sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9360c2fc3f8afa9581e05d7796e82ccb09a7af379239de9ec419d4963ed6b332 | MATLAB | 25,577 | 807 | % clear
% clc
NineMuscleMorphParaInitial = load('NineMuscleMorphParaInitial.mat');
NineMuscleMorphParaInitial = NineMuscleMorphParaInitial.NineMuscleMorphParaInitial;
G = 7; % Muscle Group Number (G = 1 to 9)
x0(1) = NineMuscleMorphParaInitial{G, 1}.MorphologicalParameters.OW.a1OW;
x0(2) = NineMuscleMorphParaInitia... |
f088843f067a0f5150a960cb28c85f16a3ce70e0c5329204e503f0f047611a29 | MATLAB | 25,579 | 627 | function varargout = eval_gv(net, condition, v_u_t, m_target_t, v, lambda, forward_pass)
%% Setup.
% Network structure.
[n_Wru_v, n_Wrr_n, m_Wzr_n, n_x0_c, n_bx_1, m_bz_1] = unpackRNN(net, net.theta);
[V,T] = size(v_u_t);
[M,N] = size(m_Wzr_n);
% Transfer functions.
rec_transfun = net.layers(2).transfun;
out_transfun ... |
6c3cd0191c5b3410b82d9285e05a3ec29340bd47f25a307cf6bcd874922a3c34 | MATLAB | 25,598 | 524 | %% This file generates all figures and tables of results to the fitting of the connectome data.
% Be sure to run FitConnectome first.
%% Create Brain figures
PATH = pwd;
fontsize = 10;
diff_time19 = (19 - 8/3)/1000;
diff_time49 = (49 - 8/3)/1000;
image1Sub = 'sub_003_rescan';
image1slice = 71;
image2Sub = ... |
ef0a3d67d3f6012bd349a2401019bcda7ee76d1888b164e3d4f86265dbf1aa8f | MATLAB | 25,603 | 471 | % Get behavior related information
% Edit by Jerry. 09/20/2022
function Behavior = GetBehaviorInfo_220920...
(szCell,szDir,szTiming,params,SaveDir)
%*********************************************************************
% this function extracts all the behavioral information
% The notation [n] refers to... |
8cf269b3d7ef93b4e86eb8edb5b586512141ea457947e0e14ab649e602b05871 | MATLAB | 25,616 | 778 | function stack = tiffread(filename, indices)
% tiffread, version 2.91 Nov 1, 2010
%
% stack = tiffread;
% stack = tiffread(filename);
% stack = tiffread(filename, indices);
%
% Reads 8,16,32 bits uncompressed grayscale and (some) color tiff files,
% as well as stacks or multiple tiff images, for example those produced... |
d09eadb299352107654b2616a012c6ae8653b96e17dc7fdecd99056d29a94b46 | MATLAB | 25,618 | 649 | %% ppDataCell
% OOP-based class for handling of point-process datatypes. Designed for use
% within the SDO Analysis Toolkit.
% TODO: Modularize Plotters
% 8.12.2024 - Added Validation to the import method to ensure that the
% arrangement of data corresponds to expectations
%_______________________________________
%... |
f294014a740ccbabd7e24071918f72b4da9120e8cb5c5451ba6046ada9a5d408 | MATLAB | 25,664 | 598 | function [headmodel, sens] = ft_prepare_vol_sens(headmodel, sens, varargin)
% FT_PREPARE_VOL_SENS does some bookkeeping to ensure that the volume
% conductor model and the sensor array are ready for subsequent forward
% leadfield computations. It takes care of some pre-computations that can
% be done efficiently prior... |
403b9b001018b444ac07853377fe9e4678ef06ce5a027c8e4f6f7edeb24ed72c | MATLAB | 25,677 | 1,015 | function GLAN = erp_stata(GLAN,cfg)
% <*LAN)<]
% v.0.0.996
%
% REALIZA ESTADISTICA NOPARAMETRICA A ERP
%
% cfg.
% subject = [{}{}{}]
% comp = [n1 n2]; % INDEX OF THE CONDITION TO COMPARED
% matdif = [-1 1 -2 2] % MATRIZ DE DIFERENCIAS, DEL MISMO TAMAGNO QUE cfg.comp.
% ... |
bbbc2c9b7ac7068ce05f0145cf850b783b71ef7c03e62fa21eba8d05612bea8f | MATLAB | 25,685 | 750 | function y = symbolise_ed_vectorised(x, dim, dly, ties)
% SYMBOLISE_ED_VECTORISED encodes Difference Patterns of a given time
% series. Patterns are encoded using vectorisation. The entries of the
% output vector are casted to the smallest admittable unsigned integer
% class (uint8, uint16 or uint32).
%
% Y =... |
cf63cd44fd6bc866d7a9b6ff467f4071186e7965ca13f31f31aa609d3fa5a3e3 | MATLAB | 25,697 | 397 | function remapping_classification_bootstrap(folders)
parameters= list_of_parameters;
master_folder= pwd;
cell_remapping= table;
% load('cell_remapping.mat');
for this_folder=1:size(folders,1)
cd([master_folder '\' folders{this_folder,1}]);
disp([master_folder '\' folders{this_folder,1}])
tic;
load... |
594b255ad44b9d87f740d65598a5b47ebba0a21b9191628f43c9dab471410705 | MATLAB | 25,747 | 525 | function [log_odd] = ground_truth_log_odd_analysis_partial(folders,timebin,posbin,BAYSESIAN_NORMALIZED_ACROSS_TRACKS)
% Input:
% Folders: Each Folder is data for a session
% Timebin: 0.02 or 1
% 0.02 -> 20ms time bin
% 1 -> 1 event time bin
% posbin: [] or 1
% [] -> 20 position bin per track (will load extracted_place_... |
91ebf203335e63e7837c518f5d35c64bcc1e133d49cbdfbbd8e72ed5827848cc | MATLAB | 25,762 | 813 | % clear
% clc
NineMuscleMorphParaInitial = load('NineMuscleMorphParaInitial.mat');
NineMuscleMorphParaInitial = NineMuscleMorphParaInitial.NineMuscleMorphParaInitial;
G = 6; % Muscle Group Number (G = 1 to 9)
x0(1) = NineMuscleMorphParaInitial{G, 1}.MorphologicalParameters.OW.a1OW;
x0(2) = NineMuscleMorphParaInitia... |
4525a67b2af936fa096a4e513c86f72e7c0758d4241f712f13699d18d6975418 | MATLAB | 25,781 | 683 | function [Y, infos, problem_description] = low_rank_dist_completion(problem_description)
% Perform low-rank distance matrix completion w/ automatic rank detection.
%
% function Y = low_rank_dist_completion(problem_description)
% function [Y, infos, out_problem_description] = low_rank_dist_completion(problem_descri... |
b95368e133186c1f1956071cf653c8394b4d3c204c941a85cebf035929b8d3b5 | MATLAB | 25,785 | 827 | % clear
% clc
NineMuscleMorphParaInitial = load('NineMuscleMorphParaInitial.mat');
NineMuscleMorphParaInitial = NineMuscleMorphParaInitial.NineMuscleMorphParaInitial;
G = 7; % Muscle Group Number (G = 1 to 9)
x0(1) = NineMuscleMorphParaInitial{G, 1}.MorphologicalParameters.OW.a1OW;
x0(2) = NineMuscleMorphParaInitia... |
679f245bbe0f4c8a3d7066c1de0249a8847c746ff254205a3ea868106a3ca1de | MATLAB | 25,946 | 522 | function [ session ] = load_beh_shef( varargin )
%LOAD_beh GUI for aligning .tif files to .mat files
%
% PARAMETERS
% tif_frame_counts ([]) - The number of frames in each .tif to be
% aligned. If left empty, tif_filepaths must/will be assigned and the
% frame counts will come from the files.
% tif_filep... |
8340765ed66db64f280cbec97610d7d03e6c58bc0114b6dbdafc93d25537a643 | MATLAB | 25,971 | 834 | % clear
% clc
NineMuscleMorphParaInitial = load('NineMuscleMorphParaInitial.mat');
NineMuscleMorphParaInitial = NineMuscleMorphParaInitial.NineMuscleMorphParaInitial;
G = 6; % Muscle Group Number (G = 1 to 9)
x0(1) = NineMuscleMorphParaInitial{G, 1}.MorphologicalParameters.OW.a1OW;
x0(2) = NineMuscleMorphParaInitia... |
0d5fe0e82b255ab1ff48d62379ec1c3d266731affd40935c1b1c452e15fd0893 | MATLAB | 25,979 | 583 | function fg=y_spm_image(op,varargin)
% image and header display
% FORMAT y_spm_image
%_______________________________________________________________________
%
% y_spm_image is an interactive facility that allows orthogonal sections
% from an image volume to be displayed. Clicking the cursor on either
% of the ... |
43a83f66870f605f3de6b05f3265c8448526ea90c414c0522829d5c4f2f4d336 | MATLAB | 25,997 | 865 | %% Load Unit Data
datRoot = '/Volumes/LaCie/Farries recordings/';
load([datRoot 'unitDat_final_culled.mat'])
uName = arrayfun(@(u) strsplit(u.name), unit, 'UniformOutput', false);
uRat = cellfun(@(u) u{1}, uName, 'UniformOutput', false);
uSes = cellfun(@(u) u{2}, uName, 'UniformOutput', false);
uTrode = cellfun(@(u) ... |
b405fedca088d688d300fcc5a471cb073d0ecd61f36f8c581cbd5df9404576e7 | MATLAB | 26,029 | 518 | classdef ProjectSetup < handle
% Widget properties
properties (Access = private, Transient)
fig_ matlab.ui.Figure
project_name_label_ matlab.ui.control.Label
project_name_edit_ matlab.ui.control.EditField
number_of_keypoints_label... |
560b48d7907a6d69ac4f1034cff5849e1bb960f23d2d9e72b402384b2d9b11f3 | MATLAB | 26,038 | 670 | % [MeanContrast, SigContrast, pValue] = PermutationTest( ...
% Data, Data2, nPerms, pValue, Paired, OneSided, TMaxDims, ...
% MultipleComparisons)
%
% One- or two-sample, paired or unpaired random permutation test of the
% null hypothesis that the samples in arrays Data and Data2 along the last
% dimension come f... |
c6dbcb6d6ffb6e5197a4a2cf0412c2582bdfa7767008c3c4dc0bf83cfbc26f85 | MATLAB | 26,080 | 469 | function shape_classification_plot_distribution(dataClass,ClassesDistance)
fig = clf(figure());
set(fig,'name','Class distribution','NumberTitle','off','color','w','units','normalized','position',[0.275 0.175 0.4 0.4],'menubar','none','toolbar','none')
CurrentAutomaticAxes = 1;
CurrentBox = 0;
CurrentGrid = 0;... |
8001742f172f311f6866c5a8571043eea6cab8733276a9e323f8a4049556d3f7 | MATLAB | 26,102 | 773 | function [pipeline] = ft_analysispipeline(cfg, data)
% FT_ANALYSIPIPELINE reconstructs the complete analysis pipeline that was used to create
% the input FieldTrip data structure. The pipeline will be visualized as a flowchart.
% In the future it will be possible to output the complete pipeline as a MATLAB script
% or... |
59c45660e4b0e35be990a43aff09e3935025414558b84c7a26ecc3c188598046 | MATLAB | 26,104 | 520 | %_______________________________________________________________________
%
% Run random dot motion experiment defined in createDotInfo
%_______________________________________________________________________
%
% Input
%
% expInfo | experiment configuration (struct)
% setup.subj | identifier of subject (string)
% con... |
affcde97f3af8e19dc2e272d6768061c294f2f4d052d3aaaa8e2d570242167c7 | MATLAB | 26,134 | 618 | function [status] = ft_hastoolbox(toolbox, autoadd, silent)
% FT_HASTOOLBOX tests whether an external toolbox is installed. Optionally
% it will try to determine the path to the toolbox and install it
% automatically.
%
% Use as
% [status] = ft_hastoolbox(toolbox, autoadd, silent)
%
% autoadd = 0 means that it will ... |
24f197917699727921935f20708ffa2e1a6142b119d66d5bc6cc3ea1c7e0853b | MATLAB | 26,150 | 779 | function [varargout] = ft_qualitycheck(cfg)
% FT_QUALITYCHECK performs a quality inspection of a given MEG/EEG dataset,
% stores (.mat), and visualizes the result (.png and .pdf).
%
% This function segments the data into 10-second pieces and performs the
% following analyses:
% 1) reads the properties of the dataset
... |
d8c4947780c47c36cb1cc4d7eed877511464b2d8d06ce91f2811c2ecbf5175fc | MATLAB | 26,155 | 779 | function [varargout] = ft_qualitycheck(cfg)
% FT_QUALITYCHECK performs a quality inspection of a given MEG/EEG dataset,
% stores (.mat), and visualizes the result (.png and .pdf).
%
% This function segments the data into 10-second pieces and performs the
% following analyses:
% 1) reads the properties of the dataset
... |
e0e094b8983965b30b6d6d1060862b1f39d32d09c9fff398c07ad62c9f9461ee | MATLAB | 26,172 | 558 | %% cytoarchitecture
% author: Casey Paquola
% email: casey.paquola@gmail.com
% feel free to get in touch if you have any questions
for init_project = 1
% set directories
GH = '/Users/cpaquola/Documents/GitHub/'; % github repo location
homeDir = [GH '/DMN']; ... |
38940f4f0673c6f3dc9d64db17a44990bdecf535f4bcdd2008276128c118dfd5 | MATLAB | 26,179 | 589 | function [cfg] = ft_interactiverealign(cfg)
% FT_INTERACTIVEREALIGN allows the user to interactively translate, rotate and scale an
% individual geometrical object to a template geometrical object. It can for example be used
% to align EEG electrodes to a model of the scalp surface.
%
% Use as
% [cfg] = ft_interacti... |
1d45611715500236256be225c89406d3e8a9619148831bcdafca2f118164332b | MATLAB | 26,205 | 613 | function [headmodel, sens] = ft_prepare_vol_sens(headmodel, sens, varargin)
% FT_PREPARE_VOL_SENS does some bookkeeping to ensure that the volume
% conductor model and the sensor array are ready for subsequent forward
% leadfield computations. It takes care of some pre-computations that can
% be done efficiently prior... |
ed6f1083cbd070913eb66bc1f4678b4c31ee385b821ca4d1bdcb9349e3e4ac48 | MATLAB | 26,206 | 457 |
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
84240e02397e14080a11db2d11b76acb69a07e08a9fe52fa4dcbf25c983478b8 | MATLAB | 26,242 | 537 | clear all; clc
% Change directory to path where sosp_vaso git has been cloned
cd /home/amonreal/Documents/PhD/PhD_2023/AROMA/publications/sosp_vaso/github/3D_SOSP_fMRI/
addpath(genpath("./pulseq/functions"))
%% Adding paths
addpath(genpath("./pulseq/functions")) % Functions to... |
fb6a51d79d42b2c557d0a7f89216f1ae3db6b66963f8573d97cbbbf9b6f2a195 | MATLAB | 26,298 | 951 | function output=model_ToRORd_Land(t,X,flag_ode, cellType, ICaL_Multiplier, ...
INa_Multiplier, Ito_Multiplier, INaL_Multiplier, IKr_Multiplier, IKs_Multiplier, IK1_Multiplier,IKCa_Multiplier, IKb_Multiplier,INaCa_Multiplier,...
INaK_Multiplier, INab_Multiplier, ICab_Multiplier, IpCa_Multiplier, ICaCl_Multiplier... |
d75f5302879c99e61993f8f682abf704ebb9b97365b1f4fd6285f78b71da6228 | MATLAB | 26,354 | 576 | % PLSR_forRunAnalysis.m
% Sarah West
% 6/6/22
% A wrapper that runs the Matlab function plsregress_fullcode via RunAnalysis.m
function [parameters] = PLSR_forRunAnalysis_Inverted(parameters)
% *** Inputs ***
% parameters.dataset.explanatoryVariables --
% parameters.dataset.responseVariables --
% pa... |
e509c9b9718eec88e51642d5ace0f684ae78dd1d7d7c2c31906854785d2f852d | MATLAB | 26,374 | 590 | function fg=y_spm_image(op,varargin)
% image and header display
% FORMAT y_spm_image
%_______________________________________________________________________
%
% y_spm_image is an interactive facility that allows orthogonal sections
% from an image volume to be displayed. Clicking the cursor on either
% of the ... |
0e09a94860c709c8c6af1b6618397ef8d350f8b069db89b165748b124e4d8c97 | MATLAB | 26,388 | 819 | function [xfinal,ffinal,exitflag,xstart] = rmsearch(fun,optname,x0,LB,UB,varargin)
% RMSEARCH: Randomly multistarted overlay to several optimizers
% usage: [xfinal,ffinal,exitflag,xstart] = RMSEARCH(fun,optname,x0,LB,UB)
% usage: [xfinal,ffinal,exitflag,xstart] = RMSEARCH(fun,optname,x0,LB,UB,prop1,val1,prop2,val2,...)... |
b137224244a5d0e4f96fe96d096de06e70a911a2a0bc198ca43122deaa8055da | MATLAB | 26,400 | 718 | % create_conditions_names.m
% Sarah West
%% Parameters for directories
clear all;
% Time for continued time chunks, in seconds.
continued_chunk_length = 1;
experiment_name=['Random Motorized Treadmill\'];
dir_base='Y:\Sarah\Analysis\Experiments\';
dir_exper=[dir_base experiment_name '\'];
dir_out=dir_exper;
mkdi... |
0776d7a3f419b086a8951a01c1a46a13bc8a7fc3e88bdd9181872b8fe1defb65 | MATLAB | 26,436 | 592 | function [cfg] = ft_interactiverealign(cfg)
% FT_INTERACTIVEREALIGN allows the user to interactively translate, rotate and scale an
% individual geometrical object to a template geometrical object. It can for example be used
% to align EEG electrodes to a model of the scalp surface.
%
% Use as
% [cfg] = ft_interacti... |
75e38fe9f4c04a8da7ddaad47a68b501ef6d0bcc7cc74c019831ca59428ae51d | MATLAB | 26,503 | 776 | function [pipeline] = ft_analysispipeline(cfg, data)
% FT_ANALYSIPIPELINE reconstructs the complete analysis pipeline that was used to create
% the input FieldTrip data structure. The pipeline will be visualized as a flowchart.
% In the future it will be possible to output the complete pipeline as a MATLAB script
% or... |
451cc123305c5a1f4ce4e46983856bd73639644678d0135067dc7c7f9166b61d | MATLAB | 26,533 | 541 | function [header] = read_4d_hdr(datafile, configfile)
% hdr=READ_4D_HDR(datafile, configfile)
% Collects the required Fieldtrip header data from the data file 'filename'
% and the associated 'config' file for that data.
%
% Adapted from the MSI>>Matlab code written by Eugene Kronberg
% Copyright (C) 2008-2009, Centre... |
a9da8f098b63327bfc98124a9e4d84974d15929d3e901abe4b8b279757a7be35 | MATLAB | 26,540 | 662 | classdef ScrollingPanel < uix.Container & uix.mixin.Panel
%uix.ScrollingPanel Scrolling panel
%
% p = uix.ScrollingPanel(p1,v1,p2,v2,...) constructs a scrolling panel
% and sets parameter p1 to value v1, etc.
%
% A scrolling panel is a standard container (uicontainer) that shows
% one i... |
ac1df58ad6e44cd946a057a1871c50bd65ad54fe747cf4c235727e4d336b0e0f | MATLAB | 26,551 | 958 | function output=model_ToRORd_Land_diffusion_current(t,X,flag_ode, cellType, ICaL_Multiplier, ...
INa_Multiplier, Ito_Multiplier, INaL_Multiplier, IKr_Multiplier, IKs_Multiplier, IK1_Multiplier,IKCa_Multiplier, IKb_Multiplier,INaCa_Multiplier,...
INaK_Multiplier, INab_Multiplier, ICab_Multiplier, IpCa_Multiplier... |
7fb4da30845fac3eea9814167a824e30633d43d9a5eed5ba57d9997d7a14d990 | MATLAB | 26,584 | 728 | function prepro_proto(LAN)
global fig_eeg;
global fig_chan;
global fig_control;
global fig_tsm;
time_win = 1;
time_start = 0;
time_trial = 1;
chansel = 1:LAN.nbchan;
chansel_ts = 1:LAN.nbchan;
str_chan = cat(2,'1:',num2str(LAN.nbchan));
chanhighlight = 0;
gapsize = 3* mean( std(LAN.data{1},[],2) , 1);
resizefact = 1;... |
e93877aaa28b58b49575f2ab23402d729ef532d48d1143d53ae7e17e8ec8159b | MATLAB | 26,599 | 726 | function elife_BH_test
clear all
num_events = 10000;
num_cells = 10;
noise = 0;
% Generate random neuronal sequence with each neuron firing 1,2 or 3 spikes
for i=1:num_events
spikes1 = [];
s = RandStream('dsfmt19937','Seed',i); % Set random seed for resampling
spikes1 = randperm(s,num_cells);
spike... |
6155656509ceff7c8cc678725d3ad8b5f9fa829bae6bd709137b8fbd6e1b5c4f | MATLAB | 26,735 | 529 | function print2eps(name, fig, export_options, varargin)
%PRINT2EPS Prints figures to eps with improved line styles
%
% Examples:
% print2eps filename
% print2eps(filename, fig_handle)
% print2eps(filename, fig_handle, export_options)
% print2eps(filename, fig_handle, export_options, print_options)
%
%... |
427bd395e48611a53c4ceb59787da0b0948d0aa9b876748cc4ccc24cd701c351 | MATLAB | 26,760 | 953 | function output=model_ToRORd_step_stimulus(t,X,flag_ode, cellType, ICaL_Multiplier, ...
INa_Multiplier, Ito_Multiplier, INaL_Multiplier, IKr_Multiplier, IKs_Multiplier, IK1_Multiplier,IKCa_Multiplier, IKb_Multiplier,INaCa_Multiplier,...
INaK_Multiplier, INab_Multiplier, ICab_Multiplier, IpCa_Multiplier, ICaCl_M... |
0dd5a7d6bf127d134b45df5e04116904795cb6cd0f4bc9859ad9d6dca2986612 | MATLAB | 26,803 | 954 | function output=model_ToRORd_diffusion_current(t,X,flag_ode, cellType, ICaL_Multiplier, ...
INa_Multiplier, Ito_Multiplier, INaL_Multiplier, IKr_Multiplier, IKs_Multiplier, IK1_Multiplier,IKCa_Multiplier, IKb_Multiplier,INaCa_Multiplier,...
INaK_Multiplier, INab_Multiplier, ICab_Multiplier, IpCa_Multiplier, ICa... |
5bd1844b79cc29e5182b079913cc34f5d72d40cb3111788615229342f8e6b6af | MATLAB | 26,822 | 954 | function output=model_ToRORd_step_stimulus(t,X,flag_ode, cellType, ICaL_Multiplier, ...
INa_Multiplier, Ito_Multiplier, INaL_Multiplier, IKr_Multiplier, IKs_Multiplier, IK1_Multiplier,IKCa_Multiplier, IKb_Multiplier,INaCa_Multiplier,...
INaK_Multiplier, INab_Multiplier, ICab_Multiplier, IpCa_Multiplier, ICaCl_M... |
99f7d1935dff3a154dbddb6728d19c301adb0d3fed5893e91d8a1ce089ca51d9 | MATLAB | 26,844 | 698 | function varargout = DPABI_DCMSORTER_TOOL(varargin)
% DPABI_DCMSORTER_TOOL MATLAB code for DPABI_DCMSORTER_TOOL.fig
% DPABI_DCMSORTER_TOOL, by itself, creates a new DPABI_DCMSORTER_TOOL or raises the existing
% singleton*.
%
% H = DPABI_DCMSORTER_TOOL returns the handle to a new DPABI_DCMSORTER_TOOL or t... |
508a88afd65ae0aa5a024d3cac1ccb53bde1fce92c78b19f5b5ec75ff1ad3eee | MATLAB | 26,850 | 954 | function output=model_ToRORd_step_stimulus_rescaled_IKs_60_percent_GKr(t,X,flag_ode, cellType, ICaL_Multiplier, ...
INa_Multiplier, Ito_Multiplier, INaL_Multiplier, IKr_Multiplier, IKs_Multiplier, IK1_Multiplier,IKCa_Multiplier, IKb_Multiplier,INaCa_Multiplier,...
INaK_Multiplier, INab_Multiplier, ICab_Multipli... |
411e2e6189ce29991f24446a4c615edb5df06aa5047df85d3ba4c206759e183d | MATLAB | 26,854 | 631 | %{
Copyright (c) 2025 Axion BioSystems, Inc.
Contact: support@axion-biosystems.com
All Rights Reserved
%}
classdef AxisFile < handle & matlab.mixin.CustomDisplay
%AXISFILE: Class that holds all Data for a loaded Axion 1.X File
%
% Calling A = AxisFile('filename.raw') or AxisFile('filename.spk') ... |
b4cf7f705fa3ce604dd4396aa210cae8ca1ddfca5a45ff3a2947dd38d06d7015 | MATLAB | 26,883 | 554 | function [O_error, O_grad]=bspline_registration_gradient(O_grid,sizes,Spacing,I1,I2,options,MaskI1,MaskI2,Points1,Points2,PStrength)
% Function registration_gradient. This function will calculate a registration
% error value and gradient after b-spline non-rigid registration
% of two images / volumes.
%
% [error, ... |
14f234a5905426a7a4897c1d41421e95c5ef47abe4b6aedf0cda9956bc92ccac | MATLAB | 27,018 | 600 | function [out,pkLocOn_all,unilateralStim,fNumOut] = plotObs(obs_allFlies,meta)
warning('off','signal:findpeaks:largeMinPeakHeight')
gender_allFlies = meta.gender;
stimIntensity_allFlies = meta.stim.Intensity;
stimFileName_allFlies = meta.stim.FileName;
stimColor_allFlies = meta.stim.Color;
flyID_allFlies = repm... |
11051d18eaeead39d243eee8972b840f6c437b5b51739dc47d723e881620d12d | MATLAB | 27,041 | 712 | function varargout = DPABI_ICC_TOOL(varargin)
% DPABI_ICC_TOOL MATLAB code for DPABI_ICC_TOOL.fig
% DPABI_ICC_TOOL, by itself, creates a new DPABI_ICC_TOOL or raises the existing
% singleton*.
%
% H = DPABI_ICC_TOOL returns the handle to a new DPABI_ICC_TOOL or the handle to
% the existing singleton... |
de8a590ef2ed248c4884605a76ab31331a64fec6bc208ae27c79fa8ecd8bc0c5 | MATLAB | 27,058 | 780 | classdef BoxPanel < uix.Panel & uix.mixin.Panel
%uix.BoxPanel Box panel
%
% p = uix.BoxPanel(p1,v1,p2,v2,...) constructs a box panel and sets
% parameter p1 to value v1, etc.
%
% A box panel is a decorated container with a title box, border, and
% buttons to dock and undock, mini... |
521f196dfe695eb1cb557e1e7549acedb6b5025333b4e38891f56afb7dae319c | MATLAB | 27,083 | 956 | function output=model_ToRORd_diffusion_current_rescaled_IKs(t,X,flag_ode, cellType, ICaL_Multiplier, ...
INa_Multiplier, Ito_Multiplier, INaL_Multiplier, IKr_Multiplier, IKs_Multiplier, IK1_Multiplier,IKCa_Multiplier, IKb_Multiplier,INaCa_Multiplier,...
INaK_Multiplier, INab_Multiplier, ICab_Multiplier, IpCa_Mu... |
8e35c878bd3f76cd80b6bcefbc50c9847784b45f2ee0b4e9c17a0f9026b962e6 | MATLAB | 27,094 | 541 | %%
% ================= SACCADE ANALYSIS =================
%%
clear all; close all; clc;
addpath('C:\toolbox\edfImport1.0.5\')
ET_details = {};
%%
for s = 1:21
if s < 10
sub = strcat('P0',num2str(s));
else
sub = strcat('P',num2str(s));
end
dir_files = strcat(... |
f96cd6047b2f891a591efa2a1b7f7be4d62b05e3abe10cd86d8e52ee82bc9d1b | MATLAB | 27,098 | 956 | function output=model_ToRORd_diffusion_current_rescaled_IKs_60_percent_GKr(t,X,flag_ode, cellType, ICaL_Multiplier, ...
INa_Multiplier, Ito_Multiplier, INaL_Multiplier, IKr_Multiplier, IKs_Multiplier, IK1_Multiplier,IKCa_Multiplier, IKb_Multiplier,INaCa_Multiplier,...
INaK_Multiplier, INab_Multiplier, ICab_Mult... |
9df058deb2264405e08d6ef8d3a6b60987bc7caad411a834af26fa3443d230e3 | MATLAB | 27,123 | 602 | classdef Quattrodlg < matlab.apps.AppBase
% Properties that correspond to app components
properties (Access = public)
UIFigure matlab.ui.Figure
pathname matlab.ui.control.EditField
CheckBox_M4 matlab.ui.control.CheckBox
CheckBox_M3 matlab.ui... |
2bc00fc7bea9b0a965e055d4af08c5302230c7cf0e11625b5680ca117b09370a | MATLAB | 27,138 | 642 | function [source] = ft_dipolefitting(cfg, data)
% FT_DIPOLEFITTING perform grid search and non-linear fit with one or multiple
% dipoles and try to find the location where the dipole model is best able
% to explain the measured EEG or MEG topography.
%
% This function will initially scan the whole brain with a single ... |
8a6b5015b4e049fd45fc5f160fd32933c38f3aa1924677b4ff9cdf27ffc69dda | MATLAB | 27,176 | 580 | function varargout = FieldmapFormat(varargin)
% FIELDMAPFORMAT MATLAB code for FieldmapFormat.fig
% FIELDMAPFORMAT, by itself, creates a new FIELDMAPFORMAT or raises the existing
% singleton*.
%
% H = FIELDMAPFORMAT returns the handle to a new FIELDMAPFORMAT or the handle to
% the existing singleton... |
5c6c46b27135d7c68f53ba4a9cdd747c77c5a858f6625ffabb32453c3951033b | MATLAB | 27,191 | 642 | function [cfg] = ft_singleplotER(cfg, varargin)
% FT_SINGLEPLOTER plots the event-related fields or potentials of a single
% channel or the average over multiple channels. Multiple datasets can be
% overlayed.
%
% Use as
% ft_singleplotER(cfg, data)
% or
% ft_singleplotER(cfg, data1, data2, ..., datan)
%
% The dat... |
c58f74a3e0a75f880fd1683e89b313ef21c28dea00b74860aa27bde2605223ba | MATLAB | 27,201 | 662 | classdef ScrollingPanel < uix.Container & uix.mixin.Panel
%uix.ScrollingPanel Scrolling panel
%
% p = uix.ScrollingPanel(p1,v1,p2,v2,...) constructs a scrolling panel
% and sets parameter p1 to value v1, etc.
%
% A scrolling panel is a standard container (uicontainer) that shows
%... |
81e32851108bcec563223456be7a5cbb3efe6dacb83d90124b821cfb5042f430 | MATLAB | 27,204 | 637 | function [cfg] = ft_multiplotER(cfg, varargin)
% FT_MULTIPLOTER plots the event-related potentials or event-related fields verus
% time, or the oscillatory activity (power or coherence) versus frequency. Multiple
% datasets can be overlayed. The plots are arranged according to their location
% specified in the layout.... |
a1fee73d2afe28e8b473bcf5552449f3546837c955dc908110a83ee14f8da760 | MATLAB | 27,205 | 923 | % Copyright (c) Hugo Gävert, Jarmo Hurri, Jaakko Särelä, and Aapo Hyvärinen.
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% any later vers... |
369e05cfa7911711a1bb718d9f06ef4aafa0044a523b29f4a94004f44ad38078 | MATLAB | 27,260 | 698 | function [interp] = ft_sourceinterpolate(cfg, functional, anatomical)
% FT_SOURCEINTERPOLATE interpolates source activity or statistical maps onto the
% voxels or vertices of an anatomical description of the brain. Both the functional
% and the anatomical data can either describe a volumetric 3D regular grid, a
% tri... |
705e1c1f60673bd02c5dc120867dd859f139962cc425d17495d559d42a5ce619 | MATLAB | 27,265 | 843 | function [z,s,exitflag] = smoothn(varargin)
%SMOOTHN Robust spline smoothing for 1-D to N-D data.
% SMOOTHN provides a fast, automatized and robust discretized spline
% smoothing for data of arbitrary dimension.
%
% Z = SMOOTHN(Y) automatically smoothes the uniformly-sampled array Y. Y
% can be any N-D noisy a... |
7060fa9c6216f6e4d52876f0285a418d989ad5a399ecb1d182f8290635e185cb | MATLAB | 27,282 | 775 | function [cfg] = ft_checkconfig(cfg, varargin)
% FT_CHECKCONFIG checks the input cfg of the main FieldTrip functions
% in three steps.
%
% 1: It checks whether the cfg contains all the required options, it gives
% a warning when renamed or deprecated options are used, and it makes sure
% no forbidden options are used.... |
4dfb29be5261f7b63eba80a5ead496693e8deceb6e5bfd53348e79fb4ed6a8a7 | MATLAB | 27,303 | 652 | classdef CompareTrackersController < handle
% Owns the figure, dropdowns, threshold edit, and listbox for the
% Compare Trackers... window.
properties (Access=private, Transient) % private by convention
labelerController_ % parent controller
labeler_ % Labeler
model_ % CompareTrackersModel
fi... |
3bf494a014b654eae68d8fc2d97fc46fb76c66102d4a78984522885764423cf6 | MATLAB | 27,312 | 586 | function headshape = prepare_mesh_cortexhull(cfg)
% PREPARE_MESH_CORTEXHULL creates a mesh representing the cortex hull, i.e.
% the smoothed envelope around the pial surface created by FreeSurfer
%
% This function relies on the FreeSurfer and iso2mesh software packages
%
% Configuration options:
% cfg.headshape =... |
e878308691c67aa144534c1a7dc7e8f587041538b79b9995d76c7a27ffdb4675 | MATLAB | 27,313 | 680 | function [dipout] = beamformer_dics(dip, grad, headmodel, dat, Cf, varargin)
% BEAMFORMER_DICS scans on pre-defined dipole locations with a single dipole
% and returns the beamformer spatial filter output for a dipole on every
% location. Dipole locations that are outside the head will return a
% NaN value.
%
% Use as... |
033a1f0c44c2ac41d8f7b668c20069735ba4427c42a34f6aee2273ecaf656c4b | MATLAB | 27,322 | 774 | function varargout = VBA_spm_mesh_render(action,varargin)
% Display a surface mesh & various utilities
% FORMAT H = spm_mesh_render('Disp',M,'PropertyName',propertyvalue)
% M - a GIfTI filename/object or patch structure
% H - structure containing handles of various objects
% Opens a new figure unless a 'p... |
aba76c4e72142d518666b6233a7756a782b5a0cbe1904cad27980d476cb1bb4d | MATLAB | 27,346 | 723 | function varargout = combat_settings(varargin)
% COMBAT_SETTINGS MATLAB code for combat_settings.fig
% COMBAT_SETTINGS, by itself, creates a new COMBAT_SETTINGS or raises the existing
% singleton*.
%
% H = COMBAT_SETTINGS returns the handle to a new COMBAT_SETTINGS or the handle to
% the existing si... |
245898a65197133dbcd758c5994395e051f485f5379085d534c7e508a4983bf6 | MATLAB | 27,380 | 442 | function [] = spearman_shuffled_data_re_analysis(folders,option)
if strcmp(option,'global_remapped')
data_folders = 'global_remapped';
elseif strcmp(option,'place_field_shifted')
data_folders = 'place_field';
elseif strcmp(option,'spike_train_shifted')
data_folders = 'spike_train';
elseif strcmp(option,'cr... |
2817fc3ee763045548bcc291a6761eaa2fb95876edf3c019aa2e52f14907279a | MATLAB | 27,425 | 630 | function populateSOI(this, SOI, varargin)
% populate SOI for spherelikeFitter
%
% populateSOI(SOI)
% populateSOI(SOI, t)
%
% if SOI is dynamic, time needs to be provided
% populate SOI object by computing desired charts and arrange them in
% the strucutres from the diffgeometry sec... |
5d0f3f3e340f2323621c5accb62cd43f82689a630611255547da654ddfe93174 | MATLAB | 27,589 | 936 | %%
close all force;
clear classes;
clc
%%
addpath f:\repo\apt6\gt
addpath f:\repo\apt6\gt2sh\
%% Load GT results and KB orig GT tables
tGT = loadSingleVariableMatfile('cpr_gtres_v00.mat');
sgt = load('SelectedGTFrames_SJH_20180603.mat');
tFrms2Lbl = sgt.frames2label;
%%
assert(strcmp(tGT.Properties.VariableNames{1},... |
6a73c1f4faf1ef27194fd48c4409f77111803bf6354afb09fbf8548cee3612c0 | MATLAB | 27,594 | 364 | function DPABI_TDA_run(Cfg)
% FORMAT DPABI_TDA_run(Cfg)
% Perform temporal dynamics analysis and concordance analysis
% Input:
% Cfg - the parameters for temporal dynamics analysis.
% Output:
% The processed results that you want.
%___________________________________________________________________________
% Writte... |
338c1d7b5ccfa6d88d7348b2f6995d1267fe034d9b7c42e9a4652536114091ec | MATLAB | 27,693 | 696 | %% xtDataCell Class (OOP)
% Class for manipulating X(t) and interconverting.
% Designed for use within the SDO Analysis Toolkit
% xtDataCell class used here to contain/operate on time series type data;
%_______________________________________
% Copyright (C) 2023 Trevor S. Smith
% Drexel University College of Medic... |
04399b65718f746f47446594c64634e9d8c6acbd43e8422ae054f02eaaf8b3bb | MATLAB | 27,707 | 687 | function [cfg, Lag] = runGLAD(cfg)
% This function runs the Lagrangian postprocessing.
addpath('./analyzeFlows','./Inverse','./Sensitivities',genpath('./utilities'));
%%
fprintf('\n =============== Lagrangian Post-processing Starts ===============\n')
fprintf('_________________________________________________________... |
59fd65c2f603fac3487a7c091ec2336b2c89fd4df204ee813a60f9c05f7de42c | MATLAB | 27,719 | 685 | function [dipout] = beamformer_dics(dip, grad, headmodel, dat, Cf, varargin)
% BEAMFORMER_DICS scans on pre-defined dipole locations with a single dipole
% and returns the beamformer spatial filter output for a dipole on every
% location. Dipole locations that are outside the head will return a
% NaN value.
%
% Use as... |
0bbf600b74553909c7a68a85f93661bab87e35f34afc1ac0a78e8bda9c5731a4 | MATLAB | 27,725 | 492 | function [] = ground_truth_log_odd_analysis(folders,timebin,BAYSESIAN_NORMALIZED_ACROSS_TRACKS)
% Input:
% Folders: Each Folder is data for a session
% Timebin: 0.02 or 1
% 0.02 -> 20ms time bin
% 1 -> 1 event time bin
% posbin: [] or 1
% [] -> 20 position bin per track (will load extracted_place_field_BAYESIAN)
% 1 ->... |
1b3fed6745927db56fbb6f4abf4982181daf20559c82274d9fe9d20a7fe8c09f | MATLAB | 27,834 | 591 | classdef ThorlabsPowerMeter < matlab.mixin.Copyable
%ThorlabsPowerMeter Matlab class to control Thorlabs power meters
% Driver for Thorlabs power meter
% It is a 'wrapper' to control Thorlabs devices via the Thorlabs .NET
% DLLs.
%
% User Instructions:
% 1. Download the Optical Pow... |
d1c2973dc0c04fdc41bebe4d43b0215ddaeabd7b3e8199a6f97f6ce5f357ebf6 | MATLAB | 27,864 | 679 | function RT = lan_detect_freq_event(LAN, cfg )
% v.0.1.4
%
% detect frequiency events in some
% channels : cfg.chan = [ch1 ,...] ; e.g. [3 4 5 ]
% frequency band : cfg.freq = [f1 f2] ; e.g. [80 200]
% minimun time duration : cfg.time = [ms] ; e.g [20]
% power threshould ... |
4801efed97280e84472d659bfba5dd9b16a6b81791f2864876ae1af8bced401e | MATLAB | 27,873 | 533 | function EpisodicImageChecker1(StatusFig,Flagged_Episodes,LastEpisodeNumber,Temp_ImageArray_FirstImages,Temp_ImageArray_Peak_DeltaF,Temp_ImageArray_End_DeltaF,MeanStartingFluorescenceVector,Temp_ImageArray_Peak_DeltaFMaxVector,Temp_ImageArray_End_DeltaFMaxVector)
warning on all
warning off verbose
warning ... |
e532c693cd60c9794db5528f6dabd9cd9580121777412b5cd382cde66dde2727 | MATLAB | 27,908 | 804 | function [hImage, hText, hXText] = heatmap(mat, xlab, ylab, textmat, varargin)
% HEATMAP displays a matrix as a heatmap image
%
% USAGE:
% [hImage, hText, hTick] = heatmap(matrix, xlabels, ylabels, textmatrix, 'param', value, ...)
%
% INPUTS:
% * HEATMAP displays "matrix" as an image whose color intensities refl... |
758b55a935fe20668c19a6ecb66821a2501808dabdda6d56fe6dfd4797e8c36f | MATLAB | 28,019 | 575 | % pop_runica() - Run an ICA decomposition of an EEG dataset using runica(),
% binica(), or another ICA or other linear decomposition.
%% NWB adjusted to output "NonConvergence=1" if fastica_symm does not converge (which causes issues with ICA cleaning)
% Usage:
% >> OUT_EEG = pop_runica( EEG ... |
1723f0ddb4edb4d7e9775cc9aaa4c34de85dfcce487abdfccfb1deec7fc82cc8 | MATLAB | 28,054 | 853 | function [samples, stats, structArray] = matjags(dataStruct, jagsFilenm, initStructs , varargin)
% MATJAGS, a Matlab interface for JAGS
% Version 1.1. Tested on JAGS 3.0.0, Windows 64-bit version
%
% This code has been adapted from MATBUGS that was written by Kevin Murphy and Maryam Mahdaviani
%
% [samples, stats... |
9a0c07fa8293a50b432ff837e4c9416acf545777c44fa3f26787c5247cac3402 | MATLAB | 28,124 | 496 | %_______________________________________________________________________
%
% Configuration for running StateSwitch experiment
%_______________________________________________________________________
%
% Output
%
% expInfo | configuration for state switch word version (struct)
% Written by Julian Kosciessa (kosciessa@m... |
3292c651ab730fdd976439ca20308e0e88d6b76c207ebd8cbe680c42c29e1cc0 | MATLAB | 28,137 | 839 | function im = metamerSynthesis(params,seed,m,opts)
%
%-----------------------------------------
% metamerSynthesis(params,seed,m,opts)
%
% generates an image matched to a set of
% statistical parameters computed within
% a set of tiling regions defined by window functions
% (see metamerParams.m and metamerAnalysis.m)
... |
6e1299a24ee26fc3acf0853e8c6b1a1ab533d2e2dfcb578f3a7e32c57379ee3a | MATLAB | 28,176 | 681 | function [stat, cfg] = statistics_wrapper(cfg, varargin)
% STATISTICS_WRAPPER performs the selection of the biological data for
% timelock, frequency or source data and sets up the design vector or
% matrix.
%
% The specific configuration options for selecting timelock, frequency
% of source data are described in FT_T... |
7c7ffcab1ab84e0260bb6c82ebb229908faf20504d4fc4f2550ccac483906665 | MATLAB | 28,176 | 681 | function [stat, cfg] = statistics_wrapper(cfg, varargin)
% STATISTICS_WRAPPER performs the selection of the biological data for
% timelock, frequency or source data and sets up the design vector or
% matrix.
%
% The specific configuration options for selecting timelock, frequency
% of source data are described in FT_T... |
1e103248a5f9e0e41d0c01012a7b684048d5c62f58c8661ae1e2d8ea941f4bd8 | MATLAB | 28,193 | 669 | function varargout = DPABISurf_ROIList(varargin)
% DPABI_ROILIST MATLAB code for DPABI_ROIList.fig
% DPABI_ROILIST, by itself, creates a new DPABI_ROILIST or raises the existing
% singleton*.
%
% H = DPABI_ROILIST returns the handle to a new DPABI_ROILIST or the handle to
% the existing singleton*.
... |
eb24a414c375d99ee25210e83938f65444d4f21ddea9b56d2caf36874470a95c | MATLAB | 28,269 | 562 | function interpret_PLS(result, numSubj, numCond, numGroups, numTrials, numSources, numSamples, numDataPoints, network, fb_interest)
%%
if network.pls.method == 1 || network.pls.method == 4
if network.pls.method == 4
[task_range,~]=size(result.TBv{1,1});
u=result.u(:,1:task_range);
v=result... |
971fc718b7970830b4a200ffd4030b20fd1dd306722a1c7dc1d37c12ed5cf5ce | MATLAB | 28,297 | 498 | %_______________________________________________________________________
%
% Configuration for running dotsExperiment
%_______________________________________________________________________
%
% Output
%
% expInfo | configuration for state switch MAT (struct)
% Written by Julian Kosciessa (kosciessa@mpib-berlin.mpg.de... |
80d6b0a8770b3e059f64d9afbd14d3ae13e696c95650578a1246090153c22ffe | MATLAB | 28,304 | 668 | function [status] = ft_hastoolbox(toolbox, autoadd, silent)
% FT_HASTOOLBOX tests whether an external toolbox is installed. Optionally
% it will try to determine the path to the toolbox and install it
% automatically.
%
% Use as
% [status] = ft_hastoolbox(toolbox, autoadd, silent)
%
% autoadd = 0 means that it will ... |
de5c499336ee7c402c011204bc4e891789e1cc2ff8dab77d7720aeddb63a8789 | MATLAB | 28,413 | 620 | %{
Copyright (c) 2025 Axion BioSystems, Inc.
Contact: support@axion-biosystems.com
All Rights Reserved
%}
%DATASET: Handle by which data is laoded from an Axion File.
% VersionMajor: Writing version (Major number) that was used to
% serialize this BlockVector.
%
% VersionMinor: Writing version (Minor... |
064a7e32be0913a37babcd3816050bddf165408e5314ca66b8c6f87dcd933c9d | MATLAB | 28,452 | 657 | function [source] = ft_dipolefitting(cfg, data)
% FT_DIPOLEFITTING perform grid search and non-linear fit with one or multiple
% dipoles and try to find the location where the dipole model is best able
% to explain the measured EEG or MEG topography.
%
% This function will initially scan the whole brain with a single ... |
2a330d43045170d3ff562e10c4a6d53ec2f88c5a5ab5d2ef9172cf02b20bd517 | MATLAB | 28,459 | 740 | classdef ParameterSetupModalController < handle
% Controller for the modal dialog used to set training or tracking
% parameters. The dialog is modal, but the constructor returns as soon as
% the dialog is up. When the user clicks Apply, the dialog writes the new
% parameters to the Labeler itself; on Cancel t... |
fe4823e95052abcf4d6569ca8322f002d01b231b0402831e9a1b869cb19656b9 | MATLAB | 28,465 | 570 | function interpret_PLS(result, numSubj, numCond, numGroups, numTrials, numSources, numSamples, numDataPoints, network, fb_interest)
%%
if network.pls.method == 1 || network.pls.method == 4
if network.pls.method == 4
[task_range,~]=size(result.TBv{1,1});
u=result.u(:,1:task_range);
v=result... |
0d47f8989549ed36c4a1bc6e6d41cd12de42bd407c8e8ba79967483185dde163 | MATLAB | 28,486 | 692 | classdef CompareTrackersModel < handle
% Holds computed data about bouts of frames where a reference tracker
% and a test tracker disagree, for the current movie.
properties (Access=private)
quantileThreshold_ = 0.99
% scalar double, the quantile threshold (0-1) for filtering bouts.
matchDistanceTh... |
8761b34359f9ea6a83b48873ca3ad52fce837d314c424c91819c43c229ea5213 | MATLAB | 28,496 | 664 | function [Ireg,O_trans,Spacing,M,B,F] = image_registration(Imoving,Istatic,Options)
% This function image_registration is the most easy way to register two
% 2D or 3D images both affine and nonrigidly.
%
% Features:
% - It can be used with images from different type of scans or modalities.
% - It uses both a rigi... |
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