sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
30a4e53abeb257b816942facaf26525e26969cb4c594b074f60ac1ceddb0baa7 | MATLAB | 3,437 | 95 | clear all;
clc;
load('vik.mat');
rdm_type = 'cosine'; % 'cosine' 'pearson'
num_listeners = 100;
all_correlations = zeros(num_listeners, 1);
% Load speaker data once outside the loop
ct_speaker_full = load('cifar100_ss20_ni1e-1_ychen_trail1.mat');
ct_speaker_data_full = struct2array(ct_speaker_full);
for listener_i... |
c951ed5037c9023947ebb2763382afdacf19bcbd635dec5ef508dc4f8d4e8e46 | MATLAB | 3,441 | 118 | function varargout = openbci_txt(filename, hdr, begsample, endsample, chanindx)
% OPENBCI_TXT reads time series data from a OpenBCI txt file
%
% Use as
% hdr = openbci_txt(filename);
% dat = openbci_txt(filename, hdr, begsample, endsample, chanindx);
% evt = openbci_txt(filename, hdr);
%
% See also FT_FILETYPE, ... |
71479410389f608b13eeeba8a1cad73bb59cbd0088bbbf2927a991372a8ca8f7 | MATLAB | 3,443 | 95 | function band_signal = modwt_single_band(data, wavelet_type, level, target_band)
% MODWT_SINGLE_BAND - Decompose and reconstruct a single wavelet band
%
% Convenience wrapper that performs MODWT decomposition and then reconstructs
% only the requested band. Optimized for memory efficiency in incremental
% band processi... |
3d681dc2c2accd88e605de0526ac417f6a730a01ca442d2395a4f53e60f9a001 | MATLAB | 3,445 | 97 | function M=timewarp(evLatency, newLatency)
% TIMEWARP - Given two event marker vectors, computes a matrix
% that can be used to warp a time series so that its
% evlatencies match newlatencies. Values of the warped
% timeserie that falls between two frames in the original
%... |
ad6b40d5e555a508aaed8b1da4b0752222e9f3b6af82e70435b24fd341745a6a | MATLAB | 3,445 | 95 | function fear_getSpindle_spike_PETH(basename)
% basename='~/data/Fear/triple/achel180320/achel180320';
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
load([basicMetaData.Basename '.pfcSpindle.events.mat'])
load([basicMetaData.Basename '.... |
459139ba7a4a5cf2bd03355ae43e420d6be6e9d267d4b57d9e0402d459a29629 | MATLAB | 3,448 | 97 | function this = MrImageGeometry_load_from_file(this, testFile)
% Unit test for MrImageGeometry Constructor from file
%
% Y = MrUnitTest()
% run(Y, 'MrImageGeometry_load_from_file')
%
% This is a method of class MrUnitTest.
%
% IN
%
% OUT
%
% EXAMPLE
% MrImageGeometry_load_from_file
%
% See also MrUnitTest
% Au... |
cce8e10b6a6b8d140cdaf3b05da8f95621f6c3aac566c03fdd32d2096a2b331c | MATLAB | 3,448 | 108 | % POSACT - Make RUNICA activations all RMS-positive.
% Adjust weights and inverse weight matrix accordingly.
%
% Usage: >> [actout,winvout,weightsout] = posact(data,weights,sphere)
%
% Inputs:
% data = RUNICA input data
% weights = RUNICA weights
% sphere = RUNICA sphere {default|0 ... |
6e08285e9346afcfaecb88ceeb9e0f3f7953d2d8a1ea0e0c0fe74b1d6ad41c68 | MATLAB | 3,451 | 114 | function Meta_interactive_point_slice_plot(MC_Setup, DB)
% Meta_interactive_point_slice_plot(MC_Setup, DB)
%
% Set up interactive point plotting on slice
%
% tor wager, nov 2007
%
% Simple example for checking points manually, rather than setting up the interactive plotter:
% load SETUP
% V = DB.mas... |
7b2bcef77ef9b2bf7e251c0bbf7f87ec3aa1d55c00430f29f509413da0c5cbfc | MATLAB | 3,451 | 114 |
clear all
spm fmri
%% Demo: fMRI searchlights LDA classifier
%
%To run MVPA with LDA classifier, crossvalidation method
%
% # For CoSMoMVPA's copyright information and license terms, #
% # see the COPYING file distributed with CoSMoMVPA. #
clear all;
%PILOT
sub(1).id = 'sub-01';
sub(1).... |
811af9f6ff04fec64ba3a8aa02405e3e3c2ba1630f4f722143d1397dee98eea3 | MATLAB | 3,452 | 92 | %% h = sepia_handle_panel_qsm_iLSQR(hParent,h,position)
%
% Input
% --------------
% hParent : parent handle of this panel
% h : global structure contains all handles
% position : position of this panel
%
% Output
% --------------
% h : global structure contains all new and other hand... |
d8fa906f2d29e51b9f8a466cb5e4276d46741c386d6569bc11891f86d4ae33a7 | MATLAB | 3,453 | 117 | function fear_coact_within_oscillation(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.templateSes=2;
param.targetHC=3;
param.tRange=0.1;
par... |
0cbb356c1f6028ed95bd1be1e9089138f8deb59f78b72c4126d142e9b912ee52 | MATLAB | 3,454 | 98 | function tapas_hgf_whatworld_plotTraj(r)
% Plots trajectories estimated by fitModel for the hfg perceptual model
% Usage: est = tapas_fitModel(responses, inputs); tapas_hgf_plotTraj(est);
%
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2013 Christo... |
bc48e0c24e91d29990062f4ad7153da0201308eaf8ace5d334af266a99cee1e2 | MATLAB | 3,454 | 87 | function [t, wv] = LoadTT_openephys(fn,records_to_get,record_units)
%LOADTT_OPENEPHYS MClust loading engine for open ephys data.
% LOADTT_OPENEPHYS loads open ephys data and fullfils all requirement for
% MClust loading engines (see MClust 3.5 documentation for details on
% MClust loading engines).
%
% Syntax... |
c65a22ce11fe3eb132a299f7709e085b0f0778ffb0c7e483ea102732b9fa0f93 | MATLAB | 3,455 | 112 | function [xvec, hmat, alignspikes] = alignSpikes(spiketimes, cond, wndw,...
bins, alignto,trialend)
%This function takes spiketimes and aligns them to the event (cpoke,
%reward, opt out, etc) specified by alignto. Timestamps are according to
%open ephys computer clock. cond is the condition found in
%behEvents (hi... |
11aa454d3d36efe2b5cccc1ccee0c321f2d5bd81a195a2d2c7ddef3633faf31e | MATLAB | 3,456 | 94 | function this = compute_masks(this)
% Segments defined input image into tissue types & thresholds to get masks
% - input image can be anatomical or mean functional
%
% Y = MrSeries()
% Y.compute_masks(inputs)
%
% This is a method of class MrSeries.
%
% IN
% parameters.compute_masks.
% nameInputImage... |
8830e99af52d69c0b0ebb3f174503c8172d910632cee5856ddb75d394e89784f | MATLAB | 3,457 | 96 | function c = tapas_rw_binary_dual_config
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Contains the configuration for the Rescorla-Wagner (RW) learning model for binary inputs and dual
% updating.
%
% The RW model was introduced in :
%
% Rescorla, R. A., and Wa... |
ad2084cda6425df2e03cf19a4d7c0c688edfc81a11299a4db6180fd3fcdf7d20 | MATLAB | 3,457 | 80 | %% PlotRepresentativeBehaviorData
%% Version1
TANK_location = 'F:\LobsterData\#21JAN5-210716-170133_PL';
dat = BehavDataParser(TANK_location);
figure('Position', [-1558, 655, 990, 254]);
plot([]);
hold on;
startTrial = 12;
numTrial = 3;
for trial = startTrial : startTrial + numTrial -1
line([diff(dat{trial, 1}), ... |
b96a6d656067491ba6c43242c6aa220b2fea565297dbb1f0779e71eb0097585f | MATLAB | 3,457 | 131 | %%%%% FIRST, DEFINE V1-hV4
% define
zz = 1;
subjid = sprintf('subj%02d',zz); % which subject
cmap = jet(256); % colormap for ROIs
rng = [0 7]; % should be [0 N] where N is the max ROI index
roilabels = {'V1v' 'V1d' 'V2v' 'V2d' 'V3v' 'V3d' 'hV4'}; % 1 x N cell vector of strings
prfang = {mod(180-cvnloadm... |
258380d9b916719528b13eea65b5df28c29fd24ca34ebcbf6aefdbbb84b9ad98 | MATLAB | 3,459 | 101 | function c = tapas_sutton_k1_binary_config
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Contains the configuration for the Rescorla-Wagner (RW) learning model for binary inputs.
%
% The RW model was introduced in :
%
% Rescorla, R. A., and Wagner, A. R. (1972)... |
637d330a418e96a174ce5cdeac92f8e3cc8c8b2bd53bada4a40826dcc2a49cc0 | MATLAB | 3,459 | 90 | function [Ax] = QSM_gradRegul(X_vector,params_in,tflag)
% X_vector = vectorized Matrix of x (susceptibility in the case where the direct )
%
% params_in has the following fields
% kernel - k-space representation of Dipole Kernel
% msk = mask represent the regions where
% dims = 3d-dimension of the field map
% Ex,Ey,Ez ... |
fc8c2d1a1c0a9b9f3e750af04b4d081cd848247336f80bd5bb0371dc06bac3ca | MATLAB | 3,460 | 116 | function status = makessense(data, field)
% MAKESSENSE determines whether a some specific fields in a FieldTrip data structure
% make sense.
%
% Use as
% status = makessense(data, field)
%
% See also GETDIMORD, GETDIMSIZ, GETDATFIELD
% Copyright (C) 2018-2019, Robert Oostenveld
%
% This file is part of FieldTrip, s... |
0922c4e5e897b60f6510a519b4678b9e4bc4cdd5b279f66b132c88cdc111b051 | MATLAB | 3,461 | 133 | %% stats
%% visDir
[h1,p1]=ttest(visDir_lS1,0.5);
[h2,p2]=ttest(visDir_lPC,0.5);
[h3,p3]=ttest(visDir_rPC,0.5);
[h4,p4]=ttest(visDir_lMTt,0.5);
[h5,p5]=ttest(visDir_rMTt,0.5);
[h6,p6]=ttest(visDir_lhMT,0.5);
[h7,p7]=ttest(visDir_rhMT,0.5);
stats.h=[h1,h2,h3,h4,h5,h6,h7]
stats.p=[p1,p2,p3,p4,p5,p6,p7]
% bonnstats.p=... |
a8d302bf95c54a1667c85c6e2aa4baa56017462ffb66a5cb0676986035c2c3fd | MATLAB | 3,461 | 94 | function out = muscimolPhysiology(muscimolPhysDataPath)
%Analyze firing rates pre and post muscimol infusion. Rat was anesthetized
%for the entire recording. Bilateral infusions and recordings.
% INPUTS:
% muscimolPhysDataPath = path to .mat file with recording data and
% spreadsheet with infusion info
% OU... |
7a08bdc9e37313e61bf7eaf1618a51f799e7d76949d189be743c1c8f74c5ba3e | MATLAB | 3,462 | 113 | %% ------------------------------------------------------------------------
% Texture and Fractal Feature Extraction
% ------------------------------------------------------------------------
% Features:
% - GLCM-based:
% 1) Mean Correlation (offset-dependent) (17th offset)
% 2) Variance Range (a... |
7df0d8cf1ea9f870d69e3528ae28b631734544936b0940ab56fcf09388d5cfab | MATLAB | 3,462 | 99 | function esmType = getChannelType_ESM(chStruct_H)
% returns string of catted ESM categories (e.g. 'motor') based on ESM label
% ESM = electrical stimulation mapping
% category = higher order of abstraction that ESM label
% categories may overlap (-> esmType is catted into 1 string)
% chStruct_H = channel structure in H... |
2727e844727484684b4a040410d8142328c8dba5ee02b5824ed05c2418dc77b2 | MATLAB | 3,463 | 75 | function h=subtightplot(m,n,p,gap,marg_h,marg_w,varargin)
%function h=subtightplot(m,n,p,gap,marg_h,marg_w,varargin)
%
% Functional purpose: A wrapper function for Matlab function subplot. Adds the ability to define the gap between
% neighbouring subplots. Unfotrtunately Matlab subplot function lacks this functionality... |
836efd84b943803d6d56a80bb240f871a844e496ef3159a95cc358d26c0f5de3 | MATLAB | 3,464 | 100 | function out = SY_RangeEvolve(y)
% SY_RangeEvolve How the time-series range changes across time.
%
% Measures of the range of the time series as a function of time,
% i.e., range(x_{1:i}) for i = 1, 2, ..., N, where N is the length of the time
% series.
%
% ---INPUT:
% y, the time series
%
% ---OUTPUTS: based on the... |
29d3e7f086b141c8835a29ac0e00554bc1d25998cc4eb9ee366d20c14c088ad1 | MATLAB | 3,465 | 74 | function [regressorScans,regressorNames] = create_fMRIregressors(tau, data, R, initialISIandSetup)
% an extract of fit_happy_model_nogain_guiltenvy(mtx,happyscore,constant)
% without fitting
if ~exist('tau','var'); load('js_temp.mat'); end
if ~exist('tau','var'); initialISIandSetup = [3 3]; end
plotFlag = 0;
%needs ... |
416c3a8e222fb60d3e75f29655f2cc9c531ac3e73dc91113ee64318e76f05b4c | MATLAB | 3,465 | 92 | % PCSQUASH - compress data using Principal Component Analysis (PCA)
% into a principal component subspace. To project back
% into the original channel space, use PCEXPAND
%
% Usage:
% >> [eigenvectors,eigenvalues] = pcsquash(data,ncomps);
% >> [eigenvectors,eigenvalues,compres... |
a9b5db080e55f9ad493e77b59980ec1097ba1a623319d762ce9751e2b25804d3 | MATLAB | 3,465 | 85 | function plot(spikeStream, cfg, varargin)
% Plot the contents of a McsCmosSpikeStream object
%
% function plot(str, cfg, varargin)
%
% Shows a raster plot of the spike timestamps. If only a single channel is
% selected, produces an overlay of the spike cutouts for this channel.
%
% Input:
%
% spikeStream ... |
1064dcf7761d5f5835b75e46b31ca40351c99289e575a1e2050d20c67c28fcd8 | MATLAB | 3,467 | 84 | function ProcessData_Figure6(datadir, codedir, savedir)
%ProcessData_Figure6 - Process raw data saved under datadir such that it can be plotted by PlotFigure6.
% INPUTS:
% datadir - Local directory where 'Golden_Nature/RawData_Figure6.mat' from Zenodo was saved
% codedir - Local directory where code (e.g., publishe... |
6394853fe18bc0b875920f464267408f5d3080f4309d15fb98adb272e293521a | MATLAB | 3,469 | 100 | function param = neuronConstants()
%NEURONCONSTANTS One-stop constants for the two-layer visual cortex model.
% Syntax
% P = neuronConstants();
%
% Description
% Returns a struct P with fields describing geometry, neuron counts,
% V1 (input) statistics, and V4/MT (recurrent spiking) connectivity and
% synaptic... |
6ebd58bef953e6ff3cb2eadd0a704ff6b7b7ad51e94407effa41bbb2d2e702e4 | MATLAB | 3,469 | 101 | % EEGLAB_EXECMENU - function called to execute EEGLAB menu
%
% Usage:
% eeglab_execmenu(label, func, parameter);
%
% Inputs:
% label - [string] label of the menu
% func - [string] name of the pop function. The function extract the
% callback from the menu, find the function and add the
% ... |
4d16e36d7c32dc7f2419e9b7cf0f047c3ca33fc9422fd4831c05d5737698c7f3 | MATLAB | 3,470 | 106 | function [SH3D,Residuals,b] = spherical_harmonic_shimming_option2(img,mask,order)
dim = size(img);
%% for volume fitting
% find non-zero elements
Indices = find(mask(:,:,:));
% get Cartesian coordinate of the non-zero elements
[x1,y1,z1] = ind2sub(size(img(:,:,:)),Indices);
% solutions of the linear operation
R = img... |
b1414de110b2e1294b550b9fb5ac47fc6ead12af4d4b079a6bc50fe12cb2c870 | MATLAB | 3,470 | 74 | function preprocess_nsd_MNIandbrainmask(subjix)
% function preprocess_nsd_MNIandbrainmask(subjix)
%
% <subjix> is 1-8
%
% Starting with the prepared 1.0-mm T1, determine MNI alignment using fnirt.
% On basis of the determined alignment, we backproject to the native subject space
% a liberal 1.0-mm brain mask. We also ... |
3f0e887702d6eaf9fdda536fa80e350b6da4b114bb146f4f99728b07b459d5d5 | MATLAB | 3,471 | 115 | function vol = read_asa_vol(fn)
% READ_ASA_VOL reads an ASA volume conductor file
%
% all data is converted to the following units
% vertices mm
% conductivities S/m
% Copyright (C) 2002, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and... |
cbf2925f08745fadbbccaf054904df08afc808927d0c8708bc3c428ad43f652b | MATLAB | 3,472 | 77 | % demonstrate usage of prior distributions
%
% See also priorDistributions.m.
%
% Copyright (c) by Carl Edward Rasmussen and Hannes Nickisch, 2022-04-04.
% File automatically generated using noweb.
clear all, close all
% 1) specify some priors
% a) univariate priors
mu = 1.0; s2 = ... |
73af41d90a406b09752ed0a6932be026af13fa2566a6b1f736cfd0db9932f4d7 | MATLAB | 3,473 | 96 | % EEG_RETRIEVE - Retrieve an EEG dataset from the variable
% containing all datasets (standard: ALLEEG).
%
% Usage: >> EEG = eeg_retrieve( ALLEEG, index );
%
% Inputs:
% ALLEEG - variable containing all datasets
% index - index of the dataset to retrieve
%
% Outputs:
% EEG - outpu... |
893cf5f6406d1daa7ff04c5446218c6b4bb6b59159f5e1ab068f592f3e618537 | MATLAB | 3,473 | 87 | function [cpulse, verbose] = tapas_physio_get_cardiac_pulses_manual_template(...
c, t, pulse_detect_options, verbose)
% Detects R-peaks via matched-filter smoothing & peak detection using a
% manually defined QRS-wave (or R-peak environment)
%
% [cpulse, verbose] = tapas_physio_get_cardiac_pulses_manual_template(... |
ca8e4ea11cc9eb84c267145e31d6c15cdef6381d9c059538b5b61a1dc12d8dbc | MATLAB | 3,473 | 118 | function [err,S] = HistoryTrace ( Opt)
%
% [err,S] = HistoryTrace (Opt)
%
%Purpose:
% returns a signature/history sting, useful for keeping a log
%
% The trace string is formed as such
% For example if script MainScript calls at line 12
% function F1 which at line 6 calls F2 wich at line 192 calls
%... |
772eaf4e4e79dfe1f945127dc6920d42b0770b49796c3f4df70349916cf43bc4 | MATLAB | 3,474 | 104 | function [source] = fixinside(source, target)
% FIXINSIDE ensures that the region of interest (which is indicated by the
% field "inside") is consistently defined for source structures and volume
% structures. Furthermore, it solves backward compatibility problems.
%
% Use as
% [source] = fixinside(source, 'logical'... |
b0b6977bf24d52174fde8385e2ded07e237b02fdfa059e006e884ad8d859f3e1 | MATLAB | 3,476 | 102 | % clc
% clear
%--------------------------------------------------------------------------
spm('defaults','EEG');
% Data and analysis directories
%--------------------------------------------------------------------------
Pdata = fullfile(Pbase, ['models' filesep 'DMN']);
Panalysis = fullfile(Pbase, ['... |
5396286dd5d2c87f806c65af433b5f7e379aadc2677fab6da84625f7e2caff85 | MATLAB | 3,477 | 101 | function params = validateField(params, fieldName, defaultValue, dataType)
% VALIDATEFIELD Validate and set default values for structure fields
%
% Syntax:
% params = validateField(params, fieldName, defaultValue)
% params = validateField(params, fieldName, defaultValue, dataType)
%
% Description:
% Valid... |
0034aac9d6796126ab705c44097c81fb65168e1ac366a8849cd992deec2b8ae3 | MATLAB | 3,478 | 87 | %% Wrapper_SWISMWI_SMWI(headerAndExtraData,output_structure,algorParam)
%
% Input
% --------------
% headerAndExtraData : structure contains extra header info/data for the algorithm
% output_structure : structure contains output file path and output NIfTI header
% algorParam : structure contains fields with a... |
484b81c23992a955cc40ca16aab598dedaac860574dfa5092f6d81684dbed73f | MATLAB | 3,481 | 94 | function [H, basis] = hessianmatrix(problem, x, basis)
% Computes a matrix which represents the Hessian in some tangent basis.
%
% [H, basis] = hessianmatrix(problem, x)
% [H, basis] = hessianmatrix(problem, x, basis)
%
% problem is a Manopt problem structure with a manifold and cost function.
% x is a point on the man... |
69164bb1ed2123eb9d900a79fed59bde54de03a396eb23f0e9228ef8cdb6c70f | MATLAB | 3,481 | 88 | function [varargout] = likGauss(hyp, y, mu, s2, inf, i)
% likGauss - Gaussian likelihood function for regression. The expression for the
% likelihood is
% likGauss(t) = exp(-(t-y)^2/2*sn^2) / sqrt(2*pi*sn^2),
% where y is the mean and sn is the standard deviation.
%
% The hyperparameters are:
%
% hyp = [ log(sn) ... |
c5b92aab5108cbe9a23ab75a1c4b148e041480f9bce91de27ac8a4959f1671a2 | MATLAB | 3,482 | 114 | function [response, x, s, f, v, q] = tapas_huge_bold( A, B, C, D, tau, ...
kappa, epsilon, R, u, L, E_0, r_0, V_0, vartheta_0, alpha, gamma, TR, ...
TE, dt)
% Integrates the DCM forward equations to generate the predicted fMRI bold
% time series.
%
% INPUTS:
% A, B, C, D - DCM connectivity matrices.
% tau ... |
00276225329ecad65da09f4b9c8ef0648539c11b81b218b78d8e954b2f082bdb | MATLAB | 3,483 | 75 | % eegplugin_eegbids() - EEGLAB plugin for importing data saved
% by the finders course (Matlab converted)
%
% Usage:
% >> eegplugin_eegbids(fig, trystrs, catchstrs);
%
% Inputs:
% fig - [integer] EEGLAB figure
% trystrs - [struct] "try" strings for menu callbacks.
% catchstrs - [struct] ... |
382fef5a1c08032a0b7bf15a0ea7eed9465b789b21146619f523ea526a34ffd0 | MATLAB | 3,483 | 116 | function [sel1, sel2] = match_str(a, b, fullout)
% MATCH_STR looks for matching labels in two lists of strings
% and returns the indices into both the 1st and 2nd list of the matches.
% They will be ordered according to the first input argument.
%
% Use as
% [sel1, sel2] = match_str(strlist1, strlist2)
%
% The strin... |
39cb98e3a72a7ededd3fbc4588026daedfdb5a5ee1724a73e7c98e32f76ce6f1 | MATLAB | 3,483 | 103 | function [pdd, pddnode, meanpdd] = dyn_pdd_pleakage(data,sample,mindur,meanfreq)
% Computes the phase difference derivative (PDD) wit pairwise
% leakage correction/pairwise orthogonalisation
%
% Tewarie et al., 2019 Tracking dynamic brain networks using high temporal
% resolution MEG measures of f... |
8c85e39e5e2ccaf44766571b1f0bb0a9fc5afa601e607b3eb1f7c3ab5c656e0e | MATLAB | 3,484 | 106 | function [ u ] = tapas_huge_boxcar( dt, nBoxes, period, onRatio, padding )
% Generate a boxcar function for use as experimental stimulus. All
% timing-related arguments must be specified in seconds.
%
% INPUTS:
% dt - Numeric scalar indicating sampling time interval.
% nBoxes - Vector indicating number of b... |
c71c01bfe2307f3d5e230df2da3e5c279c6fe5a74ad92500f1f2afb184a52a55 | MATLAB | 3,484 | 103 | function [Dat,stim,ops] = parse_stimuli_wrapper(ops)
%decides which parse_stimuli function to use. alters stim for CPD calc.
%
% inputs: ops.stimwrapper decides which function to use
%
%
switch ops.stimwrapper
case 'ofc'
%[stim_train,stim_test] = parse_stimuli_ofc(ops);
if ops.usePseudotrial
[Dat,stim]... |
43c605e50db27891c19684257c9e99b8f2ef13a910856a1e49e0280872781fea | MATLAB | 3,485 | 84 | function l = IsFirstAfter(timestamps,list,varargin)
%IsFirstAfter - Identify first item after each of a list of timestamps.
%
% For each element i of a list of test timestamps, find in a list of reference timestamps
% the first element j larger than i. Returns a list of logical indices (the elements of the
% test list... |
a1ef596ad75d320ddcdcf1ef55caa863c7a48e4a74fa21c14fa1a527ba56167c | MATLAB | 3,485 | 115 | clc;
clear;
addpath('/cbica/home/lihon/code/Download/cifti-matlab-master');
res_dir = '/cbica/home/lihon/comp_space_recover/ABCD_comp/dl_prediction/pred_res_cog_abcc_bl_cv/non_dl_pnc_res';
dat_dir = '/cbica/home/lihon/comp_space_recover/ABCD_comp/dl_prediction/data_cog_pnc_cv';
num_r = 400;
ro_covars = 1;
out_dir... |
8fbfdccc0aedcde16eefac60e3d5dfdb815fc48e6e672d0ff29de8d7a383825e | MATLAB | 3,488 | 84 | function l = IsLastBefore(timestamps,list,varargin)
%IsLastBefore - Identify last item before each of a list of timestamps.
%
% For each element i of a list of test timestamps, find in a list of reference timestamps
% the last element j smaller than i. Returns a list of logical indices (the elements of the
% test list... |
6fcb70cc6f0c7526c17a5c0ac2e8b227653df813ec25daa460b8a281f8527e65 | MATLAB | 3,489 | 101 | function organiseTsvOnset
% it is a mini function to
% to change the onsets in the tactile tasks.
deleteSuffix = 1;
% add bids repo
bidsPath = '/Users/shahzad/GitHubCodes/CPP_BIDS';
addpath(genpath(fullfile(bidsPath,'src')));
addpath(genpath(fullfile(bidsPath,'lib')));
% raw data path
rawDir=fullf... |
795e61b28fc88ceefa191f4091760a794f1e2fa3955750dbe4f709f4075ae097 | MATLAB | 3,489 | 99 | % This function loads a single file and gathers all of the needed
% information. fOutID should be the output file handle from
% main_diagnostics. singleSetFile should reflect its name.
function single_spect_diag(singleSetFile)
% Storing what's going to be written to the csv in a variable to act as
% Load:
... |
9105fc9f5914aecd02bab799af2fe9f8ab07092803ffc151c4157248b1a610e1 | MATLAB | 3,490 | 69 | clc;
clear all;
% This code calculate the vertex-level MFC/gMFC/sMFC for the demo dHCP subject(ID:sub-CC00056XX07 ses-10700)
% The program includes calculating of FC, gMC, sMC, MFC, gMFC and sMFC, and visualization of brain map
your_path = './data'; % Please set your file storage path
load './data/Label_7net_5k.mat' ... |
946cc9e75aca28257879615d8ce9eec836d5b74e471e8f31dee07665bd5c104d | MATLAB | 3,491 | 85 | function [infos, auxillary_toolboxes] = tapas_get_toolbox_infos()
% Function storing information regarding toolboxes.
%
% Each toolbox is represented by a field with its lower-case-name.
% The field has the following subfields:
% init_function [character vector]
% If specified, use that function to ... |
836d3212f03fa186c2963142e4e8346e360aaff62c6392087eda07934f931414 | MATLAB | 3,492 | 99 | % POP_REJEPOCH - Reject pre-labeled trials in a EEG dataset.
% Ask for confirmation and accept the rejection
%
% Usage:
% >> OUTEEG = pop_rejepoch( INEEG, trialrej, confirm)
%
% Inputs:
% INEEG - Input dataset
% trialrej - Array of 0s and 1s (depicting rejected trials) (size is
% ... |
a9a746db8e2a0ffae7febab81419eab0d823b9464256fc4d48f34b26f80dfcc7 | MATLAB | 3,493 | 108 | function [A] = tapas_uniqc_spm_matrix(P, order)
% Return an affine transformation matrix
% copy of spm_matrix from Version 6906 (SPM12) 20-Oct-16
% FORMAT [A] = spm_matrix(P [,order])
% P(1) - x translation
% P(2) - y translation
% P(3) - z translation
% P(4) - x rotation about - {pitch} (radians)
% P(5) - y rotat... |
2eac7761b6f0f4f43b3ba80632a6ccaf4fe2cccb235f75981cf33bd7fe9f86c6 | MATLAB | 3,494 | 101 | function [inargs,outargs,h1] = hlp_inoutargs(filename,funcname)
% Retrieve the names of input/output arguments of the given m file.
% [In-Args,Out-Args,H1-Line] = hlp_inoutargs(Filename,Function-Name)
%
% In:
% Filename : full path to an m-file
% Function-Name : optional, name of a (possibly nested) functi... |
5aca189fa3871115a7cc98b95a7708d290ada377eb20aeacb4c787daa3bcc2de | MATLAB | 3,494 | 85 | % STD_PRECOMP_WORKER - allow dispatching ERSP to be computed in parallel
% on a given cluster.
% Usage:
% >> feature = std_precomp_worker(filename, varargin);
%
% Inputs:
% filename - STUDY file name
%
% Optional inputs:
% Optional inputs are the same as for the std_precomp function. Note... |
ab9f98fafa9920b4ce4f601ca77b7a47bdcebaf2218519b40a8c9724860e4018 | MATLAB | 3,494 | 109 | function [results] = bias_analysis(config)
% Evaluates the bias in psi / mutual information estimates of the
% populations evolved in analysis01A and plots results.
% Fix cpu limit (relevant for cluster), and seed
maxNumCompThreads(config.cpu_limit);
rng(0);
% load evolved populations
populations = loadPopulations();... |
b7024dbacc44229495ac08c2e2581531065c0a0c83a3f6a43bd21035b052346d | MATLAB | 3,497 | 94 | function nirs = fieldtrip2homer(data, varargin)
% FIELDTRIP2HOMER converts a continuous raw data structure from FieldTrip format to
% Homer format.
%
% Use as
% nirs = fieldtrip2homer(data, ...)
% where the input data structure is formatted according to the output of
% FT_PREPROCESSING and the output nirs structure ... |
46a81728dd41386ee0aa84a8c7a025b5a2585d409d57c23fb2195e195701361d | MATLAB | 3,498 | 144 | function movie_in = sh_denoising(movie_in, options)
% update the movie in place to save the memory
windowsize = options.windowsize;
[m,n,p]=size(movie_in);
startno = 1:windowsize:p;
tau = 0.015; % why?
lambda =20/sqrt(m*n); % why?
rank = 10; % why jsut the 10 first components?
tic;
for i=1:numel(startno)
disp([... |
604d75ce84368de1c5c1e6f0d2adab38eea22b18ef0787d3a721f8d7a1444065 | MATLAB | 3,498 | 123 | function run_permuanova2_examples
%RUN_PERMUANOVA2_EXAMPLES Run permutation two-way ANOVA examples.
% Generates random data for 5 groups along the columns of X and 3 groups
% along the rows of X, each with 2 replicates. Each group has a mean
% value of 0, except for the first two columns which have a mean value ... |
28813126d5f1e3c8afdd0144b299fab25fc33becb16d544d71c6201fbe36c6df | MATLAB | 3,501 | 91 | load bs_results.mat
load Hippo_data_ASB_norm.mat
load cm17.mat
load dk_labels.mat
load power_data.mat
% lmedata = removevars(lmedata, {'age','CDR','MMSE','ZPHG'});
pa=["Amplitude", "Phase"];
sides=["L", "R", "L+R"];
for PhaseAmplitude=["0","1"]
dataPA = lmedata(lmedata.PhaseAmplitude == PhaseAmplitude,:);
f... |
eb10d03eb999121e0111f12b2b6df23dc9571a5869e4c8894604fab33644886d | MATLAB | 3,501 | 114 | %% Methods parameters
pars.sr = 1; % Hz
pars.bin = 0.02; % seconds
pars.dc = 0.01; % cut-off for distances
pars.ishalo = 1; % not using halo refinement of the clusters
pars.npcs = 5;
pars.maxmem = 8*10^9; % maximal Gb of RAM
pars.minspk = 3; % minimum 3 spikes per pattern
pars.nsur = 10; % surrogates for core-cells, s... |
8c99275968fdb287a768e7d2b9a7bdcbf0c0f3720b3494a674f08df97be11260 | MATLAB | 3,502 | 120 | function [R, M, config] = loadData(mouseName, sessionDate, prefix, suffix, folder, verbose)
% loadData Load an R/M neural-behavior dataset given identifying info.
%
% Inputs:
% mouseName - animal ID string
% sessionDate - date string (YYMMDD)
% prefix - file prefix (default 'R')
% suffix - fil... |
506449a9d2a2c7c5a297ad045d8e144ac94ec6e35ce6cf1c68e4b2b89c7f6542 | MATLAB | 3,503 | 92 | function MRSCont = osp_senseRecon(MRSCont)
%% MRS_struct = osp_senseRecon(MRS_struct)
% Loads complex coil sensitivity reference scans, converts them into
% NIfTI format, co-registers with MRS voxels, and determines complex coil
% sensitivities following the SENSE formalism.
%
% This is usually only used to rec... |
e132e787d65537d6378edc50bf8969630f4d74caf55f389942da8a8f3cec00a6 | MATLAB | 3,503 | 93 | function [refShift, refFWHM, refSinglets] = osp_PhantomReferencing(dataToFit)
%% [refShift, refFWHM] = osp_PhantomReferencing(dataToFit)
% Identify appropriate reference signals then derive reference shift
% accordingly, using the osp_XReferencing implementation.
%
% Handles three possible phantom scenarios:
%
% ... |
e35d6fa44ea2b81bd5f421346a661bf253d03adadad6c4fdee655e4acc96961c | MATLAB | 3,505 | 103 | function plotSkeletonEulerAngles(data, tPt, plotParams, view)
% Plots a single time point posture and annotates the angles around which
% we computed the major joint angles (mostly proximal due to over clutter
% if all are plotted)
% Figure
fig;
hA = gca;
axis off
axis equal
hold on;
set(gca,'View', view);
hA.ZLim = [... |
fba02ffa596e325d610adb3725deb74506f5bf34571e31f26b5f605df8ba7435 | MATLAB | 3,505 | 110 | function ah = add_panel_title(text1,text2,varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% ################################################################# %% DESCRIPTION
%FUNCTION short desc.
%
% USAGE:
% out = template(in) process with default settings
%
% out... |
2068ab0e0f90539b7da297c87009d4e5afec97a13185cad41d11f37f69072126 | MATLAB | 3,506 | 107 | function [cost, grad] = getCostGrad(problem, x, storedb, key)
% Computes the cost function and the gradient at x in one call if possible.
%
% function [cost, grad] = getCostGrad(problem, x)
% function [cost, grad] = getCostGrad(problem, x, storedb)
% function [cost, grad] = getCostGrad(problem, x, storedb, key)
%
% Ret... |
b4f39148a383c76f292ec4b982c39dd8b54b8dfbc30c5cae80fc6fdb95ce1555 | MATLAB | 3,507 | 77 | function osp_updatemeanOvWindow(gui)
%% osp_updatemeanOvWindow
% This function updates the mean spectra overview tab.
%
%
% USAGE:
% osp_updatemeanOvWindow(gui);
%
% INPUT:
% gui = gui class containing all handles and the MRSCont
%
%
% AUTHORS:
% Dr. Helge Zoellner (Joh... |
48bd8ebf2dae0c2735a31d16d89b57cc7c8b80bed3abae9a3e40786a5194aef9 | MATLAB | 3,509 | 89 | function arg = ptparsevarargin(varargin)
%PTPARSEVARARGIN Parse input arguments of PERMUTOOLS functions.
% [PARAM1,PARAM2,...] = PTPARSEVARARGIN('PARAM1',VAL1,'PARAM2',VAL2,...)
% parses the input arguments of the main PERMUTOOLS functions.
%
% See also PTVALIDATEPARAMIN.
%
% PERMUTOOLS https://github.com/mick... |
d6a8f3627c19649e39a866ff910510c4405f3fa9ed9d6dcf6690ede48b479bd4 | MATLAB | 3,509 | 81 | % This function loads all .ctr files in a user-selected directory into a DATA array
% Additional comments added by WF 8/7/2022 to help us newbies
function ARTwarp_Load_Data(is_cli_mode, input_folder)
global DATA numSamples tempres
% user selects folder that contains .ctr files and changes the active
% directory to... |
49cd76a5416f0d9c72891bce1077041ea6b46facd4c9713d7ff50aeed0e14578 | MATLAB | 3,510 | 106 | function [oo,ooo] = meansembar(varargin)
% function hh = meansembar(varargin)
% does barplots with SEM of input matrix.
%
% INPUTS
% if one input: the data. That's the minimum input, rest is optional.
% if >1:
% input 1: the x positions of the bars or sets of bars
% input 2: the data matrix (1 to 3 dimensions, seco... |
232d12b90614c108141aeca23535775acf844ef8136f19aa8b2d67bb1a9541e2 | MATLAB | 3,512 | 164 | function Pipeline_registerStack(params)
% This function performs motion correction on in vivo images by performing
% image registration
analysisDir = getAnalysisDir(params);
ExpInfoFn = getFileName(params, 'ExpInfo');
load(fullfile(analysisDir, ExpInfoFn));
for i = 1:numel(fn.si)
imfn = fullfile(fn.pth, fn.... |
4bbd4cdfea8f3dfa54facf9ba435c5c15a08a707f898ba69f0c0f0f4538160ca | MATLAB | 3,512 | 115 | function plotStack(obj,key)
channel = 'ch2';
global ind
global data
global pointi
global isAOD
name = fetch1( Experiments*Scans(key),'file_name' );
isAOD =strcmp(fetch1(Scans(key),'scan_prog'),'AOD');
if isAOD
if ~strcmp(fetch1(Scans(key),'aim'),'stack')
display('Detecting volume..')
u_ind = str... |
5f3e957b74ae876bc4ac6c2197ecc029e89b73db5c23bf97b601be4990d4d771 | MATLAB | 3,513 | 112 | function linidxsrs=surfing_coords2linvoxelidxs(coords,voldef,dim,mask)
% maps coordinates to linear voxel indices
%
% I=SURFING_COORDS2VOXELIDXS(C,VOLDEF)
% INPUTS:
% C: A 3xN matrix or 3xPxQ array with (x,y,z) coordinates
% VOLDEF: Struct with fields .mat (4x4 voxel to coordinate transformation matrix
% ... |
7247b68b17e64a4f658cc142139c05c1568bbc47500ebe1e6d1543df280c16e4 | MATLAB | 3,513 | 107 | function [P,Z,order]=hcluster(D,link)
%function [P,Z,order] = hcluster(D,link)
%
%PURPOSE
%
%To perform a hierarchical agglomerative clustering on a distance
%matrix. Returns partition vectors for each level of the clustering
%hierarchy and information for visualizing the clustering hierarchy
%as a dendrogram.
%
%INPU... |
88d979596b3c504230292d6866482532154491d9227831b1dfe97b1a2938be8c | MATLAB | 3,513 | 97 | function FCAsymIndex
% path = '/mnt/NCPL09/TMSRobustArticle/CBTRTData/FunImgARTCSFW'
% outdir = '/mnt/NCPL09/TMSRobustArticle/CBTRTData/CFHReliability/'
rThr = 0.25 ;
path=uigetdir;
outdir=uigetdir;
[TMSPath, fileN, extn] = fileparts(which('TMStarget.m')) ;
maskdir = [TMSPath, filesep, 'mask', filesep, 'GreyMask20BG... |
83f6186fd38c0593254edbedd1d3899fe6ba792278c2b4339c4704c06d56ce80 | MATLAB | 3,514 | 109 | function batchResultsFolder = run_QAMPER_IVIM(img_nii,bval_file,roi_nii,save_folder,optionS)
% function batchResultsFolder = run_QAMPER_IVIM(img_nii,bval_file,roi_nii,save_folder,optionS)
% Inputs: image_nii (char): path to 4-D NIfTI DWI volume with all b-values
% bval_file (char): path to .bval te... |
1edbf81914d059923dcdd3d638c913710d215d5970e552aa8061bcb8d86789b3 | MATLAB | 3,515 | 101 | % fastregress - perform fast regression and return p-value
%
% Usage:
% [ypred, alpha, rsq, slope, intercept] = fastregress(x, y);
% [ypred, alpha, rsq, slope, intercept] = fastregress(x, y, plotflag, plotleg);
%
% Inputs
% y - y values
% x - x values
% plotflag - [0|1] plot regression and legend. Default 0.
% plot... |
19eccfcd01d32056fa6d631966166f35742e09613500463911fbf994b88fec17 | MATLAB | 3,516 | 90 | function result = TS_GetFromData(dataSource,dataField)
% TS_GetFromData Load a given field from either a data file, or data structure
% (loaded from file).
%
%---INPUTS:
% dataSource: either a .mat filename or a structure generated from loading an
% HCTSA file, e.g.,
% da... |
21d63a3df161ec4ff25fdbf6f983cea1109f146ff312982c496626fa581810ae | MATLAB | 3,516 | 101 | function [nt2, Phi, lambda, omega, time_dynamics, X_dmd, Cv] = DMD_exact(X, dt, p, tde, r, var)
% DMD_EXACT Exact (or standard) Dynamic Mode Decomposition with optional
% time-delay embedding.
%
% [nt2, Phi, lambda, omega, time_dynamics, X_dmd, Cv] = ...
% DMD_exact(X, dt, p, tde, r, var)
%
% Inpu... |
94026f8f1153919b4b7abebca3f374f8510a766d20c71f9fe6ae068863c4d5b3 | MATLAB | 3,516 | 131 | function [header,m,channels] = MEA_load_bin(binfile,plt, convertOption)
% Convert bin files to mat files for MEA data
% This function takes txt file output from MC_Datatool (Multichannel
% Systems) and converts it into a matlab matrix.
% Parameters
% -----------
% binfile : str
% path to the bin file to be conve... |
39df0d3c264059829d42ff67fbfa47bdca629fd32161841ed2392eb2603d6568 | MATLAB | 3,517 | 114 | function [outmap, cfg] = nmri_interpolate_map(cfg,inmap)
%[outmap, cfg] = nmri_interpolate_map(cfg,inmap)
%
% cfg = config struct
% .layout = fieldtrip layout to use a reference
% .neigh = fieldtrip neighbourhood structure (will auto-determine
% if not set)
% .dist ... |
7796e1acd60a1c47a7faf45811b0efaf66a053458e1af3a9c8d275599c03abf3 | MATLAB | 3,517 | 89 | function imageCombined = combine(this, varargin)
% Combines multiple MrImages into a single one along specified
% dimensions. Basically MrDataNd.combine with additional
% affineTransformation-check
%
% Y = MrImage()
% imageCombined = Y.combine(imageArray, combineDims, tolerance)
%
% This is a method of class MrImag... |
a6d0db64adc57c124e93868b7b9b1e00fbb21b9d1cfa198d936f138ad048f976 | MATLAB | 3,517 | 118 | function fear_icaReac(basename,varargin)
% method used in
% Lopes-dos-Santos et al., 2013 J Neurosci Methods
% Trouche et al., 2016 Nat Neurosci
% Giri et al., 2019 J Neurosci
% basename='~/data/Fear/triple/karmeliet190901/karmeliet190901';
load([basename '.basicMetadata.mat'])
fprintf('%s start %s with data of ... |
08c6b985e3fe3ced82d62fb961f59c3c98fc1e688b2cc4d3bc3dc6d621d0af05 | MATLAB | 3,519 | 88 | % GETIPSPH - Compute "in place" (m by n) sphering or quasi-sphering matrix for an (n by t)
% input data matrix. Quasi-sphering reduces dimensionality of the data, while
% maintaining approximately the "original" positions of the axes. That is,
% quasi-sphering "rotates back" as ... |
2fcf943400ef0a519859e303735bd548b097cdc35aa51625d917b45651164bdc | MATLAB | 3,519 | 93 | %% plot values (SNR, DA) of different anatomical areas
% from different:
% - neuronal features (data_info.neurVars)
% - kinematic variables (data_info.trajVars)
% - subjects (subjList)
% (c) Jiri, Jun17
%% settings: SNR
pathBeg = 'G:\dox\proj_carGameAnalysis\data\kinVars_tuning';
figDir = 'G:\dox\proj_carGameAnalysi... |
72e274ce136066280375379cf7162c80b3aa8113e20545a352a7e1bc728c6514 | MATLAB | 3,519 | 101 | function output_txt = BrainNet_Output_txt(obj,event_obj)
% Display the position of the data cursor
% obj Currently not used (empty)
% event_obj Handle to event object
% output_txt Data cursor text string (string or cell array of strings).
pos = get(event_obj,'Position');
output_txt = {['X: ',num2str(pos(... |
a6c17d9a0a7e16fd258731b9a316e8e2f886d7c34f7cde2de76bc8794c59aaf9 | MATLAB | 3,520 | 151 | function M = spheresymmetricfactory(n)
% Returns a manifold struct to optimize over unit-norm symmetric matrices.
%
% function M = spheresymmetricfactory(n)
%
% Manifold of n-by-n real symmetric matrices of unit Frobenius norm.
% The metric is such that the sphere is a Riemannian submanifold of the
% space of nxn symme... |
31bb713a2087153ae59818bdbdc2eb9101d9aa6547fd8a9e54b8ab748f129f29 | MATLAB | 3,522 | 81 | function [b,r,SSE,SSR, T, TF_ForContrast] = TMSregression(y,X,Contrast,TF_Flag)
% [b,r,SSE,SSR, T, TF_ForContrast] = y_regress_ss(y,X,Contrast,TF_Flag)
% Perform regression.
% Revised from MATLAB's regress in order to speed up the calculation.
% Input:
% y - Independent variable.
% X - Dependent variable.
... |
57e1621344fe9b076fc670b0f849a3679fe8baddaacb8f46b5478ac2af72f87b | MATLAB | 3,523 | 106 | function val = ft_getopt(opt, key, default, emptymeaningful)
% FT_GETOPT gets the value of a specified option from a configuration structure
% or from a cell-array with key-value pairs.
%
% Use as
% val = ft_getopt(s, key, default, emptymeaningful)
% where the input values are
% s = structure or cell... |
7c6dd5aeae0806a98abd25fb487f232ec8fc6e2d08c944e0e43de3949992b5bd | MATLAB | 3,524 | 102 | function ButtonOpen_Callback(source,eventdata,h,field)
% get directory and display it on GUI
% global h
% default output base name
prefix = 'Sepia';
switch field
case 'mask'
% only read NIfTI file for mask
[maskfileName,pathDir] = uigetfile(sepia_get_nifti_uigetfile_filter(),'Select mask file');
... |
01a43c0d5b71df91418a5235596b531d2ad4a6b772524de809c1cee9046b1920 | MATLAB | 3,525 | 82 | function [numClust, clustInd, centInd, haloInd, delta,predbounds] = densityClust_fast(dist, rho, isHalo, autosel)
% DENSITYCLUST Clustering by fast search and find of density peaks.
% SEE the following paper published in *SCIENCE* for more details:
% Alex Rodriguez & Alessandro Laio: Clustering by fast search a... |
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