sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
0df005844ed6998e5bd7031d991401add5f687e800163f161006c2ccdcec18b7 | MATLAB | 2,343 | 54 | classdef CohenDTest < handle
%COHENDTEST Cohen's D Test for network tests
% This Cohen's D test is run for all of the tests
% Input:
% edge_test_results: Results from the edge tests
% network_atlas: Network Atlas
% result_object: This is a NetworkTestResult object. This needs to be passed ... |
e1c869da07071bbaa1ed662b4fa272ccd86870f64e62773f9c8993e8c251c067 | MATLAB | 2,343 | 66 | %% realization of the instantaneous model : U = L*W
%%% OUTPUT
% U: N*M matrix of filtered noises
% INPUT
% N data length
% C: input covariance matrix (may be interpreted as Su or Sw, see above)
% B0: M*M matrix of instantaneous effects (when relevant)
% when flag='StrictlyCausal':
% given Su, applies Chole... |
021e330134138e30473cf14a98436051503bb16b4deb565275cb7d063171029a | MATLAB | 2,348 | 70 | %% Generation of CFTf surrogates - useful to test the DC - VERSION FOR EXTENDED MVAR MODEL!
%%% ABSENCE OF FULL (direct&indirect) CAUSALITY FROM yj TO yi - Bim and Bmj coefficients are forced to zero
% Note: the length of the series should be not be odd
%%% input:
% Y, M*N matrix of time series (each time series ... |
3b1bc18cf8fc23c0a1cb1694bb228fbf5b03eb05d011b2ec1e02a3f0a6e7e13b | MATLAB | 2,353 | 63 | function shaded_areas(x, y, error, varargin)
% SHADED_AREAS Plots a line with shaded error areas.
% shaded_areas(x, y, error) plots the data in vectors x and y with
% shaded areas representing the error. The error can be a constant,
% a vector of the same length as y, or a matrix with two colu... |
4fd98608932eb70efcc099db892bfc892b975557af981d67bc51291c07087d96 | MATLAB | 2,353 | 53 | function O = cluster_DTI_perm_2groups_2(S_perm)
O = [];
%starting up some of the functions that I wrote for the following analysis
pathl = '/projects/MINDLAB2017_MEG-LearningBach/scripts/Leonardo_FunctionsPhD'; %path to stored functions (THIS MUST BECOME A FOLDER ON YOUR OWN COMPUTER)
addpath(pathl);
LBPD_startup_D(... |
97e01aca70e2a066b8aae2b5df9ad1cc51c28e8cdc814aa817f0a7e21a30fc98 | MATLAB | 2,357 | 106 | % Convert image of different orientations to standard Analyze orientation
%
% Usage: nii = rri_orient(nii);
% Jimmy Shen (jimmy@rotman-baycrest.on.ca), 26-APR-04
%___________________________________________________________________
function [nii, orient, pattern] = rri_orient(nii, varargin)
if nargin >... |
113c0c5061240cd514faea0b81774e9407f5416ca6cd3d73030cc9388cb98a31 | MATLAB | 2,359 | 82 | classdef NumberWithoutDefault < nla.inputField.InputField
properties
name
disp_name
min
max
end
properties (Access = protected)
label = false
field = false
end
methods
function obj = NumberWithoutDefault(name, disp_name, min, max)
... |
c0034c841bf5f103f1c381a442965b4a69791cc18bc538bab4d8267e85d01b24 | MATLAB | 2,384 | 78 | function edg = SurfStatEdge( surf )
%Finds edges of a triangular mesh or a lattice.
%
% Usage: edg = SurfStatEdge( surf );
%
% surf.tri = t x 3 matrix of triangle indices, 1-based, t=#triangles.
% or
% surf.lat = 3D logical array, 1=in, 0=out.
%
% edg = e x 2 matrix of edge indices, 1-based, e=#edges.
if ... |
366919f1ac08e03587b9133a283e023fd60b5f71dea8ba2822acfeb6dc7f37f6 | MATLAB | 2,385 | 61 | function varargout = run(func_name, varargin)
%RUN Run mex function, compiling if necessary
import nla.findRootPath
if isstring(func_name)
func_name = char(func_name);
end
if (ischar(func_name))
% hash the source file to check if we have an up-to-date binary
% already c... |
4c68846e6b34bec8182747701d3be0d271237d7c5cb218bf63777533292b6772 | MATLAB | 2,390 | 49 | function shape_classification_features_info(data)
clf(figure())
set(gcf,'name','Features Info','NumberTitle','off','color','w','units','normalized','position',[0.1 0.2 0.4 0.6],'menubar','none','toolbar','none')
no_of_classes = size(data.classes,1);
slider_one_value = 1;
if no_of_classes>1
slider_one_step=[... |
92d2d93818f2d452ee673bc608cf12b272d35493c233e5cf8c6e923cdff2b7b4 | MATLAB | 2,392 | 62 | %%% DISCLAIMER %%%
% This file is a modified version of `tt_cp_fun.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-Cla... |
63a56b5486a2d6c1bc69bfaa82b52f5abd2d58e1bfe07536d277385406c1d9da | MATLAB | 2,395 | 81 | function SurfStatWriteSurf( filenames, surf, ab );
%Writes coordinates and triangles to an array of .obj or FreeSurfer files.
%
% Usage: SurfStatWriteSurf( filenames, surf [,ab] );
%
% filenames = .obj or FS file name (n=1) or n x k cell array of file names.
% If extension=.obj, writes a .obj file... |
5a40a545cb515f2578986ef24681d3dbc91496e87ac0f250452d8025991ddeb5 | MATLAB | 2,396 | 67 | dFC_project = struct();
[dFC_project] = compute_dFC(dFC_project,1);
if ~isstruct(dFC_project)
errordlg('An error occured while computing dFC')
return
end
dFC_project = compute_variability(dFC_project);
if ~isfield(dFC_project,'var_output_dir')
dFC_project.var_output_dir =uigetdir(pwd,'Select folde... |
919b9128c470a62d4c21faa8dd224926cf9062ccd893f0cfad61c0341b6cc5e1 | MATLAB | 2,410 | 75 | %%
clear
% current working directory needs to be /path/to/scripts
mainpath= pwd;
thisSubject='S2';
workingDir=[mainpath filesep '..' filesep 'subjectData' filesep thisSubject filesep '6_EEG'];
%
addpath([mainpath filesep 'toolboxes' filesep 'fieldtrip'])
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
f... |
c468c6118c942419a3dbcbdfce6c5d71dc8a653ba152200b21ea03a863f1039c | MATLAB | 2,412 | 100 | clear
tfn = [path_ludisc '\common\Data\MIPCART pilot\Analysis\ParTable_250625.mat'];
load(tfn);
uID = unique(T.ID);
%%
clf
% pnl = {'D', 'Vi', 'MKi','ufa2', 'Va', 'MKa'};
% plab = {'{\itD} [µm^2/ms]', '{\itV}_I [µm^4/ms^2]', 'MK_I [1]', 'µFA [1]', '{\itV}_A [µm^4/ms^2]', 'MK_A [1]'};
pnl = {'D', 'Vi', 'Va'};
plab =... |
74ad84a92a540ec3ba5404fe2e37113eeb3a6cbfbfc03c1b979488fa704111de | MATLAB | 2,415 | 54 | function loc_list_color_histogram(data)
input_values = inputdlg({'number of bins:'},'',1,{'100'});
if isempty(input_values)==1
return
else
figure()
set(gcf,'name','color-histogram-plot','NumberTitle','off','color','w','units','normalized','position',[0.2 0.3 0.6 0.4],'menubar','none','toolbar','fi... |
1a7f97787bd7b8a6ff3beed6ec80c77f5b3e46621d05a4bc17c7d4795cb23149 | MATLAB | 2,432 | 55 | function loc_list_density_plot_delauny_triangulation(data)
answer = inputdlg({'Maximum Number of Localizations for Down Sampling'},'Input',1,{'1000'});
if isempty(answer)~=1
num_points = str2double(answer{1});
f=waitbar(0,'Please wait...');
for i=1:length(data)
m = length(data{i}.x_data);
... |
a9303e3b8141e2a56c2def5478c5001a70a4ddcbf2ed5fac5ac50f3dc08d9434 | MATLAB | 2,435 | 64 | function [Kmeans_results,rangeK] = LEiDA_cluster(data_dir, mink, maxk)
%
% Cluster all leading eigenvectors into a set of K clusters using
% the K-means algorithm.
% This function returns an optimal solution for each values of K.
%
% INPUT:
% data_dir directory where the LEiDA_EigenVectors file is saved
%
% OU... |
f8e6bb43a387a6550d4a7ba41ce5b51f2e5460e3019a3b449f789724d97af0b9 | MATLAB | 2,440 | 99 |
%% SPECTROGRAM
clc
clear
addpath('/Users/pelinozsezer/Documents/Science/Radboud/RGS-Project/code/ripples/fieldtrip');
addpath('/Users/pelinozsezer/Documents/Science/Radboud/RGS-Project/code/ripples/functions');
load('GC_ripple_4clusters_median_wa.mat');
%% Merge data per treatment
GC_veh=[GC_Bp_cluster1_veh_median_wa... |
27d9d9c1e882147ead64741221e9def00c31c4f6a21af3810ecea3d866d58c16 | MATLAB | 2,466 | 46 | function colorSelector(src, plot_figure, parameters, chord_type, callback_function, color_choices)
original_figure = src.Parent.Parent;
modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
[original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, or... |
ad7063d196c3b6c47014383fc7393543ee0395da3b7f10f2c604ed30383a668d | MATLAB | 2,468 | 96 | function [Label2, Perc, nbpCluster2, PercentROI2, nbpROI2] = gin_det_plabels(XYZmm, MNIY, MNID, ROI,fact)
%
% Compute Labels and % for local maxima
%
% XYZmm : Local Maxima
% MNID : atlas volume with labels values
% ROI : structure : link between labels values and label name.
% BORDER_XYZ : structure contains th... |
32d545eb4beb4e2049fe173fd769042bbe01fb795d45f7c9570d93f14dab4455 | MATLAB | 2,469 | 66 | function loc_list_montage(data,map,scatter_num,scatter_size,c_lim)
global Int
if length(data)>6
msgbox('Number of files selected should be less than or equal to 3')
else
figure()
set(gcf,'name','Montage Plot','NumberTitle','off','color',[0.1 0.1 0.1],'units','normalized','position',[0.15 0.2... |
71deea9372c8059bc64cecf3a167329129880b83462533c23114a681a79f8481 | MATLAB | 2,476 | 50 | % Code to perform flat hyperellipsoid projection. In this code we take a
% current density input which can be the output of a gradient descent
% procedure and project it inside (on the boundary) of an ellipsoid to
% satisfy the constraint of the problem. This is the generalization of
% projecting to an ellipsoid in a b... |
da9e19befdf3376be65ac5c7bd0911f60b25fe4755a02d7dbf089da9f02ad19b | MATLAB | 2,476 | 80 | function [R,eff]=randmio_und(R, ITER)
%RANDMIO_UND Random graph with preserved degree distribution
%
% R = randmio_und(W,ITER);
% [R eff]=randmio_und(W, ITER);
%
% This function randomizes an undirected network, while preserving the
% degree distribution. The function does not preserve the strength
... |
9457bf5582197d416c75c0e2600ddbf711940429b0d6e182e068ed646fc25b5f | MATLAB | 2,479 | 46 | function [data_clustered,data_not_clustered] = loc_list_voronoi_monte_carlo(data)
answer = inputdlg({'Number of Iterations:','nm per Pixel:','Analysis Pixel Size:','MC Confidence Bounds:','Maximum Number of Thresholds:','Minimum number of Localizations per Cluster:'},'Input',[1 50],{'5','116','20','99.5','8','5'});
i... |
1e1f9cda937edaded6597bcd1da168ed6cf6ed473efd30a6c772b425ade5ba0c | MATLAB | 2,482 | 88 | function osl_spinning_brain(fname,fig,duration,tight)
% Make an animation by spinning the figure
% The azimuth angle will sweep through 1 revolution, while the
% elevation will remain unchanged
% The animation will start with the current azimuth angle
% All axes will be rotated
%
% INPUTS
% - fname - output fil... |
6b7106ea0308ec427949c6b3dc0e2005a053660586cada748ebdd6754378ebe5 | MATLAB | 2,488 | 70 | function [virtChannels, validROIinds]=timelock2virtualChannels(timelockData, headmodel, leadfield, sens, ROIcoords)
%% [virtChannels, validROIinds]=timelock2virtualChannels(timelockData, headmodel, leadfield, sens, ROIcoords)
disp('compute LCMV beamformer...')
% LCMV beamformer
cfg = [];
cfg.method = 'lcmv';
cfg.grid ... |
425f5df3682239926edf0e7824b055e4a02c8cc35dd4093835ae6365894a72db | MATLAB | 2,490 | 86 | function dps = resQ_4d_fit2param(mfs_fn, dps_fn, opt)
% function dps = resQ_4d_fit2param(mfs_fn, dps_fn, opt)
if (nargin < 2), dps_fn = []; end
if (nargin < 3), opt = []; end
opt = mdm_opt(opt);
dps = mdm_mfs_load(mfs_fn);
% Convert dps.m to large numbers
f = resQ_unitSwap([], -1);
f = reshape(f, [1 1 1 n... |
60e89b7cc6ef0c66bcd4fff0bea110bc56e2521cee394c67aca93deeb4b98b19 | MATLAB | 2,490 | 75 | classdef SandwichEstimatorInput < handle
% used to pass object by reference to SandwichEstimatorInputGUI and
% receive output settings from that GUI
%
% call 'struct' function on an instance of this class to get an
% equivalent struct
properties
groupId %n x 1 vector
permute_meth... |
545273005dd481dc3c658d8a5f8dc1aacceaef2f72f2e7ebd0ebe8e1aef8e000 | MATLAB | 2,491 | 61 | function FC_project = get_roi_info(FC_project)
old_path = pwd;
switch FC_project.atlas
case 1 % AAL3 parcellation
roi_info = struct2cell(load('ROI_MNI_V7_List.mat').ROI);
all_roi_names = permute(roi_info(3,1,:),[3 1 2]);
% Get hemisphere info
roi_split = cellfun(... |
41d2f321eacc7e8d6d1cb268f5bc3c181db17f7b7b3de073f286612b5485e47e | MATLAB | 2,493 | 85 | function dFCstream = TS2dFCstream(TS, W, lag, format)
% FUNCTION dFCstream = TS2dFCstream(TS, W, lag, format)
% takes time-series (TS), size of window (W), and value of shift of window
% (lag) as input and calculates dynamic functional connectivity stream
% (dFCstream) as output.
%
% inputs: TS(t,n) --> rows are t dif... |
dcd570f453dae6db84b575850f60e3b53c2e54c082cbe7636f1d6a22ef3babcb | MATLAB | 2,495 | 75 | function [newData1,newData2,newData3] = reorganizeData(data1,data2,data3,Filter)
newData1 = cell(1,length(data1));
newData2 = cell(1,length(data1));
newData3 = cell(1,length(data1));
for i = 1:length(data1)
if ~isempty(data1{i})
Clusters1 = extract_clusters(data1{i});
end
if ~i... |
a6a3a4e246135f45387a7247033325bbde3c8f82218f470864fd17af436a1072 | MATLAB | 2,507 | 72 | function Plot_K_vector_labelled(data_dir,save_dir,selectedK,centroid,parcellation)
%
% Plot the selected centroid in vector format with the labels of each area.
%
% INPUT:
% data_dir directory where LEiDA results are stored
% save_dir directory to save results for selected optimal K
% selectedK K defined ... |
1dd006c7ba71055cd5ff4da95ef33bc46a65846d8a8dba2798cae2a553eee081 | MATLAB | 2,510 | 74 | function [alphamap] = pl_permalphavalue(data, varargin)
%
% Returns the location-specific alpha values of a statistical map created
% from a statistic applied on 'data'
% This function is part of the permutationlab software:
% Author: Dimitrios Pantazis
% The code is currently under development, please do not s... |
57f33b77e9786d91c6a2577239130ab973e6510a63c23207f6bbdd0c6d9acd3c | MATLAB | 2,513 | 64 | function loc_list_roi_module(data,scatter_num,scatter_size,map)
figure();
set(gcf,'name','ROI Selection Module','NumberTitle','off','color',[0.1 0.1 0.1],'units','normalized','position',[0.25 0.15 0.5 0.7],'menubar','none','toolbar','none');
data = data{1};
data_down_sampled = loc_list_down_sample(data,scatter_nu... |
86702aa6fa1dd1bce786ddbef8b0a700ad0eab2779611a62e2d0347a0f3ce9b5 | MATLAB | 2,514 | 44 | %% read
%prot = tblread('L:\Elite\LARS\2014\oktober\OLUF HUNT\endelig\results\proteinGroups.txt','\t')
%prot = tblread('L:\Elite\LARS\2014\november\Kamilla\combined\txt\proteinGroups.txt','\t')
prot = xlsread('L:\Elite\kamila\Heart\Sub12LFQ.xlsx')
protlfq=prot(:,[1:36])
%protlfq=prot(:,[117:128])
%protlfq=prot(:,... |
6108a63c8f5ad28150a5c6bf00c9bb82877db8d8fda3536f498fb53539ad112f | MATLAB | 2,516 | 72 | %% data
x=[220.22 223.54 1.00
223.84 237.44 1.00
258.32 287.93 0.00
241.53 267.49 1.00
241.79 281.38 1.00
253.21 280.85 1.00
256.95 292.47 0.00
209.14 207.97 1.00
251.28 290.98 0.00
246.40 283.78 1.00
240.18 290.06 0.00
239.29 274.88 1.00
239.76... |
44454c348dc039b51d37ed2711af209aaac2af0df4757d898b3343a09e4bda62 | MATLAB | 2,517 | 75 | % This script visualizes the firing activity of neurons in different sleep stages per
% treatment.
%% Loading Data
load('RGS_Session_1.mat')
% load('RGS_Pyr_S1_No_Rn3.mat')
load('Vehicle_Session_1.mat')
Pyr_RGS=RGS14_Session_1.Pyramidal_Cells;
Pyr_Veh=Vehicle_Session_1.Pyramidal_Cells;
%% Correcting for Outliers... |
d56659d7d11335de10f1402b810f67c03f3948396c922ee7d64c81b48c39d0f8 | MATLAB | 2,518 | 72 | function Plot_C_vector_labelled(data_dir,save_dir,selectedK,centroid,parcellation)
%
% Plot the selected centroid in vector format with the labels of each area.
%
% INPUT:
% data_dir directory where LEiDA results are stored
% save_dir directory to save results for selected optimal K
% selectedK K defined ... |
3fc5b90aac38a6ff4bcbbceab47865167a0ce18a86de8242b55b5b6162b34c8d | MATLAB | 2,526 | 65 | clear;clc;close all
[file_name,path] = uigetfile('*.locb','Select .txt File(s)','MultiSelect','on');
if path~=0
file_name = cellstr(file_name);
[file,path_excel] = uiputfile('*.xlsx');
if path_excel~=0
save_to = fullfile(path_excel,file);
for i = 1:length(file_name)
locs_... |
9c263b3cfa3f37773269f5f2ef206a65d3c85294ac41e796885659b9b9c582d5 | MATLAB | 2,529 | 59 | classdef PairedT < nla.edge.BaseTest
%PAIREDT Edge-level Paired T-test
properties (Constant)
name = "Paired T"
coeff_name = "Paired T"
end
methods
function obj = PairedT()
obj@nla.edge.BaseTest();
end
function result = run(obj, test_options)
... |
67d526e87037b05f65a4197457d2cbfcf3faa3ab9aa0da374df978ab7f418dc3 | MATLAB | 2,530 | 57 | function spt_motion_classification_butterfly(data)
input_values = inputdlg({'spatial threshold','distance threshold:'},'',1,{'1.5','8'});
if isempty(input_values)==1
return
else
spatial_threshold = str2double(input_values{1});
distance_threshold = str2double(input_values{2});
not_butterfly_... |
88192aa0034841bf5e3a6b6887f6eb6dfd7df641ac3450266a95215c087b87bb | MATLAB | 2,532 | 110 | function demo_saem(sim,type)
path_ = pwd;
addpath(genpath(strcat(path_,'/MVAR_simu')));
addpath(genpath(strcat(path_,'/joint_est')));
addpath(genpath(strcat(path_,'/two_step_est')));
addpath(genpath(strcat(path_,'/misc')))
meas_snr=5;
bio_snr_vals=[1 3 5 10];
num_sources=3;
bio_snr_arr=repmat(bio_snr_vals, [50 1]);
di... |
24d57d22a9ffde08653cccbf0853445351d04691ca4ab7a046197883cb9183f7 | MATLAB | 2,538 | 60 | %%
if ~(exist('mainpath','var'))
clearvars
% currrent working directory needs to be /path/to/scripts
mainpath = pwd;
else
clearvars -except mainpath
end
addpath([mainpath filesep 'fmriRegAnalysis'])
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
%%
fconts = dir([mainpath '/../subjectDa... |
316862895024a370b1de506dacf61562740ea05e57f823a9f0ea0463ff5acdab | MATLAB | 2,545 | 69 | function jds_rippleIEI(animalprefixlist)
%JDS_RIPPLEIEI Distributions of cortical ripple inter-event intervals.
% jds_rippleIEI(animalprefixlist) computes inter-event intervals between
% successive cortical ripple start times within REM bouts and within NREM
% bouts, compares the two distributions (rank-sum), and... |
0812a3d4ac64f31fabba0f63204b65aa897afde18fb5abb61765c55be93e2b1e | MATLAB | 2,549 | 55 | function h=subplot_tight(m,n,p,margins,varargin)
%function subplot_tight(m,n,p,margins,varargin)
%
% Functional purpose: A wrapper function for Matlab function subplot. Adds the ability to define the margins between
% neighbouring subplots. Unfotrtunately Matlab subplot function lacks this functionality, and the margin... |
f2959e45049199caded4b0f5fc3e8703d6f09b899cb7a0a4e61fa5fb98f427d7 | MATLAB | 2,560 | 69 | function O = InducedResponses_Morlet_ROIs_AarhusClust( S )
O = [];
% It sends one job for each subject to Aarhus University cluster (for parallel
% computing purposes).
% It makes sense (and therefore it is implemented) only for single_subject
% option.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
8e0d201188041ac7ef6f228987d47e92eb32a50c02c07a1fe3b94b3d94a0c37a | MATLAB | 2,565 | 60 | %% on the cluster
addpath('/projects/MINDLAB2017_MEG-LearningBach/scripts/scripts_osl_learningbach/Cluster')
% config of the cluster server see cluster_split.m for more deatails
clusterconfig('slot', 1);
clusterconfig('long_running', 1);
% clusterconfig('scheduler', 'cluster');
MRIsubj = dir('/projects/MINDLAB2017_... |
f5507979fe5b2167a840b492c0111a3d18c738894fd84f4ae41f6f4ed94718b7 | MATLAB | 2,565 | 67 | function computation_gavg_crosscorr(subjects,settings)
%--------------------------------------------------------------------------
% Till Habersetzer, 05.07.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% Description:
% Computes a group-level grand average from individual-subj... |
6345b58feffe68871ab5a66fbc8578004ecfa0547b3dd59c2e749ae39396ba2b | MATLAB | 2,566 | 90 | function [pwr_high, pwr_high_rel, pwr_high_rel_max, pd, pd_prop, pd_relative, freq] = mot_FFT(mot_data,TR,varargin)
% mot_FFT(mot_data,TR,varargin)
%
% mot_data = time X motionparam (assumes 6)
% TR = TR in seconds
% varargin = info about whether or not to make extra plots (if 1 = plot,
% default is not to plot)
%
% lo... |
3f030d29da4a9b17380f70acc1e679ee0ab057a8fdd15fbf9dae86548c4dee65 | MATLAB | 2,568 | 99 | %% files
beckprot=xlsread('V:\felles\PROTEOMICS and XRAY\Abundance\Beck-2011-supplementary table 1-protein copies per cell.xls')
commprot=xlsread('V:\felles\PROTEOMICS and XRAY\Abundance\Common proteins in IF studies-Supplementary from review modified GS.xls')
commprot=xlsread('X:\Elite\kamila\idcombo.xls')
%% ... |
c478668cf8a122d6d6163a005e993d6a4ae91a041e0d02d6ba8826c41401b61d | MATLAB | 2,569 | 76 | % Finding Patches from IRES Solution
% Abbas Sohrabpour
% 20/2/2018
% Zhengxiang Cai
% 30/10/2018
% This version has been vastly improved by removing extra for loops by
% using cell arrays and using the unique command and more importantly by
% defining a global pointer that avoids checking all global indices by
% defi... |
f0fca76d61f694640b2598c7abcff9fefc3c188baf009e1268c105b792c17f9c | MATLAB | 2,579 | 60 | function dynamicBC_Reslice(PI,PO,NewVoxSize,hld,TargetSpace)
% PI - input filename
% PO - output filename
% NewVoxSize - 1x3 matrix of new vox size.
% hld - interpolation method. 0: Nearest Neighbour. 1: Trilinear.
% TargetSpace - Define the target space. 'ImageItself': defined by the image itself (corre... |
f3fde6813863fc5104aa8712c1cc865889b809c7ec413eda66d06f56a1b89cf2 | MATLAB | 2,586 | 72 | function [embedding, lambdas] = laplacian_eigenmaps(data, n_components, random_state)
%LAPLACIAN_EIGENMAPS Performs non-linear dimensionality reduction using Laplacian Eigenmaps
%
% [embedding, lambda] = LAPLACIAN_EIGENMAPS(data, n_components)
%
% Performs non-linear dimensionality reduction using Laplacian Eigenmaps.
... |
ec668950cb010717e121ecd00e5e8d61a859fd2b0ee80b308e8f4eb00f3c048f | MATLAB | 2,588 | 84 | function pDM = pinv_reg(DM,lambda,regtype,breakPoints)
% pDM = pinv_reg(DM,lambda,regtype)
%
% returns pseudoinverse of design matrix DM with ridge regression
% using identity matrix multiplied by parameter lambda
% http://www.math.kent.edu/~reichel/publications/square.pdf
if nargin<2 % no regularisation
lambda =... |
c5ade6a216d8eec417f357330bdbe0dd8a40d8733afa668e26d5e6f704b20bb7 | MATLAB | 2,591 | 81 | function [cij,flag] = makerandCIJdegreesfixed(in,out)
%MAKERANDCIJDEGREESFIXED Synthetic directed random network
%
% CIJ = makerandCIJdegreesfixed(N,K);
%
% This function generates a directed random network with a specified
% in-degree and out-degree sequence. The function returns a flag,
% deno... |
cbaa9d7e4f2bd05c4f4154b16c90115b734c08269e23c16655964593e1d8ae55 | MATLAB | 2,598 | 123 | clear
tfn = [path_ludisc '\common\Data\MIPCART pilot\Analysis\ParTable_250625.mat'];
Tin = load(tfn);
%%
T = Tin.T;
T = T(contains(T.dps_fn, 'resQ_nocov_dps.mat'), :); % keep only resQ
T = T(1:2:end, :); % Remove broken retest
T = mipp_time_2_commonTime_v2(T, 105);
tstr = {'Diffusivity', 'Isotropic variance', '... |
65256d02ba65dcfbba5bd613bd7adcd183ffdabf133156b8609fa7a7d900341c | MATLAB | 2,600 | 69 | %% IDENTIFICATION OF EXTENDED MVAR MODEL: Y(n)=B(0)Y(n)+B(1)Y(n-1)+...+B(p)Y(n-p)+W(n)
% MAKES USE OF ICA (no need of prior knowledge!)
%%% input:
% Y, M*N matrix of time series (each time series is in a row)
% p, model order
% idMode, determines strcitly causal estimation algorithm (0:builtin least squares, els... |
0c7c9e95147064cc155193b295f168b00e99a3183a7682faf6e3a315136f97df | MATLAB | 2,610 | 55 | function drawConvergenceMap(edge_input_struct, input_struct, net_atlas, sig_count_mat, num_tests, names, edge_result, color_map)
%DRAWCONVERGENCEMAP View convergence map (chord plot summarizing many
%results)
% edge_input_struct: edge-level input struct
% input_struct: net-level input struct
% ... |
e5ca555a48cb4b51b611c5921ee48bfe436eae3f591fe0474b05d609dc521999 | MATLAB | 2,614 | 94 | function out = labelmean(D,L,varargin)
% LABELMEAN mean value within label
% Averages columns with the same label. D must be a two-dimensional
% matrix. L must be a row vector containing integers (NaNs allowed).
% These integers are the labels of the corresponding column in D. The
% sortbylabelvector flag wi... |
7cbb3a3dc4fd3e71ebb4be07add9a276cac32a9ef8760fad10283b98ffd41dfb | MATLAB | 2,615 | 74 | function surfw = SurfStatInflate( surf, w, spherefile );
%Inflates a surface towards two fitted hemi-ellipsoids.
%
% Usage: surfw = SurfStatInflate( surf [, w [, spherefile ]] );
%
% surf.coord = 3 x v matrix of coordinates, v=#vertices.
% w = weight in [0,1] given to hemi-ellipsoids, default 0.5.
%... |
5de4da440cbb81ba786ea6ec91a14134f88b2171ee5430e4562a5b99658d270e | MATLAB | 2,619 | 93 | %% read csv
%pep=csvread('X:\Elite\LARS\2013\mars\tobias\reverse.csv');
%pepval=csvread('M:\Results\Sissel\HeK50\mascot\peparea.csv');
%pepval=csvread('X:\Results\Sissel\HeK50\sequest\pep12.csv');
%rt=csvread('X:\Qexactive\WTH6\WTHRT9RepMHpep.csv',1,6);
%rt=xlsread('X:\Qexactive\WTH6\Multiconsensus from 9 Report... |
a6fd7677cbb8995c2a21e72102890c357b123cde5d1dcf5521a295e775925462 | MATLAB | 2,621 | 64 | function [index_old, index_young] = young_or_old(thresh)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Compute the indexes of young and old subjects that have given more than
% thresh correct answers. If thresh is empty, it just get the informations
% about old and young indexes.
% INP... |
d9c5dd0bd5c72cca7eab1586182d0f9a83c7e65eb2f4957327178386bc8b6a58 | MATLAB | 2,623 | 87 | function [GErout,Erout,Eloc] = rout_efficiency(D,transform)
% ROUT_EFFICIENCY Mean, pair-wise and local routing efficiency
%
% [GErout,Erout,Eloc] = rout_efficiency(D,transform);
%
% The routing efficiency is the average of inverse shortest path length.
%
% The local routing efficiency of a node u is the ro... |
86351cf3dc3b0d06fab4d0a5cda84b122aea07e8d079b83593efbd98266c9710 | MATLAB | 2,624 | 96 | %% read data
synergi=xlsread('L:\Elite\kamila\Copy of FA UDC IM raw data.xlsx')
%% synergy check
dLR5=synergi(2:5,1:4)'
dLR5=synergi(2:5,6:9)'
dLR5=synergi(7:10,1:4)'
dLR5=synergi(7:10,6:9)'
d=dLR5(:,2:4)./repmat(dLR5(:,1),1,3) % control normalization
p=anova2(d,1,'off')
[h p]=ttest(2-(d(:,1)+d(:,2)),1-d(:... |
93c4d173f1b08faf504e41940baa2f4b3877de731c7a6a8ed9e1115f07c98b89 | MATLAB | 2,626 | 67 | function Plot_K_tpm(data_dir,selectedK)
%
% Plot the mean transition probability matrices for each condition.
%
% INPUT:
% data_dir directory with the results from running the hypothesis
% tests on the state-to-state transition probabilities
% selectedK K defined by the user
%
% OUTPUT:
% .fig/.p... |
2a6cd3c18864fb403e843290dd0751a67d5da02de226b75f6d583638503b88c7 | MATLAB | 2,634 | 61 | function model = GenerateModelFitforPlot(data_to_fit,j)
UseWeights = data_to_fit.UseWeights;
ModelFit = data_to_fit.ModelFit;
FitLocError = data_to_fit.FitLocError;
NumberOfStates = data_to_fit.NumberOfStates;
JumpsPerdT = data_to_fit.JumpsPerdT;
JumpProb = data_to_fit.JumpProb(j,:);
JumpProbCDF = data_to_fit.JumpProbC... |
b5573cb9dddadd778710d33c5379c370dd7a66426b60d435f7fa6a4fb7e15725 | MATLAB | 2,634 | 68 | classdef WorkShopPerform2018Test < 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
... |
b8a4c29cd0d64919539f6c7a0a111e2aed99476030965255aa1a56ba9a8f7642 | MATLAB | 2,644 | 68 | function [trl, event] = my_trialfun_olsa(cfg)
%--------------------------------------------------------------------------
% Till Habersetzer, 05.07.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% Description:
% Custom FieldTrip trial function ('trialfun') for defining epochs fr... |
ad9308e62589a5000630a13f952230a28491180a8804cc60bcc4fd9d5e647985 | MATLAB | 2,649 | 70 | function loc_list_clusters_aspet_ratio_table(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')
for i = 1:length(data_to_send)
data_... |
c54e50f46f93d95c933f289ad5da4e2f305b90ee4a8d43bf8eef085c94a87ff5 | MATLAB | 2,672 | 81 | function gt = gtom(adj,numSteps)
%GTOM Generalized topological overlap measure
%
% gt = gtom(adj,numSteps);
%
% The m-th step generalized topological overlap measure (GTOM) quantifies
% the extent to which a pair of nodes have similar m-th step neighbors.
% Mth-step neighbors are nodes that are reachable ... |
69a0f367d990a04e68684318d0b4652ef6777a0dc8fe8fd4515594ed6609829c | MATLAB | 2,679 | 77 | function denoised_data_path = melodic_ICA(func_data_path,seg_data_path, stim, numIC)
% Preparation for ICA melodic pipeline
[outdir,sidename,~] = fileparts(func_data_path);
outdir_ICA = [outdir filesep 'ICA_' sidename filesep];
if ~exist(outdir_ICA,'dir'); mkdir(outdir_ICA); end
denoised_data_path = fullfile(outdir... |
7b5afaad31d4bdc2a293ec0342a3c3957b2432fe9358ce61fa2ff0e6e0fb048d | MATLAB | 2,688 | 81 | function O = Cov_GenEig( S )
O = [];
% Tests for computing covariance over averaged subjects for generalised
% eigenvector solution.
% Many solutions here are hard coded and the reason to use the cluster is
% to overtake problems about memory.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
a34acbf773df2b643f43b184a4e7c700df3de4134555a15901c8b800139ed13e | MATLAB | 2,691 | 83 | %MAT_INTO_HDR The old versions of SPM (any version before SPM5) store
% an affine matrix of the SPM Reoriented image into a matlab file
% (.mat extension). The file name of this SPM matlab file is the
% same as the SPM Reoriented image file (.img/.hdr extension).
%
% This program will convert the ANALYZE 7.5 SPM... |
b72a415f106e506e3f690a25f86fbbb8992f95c96b9b7ec1b63ae9ea4158603e | MATLAB | 2,691 | 62 | classdef Heteroskedastic_FAST < nla.helpers.stdError.AbstractSwEStdErrStrategy
properties (SetAccess = protected)
REQUIRES_GROUP = true;
end
methods
function contrastStdErr = calculate(obj, sweStdErrInput)
%Computes Standard Error, but accelerated using assumption ... |
15d14da1c21f4895b391964ead5ad607d2a05925d44dcc25cd35187cdd79b0e8 | MATLAB | 2,699 | 91 | function SurfStatViews( data, vol, z, layout );
%Viewer for slices of volumetric data.
%
% Usage: SurfStatViews( data, vol [, z [, layout ]] );
%
% data = n x v matrix of data if k=1, or n x v x k array of data if
% k>1, or a memory map of same.
% vol.lat = nx x ny x nz logical array, 1=... |
1723932c9cb5b63a24914f061dc78627aedb7d149d4daad106520a4b7f42a69b | MATLAB | 2,702 | 103 | function [g2g,Duration_off,Count_off,Rate_off,Duration_on,Count_on,Rate_on,NonREMdur_tot,NPD]=get_off_data_trial(SD_Data_Veh_Pyr,i,ii,NPD,Trial)
x=SD_Data_Veh_Pyr(i).RatxData(ii).SD_Spike_Info;
xx=struct2table(x);
xxx=table2cell(xx(:,1));
NPD=[ NPD sum(~cellfun('isempty',x... |
47a42a10a4be151bda212af32753ab561816ac31a825f970c6589d14ceb3aa31 | MATLAB | 2,712 | 121 | function [Label,Dist] = gin_det_dlabels(XYZmm, MNID, ROI, BORDER_XYZ, BORDER_V)
%
% Compute Labels and Distances for local maxima
%
% XYZmm : Local Maxima
% MNID : atlas volume with labels values
% ROI : structure : link between labels values and label name.
% BORDER_XYZ : structure contains the regions edges in... |
4a710b4d99f5dcef442df131aecae0392a8482cc0345381f6c32cd6e55ed2201 | MATLAB | 2,720 | 63 | function spt_tracks_number_of_frames_histogram(data)
input_values = inputdlg({'number of bins:'},'',1,{'100'});
if isempty(input_values)==1
return
else
number_of_bins = str2double(input_values{1});
figure()
set(gcf,'name','Tracks Number of Frames Histogram','NumberTitle','off','color','w','... |
f1b0811f62985384e53dd95aa740b1fb64a80d11f5a3001f658b16fe1196c4f3 | MATLAB | 2,720 | 70 | % Input
% DT - delaunayTriangulation object for a set of [x,y] points
% kppt - logical array indicating the [x,y] points that should have their
% neighbors identified; length(kppt) = size(DT.Points,1)
% dispStrOut - logical value whether to write updates to command window
%
% Output
% neighborList... |
65b10e0eaaf8957b64370f2b8ef8b0412ea47cb02a965c9d7292529596228bc0 | MATLAB | 2,721 | 52 | function pval=pvalvsNull(readleft1,readright1,readleft2,readright2,permno,wsname, v_exclude_left, v_exclude_right)
% Calculate the p-value of correlation between two surface maps based on
% the null distribution of spins of map 1
% FORMAT pvalvsNull(readleft1,readright1,readleft2,readright2,permno,wsname)
% readleft1 ... |
bb924736d7f4db64a6e4167fedcbf85d0776c8a95189bcd0e25fc7cee3e94230 | MATLAB | 2,726 | 65 | function [f,F]=motif4struct_bin(A)
%MOTIF4STRUCT_BIN Frequency of structural class-4 motifs
%
% [f,F] = motif4struct_bin(A);
%
% Structural motifs are patterns of local connectivity in complex
% networks. Such patterns are particularly diverse in directed networks.
% The motif frequency of occurren... |
90b571dcbd905612a5c6ea00c1a80cbfdb5ca219b80d324e292df1c4a82f63c0 | MATLAB | 2,739 | 114 | clear
% maindir =[path_ludisc 'common/Data\MIPCART pilot\Pilot MRI\'];
%
% par = 'D';
% srs = {['resq_dki_wf1_' par '.nii.gz'], ['resq_dki_wf2_' par '.nii.gz'], ...
% ['resq_dki_wf3_' par '.nii.gz'], ['resq_dki_wf4_' par '.nii.gz']};
%
%
%
% for i = 1:numel(srs)
% fnl(i).paths = fix.findFiles(maindir, s... |
d11f806627f4909e362e20a7c5de3b921a63cbc3acffbafabf420a3370f61fea | MATLAB | 2,739 | 86 | function []=acf(x, k, caption)
%ACF Plot of sample autocorrelation function.
%
% ACF(x) plots the sample autocorrelation function of the univariate
% time series in vector x. By default, the sample autocorrelation
% function is plotted up to lag 25. ACF(x,k) plots the sample
% autocorrelation function up to lag k.... |
fb368a0f411a9e09e063c92842934e8e4d5e80e3f2657cca237b80fda3d9c77e | MATLAB | 2,740 | 75 | function LEiDA_StateTime
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% LEADING EIGENVECTOR DYNAMICS ANALYSIS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Function to plot the state time courses for all participants and plot... |
589f0f06e62d5054a167292daef45717e5a0912b568fbc5ead2c9c4a192ac7a9 | MATLAB | 2,753 | 100 | function [filtdat,empVals,fx] = filterFGx(data,srate,f,fwhm,showplot)
% filterFGx Narrow-band filter via frequency-domain Gaussian
% [filtdat,empVals] = filterFGx(data,srate,f,fwhm,showplot)
%
%
% INPUTS
% data : 1 X time or chans X time
% srate : sampling rate in Hz
% f : peak frequency of ... |
5de92794a4afdc61c04290647c333058b1e2ff51914002229ae46c93fd5f2a28 | MATLAB | 2,755 | 80 | function [R,eff] = randmio_und_signed(W, ITER)
% RANDMIO_UND_SIGNED Random graph with preserved signed degree distribution
%
% R = randmio_und_signed(W,ITER);
% [R,eff] = randmio_und_signed(W,ITER);
%
% This function randomizes an undirected network with positively and
% negatively signed connectio... |
755452435904cce08434074cee8e8dc24185bf9491a373689b6bb42c48769383 | MATLAB | 2,762 | 94 | function result = getProjectionDataFromExperiment(expID)
% get projection data from Allen experiment ID
%
% function data = getProjectionDataFromExperiment(expID)
%
% Purpose
% Get projection information from ARA sample brain(s) given one or more experiment IDs.
% These can be searched for using findAllenExperim... |
e4d1b1056c7fb0b906feb9b68bad372cafa868a31dd0c3b85d5e4dfb2dd71272 | MATLAB | 2,762 | 102 | function varargout = findAllenExperiments(varargin)
% find all Allen experiments defined parameters
%
% function [IDs,json]=findAllenExperiments('param1','val1','param2','val2',...)
%
%
% Inputs
% 'injection' - search for experiments with injections in this location. not searched for by default.
% ... |
5659f5bf8e81402ddc5c7f4bf6d458404a181a28fd3114fc11b8491f2c9ed680 | MATLAB | 2,763 | 67 | function drawCortex(ax, anat, ctx, mesh_alpha, view_pos, color_l, color_r)
%DRAWROISONCORTEX Draw ROIs on cortex mesh
% net_atlas: relevant NetworkAtlas object
% anat: struct containing various inflation values of cortex vertices
% ctx: MeshType object determining what mesh inflation value to use
... |
3c30afd4be983606aa11bbfcf41c8e9b75793cf5ff102c608d925b21f6a5a026 | MATLAB | 2,766 | 80 | function [R,eff] = randmio_dir_signed(W, ITER)
% RANDMIO_DIR_SIGNED Random directed graph with preserved signed
% in/out degree distribution
%
% R = randmio_dir(W, ITER);
% [R,eff] = randmio_dir(W, ITER);
%
% This function randomizes a directed weighted network with p... |
5877ca00404bb330286c8294a6e92f7bd1a83d6a6442fd971ae617327ca7c2ba | MATLAB | 2,766 | 92 | function [cfg, varargout] = rollback_provenance(cfg, varargin)
% ROLLBACK_PROVENANCE rolls the provenance one step back and should
% be used whenever a FT function calls another FT function without
% the user being (or having to be) aware of this.
%
% Some examples for use
%
% tmpcfg = [];
% tm... |
e9efbb310157f362cb0ba33d945f45045e279fc6bccf1c91382671d8c4af6dc1 | MATLAB | 2,768 | 67 | % current working directory needs to be /path/to/scripts
mainpath = pwd;
addpath([mainpath filesep 'toolboxes' filesep 'analyzePRF'])
addpath([mainpath filesep 'toolboxes' filesep 'knkutils'])
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
addpath([mainpath filesep 'toolboxes' filesep 'OpenFmriAnalysis'... |
86c833bf3a7a513a4b2f1e6e4afc19cd0fd256d63668825bb083cbd2da3306cb | MATLAB | 2,776 | 88 | function regs_conv = tc_conv_parmod_hrf(regs, config)
%% regs_conv = tc_conv_parmod_hrf(regs, config)
% convolves input regressors with hrf function using spm
%
% Note that the function will crash (indendedly), because spm_jobman is
% exploited to do the convolution
%
% regs must be a cell array of different regressors... |
b149d5dc6b4d4d8e141bf8236c44235f7cd8eb1c1634587129142b085b0ffdba | MATLAB | 2,776 | 76 | function E=efficiency_bin(A,local)
%EFFICIENCY_BIN Global efficiency, local efficiency.
%
% Eglob = efficiency_bin(A);
% Eloc = efficiency_bin(A,1);
%
% The global efficiency is the average of inverse shortest path length,
% and is inversely related to the characteristic path length.
%
% The loca... |
c7f21bbb3aecea1bc5c3672ee80d2816db2e11cc1fc30a604e30a5d5b389ff3b | MATLAB | 2,777 | 88 | classdef PullDown < nla.inputField.InputField
properties
display_name
name
options
items_data
plot_figure = false
label = false
field = false
value = false
end
properties (Constant)
ARROW_SIZE = 15 % Size of pulldown arrow
end
... |
d8c8720eb8ba93bc79d88b3cc093d5a38318ef2e5eab02fab0f1d6151952d92c | MATLAB | 2,778 | 84 | function O = Induced_Resp_SingleSub_AAL_Coordsj_AarhusClust( S )
O = [];
% It sends one job per subject to the Aarhus cluster (for parallel
% computing)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% leonardo.bonetti@psych.ox.ac.uk
% Leonardo Bonetti, Oxford, UK, 12/06/2022
%%%%%%... |
24d60bdc92b63536bbd4b9bd5c1645871d19e3d11619c545ef5f37cf163bcf92 | MATLAB | 2,788 | 63 | function spt_tracks_last_first_distance_traveled_callback(data)
input_values = inputdlg({'number of bins:'},'',1,{'100'});
if isempty(input_values)==1
return
else
number_of_bins = str2double(input_values{1});
figure()
set(gcf,'name','Tracks Distance Histogram','NumberTitle','off','color','w... |
3203787d071702a7904ed6d8952b5dbc7e91466b815f9d1133f82f496a9dc2b3 | MATLAB | 2,791 | 82 | function shape_classification_iterative_pairwise_clustering(data)
input_values = inputdlg({'Mass Coeff. of Variation Threshold:','Lengh Coeff. of Variation Threshold:','Width Coeff. of Variation Threshold:'},'',1,{'10000000','0.15','0.15'});
if isempty(input_values)~=1
coefficient_of_variation = [str2double(inpu... |
81bc9b8db0048836f1e9cc17dda067ad3888348a758c3f032c30a054e696475b | MATLAB | 2,791 | 96 | function TS_rnd = PhaseRand_surrogates(TS, value)
% FUNCTION TS_rnd = PhaseRand_surrogates(TS, value)
% takes time-series (TS) and type of randomization (value) as inputs and
% provides phase-randomized TS as output.
%
% inputs: TS(t,n) --> rows are t different time-points;
% columns are n ... |
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