sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
d67631de95ad4390eee49eb001a65040ff63ab1b8b8704559f4a43e16f1705a1 | MATLAB | 4,556 | 165 | function BCCT_Modulate_statGUI
D.fig = figure('Name','BCCT stastic(two groups Modulations)',...
'units','normalized',...
'menubar','none',...
'numbertitle','off',...
'color',[0.95 0.95 0.95],...
'position',[0.3 0.4 0.4 0.3]);
movegui(D.fig,'center');
%%
D.O... |
ede9f63f18963c5f307bf1c8b5857901c9966a07ab0cd88a0155ad6ce687cd31 | MATLAB | 4,561 | 139 | function [index,val,foi,logRatio]=sortVirtualChannel(tmpDataTFR,freqInt,timeWinMax,BLwin,sorting)
%%
indsBL=tmpDataTFR.time>=BLwin(1) & tmpDataTFR.time <= BLwin(2);
if ndims(tmpDataTFR.powspctrm)==3
logRatio=log10(tmpDataTFR.powspctrm./repmat(nanmean(tmpDataTFR.powspctrm(:,:,indsBL),3),[1,1,size(tmpDataTFR.powspct... |
2437ef1b45728f0fdb5eb83122d0c51a6803a0684e6447cfcf55902238a03e0d | MATLAB | 4,578 | 114 | function varargout = process_nst_bootstrap_MEM( varargin )
% process_nst_bootstrap_MNE: Compute source-localization using Bootstrap
% and MEM
% @=============================================================================
% This function is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% ... |
aebdc630ba2535c1255ea72e84d7501c8d7e4358bd3772cb98093793461e8e9c | MATLAB | 4,579 | 105 | function dFC_project = get_lesion_info_v2(dFC_project)
old_path = pwd;
cd(fileparts(which('AAL3v1.nii')))
AAL3 = load_nii('AAL3v1.nii');
AAL3_origin = AAL3.hdr.hist.originator(1:3);
AAL3_img = double(AAL3.img);
AAL3_img(isnan(AAL3_img)) = 0;
cd('C:\Users\isaac\OneDrive\Documents\Grad School\Kiran Lab\DIssert... |
49ab3046283597f7b4d32913c30ff74b9662cad4b0742ea03b12b3cf139f7ca1 | MATLAB | 4,586 | 160 | function grayplot_HFmotion(QCinit,stage,subject,mvm_filt)
% function grayplot_MIND(QC,whattomask,stage,subject)
%
% This function will make grayplots to look at timeseries after different
% stages of procesing. Additionally allows for bad timepoints to be masked
% out from visualization.
% This will allow one to inspec... |
636193f830a0995284efb9ee4b7ed5c60fe75fce7cf0e442770375aaacb59478 | MATLAB | 4,591 | 108 | function sResults_hb = nst_mbll_source(sResults, wavelentghts)
%NST_MBLL_SOURCE Apply the MBLL on the data after source reconstruction
assert(length(sResults) == length(wavelentghts), 'Provide the wavelength associated with each map')
assert(length(sResults) > 1, 'Unable to compute the MNLL with only one wave... |
de49b58059a4c56b26c3de41d3b07b38f65b37f49e7c6284a30d969e7a1cd08d | MATLAB | 4,597 | 113 |
%% Get path to NLA
root_path = nla.findRootPath();
%% Create a pool of tests
tests = nla.TestPool();
tests.net_tests = nla.genTests('net.test');
% Example: Changing the edge-level test
% tests.edge_test = nla.edge.test.Spearman();
% tests.edge_test = nla.edge.test.SpearmanEstimator();
% tests.edge_test = nla.edge.te... |
f85db9cd9b22044fda872eefe885e8a09feaa1d2d5868bf3ee8f30c2691d683c | MATLAB | 4,598 | 83 | clc;close all;clear
% Change this if needed
PixelSize = 0.117; % 117 nm per pixel
PlotFigures = 1; % Decide whether or not you want to plot the images
% Do not change from this point on
Continue = 1; % Ignore this
% Do the analysis until you're tired of it
while(Continue)
[file,path] = uigetfile... |
a7c693f4e896ba6d479e2ce11bdf3f685abe5f91a56078f9a6f6a68bace4a318 | MATLAB | 4,604 | 121 | function varargout = process_nst_deglitch( varargin )
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2013 Brainstorm by the University of Southern California
% This softwa... |
576ab31a5615c58efbeca2f5323914fb55a2398d57c650ea46003873285d92c1 | MATLAB | 4,626 | 136 | function [Rlatt,Rrp,ind_rp,eff] = latmio_und_connected(R,ITER,D)
%LATMIO_UND_CONNECTED Lattice with preserved degree distribution
%
% [Rlatt,Rrp,ind_rp,eff] = latmio_und_connected(R,ITER,D);
%
% This function "latticizes" an undirected network, while preserving the
% degree distribution. The function does no... |
c65c65394aa7dc45344374d34c819b1d3db4febf4ff08d5f4508cf4afa2c87ab | MATLAB | 4,634 | 127 | function Binned_y = Model_3State( parameter_guess, JumpProb, data_to_fit)
%MODEL_3STATE Summary of this function goes here
% Detailed explanation goes here
LocError = data_to_fit.LocError;
dT = data_to_fit.dT;
HistVecJumps = data_to_fit.HistVecJumps;
dZ = data_to_fit.dZ;
HistVecJumpsCDF = data_to_fit.HistVecJumpsCDF;... |
1afbd597b758b9a1589f9d3a30f9d2919eb4c5b4dfce305a26971437465e9b49 | MATLAB | 4,640 | 113 | function [accur] = Decode_main_code(subid, timeid,iShufid)
iShuf=1;%1 real data, 2 premutation data
is.ENL1=0.001;
kfold_k=10;
rng('shuffle')
is.random_fixation = 154;
nstim=8;
is.whichTimes=1:10:750;
addpath('./Decode_Data')
dirRoot = './Decode_Data';
DirCon = dir(ful... |
e46c1ed51ad8a32c80e43820c9bd2ed884b72c196911d56bca655d5cfa96f2d9 | MATLAB | 4,651 | 122 | function [data_clustered,data_not_clustered,area_threshold] = construct_clusters(data,area_threshold,min_number_of_localizations,type,waitbar_counter)
f = waitbar(0,['Please Wait...',num2str(waitbar_counter(1)),'/',num2str(waitbar_counter(2))]);
voronoi_areas = data.vor.voronoi_areas;
neighbors = data.vor.neighbors;... |
631705c3c7c432bdb03f47ba24befb412f5ad179d64a4f46f4bee8a1123fef3a | MATLAB | 4,654 | 159 | % Code to solve the spatio=temporal IRES. Basically a block coordinate
% projected gradient descent algorithm where the edges and the solution
% itself will be updated sequentially.
% Xiyuan Jiang
% 11/17/2022
function [x, y,res_obj,J_intermediate,J_intermediate_count] = FISTA_ADMM_IRES_Tensor(alpha, W_v, V, L_v,x_0, ... |
c5ef0b572e8bfaf01d2709fe32cbfa1ab0291348e6175131f3c506d887e0efc7 | MATLAB | 4,662 | 109 | function [filtered_events] = read_events_modified(path_dataset, stim_channel, min_duration_samples)
%--------------------------------------------------------------------------
% Till Habersetzer, 06.06.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% READ_EVENTS_MODIFIED Extracts ... |
dc1c855e7d45e69b0fc13ae96a36dc45a6051c29d76dc9e22739d97853231c64 | MATLAB | 4,667 | 80 | classdef HyperGeometricTest < handle
%HYPERGEOMETRICTEST Hypergeometric (One-sided Fisher's Exact Test) to test significance
properties (Constant)
name = "hypergeometric"
display_name = "Hypergeometric"
statistics = ["two_sample_p_value", "greater_than_expected"]
ranking_statisti... |
8d16cdfaf1d14a62fb812e3923d7203f8c25011e49226ce17aaeb9d00f243f24 | MATLAB | 4,682 | 189 | % Generate X Y Z coordinates of a 3D Bresenham's line between
% two given points.
%
% A very useful application of this algorithm can be found in the
% implementation of Fischer's Bresenham interpolation method in my
% another program that can rotate three dimensional image volume
% with an affine matrix:
... |
9175500dd4adafb355e8be5f529daf4201f826ec07f0b9c28afd27ca7bcbac31 | MATLAB | 4,684 | 127 | function Binned_y = Model_3State_fitLocError( parameter_guess, JumpProb, data_to_fit)
%Model_3State_fitLocError Summary of this function goes here
% Detailed explanation goes here
dT = data_to_fit.dT;
HistVecJumps = data_to_fit.HistVecJumps;
dZ = data_to_fit.dZ;
HistVecJumpsCDF = data_to_fit.HistVecJumpsCDF;
ModelFi... |
99bb2fd06d3c06d033da1c8b836dc17ae21c5e379805b6e048dc4ae3b441ba72 | MATLAB | 4,694 | 124 | %APPEND_PDFS Appends/concatenates multiple PDF files
%
% Example:
% append_pdfs(output, input1, input2, ...)
% append_pdfs(output, input_list{:})
% append_pdfs test.pdf temp1.pdf temp2.pdf
%
% This function appends multiple PDF files to an existing PDF file, or
% concatenates them into a PDF file if the o... |
1beaed03c3a682e4e314833502e162ff4f763d2196753b51531dbcf6a134187f | MATLAB | 4,704 | 188 | clear
fnl(1,:) = {"D:\DATA_LOCAL\MIPCART pilot\Histology\Mouse 105\2023-04-13 13.21.07.ndpi_ID5_HE_42_B4_2.jpg"
"D:\DATA_LOCAL\MIPCART pilot\Histology\Mouse 105\2023-04-13 11.25.44.ndpi_ID5_Ki67_42_B3_1.jpg"
"D:\DATA_LOCAL\MIPCART pilot\Histology\Mouse 105\2023-04-13 10.31.07.ndpi_ID5_psma_44_B2_2.jpg"};
fnl... |
258543c0c190159d5c65e63aa4df7bfa4fbf6d97dbec17703636e15d074dcb7b | MATLAB | 4,705 | 81 | classdef ChiSquaredTest < handle
%CHISQUARED Chi-squared test to determine how far a result is from expectation
properties (Constant)
name = "chi_squared"
display_name = "Chi-Squared"
statistics = ["chi2_statistic", "greater_than_expected"]
ranking_statistic = "chi2_statistic"
... |
aa2b151c3aa21e96641273492c903cd060a4d0beb2813946dd59b8734acc7363 | MATLAB | 4,705 | 124 | function [V1_all,Time_sessions,Data_info] = LEiDA_data(data_dir,save_dir,n_areas,tmax,filter,flp,fhi,tr)
%
% For each subject compute the leading eigenvetor of the phase coherence
% matrix calculated at each recording frame.
%
% INPUT:
% data_dir directory where the parcellated fMRI data are saved;
% ... |
052caea075f01b861e0048099b4287de640ea702a1c43e03abdd32843635cce1 | MATLAB | 4,707 | 118 | function [spindles,phase_total,z,BST,V_pfc,v_pfc,Sx,Ex,Mx] = spindles_detection(vec_bin,NC3,NC2,fn,j,i,k)
if sum(vec_bin)~=0 %%All states
v2 = ConsecutiveOnes(vec_bin);
v_index = find(v2~=0);
v_values = v2(v2~=0);
for epoch_count = 1:length(v_index)
v_timestamps{epoch_count,1} = reshape(NC3(:, v_index(ep... |
bab315f1b2421a97e41500417f5f34a4ab7045aefb00b4053786e65a3ceaa259 | MATLAB | 4,711 | 164 | %%% DISCLAIMER %%%
% This file is a modified version of `tt_cp_fg.m` from Tensor Toolbox:
% Brett W. Bader, Tamara G. Kolda and others, Tensor Toolbox for MATLAB, Version 3.1,
% www.tensortoolbox.org, June 2019. https://gitlab.com/tensors/tensor_toolbox.
% It is therefore subject to the following license:
% BSD 2-Clau... |
5e5ea8de393e376fab1ab2d00e9822894fd7ff6a7927b6a7eb35f7ccdd3caee3 | MATLAB | 4,712 | 142 | function obj = fit(obj,connectivity_matrix,varargin)
% Computes the kernel, embedding, and alignment according the
% properties of the calling object. A data matrix or cell array of data
% matrices is obligatory as input. Valid name-value pairs of optional
% arguments are as follows:
%
% - Kernel arguments
% - ... |
b31f028f66557e08660744f49fbb2e140453b9d807336364814843b7e3ab68a9 | MATLAB | 4,713 | 207 | function [preimages,images,averages,mask] = OMimprocess(fname,im,rect,num_images,cropchoice,mask,sfilt,sfiltsize,inversion,tfilt,removef,camopt,sfiltsigma,pbefore,pafter,n,tstack)
%funtion for reading in and processimg all images in the tif stack/ rhs
[rows,cols] = size(im);
[~,~,remain] = fileparts(fname);
fileisr... |
b7ff416805774b95ca3b7eb454958760ed0637421a5710641966cfc0a4cba3a4 | MATLAB | 4,724 | 174 | function status = compute_epoch_psd_metrics(rootPath, subjectIDs, opts)
% compute_epoch_psd_metrics
%
% Compute epoch-level power spectral density (PSD) metrics from
% *_BipolarEEG_QC_Post.mat files.
%
% INPUT
% rootPath : root data directory
% subjectIDs : cell array of subject IDs
%
% OPTIONAL (opts... |
62518310135c8fd5933f3647736cdb341f70fb112740af5c5ef9d623460fbad0 | MATLAB | 4,729 | 174 | %% download and install orbitrap to mzxml convertor
wget http://unfinnigan.googlecode.com/files/Finnigan-0.0206.tar.gz
tar xvzf Finnigan-0.0206.tar.gz
cd Finnigan-0.0206/
cpan
install Data::Hexdumper
install CPAN
reload cpan
install Data::Hexdumper
install Digest::SHA1
install YAML
install Getopt::Declar... |
780e816048d54b920e5508410952f05751e3e23177d6e80d0364ac2caaabe9c5 | MATLAB | 4,732 | 129 | function varargout = process_nst_detrend( varargin )
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2013 Brainstorm by the University of Southern California
% This softwar... |
ba02f0e808c768c9e630adef8e2a999923235938927c09f5d5d1910fdfd2b01f | MATLAB | 4,735 | 141 | function MEM = compute_mem(W,varargin)
% COMPUTE_MEM computes the Moran eigenvectors.
%
% MEM = COMPUTE_MEM(W,varargin) computes the Moran eigenvectors for a
% weight matrix or a surface. If a surface is provided, then the weights
% are computed as inverse geodesic distance.
%
% Name-Value pairs:
% 'n... |
1988e61bb8ad83bfd05a64c304a7b30b8b37ae245c8356c8bd5a4e51eab42598 | MATLAB | 4,742 | 128 | function varargout = process_nst_extract_ssc( varargin )
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2013 Brainstorm by the University of Southern California
% This sof... |
0d9315476e5a382e45b6bf8b368aaba8e12b26d76b8bb71592e88c00542f4379 | MATLAB | 4,745 | 126 | % The main goal of this script is to study the phase locking behaviour of
% neurons in both treatments.
%
% It uses input data containining NREM sleep spikes and
% corresponding phases for each neuron in the entire study day.
%
% Using the neuron IDs, the script loads the sleep scoring file for each
% neuron (and St... |
f93b4f01ae4c149a0fe86c7afb8430fab881cdc584fba58b59b21adcaa136de7 | MATLAB | 4,745 | 131 | function varargout=findND(X,varargin)
%Find non-zero elements in ND-arrays. Replicates all behavior from find.
% The syntax is equivalent to the built-in find, but extended to
% multi-dimensional input.
%
% [...] = findND(X,K) returns at most the first K indices. K must be a
% positive scalar of any type.
%
% ... |
3fa4c09953d66ed0866ba950be6a54564ac072ece97731a25c05c142307875e2 | MATLAB | 4,759 | 131 | function jds_extractHighThetaPhasicREM(animalprefixlist)
%JDS_EXTRACTHIGHTHETAPHASICREM Extract high-theta (phasic) REM bouts.
% jds_extractHighThetaPhasicREM(animalprefixlist) averages the
% theta-filtered LFP envelope across all ctxriptet tetrodes, keeps
% periods more than 4 SD above the mean REM theta envelop... |
3a682b6421b4f2647ad0598d125083c416c5eb0977a22756919449e8db9c1e06 | MATLAB | 4,761 | 115 | function [OUT ] = Epoch_singletone_fl_F3 ( C,x,y,z,d,task,por)
% Epoching, concatenating trials, reshaping, averaing and removing source leakage correction
% of the memory encoding task data.
% This function was made for didactic reasons and it is not to be
% considered a general function that is very likely to be ap... |
b27cc6b5ad52a150d0336dd233c02fe6ca78c3d18c7ee1a90cd7caf8dff82078 | MATLAB | 4,791 | 129 | % Analyze behavioural data for the song familiarity task
% Also determine labels for each note (famuliar, unfamiliar, or
% recognized)
% Author: Cameron Hassall, Department of Psychology, MacEwan University
% email address: hassallc@macewan.ca
% Website: http://www.cameronhassall.com
close all; clear all; clc... |
2660602492754201d1805211b37e98cdf5ae7840f7ff1ed749066de6e8abf715 | MATLAB | 4,806 | 152 | function fitted_model = nst_glm_fit(model, y,method)
%NST_GLM_MODEL_FIT Summary of this function goes here
% Detailed explanation goes here
if nargin < 4
method='OLS_precoloring';
end
switch method
case 'OLS_precoloring'
[B, covB, dfe, residuals, mse_residuals] = OLS_prec... |
79f1e7ba27c392c3e60582acb3176432d8a16d98cb5f28a6c1c1dd079b2bd485 | MATLAB | 4,808 | 110 | function Res = BCCT_Perm_CaSCNMap_Cal(RealCompPara,maskedSignal,ROIsignals1)
% ROIsignals1: 1*N
Calmethod1 = RealCompPara.Calmethod1;
COVcond = RealCompPara.COVcond;
if COVcond(1)
RealCompPara.COVs = zscore(RealCompPara.COVs);
% else
% RealCompPara.COVs = ones(size(ROIsignals1));
end
ROIsignals1 = zsco... |
736623a3441a5f50638fefd0072128d1b1625ecc7da9cfea392fda92b2039aa7 | MATLAB | 4,810 | 181 | clear
switch 2
case 1 % Treated
onam = 'Mouse_002';
path = mipp_getDataPaths(2);
s_nrm = 3000;
slice = 11;
yl = [0.04 1.05];
case 2 % Untreated
onam = 'Mouse_115';
path = mipp_getDataPaths(115);
s_nrm = 5000;
slice = 12;
yl = [0.1... |
12d9d3dc763147a1435517b2ae0b5faf885853f589858f26e50d13e3a3928230 | MATLAB | 4,822 | 128 | function anatomy_based_full_group_pipeline_V1()
% Example for the template- and surface-based full pipeline, using the
% function NST_PPL_SURFACE_TEMPLATE_V1.
%
% This script downloads some sample data of 10 "dummy" subjects (27 Mb)
% Total max amount of data to download: (TODO) Mb, the user is asked for download... |
bb5c8ad11609d1c426f92ae81d3659b96197b62b25c71c1a98a8f23269eee9f9 | MATLAB | 4,824 | 128 | function Plot_C_boxplot_DT(data_dir,save_dir,selectedK,centroid,parcellation)
%
% Plot the boxplot of dwell time (DT) values by condition for the selected
% PL state.
%
% INPUT:
% data_dir directory where LEiDA results are stored
% save_dir directory to save results for selected optimal K
% selectedK K de... |
88fb9c0f1e8b8ece31b670728908516a7138112ae28d5c3a76743fb9cf6a2e50 | MATLAB | 4,832 | 137 | %% ISPC calculation - batch for HC + OCD (all subjects found in folders)
clear; clc; close all;
dbstop if error;
% Add FieldTrip path
addpath('D:\MATLAB\toolbox\fieldtrip-20211209\fieldtrip-20211209');
ft_defaults;
% ===================== Parameter settings =====================
parTF.minFreq = 1;
parTF.maxFreq = 50;... |
5e0e44ad9fa316e165f0d668330f5d627264959c00b4fbcda811d7226e63bcaa | MATLAB | 4,838 | 121 | function checkHeadMotion(fig, input_struct, motion, remove_index)
network_atlas = input_struct.net_atlas;
functional_connectivity = input_struct.func_conn;
if remove_index ~= 0
[new_netatlas, functional_connectivity] = nla.removeNetworks(input_struct.net_atlas, input_struct.net_atlas.nets(remov... |
c12c52b872ad841303bf1d851a63361d7088c9302ba39dd0d31480333b9a6de8 | MATLAB | 4,838 | 122 | function [nPerms pInds Perms] = uperms(X, k)
%uperms: unique permutations of an input vector or rows of an input matrix
% Usage: nPerms = uperms(X)
% [nPerms pInds] = uperms(X, k)
% [nPerms pInds Perms] = uperms(X, k)
%
% Determines number of unique permutations (nPerms) for vect... |
0658ac8b032cf640f563739934dbcfc225fd78e507f4555de578373bfdb39cbf | MATLAB | 4,848 | 135 | function [Mreordered,Mindices,cost] = align_matrices(M1,M2,dfun,flag)
%ALIGN_MATRICES Alignment of two matrices
%
% [Mreordered,Mindices,cost] = align_matrices(M1,M2,dfun,flag)
%
% This function aligns two matrices relative to one another by reordering
% the nodes in M2. The function uses a version of si... |
226afe1273d6799a36f9e1ef1fddfc5184740f69dd2de420c6716f10bf9726e4 | MATLAB | 4,849 | 138 | classdef EVTImportTest < matlab.unittest.TestCase
properties
tmp_dir
end
% This script aimed to test two functionality :
%
%
methods(TestMethodSetup)
function setup(testCase)
tmpd = tempname;
mkdir(tmpd);
testCase.tmp_dir = tmpd... |
9c5aff8910bb619e71ad6d23c17ffcfa8c85a1636ab284ed51be04e42d145161 | MATLAB | 4,851 | 130 | function fh = isolate_axes(ah, vis)
%ISOLATE_AXES Isolate the specified axes in a figure on their own
%
% Examples:
% fh = isolate_axes(ah)
% fh = isolate_axes(ah, vis)
%
% This function will create a new figure containing the axes/uipanels
% specified, and also their associated legends and colorbars. The o... |
945d0fe7b69b8986feb7589ed9bd42b23140f6298fb494560b637978cb466f52 | MATLAB | 4,856 | 108 | function [adj, names, name_hash, contig, overlap, deltafiles_ref, Startnode_name, Endnode_name] = get_reference_nodes( ...
adj, names, name_hash, contig, overlap, target_chromosome, contig_ref, ...
overlap_ref, name_hash_ref, deltafiles_ref, ...
max_chromosome_dist, distance, clipping_thrs, ref_first, ...... |
878fe731207a8e1fd290003d16bb742d4d6210bf4ddcbd8b57be2dddcd998304 | MATLAB | 4,860 | 126 | function Plot_C_boxplot_FO(data_dir,save_dir,selectedK,centroid,parcellation)
%
% Plot the boxplot of fractional occupancy (FO) values by condition for
% the selected PL state.
%
% INPUT:
% data_dir directory where LEiDA results are stored
% save_dir directory to save results for selected optimal K
% selected... |
e73c2fa6db39106de6315e7ee50e3fc93b6e52c791ddf783b841ba06973b26ca | MATLAB | 4,865 | 133 | function newmap = darkb2r(cmin_input,cmax_input)
%BLUEWHITERED dark Blue, white, and dark red color map.
% this matlab file is designed to draw anomaly figures. the color of
% the colorbar is from dark blue to white and then to dark red, corresponding to
% the anomaly values from negative to zero to positi... |
0e9b5de927c9be138acd23fb5188115619b4435cfe57bd42c46e29fbd31a6ab7 | MATLAB | 4,887 | 98 | classdef MultiLevelPermutationTest < matlab.unittest.TestCase
properties
test_options
end
methods (TestMethodSetup)
function loadTestData(testCase)
testCase.test_options = struct();
testCase.test_options.func_conn.v = [1:10].*ones(10,1);
end
end
met... |
28b0ce8a44bc2541f9bec1c388a382682c1a14ad98149f8469afad20afb27eb5 | MATLAB | 4,894 | 170 | function postproc(func_data_path,seg_data_path,stim,filter,regression,out_dir)
% Read data
func_data = double(niftiread(func_data_path));
seg_data = niftiread(seg_data_path);
% Check size match
if ~isequal(size(func_data,1:3), size(seg_data))
error('Mask size and functional size differ, check data');
end
% Calc... |
9bf6fca0bf96e02b268dc42e246a88352a6de2d862e1b695b901543829d3b0e4 | MATLAB | 4,903 | 129 | %% plot_fig7
%
% Plots time-frequency representations (TFR) of spectral Mean, SD, and CV
% for neural LFP data, plus time-course plots per canonical frequency band.
%
% Requires:
% - Fig7.mat containing: V1, M1, frq, Tt, Tl, frband, bandTitle, fs
% - shadedErrorBar.m (Mathworks File Exchange)
%
% Outputs:
% - Fig... |
51c2ef5519ca7cda1356a6a9220211f1f49ef3266f4aa1f3590ff217b7871ccd | MATLAB | 4,917 | 160 | function p = patchline(xs,ys,varargin)
% Plot lines as patches (efficiently)
%
% SYNTAX:
% patchline(xs,ys)
% patchline(xs,ys,zs,...)
% patchline(xs,ys,zs,'PropertyName',propertyvalue,...)
% p = patchline(...)
%
% PROPERTIES:
% Accepts all parameter-values accepted by PATCH.
%
% DESCRI... |
3112d488162af930ab6c0b737c5324bbe2d37fdd4a264f556cb47131ab51b7bd | MATLAB | 4,920 | 111 | function SpinPermuFS(readleft,readright,permno,wsname)
% Compute designated # of permutations/spins of the input surface data
% in FreeSurfer fsaverage5.
% FORMAT SpinPermuFS(readleft,readright,permno)
% readleft - the filename of left surface data to spin
% readright - the filename of right surface data to spi... |
b083e6d16457ca7f21b40d13fc29c7bc357369795f6fda5aa8b0e06967445184 | MATLAB | 4,921 | 154 | function motion_HFcharacteristics(subinfo,TR,mot_data)
% motion_HFcharacteristics
% This script gets FD summary measures from a group of subjects and relates
% them to subject demographic caracteristics. Edit the specific
% characteristics depending on what is available in each dataset
%
% subinfo = structure, with eac... |
f3b4ce7496859c435b68f00c028b2d636c34ac74345b2a47bd8298bb23a56fac | MATLAB | 4,928 | 148 | % This script generates ripple data for ripple response type and visualizes firing activity centered around ripples.
% Note: Variables Counts_Norm_RGS_Temp and Counts_Norm_Veh_Temp were used
% to create response type plots on GraphPad.
% Functions used: Ripple_Analysis_All.m, Ripple_Colorplot.m
%% Loading Input Data... |
13628769c17714497644a8b5f7bb838a77c0afba0d133809bf53330b4889c933 | MATLAB | 4,930 | 135 | function tc_show_contour_on_slice(configuration)
% Hack to allow plotting of sections
%
% Copyright (C) Tim van Mourik, 2015, DCCN
%
%% Parse configuration
volume = tvm_getOption(configuration, 'i_Volume');
%no default
section_sel = tvm_getOption(configuration, 'i_Section');
%no default
slic... |
5f2aa2555295066d9a56fc028dc297e0d9cdd17c4116b9de2acfac72c6ce1567 | MATLAB | 4,936 | 213 | function [num_images,rect,mask,im,I,boundaries,camopt,frame1,fluoim,rois] = OMimreload(fname,cropchoice,quinnieopt,threshop,threshman,rect,inversion,camopt,fluo_opt,roinum,roisum,frame1,num_images)
% Function for taking raw image file and applying thersholding without having to reread whole image stack, final
% outpu... |
b0b6c4a1140c1b1bb255a9e3bcd2aa8817d5fb087d35885e23c4f8830a3017b7 | MATLAB | 4,956 | 144 | function varargout = process_nst_mask_from_atlas( varargin )
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2013 Brainstorm by the University of Southern California
% This ... |
ab3ddbd43b8492fa1ff824f6d0709ded3e01840c0bf4f41e85d6d24435cf875b | MATLAB | 4,964 | 133 | function data_filtered = remove_outliers(data)
clusters = extract_clusters(data);
names = data.name;
areas = cellfun(@(x) x(1,3),clusters);
no_of_locs = cellfun(@(x) size(x,1),clusters);
ratio = log10(no_of_locs./areas);
ratio = ratio + abs(min(ratio))+0.1;
[counts,centers] = hist(ratio,100);
figure(1595)... |
ccd88c3e65166e2bf1785e0b6aa88af9bc77e28a384acfa176ec2134297ad474 | MATLAB | 4,993 | 119 | function jds_remRippleCA1CoactivitySpatialCorr(animalprefixlist)
%JDS_REMRIPPLECA1COACTIVITYSPATIALCORR Spatial correlation vs REM ripple cofiring.
% jds_remRippleCA1CoactivitySpatialCorr(animalprefixlist) computes, for
% CA1 cell pairs tracked from the preceding run epoch, the correlation
% between their place-f... |
2cec3dbf7d41cded2acf7ebb731a71e8040bf09f971654e06d26652d9bd0742d | MATLAB | 5,008 | 145 | function results = c_eeg_plot_power(mainpath, subjects)
%% EEG_regs_conv = e_eeg_power_regressors(mainpath, subject, delete_files)
%mainpath = '/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts/scriptTemplates/..';
results = [];
for subject = subjects
fprintf('computing results for subject %d\n', subje... |
a58bb3ebd74c5b3214a7adb778b8df4596fd6ee20ba0c00a12180881455e6266 | MATLAB | 5,021 | 130 | clear
switch 2
case 1 % Treated
onam = 'Mouse_002';
fn_rare = '\\uw.lu.se\research\LU22A1004-msf_fsz\Common\DATA\MIPCART pilot\Pilot MRI/MouseExternalRT_PilotJune2022\221021\20221021_091729_220210_JS_221006_mouse_2_time3_1_28\NII\010_1_Bruker_RARE_MAGNITUDE.nii.gz';
fn_qti = '\\uw.lu.se\r... |
1df47a70708df80339e8d6142fa7253845296e0c9fc8c7fbbe1598f477eb542b | MATLAB | 5,026 | 111 | function beta_results = g_average_betas(parameters, delete_files)
%% beta_results = g_average_betas(mainpath, subject, delete_files)
% mainpath = '/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts/scriptTemplates/..';
tc_struct2ws('caller', parameters.main);
%% parameters
tc_struct2ws('caller', parameters.p... |
08952b3da87094e49994ae7b4aeb474c9485cf2c03e7789f599245f2549bf065 | MATLAB | 5,027 | 128 | function varargout = process_nst_search_space( varargin )
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2013 Brainstorm by the University of Southern California
% This sof... |
66162372b0f732e7be47fcdd14d37fa90a0f5fa8b88a0092f9a1d38f651d1d4f | MATLAB | 5,033 | 118 | function surface_template_full_group_pipeline_V1_all_opts()
% Example for the template- and surface-based full pipeline, using the
% function NST_PPL_SURFACE_TEMPLATE_V1.
%
% This script downloads some sample data of 10 "dummy" subjects (27 Mb),
% as well as the Colin27_4NIRS template (19 Mb) if not available.
%... |
7395cc5ed8762c69f8926a4230c9539bb330fd9634dfb98f30586b32cdeeddd3 | MATLAB | 5,033 | 123 | classdef SciTest < matlab.unittest.TestCase
properties
tmp_dir
end
methods(TestMethodSetup)
function setup(testCase)
tmpd = tempname;
mkdir(tmpd);
testCase.tmp_dir = tmpd;
utest_bst_setup();
end
end
methods(TestMe... |
48537d30afa3844dfeffc8791a1d8cb3ead8217bb5a347250ce53fad5fb18531 | MATLAB | 5,046 | 124 | function [old, young, index_old, index_young] = young_or_old_evals(freq_path, index_old, index_young, thresh)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Load the explained variance for each frequency and divide them between
% young and old. If you want to discard subjects that gave ... |
b76a8ae354523b4b5b7baaf9a0880fdb7b11126a0345581af33e22eb4ba807ac | MATLAB | 5,052 | 85 | function spt_tracks_displacement_model_plot(data)
figure()
set(gcf,'name','Tracks Displacement Model Plot','NumberTitle','off','color','w','units','normalized','position',[0.4 0.3 0.4 0.6],'menubar','none','toolbar','none')
if length(data)>1
slider_step_one=[1/(length(data)-1),1];
slider_one = uicontrol(... |
f4d28b1f633bad972f93939c52fd4270ee92ddcfe077ea58f9ec41d57518e392 | MATLAB | 5,064 | 135 | function preprocessing_olsa(settings)
%--------------------------------------------------------------------------
% Till Habersetzer, 05.07.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% Description:
% Prepares individual OLSA sentence stimuli for a neural decoding analysis
% ... |
7be83bf73ebd1c2c28e3ed7110251410e41de2f7f1dc0ca5d89eb86133679eac | MATLAB | 5,099 | 109 | %%
if ~(exist('mainpath','var') && exist('setup_sel','var'))
clearvars
% current working directory needs to be /path/to/scripts
mainpath = pwd;
setup_sel = sprintf('%s/../subjectData/all/eeg-fMRI/setups/b_5_d_contrast_t_000_025.mat', mainpath);
else
clearvars -except mainpath setup_sel
end
cd
addpat... |
e9d981f4eb907de765a1747740de5ab7a29bff6d569d4eed695892f87ebc22c7 | MATLAB | 5,101 | 83 | function [GWpos,GWneg] = gateway_coef_sign(W,Ci,centtype)
% Gateway coefficient
%
% [Gpos,Gneg] = gateway_coef_sign(W,Ci,centtype);
%
% Gateway coefficient is a variant of participation coefficient. Similar
% to participation coefficient, gateway coefficient measures the
% diversity of intermodular connectio... |
9551d5f5eae3d8237b375479a48390d5e86995400fccb3a578d176b3c77f7e68 | MATLAB | 5,102 | 153 | %%%% EXTERNAL FUNCTION
% function taken from the BioSig package
% complete software may be downloaded from http://biosig.sourceforge.net/
function [CC,NN] = covm(X,Y,Mode);
% COVM generates covariance matrix
% X and Y can contain missing values encoded with NaN.
% NaN's are skipped, NaN do not result in a NaN output.... |
d453b7e62f10080ea5c8ff0174bf223ed402e79f9f9ff7db4b7edcaaca302ec3 | MATLAB | 5,123 | 95 | function [swr_hpc,swr_pfc,s_hpc,s_pfc,V_hpc,V_pfc,signal2_hpc,signal2_pfc,sd_swr, M_multiplets, Mx_multiplets, multiplets, ripples, Mono_hpc, Mono_pfc,total_swrs,total_NREM_min,v_index, v_values,v_timestamps, S_r, M_r, E_r] = ripple_detection(HPC,Cortex,states,ss,offset1,offset2,TT,j,i)
if leng... |
92d0caeca3a733985688528c7f6bac13d12a44ff0c5320c3dda2d5a336c4d82d | MATLAB | 5,126 | 151 | %%
if ~(exist('mainpath','var') && exist('relcrit','var') && exist('confsel','var'))
clearvars
% current working directory needs to be /path/to/scripts
mainpath = pwd;
relcrit = 5;
confsel = 1:3;
else
clearvars -except mainpath relcrit confsel
end
addpath([mainpath filesep 'fmriRegAnalysis'])
a... |
dd78d26fac3907113a54ec3ab86fd7b3922a312c93566722465ea636cac16ee3 | MATLAB | 5,133 | 157 | function [A, vA, vB, bb_rel] = crop_borders(A, bcol, padding, crop_amounts)
%CROP_BORDERS Crop the borders of an image or stack of images
%
% [B, vA, vB, bb_rel] = crop_borders(A, bcol, [padding])
%
%IN:
% A - HxWxCxN stack of images.
% bcol - Cx1 background colour vector.
% padding - scalar indicating ... |
1a7558df7378ec051a7710392a80f6cec59ed7779e06bacae4a02f490fdd6278 | MATLAB | 5,153 | 115 | function [ O ] = MEG_SR_Stats_twogroups_LBPD( S )
O = [];
% It computes statistics after beamforming (computed using MEG_SR_Beam_LBPD.m).
% It tests the difference between two experimental groups (using ttest2).
% INPUT: -S.workingdir: path where the data from MEG_SR_Beam_LBPD.m is stored
% -S... |
9044953c0814d9938d7f2b208cc25460499f3174913d7085aa07c945c18a56a4 | MATLAB | 5,153 | 107 | %% Export recruitment-figure data so the Python plotter can render in matching style.
% Inputs: figures/.../final/recruited_traces.mat (already exists)
% Outputs (same dir): recruitment_data.mat, recruitment_traces.csv, recruitment_counts.csv
clear; clc;
WIN_FRAMES = 5; % 3 = first ~101 ms (strict pre-movement); 5 =... |
a4d3c80ac2fdc8826ed9940a46408c3c7fef9ecce0e1f03850269a48c4141147 | MATLAB | 5,168 | 92 | clear
p = fix.subplot('tight');
p.nr = 2;
p.nc = 4;
p.lo = 0.04;
p.wo = -0.0;
c = 1;
clf
for j = 1:2
switch j
% case 1 % Mouse 12 control
% % fnl = fix_findFiles('\\uw.lu.se\research\LU22A1004-msf_fsz\Common\DATA\MIPCART pilot\Pilot MRI\MouseReference_Pilot_Feb2023\', '*RARE_MAGNITUDE.nii.gz... |
5adf393e02f66119ce472d56eaa0847a4571b6c4e71a4db0bcbf209f318fc33b | MATLAB | 5,171 | 148 | function CC = bwconncomp(varargin)
%BWCONNCOMP Find connected components in binary image.
% CC = BWCONNCOMP(BW) returns the connected components CC found in BW.
% BW is a binary image that can have any dimension. CC is a structure
% with four fields:
%
% Connectivity Connectivity of the connected compone... |
8ddf4df5f085d4e5e50c1aa6852dfe71a1201be5cd698b39a8ea45fabbdb8cb5 | MATLAB | 5,192 | 138 | classdef OptimalMontageTest < matlab.unittest.TestCase
properties
tmp_dir
end
methods(TestMethodSetup)
function setup(testCase)
tmpd = tempname;
mkdir(tmpd);
testCase.tmp_dir = tmpd;
utest_bst_setup();
end
end
met... |
bc0cfbfa06ce15a1193cf25543d041fecbab8f4bc8f6bceb4c69f08285858532 | MATLAB | 5,199 | 134 | function LEiDA_Start
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% LEADING EIGENVECTOR DYNAMICS ANALYSIS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This function runs LEiDA on any given dataset.
%
% Since we do not know a... |
267afe239d9b27eb545d08b6e3b714f9d5785162cd62a991ed853e456b1efca7 | MATLAB | 5,201 | 119 | %%
%%% LEADFIELD MODEL - WORKSHOP %%%
%instructions
%1)run the first section to start some functions up
%2)run the second section playing around with the three provided settings
% -source_label: nunmbers corresponding to different brain sources (voxels)
% -orientation: 1 of the 3 orientation of the brain sources... |
da86bb7e94579bdc8b6d174753270896655b9acbf52a6225e786d68217d66ab3 | MATLAB | 5,212 | 122 | clear
% Case 1 and 4 in paper
switch 4
case 1 % Treated
onam = 'Mouse_002';
fn_rare = '\\uw.lu.se\research\LU22A1004-msf_fsz\Common\DATA\MIPCART pilot\Pilot MRI/MouseExternalRT_PilotJune2022\221021\20221021_091729_220210_JS_221006_mouse_2_time3_1_28\NII\010_1_Bruker_RARE_MAGNITUDE.nii.gz';
... |
3f3a1162ec096202fa0c71916d962934d4b58721555f2a74509405e1584373a5 | MATLAB | 5,217 | 157 | function [ a, cb ] = SurfStatViewData( data, surf, title, background );
%Basic viewer for surface data.
%
% Usage: [ a, cb ] = SurfStatViewData( data, surf [,title [,background]] );
%
% data = 1 x v vector of data, v=#vertices
% surf.coord = 3 x v matrix of coordinates.
% surf.tri = t x 3 matrix o... |
6547ab794f27cc60532fd288b678b94663b93eea9fb28df051b2c626e011142a | MATLAB | 5,225 | 148 | function dFC_project = compute_dFC(dFC_project,new_project)
if ~isfield(dFC_project,'CONN_preprocessing_dir')
dFC_project.CONN_preprocessing_dir = uigetdir(pwd,'Select folder containing output of CONN preprocessing');
end
cd(dFC_project.CONN_preprocessing_dir)
cd ..
if ~isfield(dFC_project,'CONN_results... |
1d32773c4b1c1fa2f702d03db67fec4540bfea12fc4360134eae4a93ae62f5d6 | MATLAB | 5,246 | 135 | function computation_crosscorr(subject,settings)
%--------------------------------------------------------------------------
% Till Habersetzer, 05.07.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% Description:
% Performs a subject-level temporal cross-correlation analysis bet... |
3969a3782409dda7f7c7e577e475b0ece5e858698c7fba53a7bd6308ad4f1956 | MATLAB | 5,259 | 184 | function BCCT_WTA_statGUI
W.fig = figure('Name','WTA_stat_GUI',...
'units','normalized',...
'menubar','none',...
'numbertitle','off',...
'color',[0.95 0.95 0.95],...
'position',[0.20 0.15 0.5 0.5]);
movegui(W.fig,'center');
W.OutputText = uicontrol('parent',W.fig... |
29b5b03acea184a48cb608ede9e5a21adf3721c193f47d7f01bd8216dd3f11c7 | MATLAB | 5,268 | 139 | function loc_list_voronoi_density_map(data)
answer = inputdlg({'Color Percentile Value:','Down Sample Size:','Pixel Size (nm per pixel):','Scale Bar Size [x-axis (um)]:','Scale Bar Size [y-axis (um)]:'},'Input',[1 50],{'1 99','100000','116','2','0.5'});
if isempty(answer)~=1
pecentile_vals = str2num(answer{1});
... |
6d77c00219614a243f91e68f2173a8a531c8d3f6c2c3edf0b3e7a0cf56f9f38b | MATLAB | 5,277 | 169 | function [p]=wavesim(wsmat,mask,ep,beforeframes);
%% Chris O'Shea, 05/09/2018
% Function for producing waveform similarty map from 4D matix of
% (row,col,frame,windowed signal)
[rows, cols, num, Nsig] = size(wsmat)
%Nsig=Nsig-1;
%% Normalise signals by standard norm
for N=1:Nsig %ignore last AP
stno... |
0376de5bf64b1fbc5479e37a0990515424459f346edbbe1694c3edfcbf0ed80e | MATLAB | 5,283 | 122 | function [Ci,Q]=modularity_und(A,gamma)
%MODULARITY_UND Optimal community structure and modularity
%
% Ci = modularity_und(W);
% [Ci Q] = modularity_und(W,gamma);
%
% The optimal community structure is a subdivision of the network into
% nonoverlapping groups of nodes in a way that maximizes the numb... |
f2211ce1ba949707ce956f201a707059960e1bfdbd05d6e150f88d648d3083e7 | MATLAB | 5,289 | 146 | function varargout = process_nst_separations( varargin )
% process_nst_separation: compute distances between sources and detectors
%
% @=============================================================================
% This function is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (... |
716d1615256dcd4ff7b421405b63f0194508aa74e3a51badc6f7c126733318be | MATLAB | 5,298 | 101 | function betas = f_eeg_betas_feature_signal(parameters, delete_files)
%% betas = f_eeg_betas_feature_signal(mainpath, subject, delete_files)
% mainpath = '/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts/scriptTemplates/..';
tc_struct2ws('caller', parameters.main);
%% parameters
tc_struct2ws('caller', para... |
e3d1dfe3a7fafcbdf19cf937674d276cddba050826d7bc0c0fe45c6e703792bd | MATLAB | 5,316 | 124 | function [Ci,Q]=modularity_dir(A,gamma)
%MODULARITY_DIR Optimal community structure and modularity
%
% Ci = modularity_dir(W);
% [Ci Q] = modularity_dir(W);
%
% The optimal community structure is a subdivision of the network into
% nonoverlapping groups of nodes in a way that maximizes the number of
... |
0c0754d5470b5fdb1d24ce2fab4175cd671805cb0e8724031c75a7815c12b555 | MATLAB | 5,331 | 138 | function Plot_K_boxplot_DT(data_dir,save_dir,selectedK,parcellation)
%
% Plot the boxplot of dwell time (DT) values by condition for each of
% the centroids given by the specified K.
%
% INPUT:
% data_dir directory where LEiDA results are stored
% save_dir directory to save results for selected optimal K
% se... |
52fdabbc90ba04f84f27a56a2d8270623872db38fdfcc10eaa05c134c2f37516 | MATLAB | 5,343 | 111 | function [I,Q,F]=motif4funct_wei(W)
%MOTIF4FUNCT_WEI Intensity and coherence of functional class-4 motifs
%
% [I,Q,F] = motif4funct_wei(W);
%
% *Structural motifs* are patterns of local connectivity in complex
% networks. In contrast, *functional motifs* are all possible subsets of
% patterns of lo... |
a976ca9739a2394c1546eaaf1501ed9f734525e61dfe25dd98f5e4b10f866021 | MATLAB | 5,347 | 137 | %% Fig 2G - Number of neurons (left) and activation density (right) at threshold
if ~exist('DATA_ROOT','var'), run(fullfile(pwd, 'matlab', 'config.m')); end
load(FIG2_DATA);
fontsize = 8;
set(groot,'DefaultTextInterpreter','tex', ...
'DefaultAxesTickLabelInterpreter','tex', ...
'DefaultLegendInterp... |
c4e563689caccc2e688c0a914dff4ad26168bd74d370bfdcaea3cd55f74ec9e6 | MATLAB | 5,348 | 129 | function loc_list_plot_random(data)
I = randperm(length(data),10);
data_to_plot = data(I);
figure()
set(gcf,'name','Random Plot','NumberTitle','off','color','w','units','normalized','outerposition',[0.2 0.2 0.7 0.7],'menubar','none','toolbar','figure');
subplot = @(m,n,p) subtightplot (m, n, p, [0 0], [0.08 0.08],... |
932e2370ea105f7a1fef4be024bef6172053f9696fc795522395d5bd04ace0f5 | MATLAB | 5,350 | 137 | function Plot_K_boxplot_FO(data_dir,save_dir,selectedK,parcellation)
%
% Plot the boxplot of fractional occupancy (FO) values by condition for
% each of the centroids given by the specified K.
%
% INPUT:
% data_dir directory where LEiDA results are stored
% save_dir directory to save results for selected opti... |
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