputs a heatmap figure handle for your spikes
% Assume numSamp x 60 matrix
% INTPUT
% spikeMatrix
% number of samples x numChannels binary spike matrix
% where 0 means no spike and 1 means spike
... |
f7b0ac147ded2ba42a5a21fc988a1d9de27346c78d4bfdf70711096e071e97ee | MATLAB | 6,875 | 165 | function results = get_Fisher_information(data_folder, file_prefix, file_ind1, Nfile, Ntr, ds, batch_ID, opts)
% GET_FISHER_INFORMATION
% Syntax:
% results = get_Fisher_information(data_folder, file_prefix, file_ind1, Nfile, Ntr, ds, batch_ID)
% results = get_Fisher_information(..., opts)
% Description:
% Compute... |
4f09d711e30900577e4ffb24e026827f6f4e370c7c30ce72ee8208b78b546664 | MATLAB | 6,879 | 258 | function handle = imab(data, clims, bSep, noCols)
% function handle = imab(data, clims, bSep, noCols)
%
% Just show the 2D, 3D or 4D data as quickly as possible
%
% Concatenates the slice dimension from left to right, and the time
% dimension from top to bottom.
%
% When Mosaiced, lowest slice is in bottom-left corner... |
648054ffb73c5444eb1c0dd27acb4924484db18311edc7e89cb8e03d28a84ea8 | MATLAB | 6,882 | 223 | function coactPaper_figureS02()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=6;
letGapY=5;
fontsize=6;
close all
fh=initFig('width',18.6,'height',7.5,'font','Arial','fontsize',fontsize);
x=10;y=6;
panel_01(x,y,fontsize);
panelLetter2(x-letGapX-1,y-letGapY+1,alphabet(1,labelCase),'fontSize',labelSize,'isBol... |
818e430cd2404d6ad11d32745768a645506d63e143d6bca8edeb17bb71b445da | MATLAB | 6,884 | 176 | function [result,tracked,myelin,spatial] = main_script_function(save_spatial,intervention)
threshold_oligo_apop = intervention.oligo_apop;
threshold_stop_myelination = intervention.oligo_stop_my;
%% Sim Conditions
step_cap = 21600; %21600 is 300 days
%% Setup Simulation
[funcs,PB,sizing,borders,myelin] = Setu... |
5468298e959ceac21de66f5a35d651a9254b49010424ef1091c0695b1e9d847c | MATLAB | 6,886 | 191 | function [dat] = read_brainvision_eeg(filename, hdr, begsample, endsample, chanindx)
% READ_BRAINVISION_EEG reads raw data from an EEG file and returns it as a Nchans x
% Nsamples matrix.
%
% Use as
% dat = read_brainvision_eeg(filename, hdr, begsample, endsample)
% where the header should be first read using READ_... |
e99e22e5086331bab7a89a0c7c68071f0da0bd2ba8f6b86830bdf744abde3650 | MATLAB | 6,889 | 189 | function [map,lo,hi] = cubehelix(N,start,rots,sat,gamma,irange,domain)
% Generate an RGB colormap of Dave Green's Cubehelix colorscheme. With range and domain control.
%
% (c) 2017 Stephen Cobeldick
%
% Returns a colormap with colors defined by Dave Green's Cubehelix colorscheme.
% The colormap nodes are selected along... |
e764305fc027b942bd3628002448aa0c73ef1025004c3b6de76b03b89b76e50b | MATLAB | 6,895 | 172 | %% Creating imrpoved hybrid image (T1w+QSM) by matching DGM contrast accurately to the hybrid atlas
% Dependencies: (1) SEPIA v1.2.2.4
% Data: (1) ABRIM dataset (https://doi.org/10.34973/7q0a-vj19) (2) MuSus-100 (https://doi.org/10.1007/s00429-022-02547-1)
% Created by Kwok-Shing Chan
% Date created: 25 April 2023
%
fu... |
820d9472ac27a9ffbfa34660d9ec9406003f266f0ec890be1e2caadc9ee8ec53 | MATLAB | 6,896 | 198 | function [C2,cfg] = lda_iem_trialwise(dat,theta,cfg)
% [C2,cfg] = lda_iem_trialwise(dat,theta,cfg)
% author: N Myers
if nargin < 2
help lda_iem_trialwise
error('missing input arguments!')
end
ntrl = size(dat,1); % number of timepoints
nsens = size(dat,2); % number of M/EEG sensors
ntim... |
26c2b41fb184f1eabf4a3c289eff068a7858da6f912f734b12f6ded69164b158 | MATLAB | 6,898 | 192 | % prepareScan — Prepares experimental session.
% Opens window, defines parameters, device input, loads/creates textures, generates frames, and makes stimuli for drawing.
%
% Syntax
% [p, w, t, stimuli, frames] = prepareScan(p, w, t, dirs, toggles)
%
% Input Arguments
% p – structure containing scan parameters
% ... |
5371c23c05b075737b78ff48751a3b1be464d28e7c5d02db4b8074bedac525df | MATLAB | 6,904 | 220 | function [ all_subjects ] = nmri_statistics( all_subjects, opt, params )
%[ all_subjects ] = nmri_statistics( all_subjects, opt, params )
% Will do generate a tabulated overview of metrics (all that are readable)
% via nmri_load_metrics for any number of subject
%
% all_subjects = cell array of subjects (see n... |
c1c77016ba1c3d71f6664749015a57b97ff9d4e532ee683135cfea5ce5c4a716 | MATLAB | 6,908 | 145 | function inside = in_polyhedron(varargin)
%% Point within the volume test
%IN_POLYHEDRON Tests if points are on or inside a 3D triangulated surface
% (faces/vertices) or volume (tetrahedrals/vertices). There is NO
% assumption about orientation of the face normals.
%
% IN = IN_POLYHEDRON(X,POINTS) tests if th... |
f3b573999a0fb7fd6ada8134a5fc8424db9ff08e36d837cfca02569c0542c703 | MATLAB | 6,908 | 246 | % this script builds a bunch of connected reservoirs
% representing a meshing of a polygonal region
% ----------------
%% Create a decomposed geometry matrix, with line segments giving boundary of polygon
% documented here:
% https://www.mathworks.com/help/pde/ug/create-geometry-at-the-command-line.html
% set up th... |
026756ed9bc7bea248339ba7b872df5adf2479fd65d3391a85ed5af00f6d77e3 | MATLAB | 6,911 | 191 | function [map,data] = PhaseMango(spikes,phases,varargin)
%PhaseMango - Compute phase as a function of spike rate and acceleration.
%
% Compute spike phase as a function of spike rate and acceleration, as in
% Harris et al. (2002). The name of the function refers to the aspect of
% the resulting phase plot.
%
% USAGE
... |
ed64613fd23e261395268797380feb6504fbe4a07ac412829d998af8fa077163 | MATLAB | 6,917 | 163 | function spectra = spectra_stft_baseRS(params, trials)
% computes spectra for each trial using STFT
% baseline = resting state (if resting state not found, use spectra_stft_sessions)
% trials =
% data: [3073x125x500 double]
% time: [3073x1 double]
% sessTime: [3073x500 double]
% label... |
cf6217dc9e8682d0e4ff8a159f786c24feba256182f6865e8b4199bae6f5feec | MATLAB | 6,918 | 176 | function out = NL_BoxCorrDim(y, numBins, embedParams)
% NL_BoxCorrDim Correlation dimension of a time series.
%
% Estimates the correlation dimension of a time-delay embedded time series
% using a box-counting approach, via TISEAN's 'boxcount' (this operation
% previously used TSTOOL's 'corrdim').
%
% 'boxcount' estim... |
3bbc737e3a478b9abec9bb053bafa8667ccc35c8f83b4995bbf3d5e844b95d3e | MATLAB | 6,922 | 132 | %% Script to plot brain maps of subcortical MIND associations.
% Copyright (C) 2026 University of Seville
% Written by Natalia García San Martín (ngarcia1@us.es)
% This file is part of Hierarchy Longitudinal MIND Gradients Psychosis toolkit.
%
% Hierarchy Longitudinal MIND Gradients Psychosis toolkit is free... |
4338916ad0c3896f6f5a7a8e7d23b548f13b12d772dc3985de2afe2c6a2d827c | MATLAB | 6,922 | 169 | %% Creating imrpoved hybrid image (T1w+QSM) by matching DGM contrast accurately to the hybrid atlas
% Dependencies: (1) SEPIA v1.2.2.4
% Data: (1) ABRIM dataset (https://doi.org/10.34973/7q0a-vj19) (2) MuSus-100 (https://doi.org/10.1007/s00429-022-02547-1)
% Created by Kwok-Shing Chan
% Date created: 25 April 2023
%
fu... |
d72ca4e74aa0e0158102da6cbd46292d535a4afc5c3c906c943aab4af3f6beec | MATLAB | 6,922 | 159 | function [varargout] = likLaplace(hyp, y, mu, s2, inf, i)
% likLaplace - Laplacian likelihood function for regression.
% The expression for the likelihood is
% likLaplace(t) = exp(-|t-y|/b)/(2*b) with b = sn/sqrt(2),
% where y is the mean and sn^2 is the variance.
%
% The hyperparameters are:
%
% hyp = [ log(sn) ... |
2b8388d633c965fd181a446170ed2e22d5bdd42dc6600550bbd6f41b0f2858d6 | MATLAB | 6,925 | 182 | function res = arg_report(type,func,args)
% Report information of a certain Type from the given Function.
% Result = arg_report(Type,Function,Arguments)
%
% Functions that declare their arguments via arg_define() make their parameter specification
% accessible to outside functions. This can be used to display auto-gene... |
8052193b0a92bb21da17db8530d0c6bfe008b9cf924aca75c602a8936ed81a4e | MATLAB | 6,925 | 291 | %% drakontos(Enunciado)
%
% Regresa los Ciclos de Hamilton y Euler del Enunciado.
%
% Enunciado = "string"
%
%
%%
function HandE=drakontos(e)
e_c=getCiclo(e); % obtiene todos los ciclos del enunciado
n_he=0; % número de ciclos de hamilton y euler encontrados
% busca entre todos los ciclos del enunciad... |
29881aa8fba37199cb39067dfeaed5704ae0de2fef2da075f0cf72270ece0eeb | MATLAB | 6,929 | 212 | function [f,p,ci,stats,tbl,dist] = permuranova2(x,varargin)
%PERMURANOVA2 Permutation-based two-way repeated-measures ANOVA and Friedman test.
% F = PERMURANOVA2(X) performs a balanced permutation-based two-way
% repeated-measures analysis of variance (ANOVA) for comparing the means
% of data in a 3D matrix X (w... |
f5a7bb5f0bdf7c4e4468bd05679ba055c1847fed3b605159afc5805294181dbc | MATLAB | 6,931 | 167 | %% [chi,chi_para,chi_dia] = Wrapper_QSM_Chi_separation(localField,mask,matrixSize,voxelSize,algorParam,headerAndExtraData)
%
% Input
% --------------
% localField : local field map (tissue fields), in Hz
% mask : signal mask
% matrixSize : size of the input image
% voxelSize : spatial resolution of e... |
77c0b5ab365e4ce0858cd98db0bef68805a00829b1f3d511318b2638b2fa9c1b | MATLAB | 6,934 | 165 | function [updatedCategories, updatedMatches, updatedWeight,...
updatedNumCategories] = ARTwarp_Recat_Single_Cats(categories,...
matches, contours, weight, vigilance, bias, learningRate,...
compareWarped)
% A function to recategorise contours which are alone in their category, if
% they match another catego... |
2bce4d7cb9773172101a26935209358439077515b23b361d4925fc41f9d43e2e | MATLAB | 6,936 | 117 | clc
clear all
close all
anglerror =[];
distance_list= [];
x_distance = [];
y_distance = [];
whicheye = input('Please enter left or right to choose eye: ','s')
filepath = input('Enter procesed_data location: ', 's');
if isempty(dir(filepath))
disp([filepath, '" does not exist.']);
end
for user_num = 1:1 %(user_nu... |
0affa17fbf10bf675747c70c67bbb34f98ab8b52a641e5fbf196bd4beb90216f | MATLAB | 6,940 | 193 | function [mBIS, mBISp, etaBIS] = analyzeBehaviorWithEig_3way(data, Tmean)
% ---------- reshape ----------
data = permute(data,[1 3 2 4]); % [subj x epoch x comp x time]
[~, nEp, nComp, nTime] = size(data);
% ---------- ensure categorical with desired order ----------
Tbl = Tmean;
if ~iscategorical(Tbl.Subjec... |
519ff10c627c58a999483d9ae88dd9882117984ca10689a4edb8805e2c4a43fc | MATLAB | 6,941 | 219 | function [aps, speed] = fast_rcnn_evaluate(varargin)
%FAST_RCNN_EVALUATE Evaluate a trained Fast-RCNN model on PASCAL VOC 2007
% Copyright (C) 2016 Hakan Bilen.
% All rights reserved.
%
% This file is part of the VLFeat library and is made available under
% the terms of the BSD license (see the COPYING file).
run(fu... |
86afbaf983e1c89a5befce505b9544200a94e98d908e3fde66d3633354bbbda0 | MATLAB | 6,943 | 249 | function [traj, infStates] = tapas_ehgf(r, p, varargin)
% Calculates the trajectories of the agent's representations under the HGF
%
% This function can be called in two ways:
%
% (1) tapas_ehgf(r, p)
%
% where r is the structure generated by tapas_fitModel and p is the parameter vector in native space;
%
% (2)... |
76c602723112f78c7ee2cd35c6f7ff70f5e7742b4893c1298807c66d5576615a | MATLAB | 6,946 | 201 | % readneurolocs() - read neuroscan polar location file (.asc)
%
% Usage:
% >> CHANLOCS = readneurolocs( filename );
% >> CHANLOCS = readneurolocs( filename, method, 'key1', val1, ...);
%
% Inputs:
% filename - file name or matlab cell array { names x_coord y_coord }
% method - [1 2, 3, 4 or 5] different imp... |
8fd76d7c0a93fa990d965549897255df85a028af0868c351f48b0ee3389acc59 | MATLAB | 6,946 | 156 | function groupLevelTTest_cluster(output_dir)
nFiles = 16;
rsa_tool_path = 'rsatoolbox';
spm_path = '/data/holly-host/smark/spm';
data_path = fullfile('/data/holly-host/smark/fmri_sub_preproc_dir',output_dir);
addpath(genpath(fullfile(data_path,rsa_tool_path)))
addpath(spm_path)
ana_name = 'standard_L100_FSLcleaned280... |
43e2426da181a223fee0377c73735a401937054daab0ff1fe6204b6f3befd448 | MATLAB | 6,950 | 265 | function [traj, infStates] = tapas_hgf_categorical(r, p, varargin)
% Calculates the trajectories of the agent's representations under the HGF for categorical inputs.
%
% This function can be called in two ways:
%
% (1) tapas_hgf_categorical(r, p)
%
% where r is the structure generated by tapas_fitModel and p is... |
8ecc337b3ffc79b0c6eb6b93860a8f85436d71cc4a66b5524b15b946264e0f90 | MATLAB | 6,957 | 196 | function fd_ft = getMaxCCFD_FT(predTraj, respTraj, realTraj, parms)
% computes windowed CC between predTraj and respTraj, both have format:
% predTraj: samples x FD groups (freq)
% and returns its maximum freq. -> ccMax
% computes windowed FT, smoothes and returns its maximum freq. -> ftMax
% (c) Jiri, Jul12
nSamples... |
990c6640f2720a1a3b6b301299f5fab6a5750cb84583cd9455596b8cd75f6376 | MATLAB | 6,957 | 177 | function [Ephys] = firingRatesBursts(spikeMatrix,Params,Info)
% Detects firing rate bursts
% INPUT
% -----------------------
% spikeMatrix : matlab double
% Params : struct
% Info : struct
% OUTPUT
% ----------------------
% Ephys : struct
% structure with fields relating to firing rate and burst properties... |
c52e2085efb5f2e95d230540dce205f78b63fc4dd578627d1d7173ec08e3e67e | MATLAB | 6,958 | 268 | function hh = myErrorbar(varargin)
%MYERRORBAR Adds errorbars to existing plot (unlike errorbar.m, which creates a new plot, and allows only bars for y values)
% MYERRORBAR(X,Y,L,U) adds error bars to the graph of vector X vs. vector Y with
% error bars specified by the vectors L and U. L and U contain the
% low... |
09bf9d8d5086040fb8a84cd9f6ef9094cdee9dbaf7903a3bf89ba8e4f0194c2a | MATLAB | 6,959 | 265 | function [traj, infStates] = tapas_hgf_categorical_norm(r, p, varargin)
% Calculates the trajectories of the agent's representations under the HGF for categorical inputs.
%
% This function can be called in two ways:
%
% (1) tapas_hgf_categorical(r, p)
%
% where r is the structure generated by tapas_fitModel and... |
1aec7d5c5f516401eed08405706c79c600ed816e8fca2fc45cdbc14e3716c604 | MATLAB | 6,962 | 203 | function varargout = ft_version(command)
% FT_VERSION returns the version of FieldTrip and the path where it is installed
%
% FieldTrip is not released with version numbers as "2.0", "2.1", etc. Instead, we
% share our development version on http://github.com/fieldtrip/fieldtrip. You can use
% git to make a local clon... |
0f55326692f6b78959867f28ceb4119c558c3f045fcaff0141e3e6de5f4939b9 | MATLAB | 6,963 | 175 |
%% Take HOA to t1 space
analyfold = '/home/NCPL10/Desktop/Wanglu-scz/Cross_AHMU'
[TMSPath, fileN, extn] = fileparts(which('TMStarget.m'))
t1path = [analyfold,'/T1ImgNewSegment']
hoamask = [TMSPath '/mask/HOAsub25prob.nii'] ;
sublist = dir (t1path) ;
for i = 3 : length(sublist)
% cd ([t1path,filesep,sublist(i).... |
eb05b8ed4a8d5a273e00c746f544ee0bc519ab9b62b9cebc1620865c6ce307b9 | MATLAB | 6,963 | 222 | function addImageSequenceToAxes(ax,il)
% USAGE
% addImageSequenceToAxes(ax,imagelabels)
% FUNCTION
% places a set of images at equal distances along a line in a 2d
% coordinate system, which is then mapped to the axes of the RDM
% in ax. imagelabels is a struct with the following fields:... |
13258136aa1840d62dafe68bb3dcd516b8c3d4ec9fb6579c50218cffe41ef500 | MATLAB | 6,966 | 169 | function [K,dK] = covSM(Q, hyp, x, z)
% Gaussian Spectral Mixture covariance function. The covariance function
% parametrization depends on the sign of Q.
%
% Let t(Dx1) be an offset vector in dataspace e.g. t = x-z. Then w(DxP)
% are the weights and m(Dx|Q|) = 1/p, v(Dx|Q|) = (2*pi*ell)^-2 are spectral
% means (freq... |
345213d9860c2e1859dba88071c479c8b7554e2dca0fca4c56e19d4aa71d4e6f | MATLAB | 6,967 | 215 | function M = fixedrankfactory_2factors(m, n, k)
% Manifold of m-by-n matrices of rank k with balanced quotient geometry.
%
% function M = fixedrankfactory_2factors(m, n, k)
%
% The first-order geometry follows the balanced quotient geometry described
% in the paper,
% "Linear regression under fixed-rank constraints: ... |
dcc24863df9ab420efd1c113001279b636503d368ebc610557c642494d350705 | MATLAB | 6,969 | 195 | function [channels,coords] = getCoordsFromLayout(channelLayout)
%GETCOORDSFROMLAYOUT Specifies mapping from channel number to spatial
%coordinates
% We provide a few default coordinates from
% the Multichannel systems (MCS) (60 electrode In Vitro MEA set up) and
% the Axion system. Alternatively, you can specify your ... |
6e4a0a7b267c1b4f0b0200435ea1ec2af549e245c4657ff2bb22b5c845686d6c | MATLAB | 6,981 | 267 | function [traj, infStates] = tapas_hgf_whichworld(r, p, varargin)
% Calculates the trajectories of the agent's representations under the HGF
%
% This function can be called in two ways:
%
% (1) tapas_hgf_whichworld(r, p)
%
% where r is the structure generated by tapas_fitModel and p is the parameter vector in n... |
7028c1d1c5404f7f489ed565e835de091e9debd5bea12c57903d76ec046ef280 | MATLAB | 6,981 | 155 | %% plot 3D brain model: test script
% - define 3D brain structures (should be coregistered & normalized to MNI space)
% -> sees truct: params.plot_brain3D
% - define MNI coordinates and values to plot
% -> chnls_MNI_VAL = 2D: [ch x 4], where 4 = 3 MNIs + 1 VAL
% - load brain volumes -> surfaces
% -> ... |
72f97d09f48df0c2eac64ad9b6ea7c1558df54f31521dc18bb8401142583414e | MATLAB | 6,981 | 207 | function [N,X,sp] = smoothHistogram(varargin)
% HISTOGRAM generates a histogram using the "optimal" number of bins
%
% If called with no output argument, histogram plots into the current axes
%
% SYNOPSIS [N,X,sp] = histogram(data,factor,normalize)
% [...] = histogram(data,'smooth')
% [...] = histogra... |
6a4da5e4cd0ab003d2ec7a7631c5192ec6a1a5835baf60287286f6c5c362f79f | MATLAB | 6,982 | 231 | % plot3dmeshalign - align a first meshes or volume with a second mesh
% to check alignment.
%
% Usage:
% pop_roi_connectplot(file1, file2, transform, color1, color2, region);
%
% Inputs:
% file1 - [string] name of the first mesh/volume
% file2 - [string] name of the second mesh
% transform... |
614c62516854e62fd73931b171f05092b9d5f0ba15e4034281e487b3c87e9b43 | MATLAB | 6,983 | 181 | function res = hlp_varargin2struct(args, varargin)
% Convert a list of name-value pairs into a struct with values assigned to names.
% struct = hlp_varargin2struct(Varargin, Defaults)
%
% In:
% Varargin : cell array of name-value pairs and/or structs (with values assigned to names)
%
% Defaults : optional list of n... |
e8e6020343a68c08054d210f34ace8ccf90758f83ee0aeec38f29ac465787da0 | MATLAB | 6,985 | 200 | function [C2,cfg] = mahal_lin_trialwise_xtime(dat,theta,cfg)
% [C2,cfg] = mahal_lin_trialwise_xtime(dat,theta,cfg)
% authors: M Stokes, E Spaak, N Myers
if nargin < 2
help mahal_lin_trialwise_xtime
error('missing input arguments!')
end
ntrl = size(dat,1); % number of timepoints
nsens ... |
b2d3c4b6e19aab4e61c63a9a667aad9127824573e4c34fc0e06634c2bc901aaa | MATLAB | 6,986 | 210 | %% BiExpFitModelS0.m
% This function contains a biexponential diffusion model
%
% lossFunction - calculates loss function for optimizer
% forwardJacobian - calculates the forward jacobian for optimizer
% forwardModel - converts parameter struct into model prediction
% x2pars - converts x vecto... |
949b82466e6d2aefbe2b2ac14a2ed3aade01d34798312d50982f4aa01cf7d40e | MATLAB | 6,987 | 202 | function plotFigure3_expertEphys(ephysPath, processedEphysPath, codePath)
% Plot figure 3. YOU MUST RUN processEphysData_experts ON THE OFC
% ELECTROPHYSIOLOGY DATA BEFORE RUNNING THIS FUNCTION. Plots average firing
% rates for 20ul trials before and after the first incongruent trial.
% INPUTS:
% ephysPath = local p... |
9d9956668726e911bd97185f9fb1837daebca115acb6a4c4d2efe224566f4845 | MATLAB | 6,989 | 197 | function TS_LocalClearRemove(whatData,tsOrOps,idRange,doRemove)
% TS_LocalClearRemove Clear or remove data from an hctsa dataset
%
% The result is saved back to the hctsa-formatted .mat data file provided as whatData.
%
%---INPUTS:
% tsOrOps -- either 'ts' or 'ops' for whether to work with either time series
% ... |
3b64230e08b38f7e72b4432213792ae9381e298d9d39b5f36d0f153f26798818 | MATLAB | 6,991 | 150 | function [status, res] = BF_RipserSystem(ripserCommand, timeoutSecs)
% BF_RipserSystem Run a ripser command-line call with a bounded timeout.
%
% Sibling of BF_TiseanSystem.m for the ripser persistent-homology binary
% (Toolboxes/ripser), with the same timeout-wrapping and exit-code
% classification logic -- kept as ... |
5e9eed23e73b6ae70964872e05eebaa62d7487adb22f1ae5c9ea2ad3855ab9d2 | MATLAB | 6,992 | 180 | function [] = tapas_physio_write2bids(ons_secs, write_bids, log_files)
% Converts trigger, cardiac and respiratory data from physio structure into
% a .tsv file according to BIDS format. Meta data is written in a corresponding .json file.
%
% Parameters:
% IN:
% ons_secs: ons_secs (onsets in seconds... |
fcea6ca9abcbca9f32a365125e3ef1542cacc56fb66207d01d4d45569afd6d69 | MATLAB | 6,992 | 213 | function run_permuregress_examples
%RUN_PERMUREGRESS_EXAMPLES Run permutation multiple linear regression examples.
% Generates random multivariate data for a predictor sample X and
% dependent variables Y. Y contains 20 variables, each with a correlation
% of 0 to X, except for the first 5 variables which have a... |
e12b1b6ffec081ca953896d3a2676ffdff5fa80f6b2ece2014b4af787c2fe7a9 | MATLAB | 7,007 | 147 | % Group SPM preprocessing script for longitudinal data in BIDS
%
% Script prepared for preprocessing of fMRI data obtained for research project:
% "Temporal dynamics of functional connectivity changes induced by cognitive training",
% in which participants were fMRI scanned four time during intensive working memory t... |
086646132478a363e847a397db50a20c15b9d893e61cbf310e6b5926662856ab | MATLAB | 7,015 | 215 | function fear_getMeanFR(basename,varargin)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
load([basicMetaData.Basename '.SleepState.states.mat']);
load([basicMetaData.Bas... |
454568041d117a09dfd0a73b01aeb8b737123a4974d58df8e58e7521e0a5e3c9 | MATLAB | 7,015 | 212 | function [BCMatrix, BCRHS] = boundaryConditionCylindrical3D(BC)
% It creates the matrix of coefficient based on the BC structureprovided
% by the user. It also generates the right hand side vector of the linear
% system of equations
%
% SYNOPSIS:
%
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:
%
% SEE ALSO:
%
% Copyri... |
14608ae7fd3a1e81223467b009471716989582f76dbb34f6a7397683ff2fed13 | MATLAB | 7,017 | 165 | function out = CO_MatrixProfile(y, m, maxN)
% CO_MatrixProfile How well each subsequence shape recurs elsewhere in a time series.
%
% Computes the matrix profile: for every length-m window (subsequence) of the
% time series, the distance to its nearest neighbour among all other windows,
% after z-normalizing each win... |
61902bc80dcc0e30a28301db251a721f2a4475ff0c8c8ae917aa55501a77ad60 | MATLAB | 7,023 | 255 | function varargout = permcca(varargin)
% Permutation inference for canonical correlation
% analysis (CCA).
%
% Usage:
% [pfwer,r,A,B,U,V] = permcca(Y,X,nP,Z,W,Sel,partial,Pset)
%
% Inputs:
% - Y : Left set of variables, size N by P.
% - X : Right set of variables, size N by Q.
% - nP : An integer re... |
e0a19b954214626984d55ce3fae33cca4106e34a4ae09562a98521a7990ca637 | MATLAB | 7,024 | 175 | % STD_READTOPO - returns the scalp map of a specified ICA component, assumed
% to have been saved in a Matlab file, [dataset_name].icatopo,
% in the same directory as the dataset file. If this file does
% not exist, use STD_TOPO to create it, else a pre-clustering
%... |
cc8672b20c5f3214a3cd4fa034b1d56c25e7f88a096f25ee5c52c90a19115676 | MATLAB | 7,026 | 135 | classdef McsRecording < handle
% Stores a single recording.
%
% The different streams present in the recording are sorted into the
% {Analog,Frame,Event,Segment,TimeStamp}Stream fields where they are stored
% as cell arrays.
%
% (c) 2016 by Multi Channel Systems MCS GmbH
properties (SetAccess = privat... |
d8aa9e6e36d3858e56100793c3b6879371690ebfe9c30e969be7a768f3cb89c6 | MATLAB | 7,026 | 239 | function [str, p, h, stats] = signrank_nice(x,y,varargin)
%SIGNRANK Wilcoxon signed rank test for zero median.
% P = SIGNRANK(X) performs a two-sided signed rank test of the hypothesis
% that the data in the vector X come from a distribution whose median
% (and mean, if it exists) is zero, and returns the p-value... |
192db478fd6d55ed7c0c71df1e26397bbc7b9c771d6f741d675188c7f147e708 | MATLAB | 7,029 | 204 | function out = DN_RemovePoints(y, removeHow, p, removeOrSaturate, randomSeed)
% DN_RemovePoints How time-series properties change as points are removed.
%
% A proportion, p, of points are removed from the time series according to some
% rule, and a set of statistics are computed before and after the change.
%
% ---IN... |
b80d746e4d7cd8132181f7dd01d8cc34f1991074a8708223f4c067adf249bca8 | MATLAB | 7,033 | 116 | function gui = upper_navigate_box(gui, name,Selection,Overview)
MRSCont = getappdata(gui.figure,'MRSCont'); % Get MRSCont from hidden container in gui class
gui.upperBox.(name).upperLeftButtons = uix.Panel('Parent', gui.upperBox.(name).box, ...
'Padding', 5, 'Title', ['Navigate model'],... |
0c38a4e18ac2868b637a559b58cae758f8c7d8da048d2c340db5e27a3a0a6069 | MATLAB | 7,036 | 174 | function [newImg,xform,deformField] = mrAnatResliceSpm(img, xform, bb, ...
mmPerVox, bSplineParams, showProgress)
% Use SPM spline-based interpolation to reslice a volume image to a specific
% resolution in mm.
%
% Also crops the image to be constrained inside a specific bounding box (bb)
% also specified in mm.
... |
4541849f947fc406fc058ff158fe7f5eef6db9f6089ced4f8ac62e90d40fc197 | MATLAB | 7,036 | 145 | function [mu,sig,alpha,beta] = fit_eeg_distribution(X,min_clean_fraction,max_dropout_fraction,quants,step_sizes,beta)
% Estimate the mean and standard deviation of clean EEG from contaminated data.
% [Mu,Sigma,Alpha,Beta] = fit_eeg_distribution(X,MinCleanFraction,MaxDropoutFraction,FitQuantiles,StepSizes,ShapeRange)
%
... |
6a83e7f8e1c5b631434f5e7a391461309c5638242f04351fbc63d608bba057ab | MATLAB | 7,040 | 206 | % Main script for comparing laminar depth profiles of SANDI intra-soma signal fraction
% between primary motor and visual cortices
%
% Reference:
% Lee H, ..., Huang S, Communications Biology, 2026
%
% Requirements:
% - FreeSurfer installed and configured
% - FreeSurfer recon-all completed for each subject
% - FreeSurf... |
aba725f48c59629c9d65f54b0463641fcfaa6d85a8b751cf837aa48861c3e4b0 | MATLAB | 7,042 | 202 | function y = mvnpdfln(X, Mu, Sigma)
%MVNPDF Multivariate normal probability density function (pdf).
% Y = MVNPDF(X) returns the probability density of the multivariate normal
% distribution with zero mean and identity covariance matrix, evaluated at
% each row of X. Rows of the N-by-D matrix X correspond to obse... |
9c00ee1d1961f6cfea73e8f6c5ac449296f4812c234afffdf5a1f045e00f3b50 | MATLAB | 7,044 | 192 | function out = WL_cwt(y, wname, maxScale)
% WL_cwt Continuous wavelet transform of a time series
%
% Uses the function cwt from Matlab's Wavelet Toolbox.
%
% ---INPUTS:
% y, the input time series
%
% wname, the wavelet name. For a continuous wavelet transform, a proper
% continuous analyzing wavelet like '... |
e2b636a1fb1af1740bfdc54db5c22ec2256bf173323aae6e66e5c29fc2130f70 | MATLAB | 7,047 | 168 | % STD_GETTRIALSIND - return the index of the trials that comply with the
% defined values from trialinfo
%
% Usage:
% >> trialindsx = std_gettrialsind('testnewstudyfile.mat', 'type', { 'C' 'X' 'Y' }, ...
% 'load', [0 1 2 3 4 5 6], 'uncertainty1',[1 2])
% >>... |
479080b49ba9821c5d292c5f28aa45206c4d6888b9a6a5fe1b4e3179fa1619d7 | MATLAB | 7,052 | 179 | function shuffle_icaReacCCG(basename)
[rootPath,sesName,~]=fileparts(basename);
fprintf('%s load files for %s\n',datestr(now),sesName);
load(fullfile(rootPath,'data',[sesName '-icaReac.mat']))
load(fullfile(rootPath,'data',[sesName '.sleepstate.states.mat']))
load(fullfile(rootPath,'data',[sesName '.sessions.events.ma... |
6cb511c2df490ab547872af26d6889316a51682da91c8c8623a32c8ad1b8290d | MATLAB | 7,052 | 214 | function info = convert_open_ephys_to_kwik(varargin)
%
% Converts Open Ephys data to KWIK format
%
% by Josh Siegle, November 2013
%
% info = convert_open_ephys_to_kwik(input_directory, output_directory)
%
% input_directory: folder with Open Ephys data
% output_directory (optional): folder to save the KWIK files... |
c08759766f1ce9e24fef4d5d45d4c3564f41c21b162378017917d0b776ab2029 | MATLAB | 7,056 | 190 | % op_sortMRSIsdat.m
% Helge Zoellner, The Johns Hopkins University 2020.
%
% USAGE:
% out=osp_MRSIRecon(in);
%
% DESCRIPTION:
%
%
% in = input data in matlab structure format.
%
% OUTPUTS:
% out = Output dataset following zeropadding.
function out=op_sortMRSIsdat(in);
% 2D MRSI data
%Now that we've ... |
fb66e05a2dd4402413ee6b3362cd96f6b93451b6199c624d275ffdd2c7557c31 | MATLAB | 7,063 | 173 | function processBehaviorData(behaviorPath, codePath, savePath)
% Process behavior data. Must run for plotFigure1_expertBeh,
% plotFigure6_naiveBeh, plotFigureS1_rawWTexperts,
% plotFigureS9_naiveBehSupp
%INPUTS:
% behaviorPath = local path to behavior data downloaded from Zenodo
% codePath = local path to where c... |
a6d0b688e830fc83c1efacd7730c47269dfcb65e0e3c87202fe1a0ab227be6e3 | MATLAB | 7,068 | 189 | function DBAddFigure(f,eid,name,comments,parameters,mfiles,varargin)
%DBAddFigure - Save figure in current database.
%
% Save figure as MATLAB fig and PNG image. Also save code used to generate it
% (although not required, installing <a href="http://sites.google.com/site/oliverwoodford/software/export_fig">export_fig<... |
b13f3a9cd76afdd0b76e78441ba0b5ee037ef92aadd1973b63c1162d7f9b2426 | MATLAB | 7,074 | 219 | % Bang et al (2020) Private-public mappings in human prefrontal cortex
%
% Reproduces Figure 2-figure supplement 1
%
% Visualises behavioural data for prescan phases and performs associated
% regression analyses
%
% Statistical tests can be reproduced by applying one-sample t-tests to
% regression betas: e.g. [H,P,CI,... |
3ceed15c8004099f57cdc55274bbf8d140754c64a766e5fc92d44cb2c8ee3ea7 | MATLAB | 7,076 | 260 | % Collapse multiple single-scan NIFTI files into a multiple-scan NIFTI file
%
% Usage: collapse_nii_scan(scan_file_pattern, [collapsed_fileprefix], [scan_file_folder])
%
% Here, scan_file_pattern should look like: 'myscan_0*.img'
% If collapsed_fileprefix is omit, 'multi_scan' will be used
% If scan_file_fol... |
c300aab2946ca3b76efa3589267655d84ed8f86144ad73c94030677cbf17287d | MATLAB | 7,079 | 199 | function [MP2RAGEimgRobustPhaseSensitive, multiplyingFactor] = RobustCombination(MP2RAGE, regularization, HG)
% FUNCTION [MP2RAGEimgRobustPhaseSensitive, multiplyingFactor] = RobustCombination(MP2RAGE, [regularization], [HG])
%
% This script creates MP2RAGE T1w images without the strong background noise in air regions... |
adfa98ab7e2e7290676ff98d1b442ff76af357955d63f39abc78d70028d2f3e0 | MATLAB | 7,083 | 203 | function [hdr] = read_ctf_res4(fname)
% READ_CTF_RES4 reads the header in RES4 format from a CTF dataset
%
% Use as
% [hdr] = read_ctf_res4(filename)
%
% See also READ_CTF_MEG4
% "VSM MedTech Ltd. authorizes the release into public domain under the
% GPL licence of the Matlab source code files "read_ctf_res4.m" and... |
4814365dc243e54b21b788ea7a3cb45ef6881df6ef382034cd4d3447bf8a37e3 | MATLAB | 7,084 | 200 | function [rate_dat,lambda,trial_idx_final,lambda_var,data_idx,mod_idx,XKnew] = ...
cleantrials(f,trialmask,alignment, tmin,tmax,ops)
%parse up continuous data into trials and trim edges correctly to compare data and a model fit
%
%Inputs:
% f: loaded fit structure
% trialmask: (ns x 1) boolean for w... |
3b2619a3081be64f1aaf8843c545a443c9bfbb1bdeef1ce248145134f0f37b0e | MATLAB | 7,085 | 196 | function fp = hlp_fingerprint(data)
% Make a fingerprint (hash) of the given data structure.
% Fingerprint = hlp_fingerprint(Data)
%
% This includes all contents; however, large arrays (such as EEG.data) are only spot-checked. For
% thorough checking, use hlp_cryptohash.
%
% In:
% Data : some data structure
%
... |
b2e412c2c2d31479e8a551f30ca649baedea454eff2c6982ab428cd0eea6ccb5 | MATLAB | 7,087 | 232 | function varargout = semplot(x,y,color,smooth,solid,opt)
%semplot - Plot mean (line) +/- s.e.m. (shaded area) of a matrix 'y'
%
% USAGE
%
% handles = semplot(x,y,color,<options>)
%
% x abscissae (optional, default is 1 : size(y,2))
% y ordinates, each column contains multiple valu... |
6e1ac08c79b4f62781bae0bd9494a25603536ef881b95e9835526d1c5354d209 | MATLAB | 7,092 | 244 | function [channels,overall_amplitude] = eeg_amplitudearea(EEG, channels, resrate, wstart, wend)
% EEG_AMPLITUDEAREA - Resamples an ERP average using spline interpolation
% at a new sample rate (resrate) in Hz to get the exact limits
% of the window of integration. Finely sa... |
8baa68a285c299ca682ae0793adef3e50b83beb8ba8a0e27fdef11b9bd2cf6eb | MATLAB | 7,093 | 203 | % CALIPER - Measure a set of spatial components of a given data epoch relative to
% a reference epoch and decomposition.
% Usage:
% >> [amp,window]=caliper(newepoch,refepoch,weights,compnums,filtnums,times,'noplot');
%
% Inputs:
% newepoch = (nchannels,ntimes) new data epoch
% refepoch = a (nchan... |
2db564d473de4437e0edc5e04edc6498feff8892752ebea25c7b0448d8e4af9c | MATLAB | 7,098 | 183 | % TEXTGUI - make sliding vertical window. This window contain text
% with optional function calls at each line.
%
% Usage:
% >> textgui( commandnames, helparray, 'key', 'val' ...);
%
% Inputs:
% commandnames - name of the commands. Either char array or cell
% array of char. All style ar... |
78361e94c715bcbfdbbd8bfc0751524fe802fb9a45499fe840c28b687cab0ac8 | MATLAB | 7,098 | 265 | %% save_sepia_header(input,userDefine,output)
%
% Usage:
%
% Input
% --------------
%
% Output
% --------------
%
% Description:
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 23 May 2019
% Date modified:11 August 2021
%
%
function save_sepia_header(input,userDefine,output)
% constant
gyro = 42.57747... |
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