sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b6247373bd96db1ec1c7783b0614e5a18291b8be73b711adf1b5f7fe7e5113b2 | MATLAB | 7,063 | 217 | function [x,w,ww]=nt_star2(x,thresh,closest,w)
% [y,w,ww]=nt_star2(x,thresh,closest,w) - sensor noise suppression
%
% y: denoised data
% w: 1 for parts used to calculate covariance (time*1)
% ww: 0 for parts that needed fixing, 1 elsewhere (time*chans)
%
% x: data to denoise (time*chans or time*chans*trials)
% th... |
f32670cf5ed044ffc78cf735e2001c662a44d86052981c11f9cb257a63b9cc23 | MATLAB | 7,081 | 256 | function [A,B,R]=nt_cca(x,y,shifts,C,m,thresh,demeanflag)
%[A,B,R]=nt_cca(x,y,shifts,C,m,thresh,demeanflag) - canonical correlation
%
% A, B: transform matrices
% R: r scores
%
% x,y: column matrices
% shifts: positive lag means y delayed relative to x
% C: covariance matrix of [x, y]
% m: number of columns of x
... |
39c2828eefb76fbd390f1ee6052f1c68d21cf97cea21b3f6a956811860625a3c | MATLAB | 7,086 | 152 | function CBIG_AuthorTopic_VisualizeComponentsOnBrainSurface(paramsPath, ...
outputDir, discretizationRes, minThresh, maxThresh, ...
colorscaleName, doRemoveSmallClusters)
% CBIG_AuthorTopic_VisualizeComponentsOnBrainSurface(paramsPath, ...
% outputDir, discretizationRes, minThresh, maxThresh, ...
% colorsca... |
13cceca458e4dbf3aa17c70814129642738ba2d81414da7bcbdc8f9de1d63a57 | MATLAB | 7,128 | 225 | function [img_mask_f, results] = analyse_masks_SAP(img, biom_folder, fname, biom_set_folder, biom, repeat_name, normalise_imgs, normalise_brightness)
%% threshold images and create masks
close_figs = 0;
%% Settings
if biom_set_folder == 'B1'
pixel_size = 0.5682; % 581.82/1024
elseif biom_set_folder == 'B2'
pi... |
3e0cc95841bad8dadfb86583ce44a52870b70f64b2820100986be218cf07e1a0 | MATLAB | 7,133 | 255 | function u = units(varargin)
%
% SAK : Copied from somebody in the MatLab file exchange, but heavily
% edited.
%
%
% The units.m function returns a struct containing the SI values of
% many common units. The example below demonstrates how to use
% this struct to cleanly and effeciently perform matlab calc... |
ef934bf4ad4728f9ee54eb10037f9bb5049219e994390674e8529aa260d29bf0 | MATLAB | 7,176 | 164 | function aaa___ifversion___test(varargin)
%This is not a true test suite, but it should confirm the function runs without errors.
if nargin==0,RunTestHeadless=false;else,RunTestHeadless=true;end
% suppress v6.5 warning
v=version;v(strfind(v,'.'):end)='';v=str2double(v);
if v<=7
warning off MATLAB:m_warning_end_wi... |
eeeb031b62dafc4bbf849fa802bd408a59deb9333f5928e6c30c68ccd4382ea1 | MATLAB | 7,203 | 180 |
fname = 2711-p1-multifile-mHaT2_7
%% Add path
restoredefaultpath
if isunix
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/projects/hspike/
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/development/
addpath /network/lustre/iss01/charpier/anal... |
5f43477c33ed394e5abeb01831b4c378b19834f1a0d7c2cbd586725292c0aa25 | MATLAB | 7,205 | 151 | classdef CBIG_AuthorTopic_unit_test < matlab.unittest.TestCase
%
% Wrapper function to unit-test a coordinate-based meta-analysis with the author-topic model.
% The inference was performed with the following hard-coded hyperparameters
% - K = 2:3 - number of cognitive components to be estimated is 2 and 3
% - alpha =... |
8d38ff682080d3799234def147060b8589cd7899e32da375cb846413da6c41dd | MATLAB | 7,206 | 213 | function TrialPETHZScore( Fs, Ts, Pre, Post, EventTS,Ch490,Ch405,prefix, varargin)
%Original code by David J. Barker; Modified for use with PhotometryGUI by
%Carissa A. Bruno for the Barker Lab at Rutgers University.
%Trial Analysis: This code will take inputs and create Photometry
%Raster-PETH. The Raster PETH i... |
e0e6fc4aa04bfa31e85a8f64631b5a2252564ed1e3e23af4b1db3560cdaed36f | MATLAB | 7,209 | 161 | function Figure2
restoredefaultpath
if isunix
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/git/fieldtrip
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/projects/hspike/
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/shared/
addp... |
42acc055443e42bf072f7214aa17bff29cb68fa895be0c6639b94e8ba7b5238a | MATLAB | 7,219 | 183 | function Error_Bootstrap_Interval_Prediction()
% Load true observed data and predicted data
load('true.mat'); % True observed data: T_test
load('IVMD_CNN_SVM.mat'); % Model predictions: IVMD_CNN_SVM_TSIM2
% Call plotting and metrics function
plot_confidence_intervals_with_metrics(T_... |
503847c10698a3f9a48dab3f85d4fa93a69260c4b4ddfad426a9b8d64d4a787c | MATLAB | 7,254 | 215 | classdef TDTUDP < handle
%TDTUDP TDT UDP class.
% obj = TDTUDP(TDT_UDP_HOSTNAME, TYPE) connects to RZ specified by
% TDT_UDP_HOSTNAME, which can be either the RZ's IP address or
% NetBIOS name
% TYPE (optional) specifies the data type to expect. Default is
% 'int32'.
%
% ob... |
00772ff3aa34054bdf17bd8934d89c8d1fd2a9c3a35fa847ce952e72228198be | MATLAB | 7,271 | 176 | function [dz,vdz,Adz]=two_group_test_coherence(J1c1,J2c1,J1c2,J2c2,p,plt,f)
% function [dz,vdz,Adz]=two_group_test_coherence(J1c1,J2c1,J1c2,J2c2,p,plt,f)
% Test the null hypothesis (H0) that data sets J1c1,J2c1,J1c2,J2c2 in
% two conditions c1,c2 have equal population coherence
%
% Usage:
% [dz,vdz,Adz]=two_sample_tes... |
58e6ef880f76e050cabeccb3ede8fa486e766ec0486371ef76b68eac69e29a32 | MATLAB | 7,277 | 235 | function [img_mask_f, results] = analyse_masks(img, results_folder, fname, biom, repeat_name, normalise_imgs, normalise_brightness)
%% threshold images and create masks
close_figs = 0;
%% Settings
pixel_size = 0.5682; % 581.82/1024
color_map = [1,0,0];
transparency = 0.2;
% biom folder
repeat_name = strjoin(repeat_n... |
d78519e08e2f315ac95ed981cefdd83810980fb40209af610e738b222b493164 | MATLAB | 7,289 | 212 | function varargout=wtc(x,y,varargin)
%% Wavelet coherence
%
% USAGE: [Rsq,period,scale,coi,sig95]=wtc(x,y,[,settings])
%
%
% Settings: Pad: pad the time series with zeros?
% . Dj: Octaves per scale (default: '1/12')
% . S0: Minimum scale
% . J1: Total number of scales
% . Mother: Mother ... |
284c103228f3ab3c268907bc51a71d74a8eb7de79b73f0264498f7593f2b6482 | MATLAB | 7,298 | 135 | function writeSpykingCircusDeadFile(cfg, MuseStruct)
% WRITESPYKINGCIRCUSDEADFILE crawls and searches through data
% directories and markerfiles for artifact definitions for SpykingCircus.
%
% use as
% writeSpykingCircusDeadFile(cfg, MuseStruct)
%
% The input structure can be read by readMuseMarkers.m, and edited be... |
1a03ed0d0908edfd3002b6378e076dc2cace88936551f7691c491a71439bdc85 | MATLAB | 7,313 | 186 | function tab2output = compute_features(datafile, outdir, f_range, f_range_fooof)
% compute_hurst - compute the Hurst exponent
%
% INPUT
% datafile = full filename to a .mat file.
% outdir = directory to save output csv files
%
% OUTPUT
% tab2output = a table of H values and other parameters
%
% Example usage:... |
0b0bf9e3d695191228ff026480aa3535026ce2baf63838e2f48c39866be9a03d | MATLAB | 7,319 | 229 | % Online calculation of (weighted) sample mean and variance
%
% ss=SampleStatistics; xx=randn(100,1); for ii=1:numel(xx); ss.add(xx(ii)); end;
% ss.sampleMean() - mean(xx), ss.sampleVariance() - var(xx)
%
% ss=SampleStatistics; xx=randn(100,1); ww=randn(size(xx)); for ii=1:numel(xx); ss.add(xx(ii),ww(ii)); ... |
84100fcc8d67dc243ce4c54bc00da2e415e51321e0ad475a2ad50f27885f0312 | MATLAB | 7,351 | 271 | function [p,data]=nt_read_data(fname,flag)
%[p,data]=nt_read_data(fname,flag) - read data from file
%
%
% fname: file to read
% flag: specify how to deal with complex data
% 0: walk through and select
% 1: choose first of each [default]
% 2: return all as struct
%
%
VERBOSE=1;
if nargin < 1 ; ... |
bb2c180ad9cd83a8017fed27e15dd9839301b48e608fa8bcdb4df3ade92a1cf2 | MATLAB | 7,351 | 198 | function Error_LSCV_B_interval_prediction()
% Load true and predicted values
load('true.mat'); % T_test (true values)
load('IVMD_CNN_SVM.mat'); % IVMD_CNN_SVM_TSIM2 (predictions)
% Print array lengths
fprintf('Length of true_values: %d\n', length(T_test));
fprintf('Length of predictions:... |
1b0fb2e9030f2c1b8bc461d9b84f203175fb53958e465c049c2e075745abe472 | MATLAB | 7,357 | 212 | function [fileNameTSVGZ_blink,fileNameJSON_blink] = natview_eye_preprocess_blinks(fileNameTSVGZ,fileNameJSON,outputDir)
%% PURPOSE: This script converts EyeLink EDF files into the BIDS format
%
% Raw eye tracking data contains column with NaN entries during
% periods when participant is blinking... |
d1ba18cfcff9e6d1c119c8a896234415bf95f14a45b58e625d1125089518d97f | MATLAB | 7,363 | 280 | function ctpath(CT0,varargin)
% CTPATH(CT,{CMODEL},{MARKERSIZE},{OPTIONS})
% Plot the trajectory of a color table in a selected color space.
% Create a datacursor to help inspection of the trajectory.
%
% CT is a Mx3 color table of any standard image class
% The values in CT must be scaled appropriately for the ... |
cb81956ead3952a414b368079111acf3580b5e3e4fa9dca438501adb6a1667b4 | MATLAB | 7,373 | 255 | function results = run_gcmi_regression_tests()
%RUN_GCMI_REGRESSION_TESTS Deterministic smoke tests for the MATLAB package.
%
% results = run_gcmi_regression_tests() executes a small set of regression
% checks covering the public wrappers, helper fixes, and discrete-class
% validation behavior. The function print... |
9610d1e67e422fcf54143bafe300755ca7761cbe0f5a66e8e5c289fe5b06bf0d | MATLAB | 7,390 | 132 | function hspike_write_spykingcircus_cluster(ipatient)
%% Analysis script for SLURM cluster
%
% (c) Stephen Whitmarsh, stephen.whitmarsh@gmail.com
%
%% Add path
restoredefaultpath
if isunix
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/projects/hspike/
addpath /network/lustre/iss0... |
aa6a6eaa1603df064de263ea9276d69b3ec345959ee76a2be260338b75d495dc | MATLAB | 7,390 | 196 | function wpict = vectorscan(inpict,numlines,scanamp,varargin)
% OUTPICT=VECTORSCAN(INPICT, NUMLINES, AMPLITUDE, {OPTIONAL PARAMS})
% Loosely emulates the appearance of a scan processor output on a
% monochrome display with persistence. Vertical deflection and beam intensity
% are modulated by input... |
b17ab0c8b97d9cd93fcacab21afd7d371417064f152203c67e5278f830b480e9 | MATLAB | 7,396 | 187 | function tab2output = compute_features_remove_channels(datafile, outdir, f_range, f_range_fooof)
% compute_hurst - compute the Hurst exponent
%
% INPUT
% datafile = full filename to a .mat file.
% outdir = directory to save output csv files
%
% OUTPUT
% tab2output = a table of H values and other parameters
%
... |
011668d8ea0c6492b4f8f656892773827402995ae7902f17c12b52ddb0cc5155 | MATLAB | 7,397 | 215 | function varargout=wtcJA(x,y,varargin)
%% JOACHIM OUTCOMMENTED stuff about significance!!
%% Wavelet coherence
%
% USAGE: [Rsq,period,scale,coi,sig95]=wtc(x,y,[,settings])
%
%
% Settings: Pad: pad the time series with zeros?
% . Dj: Octaves per scale (default: '1/12')
% . S0: Minimum scale
% . J... |
84385e24a08116bdeaaafd5c04e3e302a948ba4d7c971452961d4d5e027be839 | MATLAB | 7,423 | 143 | classdef NullModelAnalysisBatchRunner
% Manages batch execution of null model analyses using NullModelAnalysisUnit
properties
GeneratorModel NullConnectomeGeneratorModel
NumUnits (1,1) {mustBeInteger}
HoldoutOptions HoldoutParameters
% results holder
FullDataCorr... |
e52b5d1281d50c9fc6b861d60ab94e54bb60c4c239de7c219bd680b6fb507871 | MATLAB | 7,440 | 187 | function celltype = classification_celltype(config, force, do_plot)
%
% Use as
% celltype = classification_celltype(config, force, do_plot)
%
% force : whether to redo analyses or read previous save (true/false)
% do_plot : optional (default = true), can be set to false to only compute
% value with... |
652d706e801031d25870c77e3bcc12ec910672a45a298473fea933e3f1413fdf | MATLAB | 7,446 | 232 | function plot_distributions_and_stats_with_cdf()
% ===============================
% 1. Load data
% ===============================
load('true.mat'); % T_test
load('IVMD_CNN_SVM.mat'); % IVMD_CNN_SVM_TSIM2
% ===============================
% 2. Error calcu... |
d85cb10ab039291c4d253b02092ddc36c3e0421298fdca4ff2d859f807234864 | MATLAB | 7,447 | 232 | function plot_distributions_and_stats_with_cdf()
% ===============================
% 1. Load data
% ===============================
load('true.mat'); % T_test
load('IVMD_CNN_SVM.mat'); % IVMD_CNN_SVM_TSIM2
% ===============================
% 2. Error calcu... |
7653f4f09ad1a1b4a3f5bf5276977d416bd513e79596077eb1eaebad761b2ee6 | MATLAB | 7,450 | 241 | function [z,s] = smooth1q(y,s,varargin)
%SMOOTH1Q Quick & easy smoothing.
% Z = SMOOTH1Q(Y,S) smoothes the data Y using a DCT- or FFT-based spline
% smoothing method. Non finite data (NaN or Inf) are treated as missing
% values.
%
% S is the smoothing parameter. It must be a real positive scalar. The
% large... |
0ac95fdbb3568d492d10a780be650f984624b5963caebd83f33a7a2fb31435c3 | MATLAB | 7,452 | 220 | classdef Dataset < matlab.mixin.Copyable
%DATASET Class that stores structured character data
% This class stores, and provides easy access, to the
% sturctured character data. Using the "get" method,
% you can easily access particular alphabets/characters/drawers.
% You can also pick random... |
7aca7741d121773bb0bca538379254beea7ade0149e6cb53844b68c2e5ca5779 | MATLAB | 7,461 | 219 | function varargout=xwt(x,y,varargin)
%% Cross wavelet transform
% Creates a figure of cross wavelet power in units of
% normalized variance.
%
% USAGE: [Wxy,period,scale,coi,sig95]=xwt(x,y,[,settings])
%
% x & y: two time series
% Wxy: the cross wavelet transform of x against y
% period: a vector of "Fourier" periods a... |
7ebad94eff4cee825478295f5e1ccdb4abd0f6029ffda279d7874092da48cad1 | MATLAB | 7,500 | 112 | function plotstats(cfg)
nrows = 1;
ncols = 4;
SpikeDensity_timelocked = spikeTrialDensity(cfg);
for ipart = 1 : size(SpikeDensity_timelocked, 2)
for markername = string(fields(SpikeDensity_timelocked{ipart}.sdf_bar))'
nrows = max([nrows, size(SpikeDensity_timelocked{ipart}.stat.(markername), 2)]);
en... |
7c7742660bedda7e19f78b41d5a10cd2f96b70a95d44bb918b38ee423c6ffb90 | MATLAB | 7,515 | 260 | function stats=nt_statMatrix(x,plot_params)
%stats=nt_statMatrix(x,plot_params) - calculate statistics arrays for each dim of matrix
%
% stats: array of statistics arrays
%
% x: data to stat
% plot_params: parameters
%% arguments
if nargin<1; error('!'); end
if nargin<2;
plot_params.bottom=0.1;
plot_params.... |
c87141143b8c8e07a1c40dc3304320c20673e82b7bd93e09dcabd0d4f34e1e19 | MATLAB | 7,520 | 193 | function violins = violinplot(data, cats, varargin)
%Violinplots plots violin plots of some data and categories
% VIOLINPLOT(DATA) plots a violin of a double vector DATA
%
% VIOLINPLOT(DATAMATRIX) plots violins for each column in
% DATAMATRIX.
%
% VIOLINPLOT(DATAMATRIX, CATEGORYNAMES) plots violins for each
% ... |
d983ce77b7aec837af84d97b1e37799ffbc730c1a26ecc8e444842ff84f3f953 | MATLAB | 7,540 | 150 | function [maskwalker, mperiods, mphases, nscrdots] = mmprepare_randmask(maskdata, nd, plotsize, mazimuth, msize, minvert, mscrambleoption, mmultiply)
% DC: added output "nscrdots", "nd" now = "nscrdots", added "mmultiply",
% "mwalkersoppo", etc. to equate local motion direction of display + mask
%[maskwalker, mp... |
5d5cfc984f2289f99edf7eee92a4a436b19b48e5560b410982c22b62e4bc2947 | MATLAB | 7,560 | 137 | % Help for file Mat2NlxTT.dll
%
% Purpsose
% The purpose of this program is to take extracted Neuralynx data from the matlab environment and create the appropriate Neuralynx file.
%
% Composition
% This program is a matlab mex file compilation of matlab and C++ source code.
% C++ source code is used to extract data fr... |
ac21175c3c3201ce488cdd282a92c90198c730a29b9443e8f35ccfd0bc3f98f8 | MATLAB | 7,569 | 137 | % Help for file Mat2NlxSE.dll
%
% Purpsose
% The purpose of this program is to take extracted Neuralynx data from the matlab environment and create the appropriate Neuralynx file.
%
% Composition
% This program is a matlab mex file compilation of matlab and C++ source code.
% C++ source code is used to extract data fr... |
6ddb8d13d111d8aa4d523c00c732f44b1d7fe8a1c96d2aea6f137d14673e78ad | MATLAB | 7,576 | 188 | function [marker, hypnogram, stats] = hypnogramMuseStats(cfg, MuseStruct, force)
% HYPNOGRAMSTATS creates statistics based on hypnogram and markers in MuseStruct
%
% use as
% [MuseStruct, marker, hypnogram] = hypnogramStats(cfg, MuseStruct, force)
% This file is part of EpiCode, see
% http://www.github.com/stephenw... |
ae18ccfc7449d237d15f940e1641629abf86a550bd3963bd1c6f9b650758df26 | MATLAB | 7,576 | 128 | function preictal_project(ipatient)
restoredefaultpath
if ispc
addpath (genpath('\\lexport\iss01.charpier\analyses\vn_preictal\scripts\EpiCode\shared'))
addpath (genpath('\\lexport\iss01.charpier\analyses\vn_preictal\scripts\EpiCode\external'))
addpath (genpath('\\lexport\iss01.charpier\analyses\vn_preicta... |
0e0a3ad9f7f8c067bb4c47a9d03bd95b1ca4941a5cf8ca6f2a88c68d6007af4d | MATLAB | 7,578 | 201 | function preictal_project_SW
restoredefaultpath
if ispc
addpath (genpath('\\lexport\iss01.charpier\analyses\stephen.whitmarsh\EpiCode\shared'))
addpath (genpath('\\lexport\iss01.charpier\analyses\stephen.whitmarsh\EpiCode\external'))
addpath (genpath('\\lexport\iss01.charpier\analyses\stephen.whitmarsh\Epi... |
314642afeb9d9f6666f572119a8e21460bdb59fa8485a47112e9541f75860e80 | MATLAB | 7,579 | 139 | function [mm, markers, wperiods, wphases, xcenterw, ycenterw] = mmprepare_single(mm, scrambleoption, scramblex, scrambley, invert, trans, offx, offy, plotsize, xcenter, ycenter)
%DC: if invert == 5, invert z;
%[mm, markers, wperiods, wphases, xcenterw, ycenterw] = mmprepare_single(mm, scrambleoption, scra... |
20ee0b6cd8f3cdae4e03f9b23b53c48888bb1c3f17a55cf0b26e8338fd155e20 | MATLAB | 7,603 | 269 | function Sout = learn_coefficients(B, X, alpha, gamma, L, Sinit)
% The feature-sign search algorithm
% L1-regularized least squares problem solver
%
% This code solves the following problem:
%
% minimize_s 0.5*(||xi-B*si||^2 + alpha*si'si + 2*alpha*si(sigma(Lijsj)) +
% gamma*||si||_1
% X : data matrix
% B : basis... |
40ba847b362eb4e615bacdd1b89161b63ebcd088e43a514579938df1d0a2f5f3 | MATLAB | 7,613 | 137 | % Help for file Mat2NlxCSC.dll
%
% Purpsose
% The purpose of this program is to take extracted Neuralynx data from the matlab environment and create the appropriate Neuralynx file.
%
% Composition
% This program is a matlab mex file compilation of matlab and C++ source code.
% C++ source code is used to extract data f... |
6509b0bb08e859e2893651030b8a78ab1fafdabb7b3ba55d299ae68c5838f82d | MATLAB | 7,673 | 292 | function map = viridis(N)
%VIRIDIS Perceptually uniform sequential colormap (Matplotlib viridis).
%
% map = viridis
% map = viridis(N)
%
% Input:
% N : nonnegative integer, number of colours (default: current colormap length)
%
% Output:
% map : N-by-3 RGB colormap in [0,1]
if nargin < 1 || isempty(N)
N = siz... |
f1bda0b37d423ee5013c5a9065d505ddd66b8f0aca9499b6b5ff6426db2b46b5 | MATLAB | 7,696 | 225 | function [lme,h,p] = mixed_model_SAP(data, stats_folder, filename, name, biom_1, biom_2, coloc)
diagnostics = 0;
alpha = 0.05;
tech_rep = 0;
var_names = {'Sham vs Theta'};
if iscell(stats_folder)
stats_folder = char(stats_folder);
end
if iscell(biom_1)
biom_1 = char(biom_1);
end
if iscell(biom_2)
biom_2... |
930cd86f0a4fb4f3349f54a9302737ab434da8728e334ca738f1f946a06560ac | MATLAB | 7,697 | 137 | % Help for file Mat2NlxTT.dll
%
% Purpsose
% The purpose of this program is to take extracted Neuralynx data from the matlab environment and create the appropriate Neuralynx file.
%
% Composition
% This program is a matlab mex file compilation of matlab and C++ source code.
% C++ source code is used to extract ... |
17230bd4fd778a509cbfee48bf03920a212646b4d255a13463a685cec1563b16 | MATLAB | 7,706 | 137 | % Help for file Mat2NlxSE.dll
%
% Purpsose
% The purpose of this program is to take extracted Neuralynx data from the matlab environment and create the appropriate Neuralynx file.
%
% Composition
% This program is a matlab mex file compilation of matlab and C++ source code.
% C++ source code is used to extract ... |
470ed3cf948e0951bf30bca2d8104ba712205ea8472e2f589466a3e8dc0ed818 | MATLAB | 7,718 | 164 | function [session, init_params, glm_params] = fLocAnalysisParams(session, clip)
%
% Generate data structures for preprocessing and analyzing localizer data
% using vistasoft functions (https://github.com/vistalab/vistasoft).
%
% [session, init_params, glm_params] = fLocAnalysisParams(session, clip)
%
% INPUTS
% 1) s... |
68ebd59019493009b0d35d25f7e21a0fa5a7aa92db701d872d126fd6b20cfb05 | MATLAB | 7,736 | 190 | function [covariates] = CBIG_generate_covariates_from_csv( csv_files, subject_header, ...
covariate_names, covariate_types, subject_list, FD_file, DVARS_file, outname, delimiter )
% [covariates] = CBIG_generate_covariates_from_csv( csv_files, subject_header, ...
% covariate_names, covariate_types, subject_list... |
688c919c7a964918dcf7a728feece23f99866844c02b3975986686f6cf7c2cfc | MATLAB | 7,750 | 137 | % Help for file Mat2NlxCSC.dll
%
% Purpsose
% The purpose of this program is to take extracted Neuralynx data from the matlab environment and create the appropriate Neuralynx file.
%
% Composition
% This program is a matlab mex file compilation of matlab and C++ source code.
% C++ source code is used to extract... |
830637aa4f96d8aea5a9b2f7997d70bbbcdf99c853efb1932264e00049aba87b | MATLAB | 7,755 | 212 | %%
function [varargout] = browse(path, loadables, varargin)
%----- Parse input
options = inputParser;
options.addParameter('extension', '.fig');
options.addParameter('dataExt', '.mat');
options.addParameter('figureName', []);
options.addParameter('figureTitle', []);
options.addPar... |
5b7eefce1c7b567a387fc8606fd1b93b5f0a1665fd8b00fa537004ed285670c6 | MATLAB | 7,769 | 149 | function [artefacts] = writeSpykingCircusDeadfilesMultichannel(cfg, MuseStruct, force, suffix)
% WRITESPYKINGCIRCUS_DEADFILES creates artefact files (deadtime) for
% SpykingCircus in data directories for spike analysis
%
% use as
% writeSpykingCircus_deadfiles(cfg, MuseStruct, force)
% or
% writeSpykingCircus_dea... |
328985388681410e0648f18ea2d04f745967bbb859053a3ed0eee6c0cf920d71 | MATLAB | 7,807 | 185 |
% Correlate varA with varB accounting for confounds (SPM)
clear, clc, close all
%% Paths / data
path_batches = 'D:\Projects\2023_multib\MK_multi_b\Scripts';
cd(path_batches)
load('Table_297_subjs_demographics_biomarkers_2024_05_03.mat')
n_subjects = size(T_subjects,1);
path_stats_group = 'D:\Project... |
4dae22595cc4fc638d6de5a7ea96031b0d138028aef712c59c48934a3b69ca7f | MATLAB | 7,807 | 242 | function [G ugl] = impatsort(fpathexpr,varargin)
% [PATGROUPS LEVELS] = IMPATSORT(PATHEXPR,{OPTIONS})
% [PATGROUPS LEVELS] = IMPATSORT(INSTACK,{OPTIONS})
% Read a number of image files (ostensibly tileable patterns/textures)
% and sort them into groups based on their average gray level. This is
% used as th... |
e2af6a063e41623696c58ddcf58f8d9707ea726d6227fa1bc0494bacbe876361 | MATLAB | 7,840 | 204 | %%%% Version 4 (MGG) %%%%
%%%% Cell classification in a semi-automated way %%%%
%%
clc;
close all;
clear all;
warning('off','all')
reset(0);
select_monitor = 1;
%------------------------------------------------------------------------------%
%% Select steps to run
%%% Step 1 %%%
% Select cells %
set... |
be11452d867d7e7bcba4dde6f89046c389eaf568f69386e8381861faf8cd2c30 | MATLAB | 7,866 | 211 | %%
% Inputs
folder='.\'; % Results will be saved in this folder
J_dial = "Enter number of protofilaments : ";
J = input(J_dial);
% r_dial = "Enter spacing between tracing points, nm : ";
% r = input(r_dial);
r=2; %minimal spacing between tracing points
c_dial = "Enter curvature, deg/dimer : ";
c = input(... |
ef143e7eec92b4f2f3482f0f8e94dda7aae8fb5509ae1b77150992680bbc9292 | MATLAB | 7,872 | 239 | function varargout = imcropzoom(varargin)
% IMCROPZOOM({INPICT},{WIDTH})
% OUTPICT = IMCROPZOOM({INPICT},{WIDTH})
% [OUTPICT RECT] = IMCROPZOOM({INPICT},{WIDTH})
% Interactively use IPT imcrop() to crop an image. This is a simplified utility
% that aims to improve the practical usability of imcrop() within the c... |
be6bbcca5cf11df129282c2ccceb078aaf345928ba484f6f021e8f34dcaeb831 | MATLAB | 7,874 | 194 | function outpict = lcdemu(inpict,vangle,screenprofile)
% LCDEMU(INPICT,{ANGLE},{SCREENPROFILE})
% Emulate the effect of using an old or low-quality TN-type LCD monitor
% Both horizontal and vertical viewing angle influence is emulated
% Image is assumed to be scaled to screen extents
%
% INPICT is... |
4649117fd2830331520e42dfa4c111fcb854976c362ea3b08eee0212bf3ca2f7 | MATLAB | 7,923 | 150 | function [allData_combined,DataToCombine] = combine_experimenters(save_path)
%%% Combine data from different experimenters for the same cohorts/brain slice - V2 (MGG) %%%%
%% Combine all data in a single table and generate results
% Find mat files for each dataset
files = dir(fullfile(save_path,'*.mat'));
% Re... |
565ec1a67f34a831b3656d290b6d3d5478484ffbdca526161879ed2e1098e084 | MATLAB | 7,959 | 246 | function TrialPETHDeltaF( Fs, Ts, Pre, Post, EventTS,Ch490,Ch405, prefix, varargin)
%Original code by David J. Barker; Modified for use with PhotometryGUI by
%Carissa A. Bruno for the Barker Lab at Rutgers University.
%Trial Analysis: This code will take inputs and create Photometry
%Raster-PETH. The Raster PETH ... |
d1ad2912aa2c93d03791368fa0daeae864c0502e7a42bc1717c631fe782e78d9 | MATLAB | 7,964 | 144 | %% |NATSORTFILES| Examples
% The function <https://www.mathworks.com/matlabcentral/fileexchange/47434
% |NATSORTFILES|> sorts filenames or filepaths in an array |A| (cell/string/struct)
% taking into account number values within the text. This is known as
% _natural order_ or _alphanumeric order_. Note that MATLAB'... |
75efbcec47d007ec425597e4e81575f561e2cbbbc5914a22640510977df513e8 | MATLAB | 7,977 | 215 | function err = functionalPreprocessing(session, init_params, clip, stc, QA)
% Automated preprocessing of fMRI data
% using vistasoft functions (https://github.com/vistalab/vistasoft).
%
% INPUTS functionalPrepcrocessing(session, init_params, clip, stc, QA)
% 1) session: name of session to analyze (string)
% 2) init_... |
6f0b5086edfbc020014908e4dd45983c401bce85c3d95ae3e10f60c2d906eb03 | MATLAB | 7,978 | 171 | function output = CBIG_Projectfsaverage2MNI_Ants(lh_surf, rh_surf, interp_type, MNI_mask, index_map, delimiter)
% Usage: output = CBIG_Projectfsaverage2MNI_Ants(lh_surf, rh_surf, interp_type, MNI_mask, index_map, delimiter)
%
% Function projects surface data to the volume
% Also see reverse transform CBIG_ProjectMNI2f... |
c7fb8416b13be463a98b885968f99ce1d8e95ab654155756d5dda99e6c5f935c | MATLAB | 7,989 | 220 | %%
% draw3DProjections(description, canvas, subs, histo, xyzArray, [@combiner])
% draw3DProjections(description, canvas, subs, x, y, z, xyzArray)
% draw3DProjections(description, canvas, subs, x, y, z, w, nXYZBins, xyzMin, xyzMax, [zRange], [doProfile])
%
% Units can be specified for axes by either providi... |
7f55209ee1b09ce84c32c8fff7cc04a05d1b6c963eafe6a2523c28ec6c9525a0 | MATLAB | 8,016 | 219 | function plot_kde_90p_prediction_intervals()
% load
load('true.mat'); % T_test
load('IVMD_CNN_SVM.mat'); % IVMD_CNN_SVM_TSIM2
x = 1:length(T_test);
errors = T_test(:) - IVMD_CNN_SVM_TSIM2(:);
errors = errors(~isnan(errors)); % 去除 NaN
% 设置带宽方法
bandwidth_methods = {'RuleOfThumb... |
8c163189ced4f7c5e804d186eda1071bd94999d5003a81530ad82ecea7047ccb | MATLAB | 8,036 | 201 | function [isih] = ft_spike_isi(cfg, spike)
% FT_SPIKE_ISI computes the interspike interval histogram
%
% The input SPIKE should be organised as
% a) the spike datatype, obtained from FT_SPIKE_MAKETRIALS
% b) the raw datatype, containing binary spike trains, obtained from
% FT_APPENDSPIKE or FT_CHECKDATA. In this cas... |
a3a96b5089010400a49d809cd90bb240fb14059f60d46d5722f18ea29c9829a2 | MATLAB | 8,075 | 265 | % BLEND MODE DEMOS
% depending on your filesystem, your pwd and where you stick this script,
% you may need to change the path strings used for input/output.
% some of these may be configured for viewing on an inverted display
% if something looks inverted, just check the call to imshow() or imshow2()
% This file ex... |
d7ecd3569904b2904622785d811797515f42ec8dac981fee9deb6ff4728f55f1 | MATLAB | 8,077 | 176 | function [hline,hdata] = plotPsych(result,plotOptions)
% plot your data with the fitted function
%function plotPsych(result,plotOptions)
% This function produces a plot of the fitted psychometric function with
% the data.
% In the struct plotOptions you may set a lot of options, which are listed
% here with their defa... |
613d7e58e2accb20bba3bd9e2d226bf88ceaeae2c519fbe288c0d31d58bb7e50 | MATLAB | 8,085 | 178 | %% Create filename list
clear RLfilename fout_table fout_data
% loop over patient
ifname = 1;
electrodetype = [];
for ipatient = 1:length(vect_pat)
% loop over sleep vs wake
for iperiod = 1:2
% loop over macro vs micro
for electype = 1:2
for elec = 1 : nr... |
f4183deeb68da9c467f71f477179d86dd2fab021d3e2b397e2282c589e38a1fe | MATLAB | 8,095 | 204 | %% FAQ
% Frequently Asked Questions for the Wavelet Coherence Matlab Toolbox
%
% http://www.glaciology.net/wavelet-coherence
%% How do I know whether AR1 noise is an appropriate null hypothesis to test against?
% It is usually an appropriate null hypothesis if the theoretical AR1
% spectrum is �a good model� for the ... |
a7ee368fdcf9a2dbf2407385c3786772255316444c15ad9bdc27bc29d18c6163 | MATLAB | 8,120 | 280 | function outpict = ibcomposite(outpict,FG,BG,FGA,BGA,FGhasalpha,BGhasalpha,compositionmode,blendmode,opacity,camount,nframes)
% this is the composition section of IMBLEND
% this is not intended to work independently
% i only split this because editing a 3000+ line file is a pita
% prepare things
if ~strcmp(compositi... |
89429166407ae2d3d7bae554ccd9b57347f60b2f61ae9dfe5866f0112e626d38 | MATLAB | 8,134 | 153 | %**************************************************************************
%
% create_ismrmrd_3Dvol_and_send extracts a block of 3D data in ISMRMRD
% format and sends it back to the host.
% input: Structure with fields of data and reference
% connection: Link with Gadgetron. Required to get global... |
f1369999dbd1abe18d4fa01b7b55e2a19873df93d0f7c208257c392bc6ba0dae | MATLAB | 8,149 | 162 | function [X, fX, i] = minimize(X, f, length, tol, P1, P2, P3, P4, P5, P6, P7);
% Minimize a continuous differentialble multivariate function. Starting point
% is given by "X" (D by 1), and the function named in the string "f", must
% return a function value and a vector of partial derivatives. The Polack-
% Ribiere fl... |
ff7957b24f37b19185957e393eee4173c848e8c4e9a932f16246af21f1cadc5c | MATLAB | 8,171 | 237 | clear all; close all; clc
addpath(genpath('/data/code/matlab'));
% error('to here')
% /usr/local/MATLAB/R2018a/bin/matlab -nodisplay -nosplash -r RunMacro19
% nohup /usr/local/MATLAB/R2018a/bin/matlab -nodisplay -nosplash < RunMacro19.m >&! out.1 &
CHRONUX = 0 % Use 0/1, NOT T/F
CROSSED = 0
SPLIT_UP = 0 % [0] Bre... |
daf37f65f23cb0cad0eb2b8f23d5bdff86753d113678acfc8676da3a11f08c47 | MATLAB | 8,174 | 163 | function [Xcorr, XcorrGH, PosPvalues, NegPvalues, num_pairs] = ...
computeXcorrHGonly(animal_name, spike_matrix, autocorr, max_lag, repeat_calc, save_data, output_folder)
%% By Mattia 01.02.19
% computes cross-correlograms (CCH) and their "significance" values
% as in English et al., 2017.
% requires spike matrices... |
6dac0974e6da0facb1fc4b428bb174f390d30753774316bc7a951fb9f5536040 | MATLAB | 8,216 | 279 | function outpict = imrectrotate(inpict,angle,varargin)
% IMRECTROTATE(INPICT, ANGLE, {OPTIONS})
% Rotate an image using pixel displacement to crudely maintain boundary geometry.
% Characteristic creasing effects can be maximized with iterative application.
% This is not intended for any technical pu... |
ec2886621faca2c883ee429f2810c3960b07483d791fb2b3e8e5d07cc697b092 | MATLAB | 8,239 | 220 | function preictal_project_LC
restoredefaultpath
if ispc
addpath (genpath('\\l2export\iss02.charpier\analyses\vn_preictal\scripts\EpiCode\shared'))
addpath (genpath('\\l2export\iss02.charpier\analyses\vn_preictal\scripts\EpiCode\external'))
addpath (genpath('\\l2export\iss02.charpier\analyses\vn_preictal\sc... |
c09832efdcaa1dccd19ab7d4a555d37c6c3153d5165425598abd31cc2a95db14 | MATLAB | 8,250 | 233 | % Load the Gaussian filtered FC matrices
% FC_all = load('.../FC_filtered.mat');
average_conn_matrix = squeeze(mean(FC_all.FCE, 1));
% Load saved 1-Cycle vectors & cycle coefficient to save time for subgroups
% load('/Results/kCycleVect.mat');
% load('/Results/Alpha.mat');
demographics = readtable('.../DemTable.... |
36c8c341a5ff56139b00545691e0000f52e01e93c21784b7e7ec62b89656eb3e | MATLAB | 8,292 | 203 | function seizure_infos = dtx_stats_seizure_timings(cfg, MuseStruct_concat,ipart)
% computes some descriptive stats for data with or without EMG, with
% seizure start/end (rats) or slowwave (patients). For rats, time is
% relative to the injection of DTX.
% ## INPUT :
% - cfg :
%mandatory :
% cfg.seizuretimings.mark... |
a78d848abf380ec39491841897c8e74f5db11c2357704c13b7a21b71ee37c293 | MATLAB | 8,303 | 269 | % This script provides a tutorial application of the Gaussian-Copula Mutual
% Information (GCMI) estimator to quantify temporal interactions in an
% event-related EEG response modulated by a continuous stimulus feature
%
% This script uses cell mode - cells are delimited by %% lines and can
% be run with:
% ctrl-ent... |
a2575c538dbe3f151422681733516be6294af495aa23f0d394c6d44d713ed79c | MATLAB | 8,308 | 214 | function [taskLengthDiff,percentMissingSamples,percentOffSamples] = natview_eye_data_qc(fileNameSET,fileNameTSVGZ,fileNameJSON,outputDir,saveFlag)
% PURPOSE: This function calculates quality control (QC) metrics from eye
% tracking data. Using the raw EEG file, function calculates the
% difference bet... |
02422349acb824d892d778a730df9b344190d3ec570ac3fdbf2c2f36c819d90e | MATLAB | 8,319 | 241 | clear all; close all; clc
addpath(genpath('/data/code/matlab'));
% error('to here')
% /usr/local/MATLAB/R2018a/bin/matlab -nodisplay -nosplash -r RunMacro19
% nohup /usr/local/MATLAB/R2018a/bin/matlab -nodisplay -nosplash < RunMacro19.m >&! out.1 &
CHRONUX = 0 % Use 0/1, NOT T/F
CROSSED = 0
SPLIT_UP = 0 % [0] Bre... |
b322905093b3768ca2aba4830564a8f78e3c7a9d880ccbc103f3389758a3d0f1 | MATLAB | 8,340 | 157 | function [artefacts] = writeSpykingCircusDeadfiles(cfg, MuseStruct, force, suffix)
% WRITESPYKINGCIRCUS_DEADFILES creates artefact files (deadtime) for
% SpykingCircus in data directories for spike analysis
%
% use as
% writeSpykingCircus_deadfiles(cfg, MuseStruct, force)
% or
% writeSpykingCircus_deadfiles(cfg, ... |
a8abdc731c6d80f0085a04a5a28e56554625047fae6836d78428fafb1db433d3 | MATLAB | 8,359 | 227 | %load data from csv as table GTEx version 8
T= readtable('Male+Female.csv');
%T should be (the number of samples by how ever many input and output features)
%T = (n_samples x n_features)
data = T(:,:);
%Extract ID feature
ID = table2array(data(:, {'ID'}));
%Set input parameters
x_names = {'HDAC1','HDAC2','HDAC3','HD... |
765b0c967e1baf31db5478e73d8c11df9c0988b9184196b12ba0c9f2c5a331ab | MATLAB | 8,361 | 234 | function [result] = bfopen(id, varargin)
% Open microscopy images using Bio-Formats.
%
% SYNOPSIS r = bfopen(id)
% r = bfopen(id, x, y, w, h)
%
% Input
% r - the reader object (e.g. the output bfGetReader)
%
% x - (Optional) A scalar giving the x-origin of the tile.
% Default: 1
%
% y - (Optional) ... |
05c6c9d71461f1484d630c08a2f40fc37784437cfa0c72190c77892c0fcc3229 | MATLAB | 8,363 | 269 | function [p,padj,h,lme] = stats_VMstim(results_folder, results_to_plot, biom_1, biom_2, name, coloc, allData)
%% setup
AB=1;
norm_to_zero = 0;
no_carrier = 0;
rem_outliers = 1;
if AB
sprintf('Pipeline setup for Alamar Blue!!');
end
stats_folder = fullfile(results_folder, biom_1, 'Stats');
if AB
stats_fol... |
ae9c60ccb086ebd2d5749bb6c943d83512716aa64ab3ac2f4a1c03e835133c72 | MATLAB | 8,384 | 200 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_untouch0_nii_hdr(fileprefix, machine)
fn = sprintf('%s.hdr',fileprefix);
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
hdr = read_header_load_u... |
2c2a0b101d233b68b30c51f5d62b37c83cfc3d3fa2101ca5bccadcd3864229b1 | MATLAB | 8,389 | 310 | function spm_prf_review_surface(PRF,pidx,img)
% Displays PRF results on a cortical surface
%
% PRF - estimated PRF structure
% pidx - index of the parameter to display within PRF.Ep{1}
% img - (optional) displays this parameter map (.nii)
% Default hemisphere
hemi = 'lh';
alpha = 0.8;
if nargin < 3
img = '';
e... |
b88fc34e557dc28f46af6c179344ff2357dcdeb951521582c1a9854d976dfd0a | MATLAB | 8,412 | 189 | %% Create filename list
clear RLfilename fout_table fout_data
% loop over patient
ifname = 1;
electrodetype = [];
for ipatient = 1:length(vect_pat)
% loop over sleep vs wake
for iperiod = 1:2
% loop over macro vs micro
for electype = 1:2
for elec = 1 : nr... |
0b126b30eb5f27b00a8069f85e3da1356222df447640ddd36db420bf145a2339 | MATLAB | 8,419 | 200 | %PARAMETERS
% nodestdThresh. This is the standard deviation threshold for exclusion of
% skeleton nodes based on prePeriod activity
nodestdThresh = 1;
[textFileName, textFilePathName] = uigetfile('*.txt', 'Pick txt file specifying input');
fid = fopen(strcat(textFilePathName,textFileName));
% filename pathname conditi... |
eef60bb2f3da21d38cbe824d7a4527baa096a0c7905933a4aa17f8178c8863b6 | MATLAB | 8,422 | 182 | classdef PairDataCCAResultsVisualizer
% PairDataCCAResultsVisualizer
% Visualizer for CCA analysis results, including correlation plots
% and 3D visualization of wiring PI components.
methods (Static)
function ax = scatterCCACorrelation(ccaResults, componentIdx, options)
% Scatter ... |
959abab4ec140cc421b9a2bf3ace9dda42f9b634f19336f2a1b409890dd80c32 | MATLAB | 8,426 | 172 | function stats = spikeWaveformStats(cfg, SpikeWaveforms, force)
% SPIKEWAVEFORMSTATS computes average and variance of the spike waveform.
% Then, the average is interpolated and the following parameters are
% computed : amplitude, halfwidth, peaktrough and trouhpeak.
% Input spike waveform data is get from readSpikeW... |
9cd08b1f1785d572416b9d25f6c4f55d00faf2562fc190e40d2632393d29dac3 | MATLAB | 8,434 | 259 | function outpict = nhfilter(inpict,varargin)
% OUTPICT=NHFILTER(INPICT,MODE,{BLOCKSIZE},{ORDER})
% Perform the selected sliding-neighborhood filter operation on an image.
%
% This is a passthrough to various IPT functions, with internal fallback implementations to help
% remove the dependency of MIMT tools o... |
993eeaa7e0edfcbaa463d66bb94169ee00e1eefbf5b9eea100917cb1bbb87c33 | MATLAB | 8,435 | 196 | %%
%
function [varargout] = enhanceCopying(handles, copyWholeFigure)
%----- Get axis handles if none are provided
if nargin < 1
handles = vca;
end
if nargin < 2
copyWholeFigure = all(ishghandle(handles, 'figure'));
end
%----- Available context menus
if copyWholeFigure
... |
3b68ac24f2472ea4fa1b50cf93ed3c8a2e006844ec1d5ea773be6a0d930971b4 | MATLAB | 8,447 | 284 | function varargout = cropborder(inpict,varargin)
% OUTPICT=CROPBORDER(INPICT, {WIDTH}, {OPTIONS})
% [OUTPICT WIDTHUSED]=CROPBORDER(INPICT, {WIDTH}, {OPTIONS})
% crops a border of WIDTH pixels from the edges of INPICT
% this is much more convenient than using imcrop()
%
% INPICT is an I/IA/RGB/RGBA/RG... |
323161b61fb730429fd86c874ebacafefae8c53e17e56a7b84446b41fac2385b | MATLAB | 8,457 | 217 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_untouch_nii_hdr(fileprefix, machine, filetype)
if filetype == 2
fn = sprintf('%s.nii',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.nii".', fileprefix);
error(msg);
end
else
fn = sprint... |
4d905b73f509bf83fcf72c01f371655f077fe0d30e231b59284a9ba50e3d6b34 | MATLAB | 8,511 | 207 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_untouch_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header_save_untouch_nii_hdr(hdr, fid);
return; % save_nii_hdr
end
%----------------------------------------------... |
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