sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
52e3de1017ca35fde6c25d41d79eff6ee2b83b6cd3be159e64dc5bddcc3478d4 | MATLAB | 2,434 | 67 | %% when done with all subjects, write out inflated views
% these images are our final inspections and quality assessments
% OBSOLETE
%mkdirquiet('~/Dropbox/KKTEMP/floc-faces-raw');
outputdir = '~/Dropbox/KKTEMP/floc-facesandwords';
mkdirquiet(outputdir);
todo = {{'floc-faces' 'flocfacestval'} {'floc-words' 'flo... |
dbaa84d33361adbe754cfcd4581c2b720d02e839a05453c4f03f6cc3004ce41a | MATLAB | 2,434 | 74 | function main(cfg)
% MAIN Entry point for Myelin–FC Coupling analysis (MATLAB)
% addpath(genpath(fileparts(fileparts(mfilename('fullpath')))));
% cfg = config.default_config();
if nargin < 1
cfg = config.default_config();
else
% window for user to set FC modality
cfg_default = config.default_config();
... |
321909521a101972026a844556e37266af02b64047047ecbd8c4a87647b7e9a4 | MATLAB | 2,437 | 56 | %% this raster script is for use with MClust files rather than spike 2
Neuron = 9; %%total number of neurons
Set = [1];%%%[0 2 4 5 6 7]; %% number your electrodes according to oep channels as needed oep 1, 2, 3
NeuronsInset = [9]; %%%[2 1 4 2 2 2]; %%represents the number of neurons that was sored for each for each... |
862ca643e9cc224490c33378d39660e8aee74bc0567629af1d9ef37dbbe435c9 | MATLAB | 2,437 | 129 | function Pipeline_plotInVivoData(params, plt)
% This function plots in vivo data, filtered for photobleaching.
analysisDir = getAnalysisDir(params);
ExpInfoFn = getFileName(params, 'ExpInfo');
tsFn = getFileName(params, 'TS');
load(fullfile(analysisDir, ExpInfoFn));
load(fullfile(analysisDir, tsFn));
for i = 1:nume... |
86a65fd503a25872b891e0f0e5047aebdbb46822c83806782e40a53fe3b8fbf0 | MATLAB | 2,437 | 62 |
main_path = './';
% MEG and MRI mat files can be downloaded from:
% https://osf.io/pd4h9/overview
% should be placed in the 'Dataset' folder under main_path
% Required Toolboxes to run the code:
%fieldtrip toolbox is required for anatomy transformation and preprocessing steps
% https://www.fieldtriptoolbox.org/
%b... |
c47829ad5319c43219b36f3920a3e6642fac95fa77892e8ccff38abbfb4117ca | MATLAB | 2,437 | 68 | % Here, we create some simple "probabilistic ROIs"
% whereby we transfer manually defined ROIs in each of the 8 NSD
% subjects to fsaverage and then compute the fraction of subjects
% that are labeled at fsaverage vertex.
%
% We save both fsaverage .mgz files and also create some visualizations.
%% %%%%% Compute and ... |
728dded94e2303564b11a900a9b046379f1ee2a7dd1e64cedf2d4c1f4d5ed3f1 | MATLAB | 2,438 | 82 | %% unitTest.m
% This function performs a command line unit test based on the jobTesting.m file in the
% ci folder. All Osprey modules are tested in dependence of the
% included dataset. You can change the jobTesting.m file according to your desired
% needs. The results unittest class includes detailed informati... |
50d435f3ea6f7f4ea58b960182d10a19039fc71fd79bd7f920f85eeebf36f539 | MATLAB | 2,439 | 55 | %% Figure 5 analysis
% Runs regression analysis for all model configurations, for RADICaL rates
% and for smoothed-deconvolved events
% Model configurations:
% Instantaneous, proximal-distal partial, spout-distance partial, causal
% Wiener filter, acausal Wiener filter
%% Preprocess data
% Before running this script,... |
c3320d16775e01367626074850c8500548c22e2636246fa38722ba8ffd23c778 | MATLAB | 2,440 | 69 | function [encoderNet, decoderNet] = train_vae(encoderNet, decoderNet, XTrain, XTest)
numTrainImages = size(XTrain, 4);
executionEnvironment = "auto";
numEpochs = 250;
miniBatchSize = 128;
lr = .25e-3;
numIterations = floor(numTrainImages/miniBatchSize);
iteration = 0;
avgGradientsEncoder = [];
avgGradientsSquaredE... |
2d23d8165294ce79093ec4d27275d081d9ae0ad106c50ebc688a0ebeb5fd4ed7 | MATLAB | 2,441 | 66 | function SaveRippleEvents(filename,ripples,channelID,varargin)
%SaveRippleEvents - Save hippocampal ripple (~200Hz oscillations) events.
%
% USAGE
%
% SaveRippleEvents(filename,ripples,channelID,options)
%
% filename file to save to
% ripples ripple info as provided by <a href="matlab:help FindR... |
d7cff186e9218432e916749be129130d10d30c3e275f4349129a43ab0e51980b | MATLAB | 2,441 | 76 | function pick = bbox_nms(boxes, overlap)
% top = nms(boxes, overlap)
% Non-maximum suppression. (FAST VERSION)
% Greedily select high-scoring detections and skip detections
% that are significantly covered by a previously selected
% detection.
%
% NOTE: This is adapted from Pedro Felzenszwalb's version (nms.m),
% but a... |
0aceae470ae1a56a5af14682f94c8e9829fd102d80426c0740743bd3f038018a | MATLAB | 2,442 | 101 | function hout=suptitle(str)
%SUPTITLE Puts a title above all subplots.
% SUPTITLE('text') adds text to the top of the figure
% above all subplots (a "super title"). Use this function
% after all subplot commands.
% Drea Thomas 6/15/95 drea@mathworks.com
% Warning: If the figure or axis units are non-default, ... |
274cde9fa91049e4c803458253de1e2042344fab83eaef3ea458fb1a9cf21212 | MATLAB | 2,442 | 92 | % op_combinesubspecs.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_combinesubspecs(in,mode);
%
% DESCRIPTION:
% Combine the subspectra in an acquisition either by addition or
% subtraction.
%
% INPUTS:
% in = input data in matlab structure format.
% mode = -"diff" adds the subspectra togeth... |
aa732633b38e23f891ada0dd706f761311ac2aa8232312fe4a08f81db17a770b | MATLAB | 2,444 | 57 | % VL_NNROIPOOL CNN region of interest pooling.
% Y = VL_NNROIPOOL(X, ROIS) pools each feature channel in X in
% the specified regions of interest ROIS. ROIS is a 5 x K array
% containing K regions. Each region has five coordinates `[t, u0,
% v0, u1, v1]` where `u0`, `v0` is the upper-left corner of a ROI,
% ... |
c93e1549cf8ebf9073e78786fdee2e92ef4fdd89302288700c720910165ecbc3 | MATLAB | 2,444 | 71 | function [K,dK] = covDiscrete(s, hyp, x, z)
% Covariance function for discrete inputs. Given a function defined on the
% integers 1,2,3,..,s, the covariance function is parameterized as:
%
% k(x,z) = K_{xz},
%
% where K is a matrix of size (s x s).
%
% This implementation assumes that the inputs x and z are given as i... |
e40b4f47248ae1260078672c8b736d5016b06474ce5c05615c5ff7e678732497 | MATLAB | 2,445 | 51 | % calculate dFoverF for a response window and for a moving window, taking
% the maximum response for each location
function [DF_reponse,DF_master,DF_movie] = dFoverF(movie,offset,framerate,plot1,plot2,DF_movie_yesno,f0_window,response_window)
% figure(66), plot(squeeze(mean(mean(movie,2),1)))
% xy = ginput(4);
xy = [ ... |
fd617d56c807ea115e9eb80bb73041c70d77f348eb54a5c2600036e005b6d1ea | MATLAB | 2,446 | 70 | function diff = getDirectionalDerivative(problem, x, d, storedb, key)
% Computes the directional derivative of the cost function at x along d.
%
% function diff = getDirectionalDerivative(problem, x, d)
% function diff = getDirectionalDerivative(problem, x, d, storedb)
% function diff = getDirectionalDerivative(problem... |
2d66ef85d5fbaa5f53449917f3ae013ce2f886a66f085ba8eda3444dfcb25e25 | MATLAB | 2,447 | 87 | function splitc = splitcode(code)
%SPLITCODE Split a line of Matlab code in string, comment and other
% SPLITC = SPLITCODE(CODE) splits line of Matlab code CODE into a cell
% array SPLITC where each element is either a character array ('...'),
% a comment (%...), a continuation (...) or something else.
% Note that ... |
1a2e7939c8f57f1ef11baa359a02e45e58343938ca030148537c878ad7b4d0ec | MATLAB | 2,448 | 90 | function [ DCM ] = tapas_ceode_synData_cmc()
% [ DCM ] = tapas_ceode_synData_cmc()
%
% Sets parameters and function handles to create a synthetic DCM
% structure. The resulting structure can then be used to generate
% artificial data with tapas_ceode_gen_erp.m
%
% INPUT
%
% OUTPUT
% DCM struct DCM st... |
a30ea205545e513cfce42204cd42e22e475c2772c14f54579c5064df55e74152 | MATLAB | 2,448 | 60 | function osp_ProTabChangeFcn(src,~,gui)
%% osp_ProTabChangeFcn
% This function is triggered when the process tab is changed. It refreshes
% the figure.
%
%
% USAGE:
% osp_ProTabChangeFcn(src,~,gui);
%
% INPUT: src = handle of the fit tabs
% gui = gui class containing all handles and t... |
e97c73feb289691843be701b08de033b30fbf53cdabb58a77d440089434b8db2 | MATLAB | 2,448 | 50 | % POP_STDWARN - check memory options and issue warning for studies.
%
% Usage: >> pop_stdwarn;
%
% Author: Arnaud Delorme, CERCO, 2007
%
% See also: EEG_OPTIONS
% Copyright (C) Arnaud Delorme, CERCO, 2007, arno@salk.edu
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
%... |
f633d09f432fe5dd83208a5dbc0a40d5e7e385df609148e452e1264353868576 | MATLAB | 2,449 | 101 | function plotSpectra(params, spectralData)
% plots spectra for channels
% spectralData =
% info: [1x1 struct]
% xVals: [60x1 double] ~ time
% yVals: [129x1 double] ~ freq
% cVals: [129x60x125 double] ~ time x freq x chnls
% (c) Jiri, May16
%% basic check
nCh = size(spectralData.cVals,... |
e90f5b5988a4b3d81aabd39035c0136caf3da8e5d87b60bc97f0bce3af499419 | MATLAB | 2,450 | 67 | function [embedding, scaled_eigval] = diffusion_mapping(data, n_components, alpha, diffusion_time, random_state)
% DIFFUSION_MAPPING Diffusion mapping decomposition of input matrix.
% embedding = DIFFUSION_MAPPING(data,n_components,alpha,diffusion_time)
% computes the first n_components diffusion components of ma... |
0649839a165e37a59d513735a66836a6305b9d3071564b3e21c1dec54a372523 | MATLAB | 2,451 | 95 | function [S_m_noise]= Phantom_Simulation_BiExp_Relax_Pixel(Phantom,N,b_values,TE,TR)
% This function creates a 2D IVIM phantom dataset using the input
% parameters in the phantom struct and input parametrs
%
% USAGE:
% [S_m_noise]= Phantom_Simulation_BiExp_Relax_Pixel(Phantom,N,b_values,TE,TR)
%
% INPUTS:
% ... |
805250fb17e334519e5746bd391cae39f43e4a2c0f09be88a2aa07de80f88596 | MATLAB | 2,451 | 90 | dirname = '~/proj/networkFVMsims/examples/';
%% total flux out of holes
filename = [dirname 'example1_ca.out'];
[fluxsim,tvals] = loadTotFluxSim(filename);
if (tvals(1)~=0)
tvals = [0; tvals];
fluxsim = [fluxsim(1); fluxsim];
end
vals = sum(fluxsim,2);
integ = (vals(2:end)+vals(1:end-1))/2;
dt = diff(tvals);
... |
aea2c5dc5807f852264c3d7e5b70bd01fdb7a8df5e3a6a8510cac6403f483b81 | MATLAB | 2,451 | 69 | function tapas_rw_binary_dual_plotTraj(r)
% Plots the estimated or generated trajectories for the binary HGF perceptual model for multi-armed
% bandit situations.
%
% Usage example: est = tapas_fitModel(responses, inputs); tapas_rw_binary_dual_plotTraj(est);
%
% --------------------------------------------------------... |
57b8a6565c5359ecaca6b20bf3bc5b4bcb77450ab4e481a828d69413803757dc | MATLAB | 2,452 | 72 | function grad = fif2grad(filename)
% FIF2GRAD constructs a gradiometer definition from a Neuromag *.fif file
% The resulting gradiometer definition can be used by Fieldtrip for forward
% and inverse computations.
%
% Use as
% grad = fif2grad(filename)
%
% See also CTF2GRAD, BTI2GRAD, MNE2GRAD, ITAB2GRAD, YOKOGAWA2GRAD... |
9cd3b74f72aaa0050b69d6a01c5adbceecbdc5fb6139fcd67306186b97d41e5b | MATLAB | 2,452 | 71 | function continuous_tone_cursor
% Global variables to share state between callbacks.
global currentFreq phase ap dt fs fig ax;
% Initialize frequency and phase.
currentFreq = 200; % Starting frequency (Hz)
phase = 0; % Initial phase for continuity
% Audio parameters.
fs = 4... |
d4a8fa18f97909617df8f7be908b2af95da73f81f053367fe9a26ecb29752886 | MATLAB | 2,452 | 71 | function map = tab20(N)
% Qualitative colormap from MatPlotLib, for plots using the line ColorOrder.
% In MatPlotLib 2 it is named VEGA20, for MatPlotLib 3 was renamed TAB20.
%
% Copyright (c) 2017-2020 Stephen Cobeldick
%
%%% Syntax:
% map = tab20
% map = tab20(N)
%
% For MatPlotLib 2.0 improved colormaps were creat... |
635e6aab3d5c55752c8ae1f4468db60262d943a41df40a76ea873f9e0f2d9d28 | MATLAB | 2,454 | 100 | function result = GGclust(data,param)
%checking the parameters given
f0=param.c;
%data normalization
X=data.X;
if exist('param.m')==1, m = param.m;else m = 2;end;
if exist('param.e')==1, e = param.m;else e = 1e-4;end;
[N,n] = size(X);
[Nf0,nf0] = size(f0);
X1 = ones(N,1);
% Initialize fuzzy partition matrix
rand... |
a20df7949f63f743df35b37ce32b9f0b3f6588dc2008ee2d4629bb56ec7de65e | MATLAB | 2,455 | 89 | function [swf] = read_besa_swf(filename)
% READ_BESA_SWF
%
% Use as
% [swf] = read_besa_swf(filename)
%
% This will return a structure with the header information in
% swf.label cell-array with labels
% swf.data data matrix, Nchan X Npnts
% swf.npnt
% swf.tsb
% swf.di
% swf.sb
% Copyright (C) 2... |
20150215d02c56bbfe08dec79beea4bd71ff6280de4241b61ff1d0f673b0700e | MATLAB | 2,458 | 100 | function test95()
% function test95()
%
% Test for symfixedrankNewYYquotientfactory geometry (low-rank PSD matrix completion)
% This test is different from 'test98'. We use the tuned geometry,
% symfixedrankNewYYquotientfactory.
%
% This file is part of Manopt: www.manopt.org.
% Original author: Bamdev Mishra, Dec. 30... |
e10af9cfdee256348eea50318c0cf81460519760714278eca81a44afe10bc306 | MATLAB | 2,458 | 41 | function B1Tx_GroupAverage(myelinFile, myelinAsymmOutFile, phaseFile, phaseAsymmOutFile, myelinCorrOutFile, myelinCorrAsymmOutFile, fitParamsOutFile)
%Orig Myelin, with receive corr if applicable
MyelinMap = cifti_read(myelinFile);
surfasymmnorm(MyelinMap, myelinAsymmOutFile, 'Group Myelin Asymmetry');... |
50d3a76f0bdcc376ae2951fcb75004b4b8d3c8233e9d80a9491f982194b58aeb | MATLAB | 2,460 | 85 | function p = PlotSamples(X,varargin)
%PlotSamples - Plot samples (multiple time series).
%
% Plot columns 2...M of a matrix as a function of its first column.
%
% USAGE
%
% p = PlotSamples(X,<options>,<options2>)
%
% X <a href="matlab:help samples">samples</a> to plot
% <options> optional l... |
5b029280137512daf358785ac39aa209813d9f00a23d4eb8cdd0f97eaeedee74 | MATLAB | 2,460 | 80 | function flt = constructsmoothingfilter(sd,thresh)
% function flt = constructsmoothingfilter(sd,thresh)
%
% <sd> is [A B C] with standard deviations of a 3D Gaussian filter along the
% first, second, and third dimensions. you can also specify [A B] in order
% to obtain a 2D Gaussian filter.
% <thresh> is threshol... |
6fc9bdd588bf22cd5a5857fc84188a2b973f0e69289371715471cb6b36469507 | MATLAB | 2,460 | 60 | % STD_SAVEDAT - save measure for computed data
%
% Usage: std_savedat( filename, structure);
%
% Authors: Arnaud Delorme, SCCN, INC, UCSD, 2006-
% Copyright (C) Arnaud Delorme, SCCN, INC, UCSD, October 11, 2004, arno@sccn.ucsd.edu
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and ... |
d9299c559d0de6db6fe4a948aebd6819d60c3b99d11bcf9f0601e03ced97bdf1 | MATLAB | 2,460 | 61 | function CORnet_vs_Neural_Dissimilarity(IT_Fam_FR,HC_Fam_FR,IT_Fam_VE,HC_Fam_VE,IT_Lure_FR,HC_Lure_FR,IT_Lure_VE,HC_Lure_VE,HC_Fam_FV,HC_Lure_FV,IT_Fam_FV,IT_Lure_FV,times_analyze)
%This function compares the neural similarity of CORnet to that of the
%recorded neural population. It fits both a linear and a quadratic f... |
e4cf6dabc1611025abbf7b8393a812369f5bc14fd891add8f732f185ed0fdb8c | MATLAB | 2,460 | 87 | %USER_STRING Get/set a user specific string
%
% Examples:
% string = user_string(string_name)
% saved = user_string(string_name, new_string)
%
% Function to get and set a string in a system or user specific file. This
% enables, for example, system specific paths to binaries to be saved.
%
% IN:
% string_name - ... |
0407cc6e78f05b14a55b1b31b64e6462a6efc1837def443b22c4371459e9dd40 | MATLAB | 2,461 | 71 | function map = tab20c(N)
% Qualitative colormap from MatPlotLib, for plots using the line ColorOrder.
% In MatPlotLib 2 it is named VEGA20C, for MatPlotLib 3 was renamed TAB20C.
%
% Copyright (c) 2017-2020 Stephen Cobeldick
%
%%% Syntax:
% map = tab20c
% map = tab20c(N)
%
% For MatPlotLib 2.0 improved colormaps were ... |
fe12a00daeb9f04551bceedf5fdaa97e246a3b64f6407e47b2e6086a661e0a99 | MATLAB | 2,461 | 71 | function map = tab20b(N)
% Qualitative colormap from MatPlotLib, for plots using the line ColorOrder.
% In MatPlotLib 2 it is named VEGA20B, for MatPlotLib 3 was renamed TAB20B.
%
% Copyright (c) 2017-2020 Stephen Cobeldick
%
%%% Syntax:
% map = tab20b
% map = tab20b(N)
%
% For MatPlotLib 2.0 improved colormaps were ... |
9e68911854f4aff6b5d86eccce741bbea68f80595ea162fb3125b5cbcd5e7e8a | MATLAB | 2,462 | 61 | function savefig_pdf(h,filename,orientation)
%% ########################################################################
% - Save plot as vector image in .pdf format
% #########################################################################
% [Note:] As I keep forgetting the function and criteria, here's a simple
% fu... |
842d3aa957750051e5a7df4c4398127871a990448e28e956c857939c7ebbc8fa | MATLAB | 2,463 | 78 | function make_clicky(infig,outfig,hsi_img,wavelengths)
%
%function make_clicky(infig,outfig,hsi_img,wavelengths)
%
% adds a callback to a given figure to display spectra for a pixel when
% clicked
%
% infig - figure handle of figure to add click ability
% outfig - figure handle of figure to display spectra
% hsi_img - ... |
3c20be84b283f3b1d9161b50cef66acda4692d54e45691527d8eedc5cd863509 | MATLAB | 2,464 | 84 | function [dimInfo, NewAffineTrafo] = ...
perform_world_space_operation(this, operation, parameters, dimInfoIn)
% Computes new dimInfo and affineTrafo
%
% Y = MrImageGeometry()
% [dimInfo, NewAffineTrafo] = Y.perform_world_space_operation(operation, ...
% parameters, dimInfoIn)
... |
78a50f6ac118dd06e1840f696843912e1e90b92a663acd8ac70e065d6408fee1 | MATLAB | 2,465 | 97 | %perm difference plotter
addpath("~/ER_Ca_rot/networkSpreadFVM-main/scripts/");
addpath("~/ER_Ca_rot/networkSpreadFVM-main/examples/");
dirname = "~/ER_Ca_rot/networkSpreadFVM-main/examples/inf_Perm_op/mesh_4";
dirname1 = "~/ER_Ca_rot/networkSpreadFVM-main/examples/200_perm_op";
ar = [0.0001,0.0005,0.0024,0.0111,0.0500... |
cb2d9d27f54ee4a18dce216060e702f2b3777f867213016848d5d33dcb861d14 | MATLAB | 2,465 | 84 | function gcdf = palm_gcdf(G,df1,df2)
% Convert a pivotal statistic computed with 'pivotal.m'
% (or simplifications) to a parametric p-value.
% The output is 1-p, i.e. the CDF.
%
% Usage:
% cdf = palm_gcdf(G,df1,df2)
%
% Inputs:
% G : G or Z statistic.
% df1, df2 : Degrees of freedom (non infinite).
% ... |
5b8c9c856bc13b95cc27681132e9e8ea924cbfd0fa69a168fb28887c072a1ce1 | MATLAB | 2,467 | 60 | % RSGET - get the p-value for a given collection of l-values
% (Ramberg-Schmeiser distribution)
%
% Usage: p = getfit(l, val)
%
% Input:
% l - [l1 l2 l3 l4] l-values for Ramberg-Schmeiser distribution
% val - value in the distribution to get a p-value estimate at
%
% Output:
% p - p-value
%
% Autho... |
04411938a9eb15b22029560c7157ca657574d9523d3edc34e466545e2c4a65ad | MATLAB | 2,468 | 51 | % pop_checkdatasetinfo() - Check for consistency between STUDY and ALLEEG
% Fields covered: filename, subject, condition,
% group, session, run.
%
% Usage:
% >> [STUDY, ALLEEG] = pop_checkdatasetinfo(STUDY, ALLEEG);
%
% In... |
439cbfb33911dee4e508154a44c59da1e9be52032e7d863673a008ce5b92c7c1 | MATLAB | 2,468 | 79 | function clout = weighted_knn(data,clas,k)
% function clout = weighted_knn(data,clas,k)
% used in tor_knn
%
% this function gives class assignments weighted by the reciprocal of prior class
% probabilities, so that smaller classes are not penalized.
% this is expected to optimize sensitivity (d-prime) to class membersh... |
55da53e7677b4da29fe6cb9e5d1241fbf748772136888559e9e9490b706ed84e | MATLAB | 2,468 | 72 | function [adjMs, F1] = generateAdjMs(spikeTimes, ExN, Params, Info, oneFigureHandle)
% Create AdjM for a series of lag values
%
% Parameters
% ----------
% spikeTimes :
% ExN :
% Params : struct
% MEA-NAP Parameter structure
% Info : struct
%
% Returns
% -------
% adjMs :
% F1 : figure handle
... |
f15af889b21f2b82c4e01a3ce8819cb4fcba148559da104bc8af9972e6710f3f | MATLAB | 2,468 | 97 | %% === compare timings for MULT
choice = questdlg('Run full comparison (several minutes)?', ...
'Performace Comparison', 'Yes','No','Yes');
if strcmp(choice,'No')
return
end
% number of repeats (to increase measurement accuracy)
R = 10;
% what sizes of (square) matrices do we want measure? (log spacin... |
6677676fbbf9376bd1d74861f5447857a119986c40dbfc505a046ea6906d25c8 | MATLAB | 2,469 | 54 | function [Operations,MasterOperations] = TS_LinkOperationsWithMasters(Operations,MasterOperations)
% TS_LinkOperationsWithMasters Link Operations with MasterOperations using Label field
% ------------------------------------------------------------------------------
% Copyright (C) 2013-2026, Ben D. Fulcher <ben.d.... |
822a3c5e8e83a9535262f1f81064722a935825b72f0d8db39069f49041366bfa | MATLAB | 2,470 | 93 | function fear_getHfoFrMod(basename)
% 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 '.okUnit.spikes.mat'])
load([basicMetaData.Basename '.se... |
b6f3aa969a6dfa1f102201fa5cb2cb32510fe709a1c6b339222073fc5c308580 | MATLAB | 2,470 | 72 | function matchFigureAspectRatio(varargin)
% MATCHFIGUREASPECTRATIO Match figure window to paper aspect ratio
%
% Syntax:
% matchFigureAspectRatio()
% matchFigureAspectRatio('Name', Value, ...)
%
% Description:
% Adjusts figure window size to match paper dimensions for accurate preview.
%
% Inputs (Name-Value pair... |
30457b96e956d68257a8852305cb4c3a3f3369a5b76fe468c814c30dbbb74298 | MATLAB | 2,471 | 90 | function this = append(this, otherImage)
% appends other MrImage (of same 3D geometry) via 4th dim to end of MrImage
%
% Y = MrImage()
% Y.append(otherImage)
%
% OR
%
% Y.append(fileName);
%
% OR
% Y.append(dataMatrix);
%
% This is a method of class MrImage.
%
% IN
%
% OUT
%
% EXAMPLE
% Y = MrImage()... |
b813352f6281d460bb8bd36e5c0efcf847b1a23a7cc2dadc987328d2831fa59b | MATLAB | 2,471 | 73 | function [Wrr,Wrf] = generate_weights_random(Ne,Ni,Nx,Prr,Prx,varargin)
% GENERATE_WEIGHTS_RANDOM Random (Erdos–Renyi) connectivity without spatial/tuning structure.
%
% Syntax
% [Wrr, Wrf] = generate_weights_random(Ne,Ni,Nx,Prr,Prx, Name,Value, ...)
%
% Description
% Constructs random connectivity lists according... |
1089a86c9ed9df0b75226238ff2778bdff361970e74b83484b6cb81b0756ab59 | MATLAB | 2,472 | 90 | function [ DCM ] = tapas_ceode_testData_erp()
% [ DCM ] = tapas_ceode_testData_erp()
%
% THIS IS A SCRIPT SOLELY FOR TESTING THE SPM/TAPAS SETUP. DO NOT CHANGE!
%
% Sets parameters and function handles to create a synthetic DCM
% structure. The resulting structure can then be used to generate
% artificial data with tap... |
e06f8d8a6dbf6c34883e17dde627aadd57c20eaf41866388461875a6e026f569 | MATLAB | 2,472 | 101 | % op_averaging.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_average_extra(in,which);
%
% DESCRIPTION:
% Combine the averages in a scan by adding the averages together and then
% dividing by the number of averages.
%
% INPUTS:
% in = input data in matlab structure format.
%
% OUTPUTS:
% out = Output... |
189a89647765227dda0eab169e279b57f23352879a9588a4968fcb4f87d2ac03 | MATLAB | 2,474 | 109 | function FigureS13(datadir, codedir)
%FigureS12 Males and females have comparable wait time ratios (top) and
% trial initiation time ratios (bottom)
% datadir = directory of dataset
% codedir = director of code
%% Set up paths
s = pathsep;
pathStr = [s, path, s];
onPath = contains(pathStr,...
codedir, 'Ignor... |
b3da556fb4eb32663dac40dfd2139d003e3f324e72f65c08201df2b1d4e88a08 | MATLAB | 2,474 | 54 | %% load libraries
run('set_library_paths.m');
addpath(SPM_PATH); % per spm docs, do not genpath it
addpath(genpath(CANLABTOOLS_PATH));
%% VARIABLES THAT MUST BE DEFINED BEFORE THE SCRIPT IS SOURCED
% THIS SCRIPT IS DESIGNED TO RUN ACROSS A SINGLE TASK
% aggregating over subject-level 1st-level SPM beta or contrast sta... |
bd6108371b23678256b4016b61207a9387acd146ee3b266f366228f66f8c80fc | MATLAB | 2,474 | 76 | %% draw the fig5a
clear;
working_dir = 'G:\CEST-fMRI'; % the actual directory to put the codes
gen_figure_path = [working_dir,'\gen_figures'];
addpath(genpath(gen_figure_path));
load_dir = [working_dir,'\scripts\loading'];
load([load_dir,'\Fig5_map.mat']);
set(0,'defaultfigurecolor','w');
figure;
set(gcf,'... |
5736f274b14c39fa29a0e2daa3e4bc5c6779018b1ae4c39e9bb6f62d243ffc27 | MATLAB | 2,475 | 90 | function [dimLabels, resolutions, nSamples, units, firstSamplingPoint] = ...
read_nifti(~, fileName)
% Reads nifti files and extracts properties for dimInfo
%
% Y = MrDimInfo()
% [dimLabels, resolutions, nSamples, units] = Y.read_nifti(fileName)
% used in Y.load(fileName)
%
% This is a method of class MrDimIn... |
709ced415bcbe042317a125dc3c0ae588776e435b8dcb86675212dcdd4e58b76 | MATLAB | 2,478 | 63 | % Mean functions to be use by Gaussian process functions. There are two
% different kinds of mean functions: simple and composite:
%
% Simple mean functions:
%
% meanZero - zero mean function
% meanOne - one mean function
% meanConst - constant mean function
% meanLinear - linear mean function... |
ccbc7ff595e1345adbd4fb6084170ea64606196cce5ddb574e652713a5ffeab9 | MATLAB | 2,478 | 62 | % BIDS �ļ���·��
BIDS_folder = '/mnt/e/Neuroimage/Projects/QSM_process/YT_QSM_BIDS';
% ���������ļ���·��
derivatives_folder = fullfile(BIDS_folder, 'derivatives');
% ��������� derivatives �ļ��У���
if ~exist(derivatives_folder, 'dir')
mkdir(derivatives_folder);
end
% SEPIA ����ļ���·��
SEPIA_output_folder = fullfi... |
11e8eeef73221ba4bf2e8f362067df360bc99b69a17696aedddced5251ded08c | MATLAB | 2,479 | 57 | % TRIAL2EEGPLOT - convert eeglab format to eeplot format of rejection window
%
% Usage:
% >> eegplotarray = trial2eegplot(rej, rejE, points, color);
%
% Inputs:
% rej - rejection vector (0 and 1) with one value per trial
% rejE - electrode rejection array (size nb_elec x trials) also
% made of 0 and ... |
3186ac4bc333049ea641c7045f05fbe93c3d38a0e5e268c2d88f18a1a1057e58 | MATLAB | 2,479 | 103 | function test07()
% function test07()
%
% Computes a robust mean of angles
%
% This file is part of Manopt: www.manopt.org.
% Original author: Nicolas Boumal, Dec. 30, 2012.
% Contributors:
% Change log:
% Generate the data
N = 250;
theta_true = pi*(2*rand(1)-1);
thetas = zeros(N,1);
p_true ... |
a1f1605561ce99ae40d0dc9efa50d97b3369c872cf0c2cacd0a405d2661f1b6d | MATLAB | 2,479 | 57 | function cleanExtractFiles(path)
% figure position for home workstation [1383,953,1920,970] / lab workstation [6,1241,1920,970]
options.skipCleanFile=true;
filelist = dir(fullfile(path, '**\DemixingEXTRACT'));
if isempty(filelist)
error('no extract output file detected in any subfolder')
else
k=1;
w... |
340cdd94ca70ce4e6cd30a0a04581afd006c8b0f194ac7e09f6f1372c0a9bd46 | MATLAB | 2,480 | 74 | function [corr_results, p_values] = BinderRSA(varargin)
% RSA correlation analysis between concept and semantic RDMs
%
% Usage:
% [corr_results, p_values] = rsa_correlation_analysis()
% [corr_results, p_values] = rsa_correlation_analysis('RandomConcept', true, 'Alpha', 1e-3)
%% Setup
p = inputParser;
addP... |
53d7bf1f104c0687ebf03bf141936c8666e7138f8a3d48285c259efa2d44422f | MATLAB | 2,480 | 83 | function [folderStructure,summary]=preprocPaths(preprocessedRoot,varargin)
%
% HELP
% Creating folder structdure for preprocessing outputs.
% SYNTAX
%[folderStructure,summary]= preprocPaths() - use 1 if no arguments are allowed
%[folderStructure,summary]= preprocPaths(preprocessedRoot) - use 2, etc.
%[folderStructure,s... |
212ab08af33c9e78313e4468c0fb8c94c286967bdd16443909a3681898d4b7d6 | MATLAB | 2,481 | 90 | function [cellList,figH]=extractCheckCellManual(output,varargin)
% can input your own cell list.
% % options.cellList=[];
options.waitForUser=true;
options.frameRate=700;
options.positionFig=[100,100,800,400];
%% UPDATE OPTIONS
if nargin>1
options=getOptions(options,varargin);
end
%%
if isempty(output.temporal_... |
c1c733fb10207e349e8f9ae8dae5e5f3231638ac8eb32011cc216850b37d049a | MATLAB | 2,481 | 59 | function merged = MergeStructures(structure1,structure2,dim)
%MergeStructures - merge two structures into a single structure
%
% This function concatenates each of the fields of structure1 and
% structure2 along dimention 'dim' (default = 1).
% If the sizes of the field contents are not compatible (e.g. cannot
% c... |
f314ce67e605d50c7e9d3e9ec98e1b7aed1b8048e13286f85384e886676a2af2 | MATLAB | 2,481 | 78 | function [fList,isFine] = tapas_diagnose(toolbox_names,options)
% TAPAS_DIAGNOSE Checks if toolbox uses functions which are overloaded
%
% IN
% toolbox_names [character vector or cell array of character vectors]
% Toolboxed to be diagnosed. If no toolbox is specified, all toolboxes
% are checked. This can take a wh... |
20612db11abd87a56da62cf5b65eb0acd3c28703f556ca68a82036c8866d3668 | MATLAB | 2,484 | 53 | %% tb = sepiatest.discover_toolboxes()
%
% Description: reports which of SEPIA's optional external toolboxes/add-ons
% are actually installed and reachable on this machine, by reading the
% same SpecifyToolboxesDirectory.m that sepia_addpath.m uses (auto-created
% from the template on first call if missing, all paths e... |
855bbf15e6de123b7574e501d86417a1390f5c2ec9ece639ea5a5691b6bfe534 | MATLAB | 2,484 | 65 | %%
clear;clc;
[mask,vox,header] = rest_readfile('E:\matlabtool\DPABI_V8.2_240510\Templates\GreyMask_02_61x73x61.img');
%% load input and average
patterns = {'Yumodel_*_concept','*Yumodel_*_cdp1', '*Yumodel_*_cdp2', '*Yumodel_*_cdp3'};
FolderName= {'CA1','CA2','CA3'};
RootPath = 'E:\YuLab\fMRI_results\Searchligh... |
3330ee584becf99ecfbe2bae16d39e2287bed4a5f00e5116bc8aaf14a7d69143 | MATLAB | 2,486 | 63 | %% =============================
% PALM Analysis: extinction CS × TUS
% =============================
% --- Locate repo root (relative to this script)
thisfile = mfilename('fullpath');
[scriptdir, ~, ~] = fileparts(thisfile);
cd(scriptdir); % Ensure consistent working dir
% Navigate up to FEARTUS root
% palm_code -... |
37aa4d9229ba6401c5f870613b011a7e1a195c95f09845aa24827753624df0bc | MATLAB | 2,486 | 79 | clc;
clear;
atlas = cifti_read('C:\Users\lihon\Desktop\abcd_study\atlas\Schaefer\Schaefer2018_400Parcels_17Networks_order.dlabel.nii');
atlas_parcel = atlas.cdata;
atlas_label = unique(atlas_parcel(atlas_parcel>0));
num_parcel = length(atlas_label);
% load regionwise prediction accuracy on PNC and HCP-D
pnc_dir = 'C... |
425b26b6c70302dadfceb809dca734ca39fdbbaf37983748ce1f6fdbc0b63d2e | MATLAB | 2,486 | 63 | %% =============================
% PALM Analysis: extinction CS × TUS
% =============================
% --- Locate repo root (relative to this script)
thisfile = mfilename('fullpath');
[scriptdir, ~, ~] = fileparts(thisfile);
cd(scriptdir); % Ensure consistent working dir
% Navigate up to FEARTUS root
% palm_code -... |
17d5cf6ae3eb2d37f0b56c470c8acfdfe4a42c1f3a5eb6dcb8107c56dd75c860 | MATLAB | 2,487 | 63 | %% =============================
% PALM Analysis: Acquisition CS × TUS
% =============================
% --- Locate repo root (relative to this script)
thisfile = mfilename('fullpath');
[scriptdir, ~, ~] = fileparts(thisfile);
cd(scriptdir); % Ensure consistent working dir
% Navigate up to FEARTUS root
% palm_code ... |
29c2260591e78907266f44cc87b6ec3428f5563418d781cad724773209ebe0cf | MATLAB | 2,487 | 75 | % EEG_FINDBOUNDARIES - return indices of boundary events
%
% Usage:
% >> boundaryIndices = eeg_findboundaries(INEEG);
% >> boundaryIndices = eeg_findboundaries(INEEG.event);
%
% Inputs:
% INEEG - input EEG dataset structure. Used to check if event
% types are string or numerical.
%
% Out... |
2a9264ee93506c78282716416530b68cf6f2b60c3b4965fbf0140a2576420f29 | MATLAB | 2,487 | 59 | function [event_frames,onset_delays,video_event_times,juv_present_frames] = load_align_dlc_events(paq_paths,dlc_paths,dlc_fd_name,Fs, varargin)
% onset delay > 0 if miniscope was started after video
num_sessions = numel(paq_paths);
% load dlc_struct and align to paq
recording_duration = 0;
event_frames = cell(1,nu... |
5bfc6358a373fb703e53300e869630e9f523da6ce7f67a40a4f4409c92a07ac2 | MATLAB | 2,487 | 90 | function analyzebehavior_floc(datadir,num_TR,stimulus_delay)
% <num_TR> = 312; % total number of TRs desired
% <stimulus_delay> = 12; % delay in seconds at beginning
ppdir = regexprep(datadir,'rawdata','ppdata');
mkdirquiet(ppdir);
% load behavioral files
stimulusfiles = matchfiles([datadir '/mat_files_from... |
804261ad3ed31ea92d541f234c23fff76f45e77d397db2e59ae583929d884f3e | MATLAB | 2,487 | 63 | %% =============================
% PALM Analysis: Acquisition CS × TUS
% =============================
% --- Locate repo root (relative to this script)
thisfile = mfilename('fullpath');
[scriptdir, ~, ~] = fileparts(thisfile);
cd(scriptdir); % Ensure consistent working dir
% Navigate up to FEARTUS root
% palm_code ... |
8962afd3a3980fbf17763eda6d18b1f69da1d92a13aec24a1c18bf4d1d0f6ff6 | MATLAB | 2,487 | 54 | function varargout = gpr(hyper, cov, x, y, xs)
% gpr - Gaussian process regression, with a named covariance function. Two
% modes are possible: training and prediction: if no test data are given, the
% function returns minus the log likelihood and its partial derivatives with
% respect to the hyperparameters; this mod... |
32a0ebcb7269d4d90240d602dd997b7caae06761f77be023e665a9dc9db5d7a0 | MATLAB | 2,488 | 64 | %% Standard script to validate input sepia header
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 22 Jan 2021
% Date modified: 12 August 2021 (v1.0)
% Date modified: 4 July 2025
%
function sepia_header = validate_sepia_header_4wrapper(sepia_header, outputNiftiTemplate)
sepia_universal_variables;
dis... |
8f1d41b46e7a706d848d9d7724f92cef3c4dcded743a9eedca759b80eddbfe13 | MATLAB | 2,488 | 79 | function tor_spm_mean_ui(P,varargin)
%tor_spm_mean_ui(Pinputnames,[outputname])
% promts for a series of images and averages them
% FORMAT spm_mean_ui
%_______________________________________________________________________
%
% spm_mean_ui simply averages a set of images to produce a mean image
% that is written as typ... |
2ada4a622fb6f7bc3af81005918b11564fb47cce85df611b9383391e3a45a714 | MATLAB | 2,489 | 74 | function [K,dK] = covFBM(hyp, x, z)
% covFBM Fractional Brownian motion covariance with Hurst index h from (0,1).
%
% [K,dK] = covFBM(hyp, x, z)
%
% The hyperparameters are:
%
% hyp = [ log(sf)
% -log(1/h-1) ]
%
% For h=1/2, this is the Wiener covariance, for h>1/2, the increments are
% positively correlate... |
51d9e924d46fae1bbc98ffcf45788f5e46528aa3e475cbcd6b34e09d5d690617 | MATLAB | 2,489 | 81 | function [times,id,group] = CCGParameters(varargin)
%CCGParameters - Reformat time series for CCG computation
%
% USAGE
%
% [times,id,group] = CCGParameters(series1,group1,series2,group2,...)
%
% series1... time series (one column) with optional IDs (in the second
% column, such as obtaine... |
9a2b0e82f82b3d8ce77f198f00f7fadfc552a9d56724c7be41564c08fe87a825 | MATLAB | 2,489 | 85 | function [ DCM ] = tapas_rdcm_generate(DCM, options, SNR)
% [ DCM ] = tapas_rdcm_generate(DCM, options, SNR)
%
% Generates synthetic fMRI data under a given signal to noise ratio (SNR)
% with the fixed hemodynamic convolution kernel
%
% Input:
% DCM - model structure
% options - estimation opt... |
d42148420322e6c0bc2b5eddab4b26836897a79a41df6997c92dc42dc525afe5 | MATLAB | 2,489 | 76 | %% stats = sepiatest.mask_stats(img, maskLogical)
%
% Description: computes a small set of summary statistics of img inside
% maskLogical, used as the regression-comparison payload instead of a
% full-resolution array diff (which is brittle across MATLAB/BLAS/FFT
% library versions for iterative solvers). Also returns ... |
1a203f2a7f651e52fca6a4afefe4d1d344291ba2894a025401788c5afe4147ec | MATLAB | 2,490 | 69 | function X = lyapunov_symmetric(A, C, tol)
% Solves AX + XA = C when A = A', as a pseudo-inverse.
%
% function X = lyapunov_symmetric(A, C)
% function X = lyapunov_symmetric(A, C, tol)
%
% Matrices A, C and X have size nxn. When the solution exists and is
% unique, this is equivalent to sylvester(A, A', C) or lyap(A, -... |
4692b7c40e517624f89f864a5d2a8fbcbc7242b181040e258df96aa1828dc488 | MATLAB | 2,490 | 67 | function osp_onRightExp( ~, ~ ,gui)
%% osp_onRightX
% Callback function on process click on left x voxel direction button.
%
%
% USAGE:
% osp_onRightX( ~, ~ ,gui);
%
% INPUT: gui = gui class containing all handles and the MRSCont
%
% OUTPUT: Changes in gui parameters and MRSCont are written... |
7299b53e07eb078631850e04942e9ac502b8ff6d93486dc7b0913858e921d76e | MATLAB | 2,491 | 77 | function names = osp_import_Tarquin_metabolite_names(filename, startRow, endRow)
%IMPORTFILE Import numeric data from a text file as a matrix.
% names = IMPORTFILE(FILENAME) Reads data from text file
% FILENAME for the default selection.
%
% names = IMPORTFILE(FILENAME, STARTROW, ENDROW) Reads
% data from rows ... |
cb07383cfd059ad5f32b68f112f13bfa2269df2de2128816f4a359190a1948cf | MATLAB | 2,491 | 63 | function [this_avg_activity,event_frames] = get_photo_episode_mean(mat_activity,event_frames,photo_on_frames,photo_off_frames, this_programs)
if ~iscell(this_programs)
this_programs = {this_programs};
end
fds = fields(event_frames);
for i = 1:numel(this_programs)
this_program = this_programs{i};
[t... |
0850662ad9955888281498f3d9901503ccdc1b3074933a10af7c09082f60bdfc | MATLAB | 2,492 | 72 | function this = extract(this, image, mask)
% Extracts data within mask from given image
%
% Y = MrRoi()
% Y.extract(image, mask)
%
% This is a method of class MrRoi.
%
% IN
% image MrImage of which data shall be extracted within mask
% mask MrImage (binary mask), of which voxels shall be extracted
... |
24b7a5b6e817b06089b5ce7d861632bea955815b65078e0d926077e193bfa841 | MATLAB | 2,492 | 101 | function [WUinit] = init_template(ops)
nt0 = ops.nt0;
Nchan =ops.Nchan;
Nfilt = ops.Nfilt;
Nrank =ops.Nrank;
tps = [1 5 10 25 40 50 61];
tps = round(tps * nt0/61);
vs = [0 0 0 -2 1 0 0];
fs= interp1(tps, vs, 1:nt0, 'linear', 'extrap');
W(:,1,1) = my_conv(fs, 2);
tps = [1 5 10 25 40 50 61];
tps = round(tps * nt0/... |
9c78d33764a728680e098faf149045810f5efc94e4a03b61f6240e78afd371dd | MATLAB | 2,492 | 67 | %function ch2roi_selFreq(params, groupInfo)
% groups channels into defined ROIs (anatomic areas), averages & plots
% based on the following criteria:
% - selected anatomical areas (groups)
% - selected freq. band
% - significance (difference of conditions, from baseline (TO DO), or all)
% settings (subjects, dire... |
f8d8ad7f1339eeb4d2e4e3c1f0317f500349dc759b900d6a9d16c4a8b2874a94 | MATLAB | 2,493 | 82 | %% unitTest.m
% This function performs a command line unit test based on the jobTesting.m file in the
% ci folder. All Osprey modules are tested in dependence of the
% included dataset. You can change the jobTesting.m file according to your desired
% needs. The results unittest class includes detailed informati... |
394a6311af6c76116411c3a1512a7befeacbbb9701874a6fb0fc488f8b61b627 | MATLAB | 2,494 | 83 | function y = vl_nnsoftmaxloss(x,c,dzdy)
%VL_NNSOFTMAXLOSS CNN combined softmax and logistic loss.
% **Deprecated: use `vl_nnloss` instead**
%
% Y = VL_NNSOFTMAX(X, C) applies the softmax operator followed by
% the logistic loss the data X. X has dimension H x W x D x N,
% packing N arrays of W x H D-dimensional... |
fd11738503fe8bfe00b61475057f9863c3e2f56e6d26af0637f00b5045ded132 | MATLAB | 2,494 | 59 | function [outdata, outsform1, outroi] = cifti_struct_dense_extract_volume_all_data(cifti, cropped, dimension)
%function [outdata, outsform1, outroi] = cifti_struct_dense_extract_volume_all_data(cifti, cropped, dimension)
% Extract the data for all cifti volume structures, expanding it to volume frames.
% ... |
7d863400b50ae2042402e8bdc15029bf7007b281c4823d2eb68ec1b7db1fb588 | MATLAB | 2,495 | 78 | function h = plotpval(ax, xpos, ypos, pval, color, pexact,pname,minp,plotline,numonly,minifz,fz,numsigdig)
% h = plotpval(ax, xpos, ypos, pval, color, pexact,pname,minp,plotline,numonly,minifz,fz,numsigdig)
% add pval next to significance bar in a figure
% adapted from mysigstar.m, written by Anne Urai
% (in turn adap... |
99fd5ce8b14cfda5dc5b219cc77f933a1fad0fce8239f46bc61e2c2bebf3c11a | MATLAB | 2,495 | 55 | % STD_CHECKDESIGN - Check if STUDY design is compatible with EEGLAB
% 2-categorical factor statistics
% Usage:
% >> [STUDY] = std_checkdesign(STUDY, designind);
%
% Inputs:
% STUDY - EEGLAB STUDY set
% designind - [integer] design index
%
% Authors: Arnaud Delorme
% Copyright (C) Arnaud... |
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