sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
35871842dc963d0b8880de9a50b7fade04fa4a1805732c6bf1cc213359e26337 | MATLAB | 7,595 | 264 | %% read
[data,id,~]=xlsread('L:\Results\Ishita\Log2abs0.5.xlsx');
prot = tblread('L:\Results\Ishita\Copy of Log2abs0.5 GO.txt','\t');
protcl=prot(:,1:12);
%% optimize find min variance
f = @(x,y) x.*exp(-x.^2-y.^2)+(x.^2+y.^2)/20;
ezsurfc(f,[-2,2])
fun = @(x) f(x(1),x(2));
x0 = [-.5; 0];
%options = optim... |
8c842f3016819bbd19e0554164fda025c209a83728f7842dde7713b2ae1edd76 | MATLAB | 7,601 | 221 | function preprocessing_olsa_decoding(subject,settings)
%--------------------------------------------------------------------------
% Till Habersetzer, 06.07.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% Description:
% Performs subject-level preprocessing of OLSA task data for... |
a881f993af9ee9a734bd7f0b2bcab77e9b021a80481d3ea415fdeb5b03620dd8 | MATLAB | 7,602 | 137 | %% Checking number of pyr neurons match with excel sheet.
% 101 RGS, 57 VEH.
% RGS
cd('/home/adrian/Documents/GitHub/RGS14/spiking_activity')
load('SD_Data_RGS_Pyr_clean.mat')
NPD=[];
for i=1:length(SD_Data_RGS_Pyr) % Rats
for ii=1: length(SD_Data_RGS_Pyr(i).RatxData)% Study days
x=SD_Dat... |
f3fc4e5ef68fbfe36e2ccddad12ad7bbc76930c66cc32cf62c8f52b499125ac6 | MATLAB | 7,605 | 210 | function preprocessing_audio(settings)
%--------------------------------------------------------------------------
% Till Habersetzer, 05.07.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% Description:
% Prepares audio stimuli for a neural cross-correlation analysis by
% conv... |
863428b431a1f72c0deed7a5ea38f91ebe4cbce783ecec875425bde64121bfe2 | MATLAB | 7,637 | 184 | function LEiDA_stats_FracOccup(data_dir,cond,pair,n_permutations,n_bootstraps)
%
% For each clustering solution compute the fractional occupancy of each PL
% state for all subjects. Perform hypothesis tests to check for differences
% in the probability of occurrence of PL states between conditions.
%
% INPUT:
% data_di... |
57736bc36d113d6799f29ea4c57f090be1ba75ad91b6e499a93d4ca2b5911276 | MATLAB | 7,662 | 174 | function [ ] = LF_3D_plot_LBPD( S )
% Plotting in 3D space leadfield over the MEG sensors given a brain source
% and orientation.
% This function should work for each individual subject. If you do not have
% any subject information, just for visualization and demonstration purposes,
% a previously computed subject da... |
a200f6dbd8d9f3ca403d8a2f4f4156cd613185dc59ef82f385e27f2e7c6e48a6 | MATLAB | 7,672 | 229 | function ROI = roi_extract(S);
% Extract ROI data from image volume(s), either 4D (e.g., resting state
% timecourses) or 3D (e.g., grey matter signal). Gets data from image files
% themselves; does not require SPM.mat.
%
% ROIfiles = cell array of cell arrays, ie set of files for each ROI mask
% Datafiles = cell arr... |
bad6ecbeb008afe0e8ed372260d672fa6d9a27c0f461b4af310564f0ec55f8bf | MATLAB | 7,688 | 120 | function spm_preprocess_brainageR(t1, template_dir, spm_dir)
addpath(spm_dir);
% check arguments are specified
if nargin < 3
error('T1 raw image must be specified');
end
%check SPM release
if exist('spm','file') ~= 2, error('Please install SPM12'); end
[v,r] = spm('Ver','',1);
if ~contains(v,'SPM12'), error('%s: O... |
14b1e19a976328c81fa1fa2f5676ff29c87d358fc9b9316a2168d124ff8a931d | MATLAB | 7,711 | 226 | function BCCT_Mod_mapcomputemain(Parameter)
pathfiles = which('BCCT.m');
[path nam ext] = fileparts(pathfiles);
Outputdir = Parameter.Outputdir;
RealCompPara.Outputdir = Outputdir;
Inputdir = Parameter.Inputdir;
RealCompPara.Inputdir = Inputdir;
SeedROItype = Parameter.SeedROItype;
RealCompPara.SeedROItype = Se... |
a230b69bb01db03ac48b6a273d93b76574ff0326978e003f77c265c311961260 | MATLAB | 7,785 | 198 | function [M,Q]=community_louvain(W,gamma,M0,B)
%COMMUNITY_LOUVAIN Optimal community structure
%
% M = community_louvain(W);
% [M,Q] = community_louvain(W,gamma);
% [M,Q] = community_louvain(W,gamma,M0);
% [M,Q] = community_louvain(W,gamma,M0,'potts');
% [M,Q] = community_louvain(W,gamma,M0,'negative_a... |
a247a7a8f2cb3f448625d64d86a6652e8c744774b684d83a2d8c28d754cb963f | MATLAB | 7,788 | 120 | function [BorderCoords, PolyshapeCloud] = FindBorders(Cloud)
% -------------------------------------------------------------------------
% Function that finds the inner and outer borders of a point cloud. The
% inner coordinates are only there when 'holes' are present in the data.
% The function uses a combination ... |
287b088a4eed84d88a2d4a01f6b7355602048c9bb89c9e35c90e5fd64e593c43 | MATLAB | 7,816 | 176 | function data = chanscale_common(cfg, data)
% CHANSCALE_COMMON applies a scaling to specific channel types
%
% Use as
% data = chanscale_common(cfg, data)
% where the configuration contains
% cfg.parameter
%
% For specific channel groups you can use
% cfg.eegscale = number, scaling to apply to the... |
9eb7897bae6ecf470c82538c4bbbe9c6766a50645c905c566c11377e476397e0 | MATLAB | 7,854 | 174 | function shape_classification_decision_boundary_plot(data)
clf(figure())
set(gcf,'name','Shape Classification Decision Boundary Plot','NumberTitle','off','color',[0.1 0.1 0.1],'units','normalized','position',[0.3 0.1 0.4 0.7],'menubar','none','toolbar','figure')
uicontrol('style','text','units','normalized','posit... |
48da5148d5658ed6e7d4cf47dbf6fb85d88e1916efd9a58fe4a913ebf5436bcd | MATLAB | 7,894 | 284 | function [W0, E0, P0, Delt0] = mleme_constraint_model(samp, W, M, Lo, Li, Lm, opts)
%MLEME_CONSTRAINT_MODEL Unbiased sampling of networks with soft constraints
%
% W0 = mleme_constraint_model(samp, W);
% W0 = mleme_constraint_model(samp, W, M);
% W0 = mleme_constraint_model(samp, W, M, Lo, Li, Lm);
% [W0, E... |
50e4b329c22887ef60cda7bf2605ffc4852552d1d811e5cf8be549fee1a8399b | MATLAB | 7,902 | 196 | function varargout = ghostscript(cmd)
%GHOSTSCRIPT Calls a local GhostScript executable with the input command
%
% Example:
% [status result] = ghostscript(cmd)
%
% Attempts to locate a ghostscript executable, finally asking the user to
% specify the directory ghostcript was installed into. The resulting path... |
0e92436c88914e8fc7896d27a73652cfb09ab3c28f7df5260bf87074b585c470 | MATLAB | 7,912 | 197 | function [N,E] = rentian_scaling_2d(A,XY,n,tol)
% RENTIAN_SCALING_2D Rentian scaling for networks embedded in two dimensions.
%
% [N,E] = rentian_scaling_2d(A,XY,n,tol)
%
% Physical Rentian scaling (or more simply Rentian scaling) is a property
% of systems that are cost-efficiently embedded into physical space. It ... |
4bf43780dbdee22db254b2deb70612d703cc72608d90cc15e0b0db452cc7e174 | MATLAB | 7,952 | 186 | clear;close all;clc
%% Simulation Parameters %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Module Parameters
mpool=1000; %total number of motors shared by modules
cpool=750; %total number of clutches shared by modules
totact=10^5; %t... |
b7bc201dfd131cdceb75d57fab747b4ede7d6746e9ee67adb21ca0f918461f39 | MATLAB | 7,960 | 227 | %--------------------------------------------------------------------------
% Till Habersetzer, 24.06.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% This script is for the visualization and quality control of computed
% dipole fitting results for a single subject. It loads the o... |
e12d11b6e7bca42c3320e3080683ebf50bb1a8183e1796efbc804a2b79e32b88 | MATLAB | 7,969 | 209 | function data_load = load_XML()
[files,path] = uigetfile('*.xml','select the files with SMT Tracks from TrackMate','MultiSelect','on');
if path~=0
input_values = inputdlg({'space units (micron, pixels):','pixel size (um):','time units (second, frames):','frame interval:'},'',1,{'micron','0.16','second','0.015'})... |
f74be765965e21bc0632263b7e5c7b59523edc01d1a4c89f739a122d840f8444 | MATLAB | 7,983 | 338 |
%% Granger Analysis
clc
clear
addpath('/Users/pelinozsezer/Documents/Science/Radboud/RGS-Project/code/ripples/fieldtrip');
load('GC_ripple_4clusters_median_wa.mat');
%% Merge data per treatment
GC_veh=[GC_cluster1_veh_median_wa; GC_cluster2_veh_median_wa;...
GC_cluster3_veh_median_wa; GC_cluster4_veh_median_wa];
... |
bc56a0f9516e2e3257e332d8f6231564f52625d0f98ad86b08b72b7b106017dd | MATLAB | 8,008 | 200 | function data = load_microscopy_file()
%%%%%% file type can be either "bin", "locb" or "csv".
%%%%%% example: data = load_microscopy_file('bin');
%%%%%% example: data = load_microscopy_file('locb');
%%%%%% example: data = load_microscopy_file('csv');
[file_names,path] = uigetfile({'*.bin;*.locb;*.csv'},'Select Fil... |
b9909cc82bb49c7f453097d34858b3f4e8bd3d949c0e5e66dd665406d4376c1a | MATLAB | 8,035 | 192 | %--------------------------------------------------------------------------
% Till Habersetzer, 24.06.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% This script performs dipole model fitting on averaged MEG data for a
% batch of subjects to estimate the location and time course ... |
df9ae9533f614e6ba1c513a71a0d6a0c8bb3562fc498cc5f1219f650a80c0517 | MATLAB | 8,059 | 202 | classdef EdgeLevelMatrix < nla.inputField.InputField
properties
name
disp_name
dimensions
matrix = false
matrix_ordered = false
end
properties (Access = protected)
label = false
select_file_button = false
end
methods
function ... |
51a47fef10297a77df485e0bc4b7a68ba65bc77d8f87b07c9db733dab45914c7 | MATLAB | 8,085 | 255 | % Decode extra NIFTI header information into hdr.extra
%
% Usage: hdr = extra_nii_hdr(hdr)
%
% hdr can be obtained from load_nii_hdr
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function hdr = extra_nii_hdr(hdr)
switch hdr.dime.da... |
228197ed9d2703426cee65c289b1feb531e996710577f7ab4b12bec4aa76a1c9 | MATLAB | 8,086 | 199 | function [ ROI_final_mat ] = diff_conditions_matr_degree_MCS_LBPD_D( a, b, ROI_lab, X, permut, thresh )
% It calculates the difference between the significant degree over time of brain
% areas (with the whole brain) in two conditions. Then, it calculates Monte
% Carlo simulations to assess which differences are signif... |
aa47784c942ee2c92062c7b522c8115ae59fab8df98fd0cb10c24d18bd05405a | MATLAB | 8,097 | 197 | %% plot_fig4_simulate_signal_conditions
%
% Simulates multi-trial LFP-like signals under five senarios that the
% stimulus SD varies compared to the baseline (Fixation-like period) SD.
% Computes across-trial variability (ATV), within-trial power variability
% (ITV), and their cross-subject correlation for each conditi... |
2e97bf02a2ed45f71ce23cb8b005c3eda111ad14c7daae9e7b5fe1b903350048 | MATLAB | 8,112 | 258 | function data_to_send = loc_list_extract_features(data)
counter = 0;
for i = 1:length(data)
data_to = unique(data{i}.area);
if length(data_to)>1
counter = counter+1;
data_to_send{counter} = data{i};
end
end
if exist('data_to_send','var')
f = waitbar(0,'Please Wait...');
fo... |
6bccd02ef8e00e9bce2038a9a71dbf609062e5a3b9f0deb937df6eb5daad1b86 | MATLAB | 8,119 | 261 | function cmap = tc_turbo_map
%% cmap = tc_turbo_map
%
% by Nikolas Karalis, 21 August 2019
% Adapted from https://gist.github.com/nikolaskaralis/b19a1d192e6972d73ab7a0a1005a0e17
cmap = [[0.18995,0.07176,0.23217];
[0.19483,0.08339,0.26149];
[0.19956,0.09498,0.29024];
[0.20415,0.10652,0.31844];
[0.20860,0... |
fe5a7d08adf7933648c94c2b500ff39525cc078037559668993746bf35465384 | MATLAB | 8,140 | 180 | %% Analyze Fig 3 neuron/response counts across the full pipeline
% Requires Plotter2Results and allRasterData
% Outputs a summary of counts at each processing stage
if ~exist('DATA_ROOT','var'), run(fullfile(pwd, 'matlab', 'config.m')); end
fprintf('=== Loading data ===\n');
load(FIG3_DATA);
load(FIG3_RASTER);
%% ===... |
4c4c5d724535ec4e0beece6ef4c468e186450880242e51c2dad93590e8955a4c | MATLAB | 8,171 | 264 | function OCDdraw_m16_plot26()
%% =========================================
% M16: beta distribution plot (70 x 26 mm)
% Current version:
% 1) Remove titles: subject-level / group-level
% 2) Change color to OCD blue
% 3) Use white circle settings fully matching M12:
% - rng(1)
% - jitWidth = 0.32
% ... |
c5352b7395a10b29befe8567bcda91d8ef24b5fab684c62d4629e958fcce20c8 | MATLAB | 8,190 | 261 | % function lineStyles = linspecer(N)
% This function creates an Nx3 array of N [R B G] colors
% These can be used to plot lots of lines with distinguishable and nice
% looking colors.
%
% lineStyles = linspecer(N); makes N colors for you to use: lineStyles(ii,:)
%
% colormap(linspecer); set your colormap to have eas... |
0c0de26a3a70a8d167edbe15580530232578680b48d4e82e3ce626ead26eaeca | MATLAB | 8,232 | 250 | function results = run_opnmf_stability_analysis(cfg)
% RUN_OPNMF_STABILITY_ANALYSIS
% Evaluate model order and parcel-level clustering stability for orthogonal
% projective non-negative matrix factorization (opNMF).
%
% This script was prepared for public code sharing. It uses generic input and
% output paths and does ... |
ae528a45ef7dad1c0602bff3a1b7851b8b455ab1a0520ecbc6d8ee0ca3392bea | MATLAB | 8,282 | 266 | function BCCT
clc;clear all;close all;
[pat,nam,ext] = fileparts(which('BCCT.m'));
% addpath([pat,filesep,'extendFunc']); % some immature ideas will add into this fold.
addpath([pat,filesep,'supportFunc']); % add nifti IO and reslice data.
% addpath([pat,filesep,'SomeTemplates']);
TempExistPath = [pat,filesep,'So... |
54d1121e9bed73bcc9b247af74f11f635c9b7e3ccebba39b1b6e315e9cc9e276 | MATLAB | 8,293 | 200 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_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')... |
0f138e796435b00ee1fd01483fb09001a2934f4b1ef150a5a715adc379b2a7a6 | MATLAB | 8,295 | 278 | function BCCT_WTA_SetupCal
D.fig = figure('Name','SetUp&Cal: Brain Covariance Connectivity Cor2SubCor&Winner Take All',...
'units','normalized',...
'menubar','none',...
'numbertitle','off',...
'color',[0.95 0.95 0.95],...
'position',[0.20 0.15 0.5 0.5]);
movegui(D.fi... |
9d86cf43a525489c6980a90090c2224198d19221f9c5797ad27f48bde1025cb9 | MATLAB | 8,352 | 244 |
% Hacky function for thresholding connectivity matrices across groups
% Rik.Henson@mrc-cbu.cam.ac.uk Nov 2018
function connectivity_stats(S);
try
CM = S.CM;
catch
error('Need to pass a Nsubject x Nroi x Nroi connectivity matrix in S.CM')
end
try
X = S.X;
catch
error('Need to pass a design matrix i... |
6b73ad52d31f7125246fcc5c77cddca7ebef17d3fb9cffa7c706322328058e23 | MATLAB | 8,356 | 173 | function jds_rankOrderCorrChainREMExcludeIEI(animalprefixlist,day,cellcountthresh)
%JDS_RANKORDERCORRCHAINREMEXCLUDEIEI Rank-order correlations within ripple chains.
% jds_rankOrderCorrChainREMExcludeIEI(animalprefixlist,day,cellcountthresh)
% computes, for each REM gamma chain and NREM ripple chain (treated as one... |
8263b9c2d898f1a65c21307aaa778ba45abdb40be47a8558da7b44746db5c54e | MATLAB | 8,362 | 181 | function [ ] = FC_Brain_Schemaball_plotting_LBPD_D( S )
% Given a connectivity matrix and the corresponding parcellation, it uses
% oslspinningbrain and schemaball for plotting connectivity within the
% brain (both video and specific frames) and as schemaball.
% INPUT: -S.MATF: connectivity matrix ROIs x ... |
2f17356a33609c06a327acf1e4abd6268bcd1a02b639a708f7ceefb10397e437 | MATLAB | 8,372 | 198 | classdef TriMatrix < handle & matlab.mixin.Copyable
%TRIMATRIX Lower triangle matrix
% Elements of a TriMatrix can be anything from doubles
% to multidimensional arrays of strings. However, there
% may only be one type of element overall per TriMatrix
% TriMatrix inherits from handle because... |
bf5426197b2106844e1169b72b6572ab04a6394abdcfef9e88d39c0e5ac7c141 | MATLAB | 8,396 | 167 | function perm_id = rotate_parcellation_fixed(coord_l,coord_r,nrot)
% Function to generate a permutation map from a set of cortical regions of interest to itself,
% while (approximately) preserving contiguity and hemispheric symmetry.
% The function is based on a rotation of the FreeSurfer projection of coordinates
% ... |
17cd45e8b3d864e462a4441b7e8bb35052ed74a78a6951ae0f447871c66e17c6 | MATLAB | 8,408 | 196 | function LEiDA_stats_TransitionMatrix(data_dir,save_dir,selectedK,n_permutations,n_bootstraps)
%
% For the selected K compute the transition probability matrix for each
% participant. Perform hypothesis tests to check for differences in the
% state-to-state transition probabilities between conditions.
%
% INPUT:
% data... |
026909d12c2ccb3c088ff101bf17f16121a6f6b6b67d8770f61b5bef1f0d40f5 | MATLAB | 8,411 | 208 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% RFR_Trento_Pipeline
%
% This script performs the RFR analysis on a set of subjects' data.
%
% Runing this file will:
% 1. Define pre-processing parameters
% 2. Select the subject(s) to analyse
% For each subject:
% 3. Prepare data structure a... |
e4708bed0adf0d6f4283d9751431bf07f5e318d517432c9eb4669cbfdabf59de | MATLAB | 8,418 | 281 | %% read
[data,id,~]=xlsread('L:\Elite\Celine\heatmap_data.xlsx');
prot =xlsread('L:\Elite\Aida\MM20.xlsx');
protcl = tblread('L:\Elite\Aida\RawFiles\CellLines RawFiles\combined\txt\proteinGroups.txt','\t')
protmm = tblread('L:\Elite\Aida\RawFiles\Samples\combined\txt\proteinGroups.txt','\t')
prot =xlsread('L:\Elit... |
01d4c99c51838b2fba6ed66c9fcd0514448e1af790d34fba69f6d6f0be1099b0 | MATLAB | 8,449 | 181 | function [W0,R] = null_model_und_sign(W,bin_swaps,wei_freq)
%NULL_MODEL_UND_SIGN Random graphs with preserved weight, degree and
% strength distributions
%
% W0 = null_model_und_sign(W);
% W0 = null_model_und_sign(W,bin_swaps);
% W0 = null_model_und_sign(W,bin_swaps,wei_freq);
% ... |
2482a8c1c8af954b4d264672e860603c447820838450a4e5545cdd2988ecff2d | MATLAB | 8,486 | 198 | function [netGraph,meanDeg,varDeg,numHighConnNodes,propHighConnNodes,conMat] = ...
activGraph(GlobalEventsTime,GloEvMat,cellMap,varList,T_HC,orientation,scale)
% This function builds the activation graph for one recording session
% ----------------------------------------------------------------------- %
% *** Inpu... |
0a84f1150dd60919ff2341d2505462819f826ddbed2f815536b71d0f11f18cd4 | MATLAB | 8,504 | 236 | function jds_rippleTriggeredAssemblyStrengthREM(animalprefixlist,area,state)
%JDS_RIPPLETRIGGEREDASSEMBLYSTRENGTHREM Ripple-triggered assembly reactivation, REM vs NREM.
% jds_rippleTriggeredAssemblyStrengthREM(animalprefixlist,area,state)
% aligns z-scored assembly reactivation strength to the first ripple of
% ... |
5900615f25044ebfe427a0f12776677db860f6722d0f8f26900d322c8ee68ffb | MATLAB | 8,523 | 217 | % Function for performing 2D Voronoi Tesellation and calculating the zero
% and first rank area for each [x,y] input point.
% J.Otterstrom MATLAB 2016a
%
% INPUTS
% x (required) - either a vector of 'x' positions or a matrix of '[x,y]'
% positions
% y (optional) - a vector of 'y' positions; include... |
94f3adb188cb45db15fa3521dc810e3173d3eb95b2a5955b150c10350d751ca3 | MATLAB | 8,523 | 222 | function [stats] = bootstrap_within_permutation_ttest2(data,design,niter,nboot,pthr,htest)
%
% PERMUTATION TESTS WITH WITHIN BOOTSTRAP SAMPLES
%
% INPUT:
% data a matrix where each column is a subject and each row is a
% data-point for example a voxel intensity in fMRI, a node level
% value in a n... |
b1bfc1eb5bd9a7aaf0c865510aad425b109dd13882f8953fdf206fe041284354 | MATLAB | 8,524 | 157 | classdef ResultRankTestCase < matlab.unittest.TestCase
properties
root_path
network_atlas
edge_test_options
network_test_options
edge_test_result
network_test_result
permutation_results
tests
rank_results
ResultRank
rank
... |
f6661914c14884db9329ffd356d1933cf63ecff688c07ca1d2bf22bedec3ba63 | MATLAB | 8,524 | 144 | %% Export full trial-averaged dF/F traces (pre+mid+post) for recruited ROIs
% For each tracked ROI x stim channel (4-6 uA pooled), per session:
% - trial-averaged, span-5 smoothed dF/F over PRE + MID + POST, aligned so
% t=0 is stim onset (pre = negative time)
% - per-ROI threshold thr = 2*CV (CV = regionSTD/re... |
aa5c32c9c659becfb17bc99c991eb77eb4e2b7babd68484283d6fbded061d1a9 | MATLAB | 8,525 | 226 | function varargout = process_nst_glm_contrast( varargin )
% process_nst_glm_contrast
% Compute a contrast and its variance from a GLM result
%
%
% @=============================================================================
% This function is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%... |
d4f63a786852dc3835b9b20673621f7bcb97156e82b5d6a61fdd47e9213de513 | MATLAB | 8,550 | 208 | function anovaResults = computeAnovaOnCond(obj, neus2consider, conds2consider, refWindow, anaWindow, binWidth, varargin)
% COMPUTEANOVAONCOND - Compute ANOVA comparing baseline and analysis windows
%
% INPUTS:
% obj - RecordedData object
% neus2consider - Neuron ind... |
235a0a698a24c4f6bf07d3fe57bda14baef9c1d6f268035e3714b535bf9ac69c | MATLAB | 8,560 | 276 | function HCdraw_m12_plot26()
%% =========================================
% M12: beta distribution plot (70 x 26 mm)
% M12-specific version adapted from M16 script:
% 1) Input file changed to M12_f2_drawshc.csv
% 2) Output file changed to M12_beta_distribution_70x26mm_Compact.tif
% 3) X-axis label changed to \b... |
ea1f3d1747407634845f157c606b9fd0ac34f7730fcb3afe3b9dc8395b05f71a | MATLAB | 8,575 | 172 | function vox_coor = get_AAL3_vox_coor()
vox_coor = [
25.5348837209302 60.5192853091322 61.8201928530913
65.5504288671991 59.2250813368826 62.4049097900030
34.9160164271047 81.9776180698152 54.6186858316222
56.2756535310183 80.5963714397191 55.6718689036286
27.2365209673841 80.4364322165520 51.9689372087863
64.... |
5ef0b253cc4f1a5bd46566c97853cfde0269de8e56a5ff9860009e2864bafc95 | MATLAB | 8,581 | 247 | function varargout = panel_nst_rename_montage(varargin)
% @=============================================================================
% This function is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2016 University of Southern California & McGill University
% This sof... |
7e8ccb5274e0670c3beb7094c36b182de739a88847c358a67376570cf5d15296 | MATLAB | 8,583 | 195 | function BCCT_VIEW_surfsimp
Hvs.fig = figure('Name','Simple Version for the Surface results viewer',...
'units','normalized',...
'menubar','none',...
'numbertitle','off',...
'color',[0.95 0.95 0.95],...
'position',[0.3 0.3 0.4 0.4]);
movegui(Hvs.fig,'center');
Hvs.BUT1 = ... |
3cc9b3465279e85328671f9b0ce3191ec317c674426d40f53e9530332190e528 | MATLAB | 8,587 | 261 | function HCdraw_m19_plot26()
%% =========================================
% M19: beta distribution plot (70 x 26 mm)
% This revision:
% 1) Move the left x-label (β_{ISPS-lPFC}) slightly downward
% 2) Move the right y-label ("median estimate") downward by 1 mm
% and slightly to the right
% 3) Keep the right... |
863d5d240fb22d8103f67b20a418bddccef387755a701efe18ab66f8eb2cc49c | MATLAB | 8,592 | 223 | function varargout = panel_nst_search_space(varargin)
% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2020 University of Southern California & McGill University
% This sof... |
98eb935b95770eb46dd1150280cf23231e37ca14900e0d004410e2c1cd263ff3 | MATLAB | 8,594 | 262 | function HCdraw_m16_plot26()
%% =========================================
% M16: beta distribution plot (70 x 26 mm)
% This revision:
% 1) Move the left x-label (β_{ISPS-motor}) slightly downward
% 2) Move the right y-label ("median estimate") downward by 1 mm
% and slightly to the right
% 3) Keep the righ... |
16025f2ef445eb106380ee409e59538e081c44f7e00035e01fdc5140867883f0 | MATLAB | 8,618 | 204 | function voronoi_area_percentiles_inside(data)
input = inputdlg({'Number of Percentiles'},'',1,{'2'});
if isempty(input)~=1
no_of_percentile_ranges = str2double(input{1});
for i=1:no_of_percentile_ranges
prompt{i} = ['cell ',num2str(i),' percentile range'];
default_input{i} = '10 90';
... |
c48b987db69bd5b353078bdc46fb492aab01cf2c98741a4c9c2dd7c0daf98765 | MATLAB | 8,641 | 209 | function obj = makeCSMS(filenameSpikes, filenameEvents, eventType, stateSeqs, matchOpt, otherMarkers)
% MAKECSMS - Create RecordedData from spike times and behavioral events
%
% SYNTAX:
% recordedData = makeCSMS(filenameSpikes, filenameEvents, ...
% eventType, stateSeqs, matchOpt, otherMarkers)
%
% INPUT... |
6009887e931dcc9ffeefbf7378110824fa68560f179c8fe8f081179579f52fa9 | MATLAB | 8,648 | 231 | function varargout = process_nst_channel_cluter_auto( varargin )
% process_channel_cluter_auto: Automatically create channel cluster based
% on the distance to anatomical atlas.
% @=============================================================================
% This function is part of the Brainstorm software:
% https... |
5eb65d2fb8e04710138c9b61b921149d656d12bce5fbc47ad2fd5c22a507df0d | MATLAB | 8,654 | 209 | function [N,E] = rentian_scaling_3d(A,XYZ,n,tol)
% RENTIAN_SCALING_3D Rentian scaling for networks embedded in three dimensions.
%
% [N,E] = rentian_scaling_3d(A,XYZ,n,tol)
%
% Physical Rentian scaling (or more simply Rentian scaling) is a property
% of systems that are cost-efficiently embedded into physical space. I... |
e60bb75b120deb48c8837e8534f60b4da93cec24aaedc495b2122ada5adee21a | MATLAB | 8,661 | 213 | function LEiDA_stats_DwellTime(data_dir,cond,pair,tr,n_permutations,n_bootstraps)
%
% For each clustering solution compute the dwell time of each PL state
% for all subjects. Perform hypothesis tests to check for differences
% in the dwell time of PL states between conditions.
%
% INPUT:
% data_dir directory whe... |
f5075ec3108ef161c7d6b9dc305bb764afd832c560c5d362148f2c148230e275 | MATLAB | 8,710 | 246 | %jds_compareNREMCA1SuppressionREMCofiringShifters
%Same suppression-vs-REM-cofiring analysis as
%jds_compareNREMCA1SuppressionREMCofiring, run separately for CA1 cells
%classified as REM theta-phase shifters vs nonshifters. Plots suppression
%by cofiring quartile for each group and tests whether the two
%correlation co... |
5cd8716c1e0fa1a895b35b32190388143aec53ef47ac56233bdfd0d8c9365a67 | MATLAB | 8,721 | 207 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header(hdr, fid);
return; % save_nii_hdr
%------------------------------------------------... |
0b427af1a1240404b23202a2f201f6045a9d8ce55ece0c47a47b7104273b89d9 | MATLAB | 8,739 | 217 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_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
... |
cd91a87f1b10871627d431128d2bb158aebfe3bbf31d1d2d9e1f0ea09aa908ef | MATLAB | 8,740 | 200 | %%
clear
for BL_type = [1, 2]
logRatioAvg = zeros(52,1,13,151,2,3);
counter = 0;
for subSel = [1:52]
counter = counter +1;
% current working directory needs to be /path/to/scripts
mainpath= pwd;
thisSubject=['S' num2str(subSel)];
workingDir=[mainpath filesep '..'... |
e4fb47833118e349ea71cdaa039bdb47fdd5bc2b456f9dc487a8f6ed066d27f3 | MATLAB | 8,778 | 174 | function [] = phasesynchrony_LBPD_D(S)
% Calculates the instantaneous phase synchrony between each couple of brain
% areas by extracting the instantaneous phase of each brain area with Hilbert
% transform and then calculating the cosine similarity of the
% instantaneous phases of different brain areas.
% Calculates al... |
cabe89ef1fff45320c4d7e773eed80020c56f571f952064f3cc357dd15aec667 | MATLAB | 8,797 | 211 | % fdr_bh() - Executes the Benjamini & Hochberg (1995) and the Benjamini &
% Yekutieli (2001) procedure for controlling the false discovery
% rate (FDR) of a family of hypothesis tests. FDR is the expected
% proportion of rejected hypotheses that are mistakenly rejected
% (i... |
47481bb8aba8f669e5dc3a0d6eadd42f42d6bf26e6bad659b07133ee096f7151 | MATLAB | 8,813 | 219 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header(hdr, fid);
return; % save_nii_hdr
%------------------------------------------------... |
1896d246e0b6efee8a106f2bf52948c0730d6604d3c52d29a6058f5fcab14af2 | MATLAB | 8,818 | 173 | %%
% current working directory needs to be /path/to/scripts
mainpath=pwd;
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
addpath([mainpath filesep 'fmriRegAnalysis'])
addpath([mainpath filesep 'scriptTemplates'])
addpath([mainpath filesep 'toolboxes' filesep 'OpenFmriAnalysis'])
tvm_installOpenFmriAnal... |
fe305d3c2e2dec7419e766401eb1361b2c6eddf5f902fddf35dc0980bdb051e6 | MATLAB | 8,825 | 174 | function [meanFreq,realEvts,diffToBaseAll,varList] = ...
segWithBaseCorr(signalMat,dt,dtev,minDepth,maxEvThresh,Tev,cfDown,smoothParam,evNumVec,GlobalEventsTime)
% This function segments the input signals in signalMat and extract the
% segmented events and inter-events features detailed in *Outputs*.
% ------------... |
37af2adbe2a075540c22a83dff600359833ce977e607ae8150f1011b21f391aa | MATLAB | 8,897 | 201 | function varargout = process_nst_mbll_dOD( 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... |
d8836da13cae14b008d4db4c865cafff572690671bba06fe5fb6faa74be5bb21 | MATLAB | 8,905 | 172 | classdef TestPoolTest < matlab.unittest.TestCase
properties
edge_test_options
network_test_options
tests
root_path
end
properties (Constant)
permutations = 20
end
methods (TestClassSetup)
function loadTestData(testCase)
import nla.TriMat... |
0239fe05f3c995a8e2616fee66c8c38d84ffdc7add31212d0759dad705f13e7a | MATLAB | 8,946 | 186 | %%
% current working directory needs to be /path/to/scripts
mainpath= pwd;
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
addpath([mainpath filesep 'fmriRegAnalysis'])
addpath([mainpath filesep 'toolboxes' filesep 'fieldtrip'])
addpath([mainpath filesep 'toolboxes' filesep 'OpenFmriAnalysis'])
tvm_inst... |
89102686d55925122ee7a31789344241b850ce4f02933135ddb6ebcb6d9f31c8 | MATLAB | 8,946 | 207 | function spt_compute_mean_msd(data)
f = waitbar(0,'calculating mean msd');
for i=1:length(data)
mean_msd{1} = calculate_mean_msd(data{i}.msd);
data_to_send{i}.msd = mean_msd;
data_to_send{i}.name = [data{i}.name,'_mean_msd'];
data_to_send{i}.tracks{1} = data{i}.tracks{1};
data_to_send{i}.type... |
0b50cf1eb170da51d940b8f82c21927f2ce5ed8e79400fc007ff381c5e41c98a | MATLAB | 8,965 | 205 | %jds_chainIsolatedRipplesAmpFreqDurREM
%With analyzeData = 0: detects cortical REM ripples across riptet tetrodes,
%measures amplitude and frequency of each event, and saves
%<animal>ctxripple_REM_amp_freq_<day>.mat.
%With analyzeData = 1: loads that file, splits events into chain vs
%isolated (non-chain) REM ripples, ... |
c328183418bde50ec0fcbb923cc8146e930dc86a47dcf6d00aecb9ed82bc1602 | MATLAB | 8,969 | 212 | % -------------------------------------------------------------------------
% Script: make_figureS1.m
%
% Description:
% This script generates Figure S1 for the manuscript, comparing the
% readiness potential (RP) in two datasets: original (Park et al., 2020)
% and newly collected data. The comparison is done for the 5... |
60a569db6fce8b92accf77a4b675ebfa1c7a381759b7e4b97f9f90c5779cc894 | MATLAB | 8,990 | 429 | function hb_extinctions = nst_get_hb_extinctions(wavelengths)
%% Return HB extinction coeffecients in water, at the given wavelenths
%% Unit is cm^-1.l.mol^-1
%
% Args:
% - wavelengths: array of double, size: nb_wavelength
% Wavelengths for which to return Hb extinction coefficients
%
% Output: matrix of doub... |
fdf751605cf172549a92382435faf5980afe1307b64b8cfc2976aef6d3b9945f | MATLAB | 8,991 | 234 | function [local_fns, downloaded_files] = nst_request_files(relative_fns, confirm_download, remote_repository, default_file_size, local_repository, download_title)
% Request local files: if they are not available in the given local repository
% then attempt to download them from given remote repository.
% The given file... |
56e70a88b7070f80a97e11de9ff00391a8b69f7db13b29fb54cef0aa3599131a | MATLAB | 9,003 | 165 | %%
if ~(exist('mainpath','var'))
clearvars
% current working firectory needs to be /path/to/scripts
mainpath = pwd;
else
clearvars -except mainpath
end
addpath([mainpath filesep 'fmriRegAnalysis'])
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
addpath([mainpath filesep 'toolboxes' file... |
a22bdc0115b2c5c27b1480e4dfe84f1a3013dd7ed85b4f6f699ca6d904de4432 | MATLAB | 9,025 | 188 | function [W0, R] = null_model_dir_sign(W,bin_swaps,wei_freq)
%NULL_MODEL_DIR_SIGN Directed random graphs with preserved weight,
% degree and strength distributions
%
% W0 = null_model_dir_sign(W);
% W0 = null_model_dir_sign(W,bin_swaps);
% W0 = null_model_dir_sign(W,bin_swaps,wei_... |
838212e438dadf9ba984bd50472885a61486eabc33a7957770c9e852078cabdf | MATLAB | 9,027 | 187 | %% RECORDEDDATA CLASS
% RecordedData - Load, process, and analyze neural recording data
%
% This class provides tools for loading neural recording data (spike times, behavioral markers,
% kinematic data) and performing comprehensive analysis including binning, visualization,
% decoding, and dimensionality reduction via... |
c540f019588d46279afa9f82e224487a00409b06eb59695a709385b7d1c87e80 | MATLAB | 9,076 | 237 | function forge_activity_test_data(dest_dir)
% Generate test data for activity detection processes.
% The generated file is a bst subject that is intended to be uploaded
% on the nirstorm data repository. Then this data is retrieved by
% nst_request_data({{'unittest', 'activity_test_subject', 'activity_test_subject.zip'... |
c432e947c7aacfc9d7995240c7aea8cf2beb179ff2dab9fb620ece1418b0f78f | MATLAB | 9,100 | 260 | function [clusterInfo] = doPermTest2(data,alpha,neighbours,EEG)
%DOPERMTEST Do permuation testing
% Do a t-test at each point. Look for contiguous sig.
% values according to the given alpha value. Sum the t-values to get the
% cluster mass. Do this for the actual data, then for permuted data.
% Permute data by ... |
ae491924b5ca76a2c922f198f2eb43b66f42a3860546a3255bb80ee05e436d57 | MATLAB | 9,121 | 223 | function AS_MatrixFCshow_bat(indir,outdir,enhanind)
if nargin<3
enhanind = [];
end
% indir = uigetdir(pwd,'MatrixFC dir');
load(fullfile(indir,'R_Pres.mat'));
[mpat,mnam,mext] = fileparts(which('AS_MatrixFCshow.m'));
load(fullfile(mpat,'gray.mat'))
% outdir = uigetdir(pwd,'Outdir');
R(1:size(R,1)+1:end) ... |
080e7e24306c8ce96ff515bc0b470c6c9f7d951a3b951d44fa28ce67601a475e | MATLAB | 9,135 | 206 | function jds_thetaCoherenceREM(animalprefixlist,Hz)
%JDS_THETACOHERENCEREM CA1-PFC coherence around REM cortical ripples.
% jds_thetaCoherenceREM(animalprefixlist,Hz) computes ripple-triggered
% CA1-PFC cohereograms (all riptet/ctxriptet pairs, z-scored to the
% epoch), along with a circular-shift shuffle, sa... |
57b053983defea0497cfa6d4ba6fe4206d78e7cfeb5af9697c1b1c2f9a9b6a2a | MATLAB | 9,163 | 224 | function AS_MatrixFCshow(enhanind)
if nargin<1
enhanind = [];
end
indir = uigetdir(pwd,'MatrixFC dir');
load(fullfile(indir,'R_Pres.mat'));
[mpat,mnam,mext] = fileparts(which('AS_MatrixFCshow.m'));
load(fullfile(mpat,'gray.mat'))
outdir = uigetdir(pwd,'Outdir');
R(1:size(R,1)+1:end) = 0;
Z(1:size(Z,1)+1... |
f0d8d582a0efb60c11b8919c89726d0451506b3ff555bfe7bdfba5a01e9b196a | MATLAB | 9,165 | 243 | function h = schemaball(r, lbls, ccolor, ncolor)
% SCHEMABALL Plots correlation matrix as a schemaball
%
% SCHEMABALL(R) R is a square numeric matrix with values in [-1,1].
%
% NOTE: only the off-diagonal lower triangular section of R is
% considered, i.e. tril(r,-1).
%
... |
1247ece23384a098e93d270ea173db37c7b6331bc7a730604eba81ef61cf01e0 | MATLAB | 9,217 | 223 | function AS_MatrixFCshow_bat2(indir,outdir,enhanind)
if nargin<3
enhanind = [];
end
% indir = uigetdir(pwd,'MatrixFC dir');
load(fullfile(indir,'R_Pres.mat'));
[mpat,mnam,mext] = fileparts(which('AS_MatrixFCshow.m'));
load(fullfile(mpat,'gray.mat'))
% outdir = uigetdir(pwd,'Outdir');
R(1:size(R,1)+1:end)... |
4c17ec13a7b8cad9761244fa7540292d9538f098b08d11dd2bc23e3221309733 | MATLAB | 9,225 | 244 | function jds_phaseSlopeIndexCA1PFC(animalprefixlist)
%JDS_PHASESLOPEINDEXCA1PFC Theta-band phase slope index between CA1 and PFC.
% jds_phaseSlopeIndexCA1PFC(animalprefixlist) computes the FieldTrip
% phase slope index between every CA1 riptet / PFC ctxriptet pair in
% 2-s windows around REM ripple-chain midpoint... |
3271f477e1dc02c7bd794823362be004cee869e618e3acbdf555935d4495e59a | MATLAB | 9,232 | 228 | function [FCpre,FCcorr,beta,pred_data,R] = predict_fc(SC,FC,ED,pred_var,model)
% PREDICT_FC Prediction of functional connectivity from structural connectivity
%
% [FCpre,FCcorr,beta,pred_data,R] = predict_fc(SC,FC,ED,pred_var,model)
% [FCpre,FCcorr,beta] = predict_fc(SC,FC,[],{'SPLwei_log','SIwei_log'},'quadrati... |
403527d4d30e2973c65cd42b8d2c42b63ba8b63f31c28772a110c8c27e5c3e14 | MATLAB | 9,235 | 352 | function [e,sots,stim,X,df] = fMRI_GLM_efficiency(S);
% Matlab function to calculate efficiency for fMRI GLMs.
% rik.henson@mrc-cbu.cam.ac.uk, 2005
%
% See for example:
%
% Henson, R.N. (2006). Efficient experimental design for fMRI. In K. Friston, J. Ashburner, S. Kiebel, T. Nichols, and W.... |
2def5d51680579ed92b23a65121afa2e412525460d60fc7c242b7ef4a6e214d4 | MATLAB | 9,245 | 303 |
function [map,meann,alll,onedev,vari,SE] = mapsbaby(startopt,framerate,t,maskedimage,imagestack,avbeat,outs,cmin,cmax,tfilt,before,apdblopt,apdblnum,medianfilter)
% function for taking a single beat image file and making apd/cad maps
% Chris O'Shea and Ting Yue Yu, University of Birmingham
% Maintained by Chris O... |
47ef4ece427e102d26709737af013204ad6907af17d2784b079d9ed3590bdbd2 | MATLAB | 9,267 | 245 | function BCCT_CON_computemain(Parameter)
pathfiles = which('BCCT.m');
RealCompPara.mod = 'volmap';
[path nam ext] = fileparts(pathfiles);
Outputdir = Parameter.Outputdir;
RealCompPara.Outputdir = Outputdir;
Inputdir = Parameter.Inputdir;
RealCompPara.Inputdir = Inputdir;
SeedROItype = Parameter.SeedROItype;
Re... |
8ecd0387a55c1a744de67bd3fec027c84e19bc0d55bcc74481b0ac557134e29b | MATLAB | 9,270 | 227 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~exist('hdr','var') | ~exist('fid','var')
error('Usage: save_nii_hdr(hdr, fid)');
end
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
if hdr.h... |
925689a1ee0825f629638c2099243ac71803f5209348dfeb2ec4c04220e45f9e | MATLAB | 9,283 | 228 | function BCCT_CON_Surf_compute_freesurfer(Parameter)
mfilenam = which('BCCT.m');
[pat nam ext] = fileparts(mfilenam);
RealCompPara.mod = 'surfmap';
Outputdir = Parameter.Outdir;
RealCompPara.Outputdir = Outputdir;
Indir = Parameter.Indir;
RealCompPara.Indir = Indir;
marker = Parameter.markerdir;
RealCompPara.m... |
9fa802860fd57169db5d5d2894c7a35ab535df4a60cb4f5443e06751e36f6e68 | MATLAB | 9,286 | 266 | %__________________________________________________________________________
% violin.m - Simple violin plot using matlab default kernel density estimation
% Last update: 10/2015
%__________________________________________________________________________
% This function creates violin plots based on kernel density e... |
10a8ded92627ed6033b9d6c8e387e57a4452b955ef1c8baf2b73fb66630a3e5c | MATLAB | 9,354 | 311 | function gifwrite(varargin)
% GIFWRITE(INARRAY, {DISPOSALMETHOD}, FILEPATH, {DELAY}, {WRITEMETHOD})
% GIFWRITE(INARRAY, MAP, {TRANSPARENTIDX}, {DISPOSALMETHOD}, FILEPATH, {DELAY}, {WRITEMETHOD})
% Write image stack to an animated gif
%
% INARRAY: 4-D image array
% RGB/I or RGBA/IA arrays may b... |
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