sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b4fffb686ca63f3f668f01886c2a9aeec01ddba27b5ef8bc417ab9e58b661e49 | MATLAB | 2,903 | 104 | clc; clearvars; close all;
T = readmatrix('source_data_file.xlsx','Sheet', 8);
ConFoffon_before = T(1,2:7);
ConFoffon_after = T(1,10:end);
nostim_before = T(2,2:6);
nostim_after = T(2,10:14);
% Group data into a matrix: rows = groups, columns = subjects
data = {
ConFoffon_before, ConFoffon_after;
nostim_befo... |
1483b97192d0ab758b98a86f81bda2f3f4ceb0de965057b6a6bc40490ca83622 | MATLAB | 2,905 | 104 | clc; clearvars; close all;
T = readmatrix('source_data_file.xlsx','Sheet', 4);
ConFon_before = T(1,2:7);
ConFon_after = T(1,10:end);
nostim_before = T(2,2:6);
nostim_after = T(2,10:14);
% Group data into a matrix: rows = groups, columns = subjects
data = {
ConFon_before, ConFon_after;
nostim_before, nostim_... |
3f48f7f2a1775522bf1190224b640da4216725cfd39edfa103420166f6d90818 | MATLAB | 2,906 | 72 | %% demo_007 Legacy option conversion
% Demo_007 demonstrate the use of psignifit 4 for users of the Wichmann & Hill (2001) "legacy-toolbox" psignifit 2.5.
%
% The bootstrap-based psignifit 2.5 toolbox allowed the user to change the
% behaviour of the (constrained) ML-estimation, statistics and plots via a
% list of opt... |
f87fd50e3919c218f023c652e5626345ef3d88209c907eaab8dde113f9a608a1 | MATLAB | 2,907 | 81 | %% Gergely Tarcsay, 2024 Ewell lab. Script to generate performance for the lesion experiments (Fig 1)
close all
warning('off','all')
if ~exist("lesion_struct", "var")
load ("G:\HPC lesion\LesionData.mat")
end
%get all days starting from day when passed
ctrl = find(lesion_struct.details.Group == "c");
le... |
45653bb18cc632a82a2b5237ae37e0bdb2bf538067a96620cf1d66be176fbd03 | MATLAB | 2,914 | 80 | function [ feat_train, feat_test ] = CBIG_FC_FeatSel( FC_train, FC_test, y_train, threshold )
% [ feat_train, feat_test ] = CBIG_FC_FeatSel( FC_train, FC_test, y_vec, fold_index, threshold )
%
% This function selects a subset of functional connectivity (FC) entries as
% features for future predictive models. The sele... |
62a26c0fd6cafbe493c3aec8d668db2145cffa327609a78ae736bfc308f20ab8 | MATLAB | 2,914 | 123 | function outpict = imecho(inpict,nechoes,varargin)
% IMECHO(INPICT, NECHOES, {OPTIONS})
% blends delayed frame copies with an image animation
%
% INPICT is a multiframe I/IA/RGB/RGBA image of any standard image class
% NECHOES is the number of image copies to be blended
% OPTIONS include the following key... |
98d70611548da2eaf0eeeb02db473af61ce5bcbd3dd51974299e369e4cafac68 | MATLAB | 2,918 | 70 | % Script to perform motion regression by fitting a GLM to each voxel time series using the six motion parameters
% as regressors to remove motion-related variance.
function S03_GLM_empty(subject, game)
root_path = 'YOUR_DATA_PATH';
main_dir = strcat(subject, '/', game) ;
sess_no = 5;
GLM_name = 'GLM_empty';... |
36843dd186182e54e6c1deb80d1216ef2d325b230cf4a310a07737ac6ee0ab2e | MATLAB | 2,923 | 107 | function allP = factor3(innum,varargin)
% P = FACTOR3(N,{OPTIONS})
% Find the factor triples of an integer. This is useful for finding
% the 3D geometries into which a given vector can be arranged,
% for instance, when devectorizing images of unknown geometry.
%
% N is a positive scalar integer (not necessar... |
a962044ad8c49e8e6dd87afc8705f8e1065e5231bc939d93d41660dd67b6a0ec | MATLAB | 2,928 | 77 | function [g,a,mu2]=ar1(x)
%% AR1 - Allen and Smith AR(1) model estimation.
% Syntax: [g,a,mu2]=ar1(x);
%
% INPUTS
% x: time series (univariate).
%
% OUTPUTS
% g: lag-one autocorrelation estimate.
% a: noise variance estimate.
% mu2: estimated square on the mean.
%
% AR1 is based on the approac... |
f8bf92a053ebe47c25a1f458ea7a13b6e2ba6c6dbdbf37f0980901f50adc7994 | MATLAB | 2,930 | 83 | % If handles is a matrix, columns will be interpreted as graphics for multiple selections
function selector = plotDataSwitcher(handles, container, dataList, description)
% Default arguments
if nargin < 4
description = '';
end
% Case for enabling multiple selections
isMultiple ... |
3824057aab0baff479b7f16c2ab5e09214e644bf25539f10d05cebd523e79700 | MATLAB | 2,932 | 72 | %WAVE_BASES 1D Wavelet functions Morlet, Paul, or DOG
%
% [DAUGHTER,FOURIER_FACTOR,COI,DOFMIN] = ...
% wave_bases(MOTHER,K,SCALE,PARAM);
%
% Computes the wavelet function as a function of Fourier frequency,
% used for the wavelet transform in Fourier space.
% (This program is called automatically by WAVELE... |
0e3f24a9acda9d505b899a92c112900600183a32fad5093f92998092cc3bee4d | MATLAB | 2,935 | 71 | clear all;close all;clc;
restoredefaultpath;
addpath(genpath('/home/ajoshi/coding_ground/bfp/dev/gifti-1.6'));
addpath(genpath('/home/ajoshi/coding_ground/svreg/src'));
addpath(genpath('/home/ajoshi/coding_ground/svreg/3rdParty'));
addpath(genpath('/big_disk/ajoshi/freesurfer/matlab'));
%% Resample from one sphere to ... |
479e34d5313705377b1eeeeb9df72f29a7fafb2ee8c554581d071a8b5bf2bf6c | MATLAB | 2,939 | 61 | function [TFR] = dtx_TFRtrials(cfg, Trialdata, force)
% This file is part of EpiCode, see
% http://www.github.com/stephenwhitmarsh/EpiCode for documentation and details.
%
% EpiCode is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% ... |
b26c80d29ff3236af65bd527a869ee2827b59e7438d59e0382f9787484c6d275 | MATLAB | 2,940 | 78 | function fLocGroupAnalysis(sessions, clip, stc)
% Automated group analysis of fMRI data from fLoc localizer experiment
% using vistasoft functions (https://github.com/vistalab/vistasoft). If
% there is an error, the code terminates the analysis of that session but
% then continues on to the next session.
%
% INPUTS
%... |
db85e94dabe8fc4e0afddd3733463ed6c16130480869134db7f92beb44acc3f7 | MATLAB | 2,940 | 109 | function outpict = dilatemargins(inpict,margins,se,varargin)
% DILATEMARGINS(INPICT, MARGINS, SE, {OPTIONS})
% Performs selective dilation & erosion on lightest and darkest pixels.
%
% INPICT is an I/IA/RGB/RGBA image of any standard image class
% MARGINS is a 1x2 vector specifying the width of black and wh... |
5ade8ed2c29028b19dadeb56046212aee66a9f7571c402d5ece617d16603a0b0 | MATLAB | 2,948 | 83 | % this script allows to convert .h5 to .nii files
% dependencies: spm
% @FIL UCL
% written by Oliver Josephs
% modifications for extra contrasts: Barbara Dymerska
% select nr of contrasts to convert
% 1 - magnitude, 2 - magnitude + phase, 3 - magnitude, phase, B1+ map
nr_of_contrasts = 3 ;
% select your h5 directorie... |
cd88536528ff2954b8a596d6f71a94f95825ebce3889f1ba4f4600cf63d17573 | MATLAB | 2,953 | 92 | function outpict = tonergb(inpict,Tr,Tg,Tb,Tsat,enforcement)
% OUTPICT = TONERGB(INPICT,TR,TG,TB,TSAT,RANGETYPE)
% Adjust image tone by adjusting RGB components relative to the
% RGB and saturation distribution in an image.
%
% This is based on Iain Fergusson's GMIC tools.
% https://github.com/dtschump/gmic-commun... |
2a891edf611219a0b88a632fe76020bf6f5d4ea2bdb903f62b4dc790c204042e | MATLAB | 2,954 | 67 | % Constructs an array B that contains a subset of the specified indices in A for dimension dim.
%
% Suppose that A is of size n-by-m-by-k, and indices is of size n-by-1-by-k. Then the call
% B = selectarray(A, 2, indices)
% will produce a n-by-k array B where for each index i of the first dimension (rows) and eac... |
c64d0ceb425768d86a594dc11c9cca521793f857f8e62efb8c2981860475e829 | MATLAB | 2,956 | 42 | classdef activityMapParams
% activityMapParams: This class holds the parameters needed to construct an activityMap object
% Open activityMapParams.m to see what the parameters are and which need to be set
properties
% these need to be set before constructing an activityMap
preLimit... |
63354390d6d99a138b55cf8777eca97228ff40027cf41c5b1226cea0dc537a2b | MATLAB | 2,958 | 76 | function maskdots=computelinmask(nd, plotsize, xcenter, ycenter, lifetime, min_sp, max_sp, fr)
%maskdots=computelinmask(nd, plotsize, xcenter, ycenter, lifetime, min_sp, max_sp, fr)
%
%Calculates the display dot matrix for a linear mask
%
%INPUTS
%nd number of mask dots
%plotsize
%x... |
9628527ba8339af73053ba04baccd660455cc20e75fae5c56a3386a425e0a098 | MATLAB | 2,958 | 74 | clear all;close all;clc;
restoredefaultpath;
addpath(genpath('/home/ajoshi/coding_ground/bfp'));
addpath(genpath('/home/ajoshi/coding_ground/svreg/src'));
addpath(genpath('/home/ajoshi/coding_ground/movie1/subaxis'));
p_dir_ref = '/big_disk/ajoshi/HCP_data/'
cmap=bipolarcmapW(100,[-1.5,1.5],'linear','br')
hemi = 'left... |
92786d75470fc71f06e4e1db81ab1fbfe9c9bb1f2b3ecb38fbe331cd5f15e115 | MATLAB | 2,967 | 86 | %
% BDP BrainSuite Diffusion Pipeline
%
% Copyright (C) 2019 The Regents of the University of California and
% the University of Southern California
%
% Created by Chitresh Bhushan, Divya Varadarajan, Justin P. Haldar, Anand A. Joshi,
% David W. Shattuck, and Richard M. Leahy
%
% This program is free sof... |
a18272fb2e03a7f11c84f05c7aec1e3d800c6b69d4a2722f66f89b762bc2129b | MATLAB | 2,975 | 68 | clear
experiments = get_experiment_redux;
fs = 32000; % from data
save_data = 1;
downsampling_factor = 32; % downsample for LFP analysis
fs_LFP = fs / downsampling_factor;
high_cut = fs / downsampling_factor / 2; % nyquist
ExtractMode = 1; % extract from neuralynx into matlab
threshold = 7; % threshold sharp waves de... |
6ecca165524df6a15869bfc96613284ea84f72952bd6747cb9fe6b230c946d76 | MATLAB | 2,978 | 87 | function [outpict TF] = histeqFB(inpict,varargin)
% OUTPICT=HISTEQFB(INPICT,{NBINS})
% OUTPICT=HISTEQFB(INPICT,{HGRAM})
% [OUTPICT TF]=HISTEQFB( ... )
% Adjust the contrast of an image such that its intensity distribution conforms to that described
% by a given histogram. If no histogram is given explicitly,... |
e173da507bb0a55ca8b7127d7c9c87275d638c0e509fb9d8b134f81fe5d766cd | MATLAB | 2,982 | 86 | classdef varMenus < handle & dynamicprops
properties
extra_room = 75;
length_slider = 375;
width_slider = 15;
left_slider = 160;
bott_slider = 40;
left_str = 50;
curr_left_str = 0;
min_left_str = 90;
... |
11505fbb12634f8a6c4a2ffaa25b727f8b64ab33470c4a1ddb8a85c01ae8fe74 | MATLAB | 2,983 | 65 | function [trialinfo,circuspath] = writemicroforspykingcircus(cfg, MuseStruct_micro)
fname_output = fullfile(cfg.datasavedir,[cfg.prefix,'single_pattern_',cfg.label,'_SC_trialinfo.mat']);
if exist(fname_output,'file') && cfg.force == false
fprintf('Loading trialinfo: %s \n',fname_output);
load(fname_output... |
d6daef69d6856da1b146f5458eff9eede5b89ffe2b1df70488a7b63a896bec88 | MATLAB | 2,983 | 87 | % ACCUMSTATS Output combined arithmetic mean and variance of all arguments
%
% Inputs
% ========
% nSamples : Number of samples used to compute the mean and variance of each input argument. If
% only one entry is provided, the same nSamples is assumed for each input.
% dim : Dim... |
d2040701eaeb7a62e175e20c19ba007378496156ce31a8d6b84f3e63023aaa10 | MATLAB | 2,984 | 102 | function [spE,sEp,prior_pd,post_pd] = spm_prf_get_ppd(PRF,xy,idx,nsamp)
% Sample from the prior (or posterior) of a pRF model and run samples
% through the likelihood, to give the prior (or posterior) predictive
% density (PPD).
%
% PRF - estimated PRF
% xy - coordinates in stimulus space to sample
% idx - ind... |
2c382af70e237a1daaf801c41a563cf2a8203a47aee6e0efc14efcf0118db752 | MATLAB | 2,990 | 90 | function clickPlot(im, mask, R, tbl, count, O)
imsize = size(im.(O{1}));
spotRow = table2array(tbl(:, 5));
spotCol = table2array(tbl(:, 6));
nSpots = size(spotCol, 1);
figure('Name','spotspotcheck','NumberTitle','off','units', 'normalized', 'position', [0 0 1 1]);
ax = imagesc(im.(O{1}));
s... |
84f33d973252269b0f8537f2a001059262c9ec12349870720a43eb459a2bd3d7 | MATLAB | 2,992 | 94 | clear
close
%% PLOTTING
lwd = 0.2; % Vs, Ca_pc
lwd2 = 0.7; % I_ast
figure;
t = tiledlayout(7,26,'TileSpacing', 'compact','Padding','tight');
PATH = './../Systems/Pyramid_astro/transients/';
% FIG. 2b
fileNames = {'1_IPeq_02', '2_IPeq_02', '3_IPeq_02', '4_IPeq_02', '5_IPeq_02', '6_IPeq_02', '7_IPeq_02'};
tlims = [0... |
313c04616d6dbf6e5b4806a6ff931824a4ffcf2c497a0c8fbe3a2baefde85e0b | MATLAB | 2,993 | 89 |
function next = cosine_filter(input,W)
disp("Cosine filter setup...")
function cosFilter = CosineFilter(N, w, symmetric)
%**************************************************************************
% profile goes from 1 to 0 over some specified width. The square of the
% cosi... |
20dac830ffad7cf36580c98ed825b541bfab2ff9ae4e80d7be541a5347019f79 | MATLAB | 2,994 | 119 | function outpict = meanlines(inpict,dim,mode)
% MEANLINES(INPICT, DIM, {MODE})
% Returns an image wherein all pixels in row or column vectors have
% the mean, max, or min values in corresponding vectors of INPICT.
% Can be used for shading or shifting images.
%
% INPICT is an I/RGB image of any ... |
321772533867dab64264d5923577efab921396394c779cb11187ca7aa9a8c3b6 | MATLAB | 3,000 | 100 |
addpath( genpath('/usr/share/fsl/5.0/etc/matlab'));
%% Reading Files
clear all
tic;
seg=read_avw('T1w_acpc_dc_restore_brain_seg.nii.gz');
wm=read_avw('T1w_acpc_dc_restore_brain_pve_2.nii.gz');
gm=read_avw('T1w_acpc_dc_restore_brain_pve_1.nii.gz');
csf=read_avw('T1w_acpc_dc_restore_brain_pve_0.nii.gz');
t1t2=read_avw(... |
5b98b716ad997e795f1f2cd4aaa6d04739f75c3db5230e83222c81f91a44766d | MATLAB | 3,007 | 42 | classdef activityMapParams
% activityMapParams: This class holds the parameters needed to construct an activityMap object
% Open activityMapParams.m to see what the parameters are and which need to be set
properties
% these need to be set before constructing an activityMap
preLimit... |
5313611e16913c16ae44de943f86099a9d9850ecbc246d549a17828a22dad9a3 | MATLAB | 3,009 | 122 | function [tosquare,quad,tosquare2,quad2,D]=nt_qca02(x,npcs,nsmooth)
%[tosquare,quad,tosquare2,quad2,D]=nt_qca02(x,npcs,nsmooth) - maximize induced power using quadratic component analysis
%
% tosquare: matrix to most reproducible induced component
% quad: most reproducible quadratic component
% tosquare2: matrix to ... |
bb5ea3c6876c857ad668cbdd65124b5d35fe5a92e92d629a9835c6025a372444 | MATLAB | 3,011 | 63 | function [hist_count, bin_center, hist_count_total, bin_center_total] = histcParzen(x, x_range, nbins, win_width, nthreads)
% Computes parzen window estimate of the histogram of input data. The histogram bins are uniformly
% spaced in the specified x_range. Cubic B-spline window with variable width is used as the parze... |
92ff6b4364266c2c0dc1b6c4b2740339014e838bbd7a78f899e6d7ed74f7bca2 | MATLAB | 3,012 | 101 | function [BS,bs_name,attysflag] = getBSdata(BSfolder)
%usage [BS,bs_name,attysflag] = getBSdata(BSfolder)
% BS folder -> insert the path of the folder up to the subject code as in 'C:\Users\Post_Box\AG06\'
% Output the BSData in struct and the corresponding starttimes
% BS.triggers contains the voltage values corr... |
e66bf563c5516f3d4a7c413964b8d551a191bebf0978fe5174ed55b2b1417fd3 | MATLAB | 3,014 | 44 | function pptwrite(data, fname, check)
%pptwrite(data, fname, check)
%
% writes the data created by runtrials_single, runtrials_double,
% or runtrials_ident (completed trials variable) into an ascii file.
% If check is set to 1, existing files will not be overwritten
% and a warning will be issued.
%
%INPUTS
... |
f2c8262052b7f7acb9c79f9b601bb3e07f6798da3ea535cf2da0cfa3a3f0d700 | MATLAB | 3,020 | 88 | %FilterLFP - Filter the local field potentials, e.g. in the theta band.
%
% Filter the local field potentials using a cheby2 filter.
%
% USAGE
%
% filtered = FilterLFP(lfp,<options>)
%
% lfp local field potentials, list of (t,v1,v2,v3...) tuples
% <options> optional list of property-value pair... |
44376a3e0c4e13aa856da6ac81b1f219b669452958e95aa0f2bce022d6c4c5eb | MATLAB | 3,027 | 129 | %%
% xbar(data, 'Legend', {'x', 'y', ...}, [... legend options ...])
% xbar(x, h, 'Legend', {'x', 'y', ...}, [... legend options ...])
% xbar({u, xU, yU}, data, ...)
%
function [handles] = xbar(varargin)
% Parse input config
narginchk(1, inf);
if iscell(varargin{1})
[units, xUnit, yUnit] = g... |
187c311fcbb7caac72b9dce538b0192b2a657ffc42f14070dc86c64e531aea20 | MATLAB | 3,035 | 87 | function [fwhm1,fwhm2] = mwave(meanwave,si,varargin)
% [fwhm1,fwhm2] = mwave(meanwave,si,varargin)
% computes the widths of the first and second response peaks of
% the spike waveform (full width at half maximum)
%
% ARGUMENTS
% meanwave required - vector containing the mean spike waveform
% si required - s... |
a4f292674c0007f19710084205e888d52b3cf50063363fc41153e53a6c10f55f | MATLAB | 3,044 | 108 | function z=nt_double2int(x,param)
%nt_double2int() - recode/decode double as integer to save space
%
% z=nt_double2int(x,intsize): recode double as integer
% z: coded data
% x: data to code (matrix or array of matrices)
% intsize: [default: 'int16']
%
% x=nt_double2int(z,indices): decode back to double
% x: dec... |
8e21205463457b33a3f8cc6b5c9cd55fc7f158a8ad1ec2a67d16319194c6c84d | MATLAB | 3,048 | 100 | function plotdata_stim_trial(cfg,dat_micro, dat_macro)
% select data for plotting
if ~strcmp(cfg.frequency,'all')
selfreq = cfg.markers.Frequency == cfg.frequency;
else
selfreq = ones(height(cfg.markers),1);
end
if ~strcmp(cfg.current,'all')
selamp = cfg.markers.Current == cfg.current;
else
selamp = ... |
08827a2be4a2e581d45d222cd8ed868b06eea14da166ec603d08175de2e30154 | MATLAB | 3,052 | 135 | function y=nt_cell2mat(x)
%y=nt_cell2mat(x) - convert cell matrix of nD matrices to (n+1)D matrix
%
% y: (n+1)-dimension matrix
%
% x: cell matrix of matrices
%
% Similar to matlab's cell2mat() but much more flexible.
%
% If matrices in x are of different dimensions or sizes, the result is
% based on the largest di... |
06ec3e8066fbf54c2a986561e5b287851b4df4f7701c0d2cb2bd8cb838006dd8 | MATLAB | 3,057 | 130 |
load data/MGB_FR.mat MGB_FR
MGB_FR_laser = MGB_FR;
load ../PV_SOM_inh/TRN_recip/data/MGB_FR.mat MGB_FR
MGB_FR_recip = MGB_FR;
load ../GJ_PV_SOM/PV_SOM_inh/TRN_recip/data/MGB_FR.mat MGB_FR
MGB_FR_gj = MGB_FR;
load ../recip_div_TRN_inh/data/MGB_FR.mat MGB_FR
MGB_FR_div = MGB_FR;
load ../recip_div_TRN_wSOMlat_in... |
6111832442e9a30e723fefd51bd271ebf0aa542aca44f43418e842f52170f61f | MATLAB | 3,057 | 99 | %
% BDP BrainSuite Diffusion Pipeline
%
% Copyright (C) 2019 The Regents of the University of California and
% the University of Southern California
%
% Created by Chitresh Bhushan, Divya Varadarajan, Justin P. Haldar, Anand A. Joshi,
% David W. Shattuck, and Richard M. Leahy
%
% This program is free sof... |
6843285e053f060a72feb018bb0fb1daa413caa420aa1c8e2f057b09802b81a3 | MATLAB | 3,057 | 67 | function p = CBIG_corrected_resampled_ttest(accuracy_vec, portion, threshold)
% p = CBIG_corrected_resampled_ttest(accuracy_vec, portion, threshold)
%
% This function tests whether an accuracy vector (obtained from cross-validation)
% is statistically different from a threshold. The accuracy vector can also
% repres... |
6df38c20f7129cb72d9eca0f5c75ede7aef8eea0c381e20027992fd466a17689 | MATLAB | 3,066 | 89 | function text2spectrogram(instring,outpath,textheight,textlocation,alteraspect,volume,blursize)
% IM2SPECTROGRAM(INSTRING, OUTPATH, {HEIGHT}, {LOCATION}, {ALTERASPECT}, {PADBAR}, {VOLUME}, {BLURSIZE})
% use inverse short-time Fourier transform to encode a text string as a marquee in audio spectra
% Output... |
1c0744db3227d44ccc3619ce5464980dcbb595d549bc175a06497e062f3c5125 | MATLAB | 3,067 | 116 | function [a, varargout] = rwLCA(x, phi, thrtype, eta, gamma_val, maxIters, group_cell, varargin)
% test for number of required parametres
if (nargin-length(varargin)) ~= 7
error('Wrong number of required parameters');
end
% set the defaults for the optional parameters
compute_mse = 0;
% read the optional paramete... |
6a288f8a46aa6405a0ff30484371d33e3c8336582d0285fb75d776e6bae48bec | MATLAB | 3,067 | 82 | %%
function [kernel] = kdeBhattacharyya(alpha, beta, varargin)
%----- Sanity check for format of input
narginchk(3, inf);
example = varargin{1};
nDims = numel(varargin);
nComponents = size(example, 1);
nData = size(example, 2);
if nComponents > 100
w... |
a75e27163dca92ff9780081f5c4c068d6ac1977a22cd186748c1abb18c1643b7 | MATLAB | 3,067 | 86 | function out = effprint(effects, effectType)
%% Interpret effect sizes of a certain types in terms of 'small', 'medium'
%% and 'large' according to Cohen's rule of thumb.
% Source: Cohen, J. 1988. Statistical Power Analysis for the Behavioral
% Sciences. Vol. 2nd. Hillsdale, New Jersey: Lawrence Erlbaum Associates.
%
... |
ec4b7d4d0add9aede9fbe6a41dca6a363e27a1c3e285efc3aaadfa1c8b9d387e | MATLAB | 3,069 | 118 | function I = cmi_ggg_vec(x, y, z, biascorrect, demeaned)
% CMI_GGG Conditional Mutual information (CMI) between two Gaussian variables
% conditioned on a third
%
% I = cmi_ggg(x,y,z) returns the CMI between two (possibly multidimensional)
% Gassian variables, x and y, conditioned on a third, z, with bias cor... |
c537c18a84e127a36fa7e01e4f089589bd8fb802222e9c6aca0b3700d9a70f0e | MATLAB | 3,071 | 81 | function out = Pyramid_only
out{1} = @init;
out{2} = @fun_eval;
out{3} = [];
out{4} = [];
out{5} = [];
out{6} = [];
out{7} = [];
out{8} = [];
out{9} = [];
% --------------------------------------------------------------------------
function dydt = fun_eval(t,kmrgd,par_Is,par_Id,par_gsd,par_gCa,par_p)
gKCa_h=15;
C_h=3;... |
f0790101ae569a8f1350cbba301ecefedefaef42dafe3ca0610d9af7419c2763 | MATLAB | 3,083 | 86 | function cohSpikeLFP(suffix)
% WAVELET ANALYSIS
% Determine phase consistency between LFP and spikes over the frequency
% spectrum. LFPs are decomposed with the wavelet transform.
%
% Read parameters
Params = read_params(suffix);
freq = Params.freq_start_1 : Params.freq_step_1 : Params.freq_end_1;
... |
d651bda8adbebb590fe5ae3aa758e5019d4266dc36c9b4df6dc8a6a85e3e7c4b | MATLAB | 3,086 | 79 | function nlx2DAT(animal, experiments, channels, broken_channels, folder2save, common_average_reference)
% by Mattia 8.11.18 based on https://github.com/kwikteam/klusta/issues/48
% Convert .nlx files to .dat:
% - Estimate chunksize for the data (max allowed by memory)
% - Copy data from server to local disk
% - Write ... |
51f16ac2426f2724ef9a9a4d6e4edf01d74efd7f0482a79feabeeb70ba2b8940 | MATLAB | 3,089 | 104 | function [y_final,SEM_final,x] = bar_plots_OPS_results(final_ind1,final_ind2,position_analysis,DI2,variable,fig_title,groups_legend,y_label)
% [y_final,SEM_final,x] = bar_plots_OPS_results(final_ind1,final_ind2,position_analysis,DI2,variable,fig_title,groups_legend,y_label)
% plot rm ANOVA results for OPS data
%
% ... |
dbf66c6554841d3e7832f08b7b7a91713c60e5108e2f047ade16d7c103f3c98c | MATLAB | 3,092 | 72 | function CoherenceStuff = ...
getCoherence(LFP1, LFP2, fs, win_length, overlap, nfft, ...
folder2save, animal_name, repeatCalc, save_data)
% calculates Coherency and Coherence as in Nolte et al., 2004
% by Mattia, 01/21, adapted from a script of Joachim and Sebastian
% inputs: - signal & 2: two signal b... |
41fb8bc01299d28b68b24edf0e4fac48f9d99dea8e41ca9595aa51ea19ec80bc | MATLAB | 3,098 | 123 | %%
function [position] = findhelper(array, inReverse, varargin)
narginchk(3, inf);
sequence = 1:numel(array);
% Special case with index range as input
if numel(varargin) > 1 ...
&& ~islogical(varargin{end}) ...
&& isnumeric(varargin{end})
select ... |
87789d02b5e2a9b404c30d85817b98dbb68a945d362e2e2db71a60fdf3c71b36 | MATLAB | 3,098 | 88 | function plotSwitcher(figureHandles, monitor, varargin)
% Default arguments
if nargin < 1
figureHandles = findall(0, 'Type', 'figure', 'Visible', 'on');
end
if nargin < 2
monitor = -1;
end
if isempty(figureHandles)
return;
end
% Create GUI
guiWidth ... |
58efe7ccb2ae001ba428e08cffb98f63a6fd077320139c38e91bd133161c55ff | MATLAB | 3,107 | 91 | % ALIGNFIGS Align all figures to a common position on screen
%
% Inputs
% ========
% figHandle : a list of figure handles to align
% displacement : [left, bottom, width, height]
% resize : min, max
% alignment : North, South, East, West
% monitor : monitor index that fi... |
0a3dc18f796e18667bad275453a6d3a87a33da534ad999cd0464061d65e873e9 | MATLAB | 3,110 | 75 | function pinv_sens = morse_calc_pinv(ref, PPIparams)
%**************************************************************************
%
% morse_calc_pinv
% input ref: data for sensitivity estimation [RO, PE1, PE2, N_coils]
% PPIparams: parameters of the acceleration
%
% output pinv_sens: image... |
b176e9e6c55cecbec76a488aa8c372b8fc2bb0c6ace84cb8e48da14d4385f6ce | MATLAB | 3,114 | 62 | function hspike_spike_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/iss01/charpier/ana... |
fc1ac70c88d2e9d54140480b578a89fcc6af1eb46704b45833572544acd4740a | MATLAB | 3,119 | 74 |
% example script on how to detect oscillations in discontinuous signal
% using:
% - normalized squared signal (NSS)
% - thresholding the baseline
% - merging neighboring events
% - thresholding the peaks (absolute and relative) - the absolute part is the
% main difference with the old version. The specific of this ... |
b36c643e58aea4c67aa8762347057d8828e7718007b3bdbc1cb568a2dad5fbb1 | MATLAB | 3,121 | 90 | function writeMuseMarkerfile_Brainvision(MuseStruct, fname)
% WRITEMUSEMARKERFILE writes markerfiles for Muse from Brainvision data format.
% use as
% function writeMuseMarkers(MuseStructt, fname)
%
% The input structure can be read by readMuseMarkers.m, and edited before
% writing it back into the Muse file.
% Thi... |
c67a7d636fde5b93e6e4d391dedabe747daa159e9cda85a0a69e3c140fb0e86d | MATLAB | 3,121 | 84 | function writeMuseMarkers(MuseStruct)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% function writeMuseMarkers(MuseStruct)
%
% Crawls and searches through patient- and recording-directories and
% writes markerfiles for Muse. The input structure can be read by
% readMuseMarkers.m, and edi... |
c984ee0a4f6a9de5b81214d9196ed8a68ad80f4ad8e5bec7cf0a3e7a11fc5b54 | MATLAB | 3,124 | 91 | function [offsets, xmin, xmax, ymin, ymax, biggestMapIndex] = registerImages(images)
% Takes cell array, each cell is a 2d or 3d image
% Usage:
% [offsets, xmin, xmax, ymin, ymax, biggestMapIndex] = registerImages(images)
% Inputs:
% images: a cell array, each cell is a 2d or >2d image
% the dimensions of the cell ar... |
2e622c2b409c17e43d78c561e200c0b80eb9f84216f53fb75bf9205896a061f4 | MATLAB | 3,127 | 76 | function [erp_data, indx] = generate_erp_data(EEG_integrals_am, EEG_integrals_nam,participant, indx, erp_data, options)
%% Calculates ERP per participant
%
% **Usage:** [all_data] = generate_erp_data(EEG1_i, EEG1_d,participant, indx, all_data)
%
% Input(s):
% - EEG1_i = EEG struct with epoched integral data
% - EEG... |
30dfa9dca27b50744cbed6ad58285b8c21656d29c1bda8a91b5e39a81756fc3d | MATLAB | 3,135 | 120 | function outpict = bicoloradapt(inpict,missingch)
% BICOLORADAPT(INPICT, MISSINGCHANNEL)
% Emulates the effect of long-term use of a crt monitor with
% a missing cathode amplifier, where sensory adaptation tends to
% relate the secondary color as a new white point. Also includes
% background glow from the pres... |
df748a3d56b09c6155b795e3b0614d8a3667f2fd7dc082f69989b92efcec16ba | MATLAB | 3,136 | 70 | function [rotated_subset_members nct_subset_rotated]=nct_analysis_subset_rotated(A,T,rho,x0,xf,subset_ids,perm_id)
% function computes control energy and stability for two states within an
% task, when a subset of regions is as a network prohibited from control
% Sebastian Markett (2022),
% using code from Urs Bra... |
50f674e5bedf95242c3ca54be54bef5aa0bb285b528aa86c8f689a3b68308e6a | MATLAB | 3,138 | 84 | function theta = getStandardParameters(theta,type,widthalpha)
%function theta = getStandardParameters(theta,type,[widthalpha])
% this function transforms a parameter given in threshold, width to a
% standard parameterization for comparison purposes
%
% theta = parameter
% type = Name of the Sigmoid
%
% if you changed ... |
6eaa73fc2b574540a0e146d487e85f00cd20ea88195c5099a936400c162e9572 | MATLAB | 3,143 | 111 | %% Pierce's criterion for rejecting outliers.
% Adapted from https://r-forge.r-project.org/R/?group_id=1473
function [accept, reject] = peirceCriterion(v, sdv, m)
%%
if nargin < 2
sdv = std(v);
end
if nargin < 3
m = 1;
end
v = v(:);
%%
lenv = numel(v);
mo1 = lenv-1; ... |
f226144b8524e0e76770d02c91d24cfc69b40043e190f41160b31fda6681cf0c | MATLAB | 3,148 | 78 | function [fun,varargout] = bilin_fun(S, Y, A, h, D, opt)
% function [fun,varargout] = bilin_fun(S, Y, A, h, D, opt)
%
% Function to calculate function value and gradiet for a bilinear
% function.
%
% 2018 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
S = reshape(S(:),[... |
b9f68a3707f3d1649223cb4b731f4e64825ae5c63c73cd4ba0b779d21cb3e73e | MATLAB | 3,155 | 73 | %% CREATEHEADERCOMMENT Parses the current document pane for the first function definition, and generates comment text suitable for documenting the use of this function.
%
% This code is not meant to be used standalone, but as an insertion function provided to
% EditorMacro(). One easy way to use this is to insert... |
3c2f99b04c3242fcf9fe64337ca824d04515966d94927190f5618f60949c90c7 | MATLAB | 3,168 | 95 | function plotTimeCourses(cfg,dat_micro,dat_macro)
for imarker = 1 : size(cfg.name,2)
fig = figure;
for ifile = 1 : size(cfg.plot.fname{imarker},2)
cfgtemp = [];
cfgtemp.dataset = cfg.plot.fname{imarker}{ifile};
hdr = ft_read_header... |
ca6a77be0e152ecf8b53367f9e878b21ef7a520ffb905cab055fbba7ee1090ed | MATLAB | 3,168 | 126 | function outpict = despeckle(varargin)
% OUTPICT=DESPECKLE(INPICT,MINSIZE,{MODE},{CONN})
% Removal of small features in a binary image by connected group size. Depending
% on the settings, this is equivalent to group-size-based image opening or closing.
%
% INPICT is a binary image. Multichannel and multifr... |
f6d2098fcf7bf9acc5c81472ca570a5b250cbdc2a995b2d7ab74937d3c317001 | MATLAB | 3,170 | 80 | function varargout = call_func_for_all_participants(path,save_path,f, options)
%% Calls a function for all the participants (reads the EEG struct of the participant)
%
% **Usage:** [] = call_func_for_all_participants(path,save_path,f, options)
%
% Input(s):
% - path = path to raw data
% - save_path = path to save ... |
d118c6141a7394d455d0ac15d12fbf0aa6a6457cb296fa3d8916ae6c8ac92148 | MATLAB | 3,173 | 95 | function matchPursuitLFP(suffix)
% LFP POWER
%
% Output:
% Power Matrix (trial type x freq x time).
% Data is written to a text file. Each row is a time series of power for
% a given frequency and trial type. Rows are grouped in blocks of trial type,
% with each row being the next frequency.
%
% AUTHOR: Charle... |
519c022948974c95f385f56378824b5a1921b7e10a66dfe1f496a08346c9ee39 | MATLAB | 3,174 | 96 | function plotsModelfit(res)
%function plotsModelfit(res)
% plots some standard plots, meant to help you judge whether there are
% systematic deviations from the model.
%
% These are the same plots as presented in psignifit 2 for this purpose.
%
% The deviance bootstrap samples plot is generated with getDeviance, i.e.
%... |
5a76ca9b8c256e81201b7299e98c1a72146e7ad22388f227e7d8583215700530 | MATLAB | 3,174 | 71 | clear all;close all;clc;
restoredefaultpath;
addpath(genpath('/ImagePTE1/ajoshi/code_farm/bfp/dev/gifti-1.6'));
addpath(genpath('/ImagePTE1/ajoshi/code_farm/svreg/src'));
addpath(genpath('/ImagePTE1/ajoshi/code_farm/svreg/3rdParty'));
addpath(genpath('/big_disk/ajoshi/freesurfer/matlab'));
%% Resample from one sphere ... |
5b4182f41c93b1735331eb264038f104084778c7acfbbc611c17578ce4e762d3 | MATLAB | 3,174 | 81 | function [fun,varargout] = bilin_fun(S, Y, A, h, D, opt)
% function [fun,varargout] = bilin_fun(S, Y, A, h, D, opt)
%
% Function to calculate function value and gradient
%
% 2018 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
S = reshape(S(:),[size(Y,1), size(A,1)]); ... |
f11ba3ab16aded8b680b78603f7e4f286609d9cc7f04cc1f4eef82fbb6aa778e | MATLAB | 3,176 | 68 |
% This is a sample main file that reads two grayordinate fmri files generated by bfp and outputs the synced files.
clc;clear all;close all;
addpath(genpath('/home/ajoshi/coding_ground/svreg'));
addpath(genpath('../'));
load LBO_right
LBOr=LBO;
load LBO_left
ids={'sub18604','sn4055','sub08224','sub05676','sn8133','tr4... |
6b5ac5142cc2450e97c342c6072a1dd3ffd64bebc64b01c6c60d9206aa6f8a37 | MATLAB | 3,190 | 93 | function [copyHandle] = copyGraphics(sourceHandle, targetHandle, positionType, offset, scaleFactor, units)
% COPYGRAPHICS Copies a graphical object with smarter preservation of
% properties.
%----- Basic copy function
copyHandle = copyobj(sourceHandle, targetHandle);
for iObj =... |
d01adbe1badbadfa3247b122dfb547043f31988fbf127a3267c9e1c301570614 | MATLAB | 3,199 | 107 | % main_gene_surrogate.m
load(strcat(projectRoot,"/data/processed/surrogate_genes_org.mat"));
surrogateGeneMatrices = permute(surrogate_genes,[2,3,1]);
clear surrogate_genes
%% Calculate Moran's I
%{
surrogateGeneMoransIMatrix = SpatialAutocorrelationCalculator.calculateMoransIMatrix_forSurrogates(...
surrogateG... |
2a9d30a0bd19b6c3c06e74b5d8703d05cbf902e6495983602b7b631d6dd58165 | MATLAB | 3,200 | 81 | % wrapping function analyze rate overlap
function [All,Cohort, Individual] = WrapRateOverlap(workdir, discrimination)
All.ROS = [];
All.RewROS = [];
All.OutROS = [];
All.RewDist = [];
All.RZID = [];
All.Pref = [];
All.MeanRate = [];
All.N_events= [];
All.Size = [];
All.NFields = [];
Cohort.ROS = ... |
2e5ce16ca23d7dde6b8282f161dc72d009a45869a385f35f20b8920ac4f842eb | MATLAB | 3,202 | 71 | function [out_nii, file_out] = fixBSheader(hdr_src_file, infile, output_file)
% A hack for (inconsistent) headers of BrainSuite/SVReg files. If input files, hdr_src_file and
% infile, overlay correctly in BrainSuite then this function modifies header of infile such that it
% is consistent with the hdr_src_file and stil... |
97ec3a2f6fc0f449c5b7a93a60cecbdbadcedf17603956dac52c1a9eea38a9f2 | MATLAB | 3,205 | 77 | classdef PairDataCCAAnalysisModel
% PairDataCCAAnalysisModel
% Performs CCA analysis and computes Wiring PI in a single workflow.
properties
CCAResultsData CCAResults % Stores CCAResults object
WiringPIPairsData WiringPIPairs % Stores WiringPIResults object
Rec... |
22a0bc2d29c018f91ff4a27a42a61716a2939bea072038c669b0322e5281a0e9 | MATLAB | 3,206 | 68 | function [trialinfo,circuspath] = writemicroforspykingcircus(cfg, MuseStruct_micro)
fname_output = fullfile(cfg.datasavedir,[cfg.prefix,'single_pattern_',cfg.label,'_SC_trialinfo.mat']);
if exist(fname_output,'file') && cfg.force == false
fprintf('Loading trialinfo: %s \n',fname_output);
load(fname_output... |
ac32ed73892394850c39838cc195a6c678a1c6f0d886fc23f8460f0942e2120c | MATLAB | 3,212 | 86 | function [img_1_mask, results_1] = process_images(files, biom_1, results_folder, repeat_name)
%% Process the images to create and save masks for further analysis
%%G&B colormaps
[r_colormap,g_colormap,b_colormap, y_colormap] = create_rgb_colormaps();
%% Plot settings
color_map = [0,0,1];
transparency = 0.5;
... |
238e894be0f2d5cfcfd04cb3c536f1892063e0d567482ea69bc035885b38ccc9 | MATLAB | 3,215 | 68 | function unit_features = getSpikeFeatures(waveform)
% by Mattia 01.19
% this functions extracts waveform features that should be useful for
% distinguishing PYR from IN. Not yet there in neonatal mice, but it should
% work for juvenile/adult.
% input : waveform (thought for the output of klusta, not everything might
%... |
d13595188e52bfac3bfcddad916a891e9e66ebca7b6fb22673cb145ada11da70 | MATLAB | 3,215 | 82 | function [img_1_mask, results_1] = process_images(files, biom_1, biom_folder, repeat_name, biom_set_folder)
%% Process the images to create and save masks for further analysis
%%G&B colormaps
[r_colormap,g_colormap,b_colormap, y_colormap] = create_rgb_colormaps();
%% Plot settings
color_map = [0,0,1];
transp... |
46d15144ae710c0a384e2cfd3584bade42805be6835b86c52ea79cde6c3ff3ad | MATLAB | 3,218 | 86 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% dictionary_learn_script.m
% This scrips it an example script for basic sparse dictionary learning
% based on the Olshausen and Field, 1997 paper 'Sparse Coding with... |
7cfc6b8a1fbe5dfe1320d25419233114089158a576a623d085af33e501ff93e0 | MATLAB | 3,222 | 91 | function [result, montageDims] = stackToMontage(stack, varargin)
% STACKTOMONTAGE: Turn a 3D stack into a montage
% Behaves the same as Matlab's builtin montage function in
% the mode montage(I) except it doesn't display the function
%
% Usage:
% [montage, montageDims] = stackToMontage(stack, numRows, numCols)
% st... |
19ced5840d07e71e56dceea78b3ab6fdd90e582d8c306d0497329734ac9888f2 | MATLAB | 3,233 | 82 | function timeSpikeLFP(suffix)
% TIME SPIKE LFP - Spike triggered average of LFP.
%
% Read parameters file
Params = read_params(suffix);
time_start = Params.time_1;
time_end = Params.time_2;
pass_band = [Params.freq_start_1, Params.freq_end_1, Params.freq_step_1];
if not(all(pass_band >... |
b2bf65f62bb9f01dbe1427870c907a4670c17b29c6fcc008ecd58ed3606bf1af | MATLAB | 3,235 | 89 | function writeMuseMarkerfile(MuseStruct, fname)
% WRITEMUSEMARKERFILE writes markerfiles for Muse.
% use as
% function writeMuseMarkers(MuseStructt, fname)
%
% The input structure can be read by readMuseMarkers.m, and edited before
% writing it back into the Muse file.
% This file is part of EpiCode, see
% http://w... |
ece30c8549494ecaca63e8647ea7387627485d308f8b2aa2afee4a67540aa240 | MATLAB | 3,236 | 75 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
01ae2235a3d0d6af6a1a17497aaae2b060051bfb211afa0aeaad19617ca6d228 | MATLAB | 3,238 | 73 | function SUAdata = getRampSpikeMatrix(experiment, save_data, repeatCalc, ...
folder2save, folderSM, folder4stim_props)
% by Mattia 10/20
% create a spike matrix (actually a tensor) for ramp classic stimulations
% this script arbitrarily divides the 9s stim period in pre
% (3s) stim (3s), taking into account the (... |
01a3f1c7b6a3d1fc3d3204628a704d359504ba6f22c161cddafa098fb67e8708 | MATLAB | 3,242 | 127 | function [ data ] = load_untouch_eig_gz(file, workdir)
% Loads .eig file to nii structure. Each voxel has 12 elements which follows following eig
% structure:
% [v1.x v1.y v1.z v2.x v2.y v2.z v3.x v3.y v3.z l1 l2 l3]
%
% v1, v2, v3 are eignvectors and l1, l2, l3 are eigenvalues, in sorted order.
%
% Also se... |
856dca9def02851e2d940a9a1b4920c689d4f7181327915ceb352378e7cc3e43 | MATLAB | 3,247 | 113 | function mask = rangemask(inpict,channel,range,compmode)
% RANGEMASK(INPICT, CHANNELS, RANGE, {COMPMODE})
% returns a 2-D logical map of all pixels in INPICT specified via
% a set of channel value ranges. This is similar in purpose to
% MULTIMASK() or FINDPIXELS(), but it is much simpler to use
% ... |
e1ba392c02d46abe36161bd69ed84086b5c8cfe212504ce5864edb9c5f7b15c6 | MATLAB | 3,247 | 60 | % -------------------------------------------------------------------------------------------------
% (c) 2025 Leon F. Heffer, David J. Sly, James B. Fallon, Rick Minter, Rebecca C. Felsheim,
% Mathias Dietz and Stephen J. O’Leary.
%
% This file is part of a repository that contains the data originally recorded by He... |
a3533951df493e088608a4d01325e869af2a2afcb3587f23ea42ed836169bbe6 | MATLAB | 3,250 | 79 | function [MuseStruct] = readMuseMarker(name_mrk)
% READMUSEMARKER extracts marker timings (time and samples) created by Muse.
% use as
% [MuseStruct] = readMuseMarker(name_mrk)
%
% with help (code) from Jean-Didier Lemarechal & Craig Richter
% This file is part of EpiCode, see
% http://www.github.com/stephenwhit... |
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