sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
68662225765e6c1a51b91f821ccf8cc5fa584fb4e7167ffe5ff428e64438aa43 | MATLAB | 15,573 | 395 | function [data] = ft_redefinetrial(cfg, data)
% FT_REDEFINETRIAL allows you to adjust the time axis of your data, i.e. to
% change from stimulus-locked to response-locked. Furthermore, it allows
% you to select a time window of interest, or to resegment your long trials
% into shorter fragments.
%
% Use as
% data = ... |
2ea27f93f75c75868501513170e5f6befe6960486706669e4adc39bde7f0f458 | MATLAB | 15,574 | 528 | function data = loadubjson(fname,varargin)
%
% data=loadubjson(fname,opt)
% or
% data=loadubjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% created on 2013/08/01
%
% $Id: loadubjson.m 460 2015-01-... |
dfab5f505c6270aac765f2a47e9ecadf0990d7c7725883c3e720742e6654c127 | MATLAB | 15,588 | 416 | % AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Bioinformatics Lead: Wayne Moore <wmoore@stanford.edu>
% Provided by the Herzenberg Lab at Stanford University
% License: BSD 3 clause
%
classdef Label... |
4b3b6c65726abfdc8c1560212f2796ac204926d0499bccd5181212c716be7184 | MATLAB | 15,595 | 396 | function [data] = ft_redefinetrial(cfg, data)
% FT_REDEFINETRIAL allows you to adjust the time axis of your data, i.e. to
% change from stimulus-locked to response-locked. Furthermore, it allows
% you to select a time window of interest, or to resegment your long trials
% into shorter fragments.
%
% Use as
% data = ... |
0225c000cd78213e60c9b3961f46dcba2073875cc5255bdc622c9bc7119e6a26 | MATLAB | 15,696 | 377 | function RokJ_PSTH_meanSpikeRate()
% Function reads data containig spike times recorded in a leg nerve of
% Nezara viridula in response to a female calling song (FCS) and/or noise.
% It analyses the data and calculates PSTH and mean spike rate. The results
% can be saved as figures, referenced in the paper as Fig... |
fda0ab2e4948aa626ea603dc2b31ad5ea425eb0c9fd8623bc5857fb07d19fa0a | MATLAB | 15,698 | 445 | %{
Once you have your results, time for plotting and making the graphs
look beautiful already in Matlab! Rather than prettifying your plots
in Illustrator, I highly recommend doing as much as possible already
in Matlab. Chances that you'll have to regenerate the figures at some
point (because you decide to change one s... |
e378b1dc99abb33f8913d1faef75abd7097058f24cc368e474fb8d90189a8127 | MATLAB | 15,709 | 560 | classdef ( Hidden ) Text < matlab.mixin.SetGet
%uix.Text Text control
%
% t = uix.Text(p1,v1,p2,v2,...) constructs a text control and sets
% parameter p1 to value v1, etc.
%
% A text control adds functionality to a uicontrol of Style text:
% * Set VerticalAlignment to 'top', 'mid... |
50b9707040cbc07097e7be0f16d222c8a9e70ce9ea18eeb3928b220d819102a2 | MATLAB | 15,713 | 440 | classdef GTManagerController < handle
% Controller for the "Groundtruth Navigator" window, which lists the
% groundtruth to-label suggestions per movie/frame/target and lets the user
% navigate to them and compute GT accuracy.
%
% This replaces the bare uifigure function GTManager.m: state and widget
% hand... |
bfa4925cdf6b230eba3e9d8e7b24426de89d77852ac4fc245c472df293e9e56b | MATLAB | 15,716 | 408 | % sim_grid.m
%
% Runs simulations of both PFs and preplay across a grid of parameters. It
% saves the spikes of each as PFSpikeTimes_grid and preplaySpikeTimes_grid
% -Each parameter point is simulated by the function run_param_sim()
% It then runs Bayesian decoding using those spikes.
% -Decoding is performed by the f... |
f7d8f2fbaa932bb84c5b053a323041c17725cb61302510bbdeecd7f1799fb980 | MATLAB | 15,716 | 243 | function remapping= rate_remapping_TRACK_PAIRS(folders,varargin)
% folders is [] for individual session, or cell array of folders
% varargin can be 'spearman' or 'wcorr'
if isempty(folders)
a=pwd;
folders={a};
cd ..
end
cd(folders{1});
if ~isempty(varargin)
method= varargin{1};
disp(['running for..... |
94dc3d6f546092aba45c6a3b1d730eeeea1e21f822ef1340ff3b1a67382b4c8b | MATLAB | 15,718 | 372 | function [data] = ft_megplanar(cfg, data)
% FT_MEGPLANAR computes planar MEG gradients gradients for raw data or average
% event-related field data. It can also convert frequency-domain data that was computed
% using FT_FREQANALYSIS, as long as it contains the complex-valued fourierspcrm and not
% only the powspctrm.
... |
85e06205e5c6f093b759d1d439461be1839e3a0fb7aa0cb67ac5622a2307847a | MATLAB | 15,739 | 450 | function varagout = boney_xml2csv(job)
%boney_xml2csv(job). Wrapper to call cat_io_xml2csv for boney structure.
% See cat_io_xml2csv.
%
% varagout = boney_xml2csv(job)
%
% report
% 'boney_default' .. only the most relevant fields
% 'boney_details' .. some additional selected fields
% (reg... |
88c7d4225e464a45385336541a67f9c607df4458ea7b734d93cb737e347aa6f0 | MATLAB | 15,750 | 445 | function [grad, elec] = mne2grad(hdr, dewar, coilaccuracy)
% MNE2GRAD converts a header from a fif file that was read using the MNE toolbox into
% a gradiometer structure that can be understood by the FieldTrip low-level forward
% and inverse routines.
%
% Use as
% [grad, elec] = mne2grad(hdr, dewar, coilaccuracy)
%... |
c5bc6d47673cbfa7086a56fb42977d3ddecec4ec868f65f437c6e0bf179b891f | MATLAB | 15,752 | 467 | function [Gain, errMsg] = bst_duneuro(cfg)
% BST_DUNEURO: Call Duneuro to compute a FEM solution for Brainstorm.
% Modificado para LAN Pablo billeke
% USAGE: [Gain, errMsg] = bst_duneuro(cfg)
% @=============================================================================
% This function is part of the Brainstorm s... |
54834b455edde96293f170b4b5ac471f5bc1929e8584d553cde948629d6aa3c4 | MATLAB | 15,764 | 487 | //========================================================================
// GLFW 3.4 Cocoa - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2009-2019 Camilla Löwy <elmindreda@glfw.org>
// Copyright (c) 2012 Torsten Walluhn <tw@mad-cad.net>
//
// This software ... |
338cac65cba5c981b7f0e55d8a54716eb98eb309c8dca3a40b2a8946fc3ac1b0 | MATLAB | 15,776 | 445 | function [grad, elec] = mne2grad(hdr, dewar, coilaccuracy)
% MNE2GRAD converts a header from a fif file that was read using the MNE toolbox into
% a gradiometer structure that can be understood by the FieldTrip low-level forward
% and inverse routines.
%
% Use as
% [grad, elec] = mne2grad(hdr, dewar, coilaccuracy)
%... |
93924023cc15ebde9c161ba0f608b8947456f775484943ff5f46122c19263fda | MATLAB | 15,786 | 444 | % note: change current folder to figure "number"
clear all;close all;clc;
rawPath=pwd; %displays the current working directory - set it to the figure "number"
savePath=rawPath;
addpath Panels/
addpath Functions/
load("ExampleCellFig1")
load("Bars_WB_DSI0.30NVS0.15_Allcells")
colors=[0.5586 0.7344 0.5586];
%% Figure ... |
a87dbd1af254a13d412feb84dc7ce41e1b7ba29c218355c8c57d703b41c3287b | MATLAB | 15,787 | 350 |
function [UDStates] = detectUD(varargin)
% Detect up and down states from LFP.
%
% USAGE
%
% [spikes] = bz_loadPhy(varargin)
%
% INPUTS
% (OPTIONAL)
% basePath -(default: pwd) basePath for the recording file, in buzcode format:
% whateverPath/baseName/
% folder mus... |
c49c4a5732caf122684602a161c578184b729951c2d444d59c89336a0550e7c7 | MATLAB | 15,821 | 246 | function block_results(stat_path,exp_folder,q_level,ground_truth)
% ========================================================================
% Ruslan Masharipov, October, 2023
% email: ruslan.s.masharipov@gmail.com
% ========================================================================
load([stat_path filesep exp_... |
f0de84239ba2d9ba9f00545dd38cc36ed180eaca12f2c8fe2487876623d087d5 | MATLAB | 15,832 | 483 | function mesh = read_ply_mod(filename)
% read_ply - read data from PLY file.
%
% mesh = read_ply(filename);
%
% mesh.v : vertices
% mesh.f : faces
% mesh.vn: vertex normals
%
% IMPORTANT: works only for triangular meshes.
%
% Copyright (c) 2003 Gabriel Peyré
%
% Modified 2015 by Idse Heemskerk t... |
21cf8a0a5842770513cf7ecea52fcbfa955288912d751c26cf278daf5b248f6b | MATLAB | 15,836 | 396 | function [data] = ft_resampledata(cfg, data)
% FT_RESAMPLEDATA performs a resampling or downsampling of the data
%
% Use as
% [data] = ft_resampledata(cfg, data)
%
% The data should be organised in a structure as obtained from
% the FT_PREPROCESSING function. The configuration should contain
% cfg.resamplefs ... |
247e6df4bd585fcf0ab46fca4f7db517be5f3b146cf67bc8cb3eb4e98594d773 | MATLAB | 15,857 | 414 | function varargout = w_ApplyMonteCarlo(varargin)
% W_APPLYMONTECARLO MATLAB code for w_ApplyMonteCarlo.fig
% W_APPLYMONTECARLO, by itself, creates a new W_APPLYMONTECARLO or raises the existing
% singleton*.
%
% H = W_APPLYMONTECARLO returns the handle to a new W_APPLYMONTECARLO or the handle to
% t... |
2a74e57715fa5a5300a1b4e6d6b34fbb34411a307d2cab1eb9df59780c4c78b7 | MATLAB | 15,873 | 393 | % Author: Ulrike Horn
% uhorn@cbs.mpg.de
function varargout = manual_rpeak_selection(varargin)
% MANUAL_RPEAK_SELECTION MATLAB code for manual_rpeak_selection.fig
% MANUAL_RPEAK_SELECTION, by itself, creates a new MANUAL_RPEAK_SELECTION or raises the existing
% singleton*.
%
% H = MANUAL_RPEAK_SELECTION... |
57fc39f9c970a10d017858b9658a8c0550921349d7da216092bc16d969a09c55 | MATLAB | 15,911 | 442 | function [cfg] = ft_neighbourplot(cfg, data)
% FT_NEIGHBOURPLOT visualizes neighbouring channels in a particular channel
% configuration. The positions of the channel are specified in a
% gradiometer or electrode configuration or from a layout.
%
% Use as
% ft_neighbourplot(cfg)
% or as
% ft_neighbourplot(cfg, dat... |
a1883f737f3b34ca5fa3cb4141feb850620aca2f36f2ea800ffe8d1d4314ca7e | MATLAB | 15,927 | 447 | %% WT
clear all; close all;clc;
%%
fps=30;
trail=[];
date='0729';EN=[13 14 15];mouse='9';
trail=[trail;loadtrail(date,EN,fps)];
date='0731';EN=[10 11];mouse='7';
trail=[trail;loadtrail(date,EN,fps)];
date='0810';EN=[22 23 24];mouse='2';%2 4
trail=[trail;loadtrail(date,EN,fps)];
date='0810';EN=[32 33 34];mo... |
638cd25569450650922062c2c6f38878af3e4229081e6a9a9ad7fafeaf4498a1 | MATLAB | 15,942 | 315 | function [Ybonepp, Ybonethick, Ybonemarrow, Yheadthick, vROI, bnorm] = ...
boney_segment_extractbone(Vo,Ym,Yc,Ye,Ya,Ymsk,trans,seg8t,tis,tismri,out,job,vx_vol,YaROIname,YaROIid,RES,BB)
%% * Report:
% - better an upper slice?
% - optimize print font size
% - add basic parameters (reduce,mask,Atlas,tpm)
% - ad... |
b594ee816c2c92a08f16af454e5ce3e3e7cbddf2fab7248b166e3a74b7c1228a | MATLAB | 15,949 | 361 | function [RawData,HarmonizedBrain, HarmonizedBrain_LH, HarmonizedBrain_RH, Header_LH, Header_RH, OutNameList_LH, OutNameList_RH] = yw_Harmonization_Surf(ImgCells_LH, ImgCells_RH, MaskData_LH, MaskData_RH, MethodType,AdjustInfo, ParallelWorkersNum,OutputDir)
% [HarmonizedBrain_LH, HarmonizedBrain_RH, Header_LH, Header_... |
924426cf9f115ccc820305a243770756ad7d7d0c9dae2de5a9b3799a34b95be7 | MATLAB | 15,981 | 348 | % regularize_ICs.m
% Sarah West
% 9/1/21
% Takes calculated ICs, thresholds them, and regularizes them into
% contiguous areas
function []=regularize_ICs(parameters)
% Establish input and output directories
disp(['output saved in ' parameters.dir_output_base{1}]);
% For each mouse
for mou... |
4ab34ac67310846ea002e28a0a392e0d3a852e3c09452393a188af1a59cbf2e9 | MATLAB | 15,994 | 361 | function [spectrum,ntaper,freqoi] = ft_specest_mtmfft(dat, time, varargin)
% FT_SPECEST_MTMFFT computes a fast Fourier transform using multitapering with
% multiple tapers from the DPSS sequence or using a variety of single tapers.
%
% Use as
% [spectrum,ntaper,freqoi] = ft_specest_mtmfft(dat,time...)
% where
% da... |
f58af2db07cb49aed17c164ddfee128c57ea2a4cae064d003cbff863f35008e7 | MATLAB | 15,995 | 361 | function [spectrum,ntaper,freqoi] = ft_specest_mtmfft(dat, time, varargin)
% FT_SPECEST_MTMFFT computes a fast Fourier transform using multitapering with
% multiple tapers from the DPSS sequence or using a variety of single tapers.
%
% Use as
% [spectrum,ntaper,freqoi] = ft_specest_mtmfft(dat,time...)
% where
% da... |
b74d998823c30cc29af01ac8f2bbbe010d57c4890f6c67292442b9d5548cf761 | MATLAB | 15,999 | 427 | function avw_hdr_write(avw, fileprefix, machine, verbose)
% AVW_HDR_WRITE - Write Analyze header file (*.hdr)
%
% avw_hdr_write(avw,[fileprefix],[machine],[verbose])
%
% eg, avw_hdr_write(avw,'test');
%
% avw - a struct with .hdr field, which itself is a struct,
% containing all fields of an Ana... |
78a195bdc22683fa191a5aeb8e20c209bff2dc1b3b66da9c80174a63168b9daf | MATLAB | 16,007 | 581 | % Field Trip-related test scripts - Synthetic FT data - "Custom" tests.
%
% This tests the ability to specify "custom" (lambda-function) segmentation
% and parameter extraction algorithms.
%
% See LICENSE.md for distribution information.
%
%
% Includes.
do_ft_init
% Grandfather in "synthetic trace" configuration.
do... |
6602b7bf94f84441171b6c7460d1c3006f41e7f7f928d54bbd00745d50b1555b | MATLAB | 16,022 | 425 | function varargout = CommunicationModelSetting(varargin)
% COMMUNICATIONMODELSETTING MATLAB code for CommunicationModelSetting.fig
% This GUIDE dialog returns a communication-model setting structure.
%
% Usage:
% newSettings = CommunicationModelSetting(oldSettings, dialogTitle)
%
% Returned structure fields:
% Pred... |
2f22fe46327b295b80215ad0a2e7cd989a1b0fdd724e419b1609c951502fa68b | MATLAB | 16,030 | 398 | function varargout = h_roiControlGUI3(varargin)
% H_ROICONTROLGUI3 M-file for h_roiControlGUI3.fig
% H_ROICONTROLGUI3, by itself, creates a new H_ROICONTROLGUI3 or raises the existing
% singleton*.
%
% H = H_ROICONTROLGUI3 returns the handle to a new H_ROICONTROLGUI3 or the handle to
% the exi... |
b144b8c9775b56c754ea07aa9e91d108cd84edb573833822f4ef72470a75e3c9 | MATLAB | 16,032 | 375 | function varargout = h_animalStateTrackerGUI3(varargin)
% H_ANIMALSTATETRACKERGUI3 MATLAB code for h_animalStateTrackerGUI3.fig
% H_ANIMALSTATETRACKERGUI3, by itself, creates a new H_ANIMALSTATETRACKERGUI3 or raises the existing
% singleton*.
%
% H = H_ANIMALSTATETRACKERGUI3 returns the handle to a new H... |
0119b0b1def77cd8c65c037f4a2f392e3de76299ac5e8cb1ba3552ee480bfd4f | MATLAB | 16,041 | 335 | function coreg = spm_cfg_coreg
% SPM Configuration file for Coregister
%__________________________________________________________________________
% Copyright (C) 2005-2016 Wellcome Trust Centre for Neuroimaging
% $Id: spm_cfg_coreg.m 7665 2019-09-23 11:27:40Z john $
%------------------------------------------------... |
6d50b370c802fb24935f5234f77b36acc28418443d337ae52fbab12f10065491 | MATLAB | 16,060 | 374 | function process_positions_PRE
% Input: data extracted from NLX 'VT1.nvt'
% - x: x position of largest tracked blob
% - y: y position of largest tracked blob
% - timestamps: timestamps (in seconds)
% Output: linear structure containing new X,Y,T and linearized position template
% this function calls 'crop_in_time.m'
... |
e60d692daea0e56cd2d320f26a49a144f402c1c6373f0953f8406ae82e38323c | MATLAB | 16,076 | 392 | function [data] = ft_megplanar(cfg, data)
% FT_MEGPLANAR computes planar MEG gradients gradients for raw data or average
% event-related field data. It can also convert frequency-domain data that was computed
% using FT_FREQANALYSIS, as long as it contains the complex-valued fourierspcrm and not
% only the powspctrm.
... |
664fc73eab61d834a82a892fa29f4815600145e5e9322f13781d599a4f1370cb | MATLAB | 16,083 | 395 | classdef DatasetReader < matlab.mixin.SetGet & dynamicprops
% DatasetReader Read Imaris ims file DataSets
%
% © 2015–2016, Peter Beemiller (pbeemiller@gmail.com)
%
% See also ImarisReader
properties (SetAccess = 'immutable', GetAccess = 'public', Transient = true)
... |
ddd4a03c25eef4b406edef265d5bc4c55e85fc6f48dbd495927b05d99c2876af | MATLAB | 16,089 | 440 | function VBA_updateDisplay(posterior,suffStat,options,y,it,flag)
% // VBA toolbox //////////////////////////////////////////////////////////
%
% VBA_updateDisplay(posterior,suffStat,options,y,it,flag)
% updates display of sufficient statistics
%
% This function deals with the screen display of iterative sufficient
% st... |
4806b3f1beb87327d9bf455b53bf25dead5ebf4ee1a967fa7f510ebb94a64094 | MATLAB | 16,094 | 322 | function [ReHoBrain_AllWindow, Header] = y_reho_Window(WindowSize, WindowStep, WindowType, AllVolume, NVoxel, AMaskFilename, AResultFilename, IsNeedDetrend, Band, TR, TemporalMask, ScrubbingMethod, ScrubbingTiming, Header, CUTNUMBER)
% Calculate dynamic regional homogeneity (i.e. ReHo)
% FORMAT [ReHoBrain_AllWind... |
f8a0b3fad9034f560c0d43c384f6e346d872511074c32c2c33068238cb3b8f42 | MATLAB | 16,101 | 401 | function [normalised] = ft_volumenormalise(cfg, mri)
% FT_VOLUMENORMALISE normalises anatomical and functional volume data
% to a template anatomical MRI.
%
% Use as
% [mri] = ft_volumenormalise(cfg, mri)
% where the input mri should be a single anatomical volume that was for
% example read with FT_READ_MRI.
%
% Con... |
41d90dc246cb99eccddc8b745500e5e51106296aea675509c6303cc97e910bfa | MATLAB | 16,107 | 444 | function han = showsurface(vertices, faces, para, varargin);
% plots volume conductor/cortex as surfaces
% eventually plus sources/dipoles
% usage: showsurface(vc,para,source1,source2,....);
%
%
% vc is a structure with two fields:
% vc.tri is Nx3 matrix of integers where each
% column denotes the indice... |
e24e3bcc1a11b37eaeb1446c79ad2632738a1616d26534db4cafd0ccd09c5f1f | MATLAB | 16,109 | 444 | % krr_predict_FK - kernel ridge regression estimation
% using (stratified) LOO and permutation testing
% Diego Vidaurre
% adapted to use feature matrix as input, different kernels (Fisher kernel)
% Christine Ahrends
%
% [predictedY,stats] = krr_predict_FK(Yin,Xin,family,parameters);
% [predictedY,stats] = krr_predict... |
6b1df00e2c6e5d9c15c05075f8d08db692f71fd90206ef171c1f497a8bda22d2 | MATLAB | 16,123 | 504 | function json=saveubjson(rootname,obj,varargin)
%
% json=saveubjson(rootname,obj,filename)
% or
% json=saveubjson(rootname,obj,opt)
% json=saveubjson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a Universal
% Binary JSON (UBJSON) binary string
%
% author... |
b54ae0908efb1281dadd7ab0063136ca04ff65147227492adbff981a19953797 | MATLAB | 16,129 | 372 | function [p]=initialize_group(p)
% remove '/' from end of base path
temp_base_path = strsplit(p.paths.base,'/');
if isempty(temp_base_path{end})
p.paths.base = strjoin(temp_base_path(1:end-1),'/');
end
% Path to subjects directories
[LIST, ISDIR] = glob([p.paths.base,'/*']);
% exclude groupANALYSIS directory
if ... |
3b0fb945dfd2189cd5259944772da6cd42f08e85bfdb70a38dca9e2671fc1f19 | MATLAB | 16,142 | 388 | function [] = plot_ground_truth_compare_global_remapped_combined(folders,method,option)
total_number{1}(1:3) = 0;
total_number{2}(1:3) = 0;
for nfolder = 1:length(folders) % Get total number of replay events
cd(folders{nfolder})
load decoded_replay_events
[~,time_range]=sort_replay_events([],'wcorr');
... |
1ac0d6f2d864ac5e86a6b30f8daffd0e7e0aa920c9bcbfe569762cc19f41a23c | MATLAB | 16,168 | 457 | function res = vl_simplenn_feattopix(net, x, dzdy, res, varargin)
% VL_SIMPLENN Evaluates a simple CNN
% RES = VL_SIMPLENN(NET, X) evaluates the convnet NET on data X.
% RES = VL_SIMPLENN(NET, X, DZDY) evaluates the convnent NET and its
% derivative on data X and output derivative DZDY.
%
% The network has a s... |
4c8f5d604edf467d899b30f22563aee12bfb87fad4871ef5ed9da6b83c26f722 | MATLAB | 16,176 | 230 | function gtfileinfo = GTFileInfo(exptype)
cprdir = '/groups/branson/bransonlab/apt/experiments/res/cprgt20190407';
gtimagefile = '';
annoterrfile = '';
switch exptype,
case {'SHView0','SHView1'}
if strcmp(exptype,'SHView0'),
vwi = 1;
else
vwi = 2;
end
gtfile_trainsize_cpr = fullfile... |
30e1e44af9fef80e5deb500af726527f447ac23f697aac3f25949c9125dcfc49 | MATLAB | 16,180 | 425 | function tom_mrcwrite(varargin)
%TOM_MRCWRITE writes data to MRC format file.
%
% tom_mrcwrite(Data)
%
% tom_mrcwrite(Data)
% tom_mrcwrite(Data,'name',property1,'style',property2)
%
% Writes 'Data' in a MRC format under the name property1. If 'Data' is not a
% structure, a default header is created 3 differen... |
ddac0d1d87ba6f175d1bcbb9e619054fb88b63aaa4510c7ef2b58c84dbffec52 | MATLAB | 16,185 | 367 | function lead_job_dmri(opt)
% - Lead-DBS Job created on 16-Apr-2019 18:09:49 -
% --------------------------------------
lead path;
options = getoptslocal;
options.lcm.seeds = opt';
ea_run('run', options);
function options = getoptslocal
options.endtolerance = 10;
options.sprungwert = 4;
options.refinesteps = 0;
op... |
280be1cf0d5e8f8dd002c33421d88121d8759f97023ef96fd506749286798d81 | MATLAB | 16,186 | 247 | function block_results_FIR(stat_path,exp_folder,q_level,ground_truth)
% ========================================================================
% Ruslan Masharipov, October, 2023
% email: ruslan.s.masharipov@gmail.com
% ========================================================================
load([stat_path filesep ... |
7374f1546f45de6ea8f23b0373d293d41fac17751d180ef8e0841fd6958691d3 | MATLAB | 16,194 | 446 | % AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Bioinformatics Lead: Wayne Moore <wmoore@stanford.edu>
% Provided by the Herzenberg Lab at Stanford University
% License: BSD 3 clause
%
classdef SortT... |
ca39ba9701ba4b4034cccc0e8574a90b6252fcb2992e206f8a1bbb9b24e6db97 | MATLAB | 16,197 | 421 | % MATLAB code provided by Seyed Mohammad Ali Rahmati
% Affiliation: Biomechanics and Motor Control Lab, Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA.
%
% Description:
% This script calculates the biomechanical variables of a selected
% musculotendon unit (MTU) during locomotion based... |
284aaecefd98f71f870d3091a4f88e4b3429dab3308e044a379b7c6563c0dbbc | MATLAB | 16,204 | 408 | function varargout = colorCorrection_manual(varargin)
% COLORCORRECTION_MANUAL MATLAB code for colorCorrection_manual.fig
% COLORCORRECTION_MANUAL, by itself, creates a new COLORCORRECTION_MANUAL or raises the existing
% singleton*.
%
% H = COLORCORRECTION_MANUAL returns the handle to a new COLORCORRECTI... |
7f41e6061306c3fa998f69b82ec840bd7e76b304d641a47b1947040e834cb157 | MATLAB | 16,206 | 431 | function [logDat ts] = ExtractBehavior(datDir, logFile, task)
% flag active reward port (L = 1, R = 2)
rwdPort = 2;
altPort = 1;
% load RHD info
rhdFile = [datDir filesep 'info.rhd'];
rhdInfo = ReadRhdInfo(rhdFile);
%% Extract All Box File Timestamps
% get recording duration
info = dir([datDir,'/board-ADC-00.dat']... |
e733d85ee44c105b748cacb1e6659ddc394e0a066db83b61bbd4306d1a13fead | MATLAB | 16,229 | 376 | %
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Jonathan Ebrahimian <jebrahimian@mail.smu.edu>
% Provided by the Herzenberg Lab at Stanford University
% License: BSD 3 clause
classdef N... |
70c9bf1c9f32aa7b417e1f010c5913aec1b8255c0f6761bf0d54af248f908cfa | MATLAB | 16,242 | 370 | % fMRI lead mapper (resting_state > first 100 subjects)
%%
function lead_job(opt)
% - Lead-DBS Job created on 11-Apr-2019 15:49:11 -
% --------------------------------------
lead path;
options = getoptslocal;
options.lcm.seeds = opt';
ea_run('run', options);
function options = getoptslocal
options.endtolerance = 1... |
92f52111d36e7ec8b018501f988e2fec2706456be8614288a28cbfeca5694d06 | MATLAB | 16,249 | 344 | function [] = plot_ground_truth_multitracks_event(folders,option,method)
total_number(1:3) = 0;
for nfolder = 1:length(folders)
cd(folders{nfolder})
load decoded_replay_events
[~,time_range]=sort_replay_events([],'wcorr');
for event = 1:length(decoded_replay_events(1).replay_events)
... |
e7deb9a0649581adefa8dab8b4d2cf7480d66fc44cd5d365d2a177a64f17f22b | MATLAB | 16,277 | 354 | function x = ifdct_wrapping(C, is_real, M, N)
% ifdct_wrapping.m - Inverse Fast Discrete Curvelet Transform via wedge wrapping - Version 1.0
% This is in fact the adjoint, also the pseudo-inverse
%
% Inputs
% C Cell array containing curvelet coefficients (see
% description in fdct_wrapping.m)... |
74e852b9683733195906e60bd106459dca1fad75be3ad8cabce4c6107404b4c2 | MATLAB | 16,289 | 442 | function obj = subsasgn(obj,subs,varargin)
% Subscript assignment
% See subsref for meaning of fields.
%__________________________________________________________________________
% Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging
%
% $Id: subsasgn.m 7744 2019-12-03 12:38:47Z guillaume $
switch subs(1).... |
2681013a7b11a966d8fbfd3cafbfd5042800a8ad153a7e828cc0fa2a319d1ea1 | MATLAB | 16,345 | 361 | function [sourcemodel, cfg] = ft_prepare_leadfield(cfg, data)
% FT_PREPARE_LEADFIELD computes the forward model for many dipole locations
% on a regular 2D or 3D sourcemodel and stores it for efficient inverse modelling
%
% Use as
% [sourcemodel] = ft_prepare_leadfield(cfg, data)
%
% It is necessary to input the dat... |
ac352ff7eaa2c469280704073eacf63c86596df8044d27510e8a9e877d25ed38 | MATLAB | 16,353 | 310 | function [R_i,R_amp,S_i,S_amp,T_i,T_amp,Q_i,Q_amp,buffer_plot] = SimpleRST(ecg,fs,gr)
%% function [R_i,R_amp,S_i,S_amp,T_i,T_amp]=peakdetect(ecg,fs,view)
%% =================== Online Adaptive QRS detector ==================== %%
%% ========================== Description ============================= %%
% QRS detection... |
10f5817d2ddde524d2457824fe6d9befffc7b30e5b559a32093220cc410d03a4 | MATLAB | 16,366 | 308 | %% This file produces and saves the data for all of the connectome data fitting results.
%% Machine and simulation parameters
delta = 8*1E-3; % pulse duration (s)
gyroRatio = 267.522E6; % gyromagnetic ratio in units of rad/s/T
G = [31, 68, 105, 142, 179, 216, 253, 290]' * 1E-3; % Gradient strengths in units of T/... |
3ef032797b25ed8ecd0555e8299462877f71af22f37239e0616411fd862ba7d5 | MATLAB | 16,396 | 253 | %% Creating dissimilarity matrices for each subject
% Defining working directories
all_subjects_files_dir = 'C:\Users\michaelpeer1\Google Drive\bar_mord_shared_files\Experiment_data\Graphml_files'; % Contains GraphML format files of subjects' social network, extracted using the LostCircles tool (https://lo... |
bf7cd432b730ed609c3b8cd5bb38ee0dcdff08c7bd17b8557fb28ee9c9a9f231 | MATLAB | 16,397 | 552 | %PMTKslow
% Compare various joint density models on categorical (mostly binary) datsets
% We visualize the learned structuers and evaluate loglik and
% imputation error on test sets
%% Data
% labels is N*D, where labels(n,d) in {1..Nstates(d)}
Nfolds = 1;
% pcTrain and pcTest do not need to sum to one
% This way,... |
b0d8feb7a1ef568fa8fa21292517c7353fa5144d1b1877d34ffb7cced26e984d | MATLAB | 16,398 | 439 | function varargout = DPABI_ResultsOrganizer(varargin)
% DPABI_ResultsOrganizer MATLAB code for DPABI_ResultsOrganizer.fig
% DPABI_ResultsOrganizer, by itself, creates a new DPABI_ResultsOrganizer or raises the existing
% singleton*.
%
% H = DPABI_ResultsOrganizer returns the handle to a new DPABI_Results... |
4c0a6d343efce9bb6bd285a0dadaf877913fc0fe47a8a6fe9f59d898c3fb189f | MATLAB | 16,416 | 480 |
load(fullfile(saveLoc, 'cosine_sim'), 'cosine_sim')
load(fullfile(saveLoc, 'resCorr_wiTrial'), 'all_zrMean', 'resCorr');
load(fullfile(saveLoc, 'cosine_sim_randperm'), 'cosine_sim_randperm') % cosine_sim_randperm(sess, d1, d2, :)
load(fullfile(saveLoc, 'resCorr_wiTrial_rand_gauss'), 'par_sess', 'filtW50b', 'rz_ses... |
785966dc562bd7d18fde34be4478e9fe38cbb5891a4c82bde25e326307e7ae97 | MATLAB | 16,418 | 363 | function fcp_4_beamforming_tmplGrid(paths)
% FCP_4_BEAMFORMING carries out beamforming and source projection on
% cleaned data. A T1 template head model is loaded in (normalizing across
% particpants) to create a volume conduction model and subsequently, a
% source model. Each participant's MRI data is then loaded in ... |
8493b14c31b5ac3d96c50529f48292d49aadce659f03196e0b98ec379a4d029d | MATLAB | 16,423 | 562 | load trnDataSH_20180417T094303.mat;
load trnDataSH_20180417T094303_IFinalReconciled.mat;
%% Remove outliers, nan rows
tLook = tGT;
hFig = figure;
axs = createsubplots(4,5);
for i=1:20
axes(axs(i));
histogram(tLook.pLbl(:,i));
end
%%
idxOut = find(tFinalReconciled.pLbl(:,3)>1e3)
idxNan = find(any(isnan(tFinalRecon... |
bbc28ebb9a1b6aecec58e3fecc7240ac960505c9c12b6987e07cf001d1e11ca8 | MATLAB | 16,429 | 285 | function P = boney_segment_preprocessing(P,out,ctpm,pmethod,bias,rerun)
%boney_segment_preprocessing. Call SPM12 or CAT12 segmentation.
%
% P = boney_segment_preprocessing(P,out,method,bias,rerun)
%
% P .. updated structures of processed files
% out(:).P .. other input files
% ctpm .. TPM selector (1-... |
2d1c40405b221626ff5280f59e6e12d01fae056cf3732b77ceb1a6b2d322adbf | MATLAB | 16,444 | 374 | function [ titleStr, settings, results ] = collapseSources( dataview, settings )
% This functions summarizes one or multiple datasources as a new 'collapsed'
% datasource. It bins all datapoints according to a number of binning variables
% and then computes summary statistics over all datapoints in ea... |
58c21e8238271ca0dae90dbe2ccc59ff837b21d7f02f3eadf3282af61227c51f | MATLAB | 16,444 | 466 | classdef SuhWindow < handle
properties(Constant)
TESTING=false;
end
properties(SetAccess=private)
handlingMoved=false;
movedByBtnClick=false;
followed;
where;
followers; %key is window, value is struct of follower dlg + where info
figMap;
alway... |
8b77f940d12e051025868909fd596ff288e6539615bdaf36e1db7fcb31a219f9 | MATLAB | 16,444 | 394 | function [dataout] = ft_eventtiminganalysis(cfg, data)
% FT_EVENTTIMINGANALYSIS computes a model of single trial event-
% related activity, by estimating per trial the latency (and
% amplitude) of event-related signal components.
%
% Use as
% [dataout] = ft_eventtiminganalysis(cfg, data)
% where data is single-chann... |
eac72b75cdf14ae98a69a51a8d16e17b1936348b0cfbe7dffa459cea74327351 | MATLAB | 16,446 | 292 | %% RELAX EEG CLEANING PIPELINE, Copyright (C) (2024) Aron Hill & Neil Bailey
% 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... |
0dd1b4eb28c71fffc9656177f47322589c50d23839488b813c4b95b8e5134ed4 | MATLAB | 16,470 | 345 | function detector = acfTrain( varargin )
% Train aggregate channel features object detector.
%
% Train aggregate channel features (ACF) object detector as described in:
% P. Dollár, R. Appel, S. Belongie and P. Perona
% "Fast Feature Pyramids for Object Detection", PAMI 2014.
% The ACF detector is fast (30 fps on a ... |
cea7658be327a87adf68ffa408424ee7f6808482ad25929784cb83588a8dcdf7 | MATLAB | 16,481 | 471 | function [x, y] = HistorySection(obj, action, varargin)
GetSoloFunctionArgs(obj);
switch action,
% ------------------------------------------------------------------
% INIT
% ------------------------------------------------------------------
%%% list all the way the rat can do wel... |
784ca0b0144612b26944e6017298ab5ee91096dad8c5db749c50bb3114f02bb4 | MATLAB | 16,485 | 487 | function [mri] = ft_read_mri(filename, varargin)
% FT_READ_MRI reads anatomical and functional MRI data from different
% file formats. The output data is structured in such a way that it is
% comparable to a FieldTrip source reconstruction.
%
% Use as
% [mri] = ft_read_mri(filename)
%
% Additional options should be ... |
c3633dfcd3be910b5098b5e0c9ecee0c57ca3e90ec2c14221cc862fd3ca1008e | MATLAB | 16,492 | 512 | function [posterior,out] = VBA_MoG(y,K,options)
% function [posterior,out] = VBA_MoG(y,K,options)
% This function is a VB scheme for the MoG classifier.
% IN:
% - y : the pxn data matrix, where n is the number of 'observations' to be
% classified, and p is the dimension of each of these observations
% - K : the m... |
35aea779e11a848c4f484c94d8ce3cd5cd2c8f80e199942c4b04f6d564d5bc15 | MATLAB | 16,499 | 369 | function [posterior,out] = VBA_NLStateSpaceModel(y,u,f_fname,g_fname,dim,options,in)
% [posterior,out] = VBA_NLStateSpaceModel(y,u,f_fname,g_fname,dim,options,in)
%
% This function inverts any nonlinear state-space model of the form:
% y_t = g( x_t,u_t,phi ) + e_t
% x_t = f( x_t-1,u_t,theta ) + f_t
% using a variat... |
14780612048d73936a8069dab14d107892d101525b9b8203252fda20c9d0687f | MATLAB | 16,508 | 466 | % IFMM Interpolative fast multipole method.
%
% This is an implementation of a kernel-independent fast multipole method
% based on the interpolative decomposition for hierarchical low-rank
% compression. The algorithmic framework is fully algebraic and supports
% multiplication with both the matrix and its... |
d1d344b4076937ed58c53b1f14a8bdc487fb2201a9360b9139ec074f2b74e189 | MATLAB | 16,526 | 220 | function [remapping, remapping_raw] = rate_remapping_TRACK_PAIRS(folders,varargin)
% Input:
% folders is [] for individual session, or cell array of folders
% varargin{1} is for methods, and can be 'spearman' or 'wcorr'
% varargin{2} as save toggle - can be 1 (default) or 0
% Output:
% remapping: diffe... |
5688e579ea18eb57d091bb66c3be78495f83994cabdb584bfdfddebe075e76a0 | MATLAB | 16,534 | 537 | %% INITIATE
clear
close all
cc=[58 112 182; 97 168 125; 100 96 133]./255;
structure={'GPi', 'GPe','STR'};
%% PAT INFO
bfmdrs=[15; 8; 10; 5.5; 11.5; 4.5; 36.5; 22; 30; 6]; %62.5
cervical=[1 1 1 1 0 0 1 1 0 0 1 1 1 0 0 0 0 1 1];
genseg=[0 0 0 0 1 1 0 0 1 1 0 0 0 1 1 1 1 0 0];
%% PSD STRUCTRE: pow
close ... |
50993e40e82e5a22222635a7e3f97adc1f3f7a94bd1954c869e7644137ed2d19 | MATLAB | 16,537 | 487 | function [ EMGwhisk ] = GetWhiskFromEMG( basePath,varargin )
%[ EMGwhisk ] = GetWhiskFromEMG(basePath )
%This is a detector that extracts whisking/nonwhisking epochs from
%implanted EMG in the whisker pad. Extracts also the EMG and EMG envelope.
%
%INPUT
% basePath
% Assumes presence of the following files:
%... |
04e5dc923dac739c025ba98edd4e114bf08d5a8287b6a330b7e2030d87f440cf | MATLAB | 16,569 | 389 | %% calculate pixel-wise correlations of roi crops
data_stability = roi_correlations(data_stability,2,'stability');
%% plot settings
set(groot,'DefaultAxesTickDir', 'out')
set(groot,'DefaultAxesTickDirMode', 'manual');
set(groot,'DefaultAxesFontWeight', 'normal');
set(groot,'DefaultAxesFontName', 'Arial');
set(... |
cff0aa38bdb11a02f6107c631c34c5562de7699ac1ace2a2b9774a1442b99675 | MATLAB | 16,575 | 423 | function [data] = ft_channelrepair(cfg, data)
% FT_CHANNELREPAIR repairs bad or missing channels in the data by replacing them with the
% plain average of of all neighbours, by a weighted average of all neighbours, by an
% interpolation based on a surface Laplacian, or by spherical spline interpolating (see
% Perrin e... |
f6d773b7f1782c584d19e4024a8d78b6291b0819d7fcc9d713725648915931e1 | MATLAB | 16,576 | 425 | function [ titlestr, settings, results ] = linearRegression( dataview, settings )
% Regresses Coordinates onto Variable using leave-1-out CV or k-fold
% CV.
%
%
%
%<PRE>
% This file is part of dspace-core.
%
% Copyright (C) 2020 University Zurich, Sepp Kollmorgen
%
% Thi... |
bc6e38ef9d1bcc2ed6d3f40b70bec6d7998503c31a2bd1a5e6688985a287cbce | MATLAB | 16,608 | 421 | classdef (Abstract) surfaceFitter < handle_light
% Fit a surface to a point cloud
%
% This is an abstract class that needs to be implemented for
% specific cases. For examples see the tpsFitter or spherelikeFitter
%---------------------------------------------------------------------
... |
f55dc332e9ae5ae3020e504e36aae49b9cbfc13fab498d2e593b709e9c3d534f | MATLAB | 16,626 | 457 | classdef InfoTimelineModel < handle
% A domain model to hold application state that just happens to correspond
% (roughly) to what is shown in the two APT timeline axes. Normally the
% Labeler object holds a reference to one of these in the infoTimelineModel
% property. Note that this class does not define an... |
ed46e653d28e8fe1378b511328e496a1d1cab775bd2a49dc8092361ca2e8077b | MATLAB | 16,627 | 389 | function varargout = w_GRFCorrection(varargin)
% W_GRFCORRECTION MATLAB code for w_GRFCorrection.fig
% W_GRFCORRECTION, by itself, creates a new W_GRFCORRECTION or raises the existing
% singleton*.
%
% H = W_GRFCORRECTION returns the handle to a new W_GRFCORRECTION or the handle to
% the existing si... |
e13c58a31bde7aa610a5ba68d4fd690a44019a06d5e68c93e4395e21f2b41d79 | MATLAB | 16,646 | 408 | function [x, cost, info, options] = conjugategradient(problem, x, options)
% Conjugate gradient minimization algorithm for Manopt.
%
% function [x, cost, info, options] = conjugategradient(problem)
% function [x, cost, info, options] = conjugategradient(problem, x0)
% function [x, cost, info, options] = conjugateg... |
81a628eed9f113d86b0b50dde93e9737e7cde93960f0690847e7bc7ad24e8824 | MATLAB | 16,662 | 326 | function [ReHoBrain, Header] = y_reho(AllVolume, NVoxel, AMaskFilename, AResultFilename, IsNeedDetrend, Band, TR, TemporalMask, ScrubbingMethod, ScrubbingTiming, Header, CUTNUMBER)
% Calculate regional homogeneity (i.e. ReHo) from the 3D EPI images.
% FORMAT [ReHoBrain, Header] = y_reho(AllVolume, NVoxel, AMaskFi... |
492dcc583b7591461f1a78b753bc2f24efed24e219f0bd548ee396ee722a7e40 | MATLAB | 16,669 | 444 | function varargout = SurfSpace(varargin)
% SURFSPACE MATLAB code for SurfSpace.fig
% SURFSPACE, by itself, creates a new SURFSPACE or raises the existing
% singleton*.
%
% H = SURFSPACE returns the handle to a new SURFSPACE or the handle to
% the existing singleton*.
%
% SURFSPACE('CALLBACK',hO... |
21883ec65827cf6e566770a1110e2e9ba84ec7156aabb9993340940fa95c4e3e | MATLAB | 16,673 | 422 | function [data] = ft_rejectvisual(cfg, data)
% FT_REJECTVISUAL shows the preprocessed data in all channels and/or trials to
% allow the user to make a visual selection of the data that should be
% rejected. The data can be displayed in a "summary" mode, in which case
% the variance (or another metric) in each channel ... |
e931c9cf23e29c1faea5a7e91f91ec64a0c43ab08a0a409078c5f4b1f4241bfd | MATLAB | 16,674 | 395 | classdef RayRaster < handle
properties ( SetAccess = private, Dependent )
interior_array(:,:,:) logical
end
methods
function obj = RayRaster( X, Y, Z, mesh )
shape = [ numel( X ) numel( Y ) numel( Z ) ];
x_index_range = obj.compute_index_range( X, mesh( :, 1... |
e791bf63e0068fdb7f720b07b14a9442fef1c70b71009acdc80df2a69978c2a2 | MATLAB | 16,684 | 431 | % Class for probability binning described at
% https://www.ncbi.nlm.nih.gov/pubmed/11598946
%
% Bioinformatics inventors
% Original: Roederer M1, Moore W, Treister A, Hardy RR, Herzenberg LA.
% Incorporation into QF matching:
% Darya Orlova <dyorlova@gmail.com>\
% Guenther Walther... |
f713f21bf38ba71c6622a390adc99fcc9df71c45886c4fb662cb8c4c572e4f74 | MATLAB | 16,700 | 427 | function runMMIVA
% % Instructions to run this script:
% % Set current folder to be the MISA folder, e.g.:
% cd . % cd('~/MISA')
% % Add the folder containing this file to the path, e.g.:
% addpath('./scripts/tests')
% % Clear all and RUN:
% close all; clear all; clc
% % run this script
comps=30;
P=0;
addpath('/trdapps... |
78ae627cf5325893979291a4f0709f8d6ac1783fff14ffd19804558a525866db | MATLAB | 16,712 | 397 | % pipeline_preprocessing_randomMotorizedTreadmill.m
% Sarah West
% 8/17/21
% This script allows you to run all steps of the preprocessing pipeline via
% the "Run Section" feature of the Matlab Editor. Each step of the preprocessing
% is called as a function.
% Use "create_mice_all.m" before using this.
% ** shoul... |
4067244374988ce4620cf9615cab957618a75136884a73cb2e5bb16bd0eb8c83 | MATLAB | 16,727 | 603 | clear srcinfo
ns = 4000;
srcinfo.sources = rand(3,ns);
srcinfo.charges = rand(1,ns)+1i*rand(1,ns);
nt = 3999;
targ = rand(3,nt);
eps = 1e-5;
ntests = 36;
ipass = zeros(ntests,1);
errs = zeros(ntests,1);
zk = complex(1.1);
ntest = 10;
stmp = srcinfo.sources(:,1:ntest);
ttmp = targ(:,1:ntest);
% Test sources to s... |
79a9b6efe0a59d443615f553acacf7c93078a550f4759ca1b24d7e0aa227cdda | MATLAB | 16,743 | 503 |
%% refrence and citation
%%%%%%%%%%%This code is a modified version of the the available code in Zajkowski et al 2017 article
%%%Zajkowski, Wojciech; Kossut, Malgorzata; Wilson, Robert, 2017, "A causal role for right frontopolar cortex in directed, but not random, exploration", https://doi.org/10.7910/DVN/CZT6E... |
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