sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fa5406cfa9cdb3344473bc4040ed0c37d3f702cf681204b02951a995499213a5 | MATLAB | 6,153 | 191 | % FORMATTING
clear all
close gcf
load Transient081_2-train
% Go to directory
cd C:\matlab\work
DATA = dir('C:\MATLAB\work\*.ctr');
DATA = rmfield(DATA,'date');
DATA = rmfield(DATA,'bytes');
DATA = rmfield(DATA,'isdir');
[numSamples x] = size(DATA);
o = zeros(1, 250);
for c1 = 1:numSamples
eval(['load ' DATA(c1).n... |
d7d0bb3592af4f56f602159bfc313ff66aedaf96550e9f844e0ba9330ad958fd | MATLAB | 6,160 | 168 | function [Z, P, X, A] = sparse_pca(A, m, gamma)
% Sparse principal component analysis based on optimization over Stiefel.
%
% [Z, P, X] = sparse_pca(A, m, gamma)
%
% We consider sparse PCA applied to a data matrix A of size pxn, where p is
% the number of samples (observations) and n is the number of variables
% (featu... |
28689f245fdcc47f95f0b3fedd92951957149f14352e854557176fcd70db6d1f | MATLAB | 6,168 | 180 | function [distmat,cfg] = mahal_iem_mds_xgen_1fold(dat,theta,task,cfg)
% [distmat,cfg] = mahal_iem_mds_xgen_1fold(dat,theta,task,cfg)
if nargin < 3
help mahal_iem_mds_xgen
error('missing input arguments!')
end
ntrl = size(dat,1); % number of timepoints
nsens = size(dat,2); % number of M/E... |
8ef584768a7125855a6a4055b728a6093e90c06347dc3373c0f4b09f1594cd06 | MATLAB | 6,170 | 102 | %% the beta parameters from a ROI
%% extract beta estimates from TML task
clear
% sub-pil001 and sub-pil002 have no localizer
%'sub-011' have no hMT;'sub-013' no (rhMT rMTt),'sub-014' no MTt
%'sub-008' have only right mst - !! do manually
subjectList= {'sub-001','sub-002','sub-003','sub-004','sub-005','sub-006','sub... |
18f1d9480b232c34ba9f2342c07bc192f1ff67bef6d6951b2e3015dffda014a3 | MATLAB | 6,173 | 118 | function plot_metrics(plotStructs, plotColors, figure_save, saveLocation, ...
y_param, x_axis_lim, y_axis_lim, x_axis_ticks, y_axis_ticks, y_axis_label, ...
pulse_width, optional_outline_color, specific_num, custom_stats, each_acq, acq_range, ...
x_axis_label, x_tick_labels, y_tick_labels)
fig = f... |
d5a70651cc7a787366c4978e1389a79874fedf710011c4b76cefb80d667934cb | MATLAB | 6,174 | 193 | % EEG_EVENTTYPES - return a list of event or urevent types in a dataset and
% the respective number of events of each type. Output event
% types are sorted in reverse order of their number. If no
% outputs, print this list on the commandline instead.
%
% U... |
29442e1276ea877e7487aca3f160721e121be0108f8711201cce18f65cc7b74d | MATLAB | 6,175 | 194 | % presentStimuli
% Presents SF bandpass filtered noise stimuli to the subject for a fixed number of blocks.
% The subject responds to a change in luminance at fixation with a button press.
% The subject is provided a blank period between blocks.
%
% Syntax
% run_info = presentStimuli(p, w, t, stimuli)
%
% Input... |
3ca2d56cf0e49146e594f80bd7feac1cd1cbacbf378e5655fc93a1c3ad57783b | MATLAB | 6,180 | 224 | % READEGI - read EGI Simple Binary datafile (versions 2,3,4,5,6,7).
% Return header info, EEG data, and any event data.
% Usage:
% >> [head, TrialData, EventData, CatIndex] = readegi(filename, dataChunks, forceversion)
%
% Required Input:
% filename = EGI data filename
%
% Optional Input:
% dataChunks = vec... |
286353c27593788013ceb46b8daa11c56f1859cea82e1173aadb6d9bf6d5d0c9 | MATLAB | 6,183 | 260 | function OUT = db_cluster_table(clusters,DB,varargin)
% function OUT = db_cluster_table(clusters,DB,varargin)
%
% tor wager
% counts studies and contrasts in each cluster
%
% clusters is a struct in which XYZmm field has list of points
% --should be output of database2clusters, which contains all fields
% DB is databas... |
f5413b2a853779c6ad847ee1f108440d953a103e4c23fb3619e416fa6ad18a81 | MATLAB | 6,183 | 143 | %************************************************************************************%
%************************************************************************************%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Master file for D.sort%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%**********************************************************... |
22d87175f904e451b8b487424782aa8c31350d6d68964764143b68fa3aeeabfb | MATLAB | 6,184 | 177 | % GRADPLOT - Compute the gradient of EEG scalp map(s) on a square grid
%
% Usage:
% >> [gradX, gradY] = gradplot(maps,eloc_file,draw)
% Inputs:
% maps - Activity levels, size (nelectrodes,nmaps)
% eloc_file - Electrode location filename (.loc file) containing electrode
% - coordinates... |
efd1ff19bf324599580cb1c199b0714ab6e01e102ea312289336bf880d7a54a7 | MATLAB | 6,190 | 105 | function ops = Config_file(sessionpath)
<<<<<<< HEAD
ops.datatype = 'OpenEphys'; % binary ('dat', 'bin') or 'openEphys'
ops.root = sessionpath; % 'openEphys' only: where raw files are
% ops.fbinary = strcat(ops.root,'\example.dat'); % will be created for 'openEphys'
=======
ops.da... |
641a757c0cb8f1b827ecdf474c9aa9c4f0b4dfd74af26d9ef267af8bd2dc2ff8 | MATLAB | 6,192 | 156 | function [movie,movie_batch,summary]=loadDCIMGchunks(filePath,varargin)
% Loading DCIMG in chunks, clearing mex buffer inbetween chunk loading.
% This function makes sense when you want to resize the file on the fly
% while loading. Otherwise, there is no memory benefit. Loding to H5
% possible too.
%
% SYNTAX
% [movie... |
a299d106c3eac26ceb9722601b1789227d74b9a4c9608dd1dcf5d67509eba275 | MATLAB | 6,192 | 173 | function PlotExtendedData7(datadir, codedir)
%PlotExtendedData7 - Plots Extended Data 4.
% INPUTS:
% datadir - Local directory where ProcessData_ExtendedData7.mat was saved after running ProcessData_ExtendedData7
% codedir - Local directory where code (e.g., published/EstrousRPE/) was saved
%% Set up paths
s = pa... |
021066ac0f81e547f4d6842cb8b8425788aefc10e08d6866288631833f241fb6 | MATLAB | 6,193 | 162 | function out = FC_LoopLocalSimple(y, forecastMeth)
% FC_LoopLocalSimple How simple local forecasting depends on window length.
%
% Analyzes the outputs of FC_LocalSimple for a range of local window lengths, l.
% Loops over the length of the data to use for FC_LocalSimple prediction
%
% ---INPUTS:
%
% y, the input ti... |
643ab6417eb47ee18cc4977a4b50db49e4de0fa221b871a0abe4b80f821fc8e1 | MATLAB | 6,199 | 152 | % fig8_v1_noGUI.m
% RF parameters:
% LW ratio: 4 to 2
% # subregions: 2
% center frequency: 0.08 cpd
clear
close all
% simulated response parameters
deltaFMax = 1;
noiseStd = 0.01;
% visualization parameters
gOSIThresh = 0;
alphaExp = 0.00001;
disableLabels = 1;
customFile = "~/Documents/MATLAB/mousesc-ori-model/fi... |
e5c35e001fa684019892552b8f58bbbb1cf8c09d95314535b753d22e48a317d8 | MATLAB | 6,199 | 177 | function NAMES = fieldnamesr(S,varargin)
%FIELDNAMESR Get structure field names in recursive manner.
%
% NAMES = FIELDNAMESR(S) returns a cell array of strings containing the
% structure field names associated with s, the structure field names
% of any structures which are fields of s, any structures which are
% ... |
cd48f7909ed16b4ac8f8d034cae38e5cf264a6e4ceae1e8d183dfccd9277223c | MATLAB | 6,204 | 148 | %% Wrapper_CLEARSWI(headerAndExtraData,output_structure,algorParam)
%
% Input
% --------------
% headerAndExtraData : structure contains extra header info/data for the algorithm
% output_structure : structure contains output file path and output NIfTI header
% algorParam : structure contains fields with algor... |
97c8d9f32619582db1f70735be6a359353a05e2b0d387c92481e23e4c2c68d6d | MATLAB | 6,207 | 144 | function processMuscimolData(muscimolDataPath, codePath, savePath)
% Process muscimol data. Must run for plotFigure2_muscimol, plotFigure_S4
%INPUTS:
% muscimolPath = local path to muscimol behavior data downloaded from Zenodo
% codePath = local path to where code was saved
% savePath = local path to where yo... |
969c60694916a194c51700a7efd2a3c8e936d395d109ec6630261995326edb9d | MATLAB | 6,211 | 166 | function [net, info] = cnn_imagenet(varargin)
%CNN_IMAGENET Demonstrates training a CNN on ImageNet
% This demo demonstrates training the AlexNet, VGG-F, VGG-S, VGG-M,
% VGG-VD-16, and VGG-VD-19 architectures on ImageNet data.
run(fullfile(fileparts(mfilename('fullpath')), ...
'..', '..', 'matlab', 'vl_setupnn.m... |
f76cdfc19e369e44a1f414c4d59a271713277bdec6fea46cf71b571fd1d6b0ab | MATLAB | 6,214 | 108 | % STD_SPECPLOT - plot STUDY component cluster spectra, either mean spectra
% for all requested clusters in the same figure, with spectra
% for different conditions (if any) plotted in different colors,
% or spectra for each specified cluster in a separate figure
% ... |
1e27a96ebe7a3da700882ff6272ce71b087c9f8ee7fa64a211422b1428cd8025 | MATLAB | 6,215 | 159 | function plotNMF(experimentMatFolder, plotSaveFolder, Params)
% Plots components and variance explained using non-negative matrix
% factorisation (NMF)
% Parameters
% ----------
% experimentMatFolder : str
% path to where experiment mat files are located
% plotSaveFolder : str
% path to save plot
% Params : st... |
c9daa02de39330f1c41bbcb3eb13b65e3f2c2d6cb118e31c649ce727900f930e | MATLAB | 6,215 | 214 | function [err,Fname] = wryte3 (M,Fname,Opt)
%
% [err,UsedName] = wryte3 (M,Fname,[Opt])
%
%Purpose:
% Write matrix M to a text file
%
%
%Input Parameters:
% M : NxK matrix
% Fname : string containing the file name to write the matrix to
% Opt is either a flag (0/1) or an optional structure with the following ... |
fe4eb9faf91dfe2b365f34e5ceaf91434e0447e7a38eaad2a270959589d65b7a | MATLAB | 6,223 | 141 | %VL_IMREADJPEG Load and transform images asynchronously
% IMAGES = VL_IMREADJPEG(FILES) reads the specified cell array
% FILES of JPEG files and returns at cell array of images IMAGES.
%
% IMAGES = VL_IMREADJPEG(FILES, 'NumThreads', T) uses T parallel
% threads to accelerate the operation. Note that this is ind... |
c921e95107a6b7df8197f22e3f7b51ea4d01247b37f63dc97e8f6fbb08bc3f19 | MATLAB | 6,225 | 207 | % output = demo_image_math_imcalc_fslmaths()
%
% IN
%
% OUT
%
% EXAMPLE
% demo_math_with_two_images
%
% See also
% Author: Saskia Klein & Lars Kasper
% Created: 2014-11-18
% Copyright (C) 2014 Institute for Biomedical Engineering
% University of Zurich and ETH Zurich
%
% This file is part of ... |
90347edd246696c7a5056ecff64b56875cdc59097fb4278b7af431d67e64243a | MATLAB | 6,228 | 153 | function transform_to_ctf(input_img, numverts, maxvoxelvol, num_sources)
%
% Input: input_img <string> fullpath to T1 MRI image to be segmented
% numvertices <integer> number of desired mesh vertices.
% maxvoxelvol <float> desired maximal volume per tetrahedra
% num_sour... |
6469eccfd20be80a89d8188b30d894674d1ba1244398737abdb7b25eb9a3f699 | MATLAB | 6,229 | 148 | function [trl] = iEEG_func_rippleDetector2(x, srate)
%% ########################################################################
% [trl] = iEEG_func_rippleDetector2(x, srate)
% #########################################################################
%
% Ripple detection
%
%--------------------------------------------... |
ae252640ced0d0586cffe6cba3302dd47602d9915675b60719d050ec30ca4043 | MATLAB | 6,231 | 255 | disp('The only input needed is a distance matrix file')
disp('The format of this file should be: ')
disp('Column 1: id of element i')
disp('Column 2: id of element j')
disp('Column 3: dist(i,j)')
%Change the line below to match the actual file name
mdist='s1cPROT_kept.dmtx';
xx=load(mdist);
%Set upper and lower bounds
... |
eb3e40bf50b923be35203ddfca9bb33025b18e510d0d89e5bac9f5774169bbe0 | MATLAB | 6,231 | 255 | disp('The only input needed is a distance matrix file')
disp('The format of this file should be: ')
disp('Column 1: id of element i')
disp('Column 2: id of element j')
disp('Column 3: dist(i,j)')
%Change the line below to match the actual file name
mdist='s2cPROT_kept.dmtx';
xx=load(mdist);
%Set upper and lower bounds
... |
3e02fad4a44a102b845e413a52d53e8789e96ec3861a2bac57853acfbf050198 | MATLAB | 6,234 | 199 | function V = tapas_uniqc_spm_create_vol_with_tr(V)
% Create a NIfTI image volume
% FORMAT V = spm_create_vol(V)
% V - image volume information (see spm_vol.m)
%__________________________________________________________________________
% Copyright (C) 2005-2014 Wellcome Trust Centre for Neuroimaging
% John Ashbu... |
31fbda9d99549ab3d36189241bd25da177dce8534e5561cba97e5c90f1a76e48 | MATLAB | 6,239 | 166 | function TS_SingleFeature(whatData,featID,makeViolin,makeNewFigure,whatStat,beVocal)
% TS_SingleFeature Plot distributions for a single feature given a feature ID
%
%---INPUTS:
% whatData: the data to load in (cf. TS_LoadData)
% featID: the ID of the feature to plot
% makeViolin: makes a violin plot instead of overlap... |
eb3ac46e28d338771bd8b097e89f99b73120d229ffbc0e99e270816287fbb784 | MATLAB | 6,240 | 174 | % FLOATREAD - Read matrix from float file ssuming four byte floating point number
% Can use FSEEK to read an arbitrary (contiguous) submatrix.
%
% Usage: >> a = floatread(filename,size,'format',offset)
%
% Inputs:
% filename - name of the file
% size - determine the number of float element... |
f68abf18190e0a5825a05a0b9f7a1e73a849faf75bb470f132a6820faf227d40 | MATLAB | 6,243 | 155 | function out = PP_ModelFit(y, model, order, randomSeed)
% PP_ModelFit Investigates whether AR model fit improves with different preprocessings.
%
% After performing the range of transformations to the time series, returns the
% in-sample root-mean-square (RMS) prediction errors for an AR model on each
% transformed t... |
5e9fb858324a73556ba41ed1dc3d53cd61a7145ab3b348102779359b622a65b1 | MATLAB | 6,244 | 160 | %{
pre.SegmentMask (computed) # mask of a segmented cell
-> pre.Segment
mask_id : int # id of the mask
-----
mask_pixels : longblob # indices into the image in column major (Fortran) order
mask_weights : longblob # weights of the mask at the indices above
%}
classde... |
f28d9e323e15fe8b4c992e909190076ff8108a74f3048416dc8766dd6b8bb89a | MATLAB | 6,247 | 141 | %VL_IMREADJPEG Load and transform images asynchronously
% IMAGES = VL_IMREADJPEG(FILES) reads the specified cell array
% FILES of JPEG files and returns at cell array of images IMAGES.
%
% IMAGES = VL_IMREADJPEG(FILES, 'NumThreads', T) uses T parallel
% threads to accelerate the operation. Note that this is ind... |
a3f8d81ee238fcfba8364db0297b87778b767f2aa04fd5afa9b04e540f51f984 | MATLAB | 6,253 | 170 | function [ output_args ] = findCOREassemblies( spike_probability_raster , spike_probability_coactivity_threshold )
%FINDCOREASSEMBLIES( spike_probability_raster , spike_probability_coactivity_threshold )
%
%
% === Jan Moelter, The University of Queensland, 2018 ===================
%
%% > EXTRACT ENSEMBLES
printConso... |
523218fa27c3fb5387b8106e8f8ecf9ba4879276c2fc04a2ce37bfc1e1152557 | MATLAB | 6,255 | 159 | clc, clear, close all;
filepath = fileparts(mfilename('fullpath'));
addpath(genpath(filepath));
% Select an example to run
exampleID = 3; % 1, 2, 3, 4, 5
%% Example 1
% Research question:
% - I have an imaging map (a nifti file) and a gene set. I want to test if
% the imaging pattern correlates to the expression ... |
f1508c8a8403b0bc860e679e70fb1ad8af9aed1d93177e444f40530d5269e3a6 | MATLAB | 6,256 | 210 | function warp_HArtMuT_sources_iso2mesh( ...
srcScalpFile, srcSkullFile, ...
tgtScalpFile, tgtSkullFile, ...
hartmutMatIn, hartmutMatOut, ...
mean_pnt)
%WARP_HARTMUT_SOURCES_ISO2MESH
% Warp HArtMuT artefact source positions from a source head (e.g., NYHead)
% to an individual target head using radial dep... |
b253d3d188ab445eda781138e5267e11a19c945e7d2ba0503e7f15eed0d0f4b3 | MATLAB | 6,259 | 216 | function [ output ] = tapas_rdcm_ridge(DCM, X, Y, args)
% [ output ] = tapas_rdcm_ridge(DCM, X, Y, args)
%
% Variational Bayesian inversion of a linear DCM with regression DCM. The
% function implements the VB update equations derived in Frässle et al.
% (2017).
%
% Input:
% DCM - model structure
% ... |
cd53e4a6f0c93e41f833896bd1e56356d33f7e9340f87f19f778d1e841446b62 | MATLAB | 6,260 | 149 | function [data, timestamps, info] = load_open_ephys_data_faster(filename)
%
% [data, timestamps, info] = load_open_ephys_data(filename)
%
% Loads continuous, event, or spike data files into Matlab.
%
% Inputs:
%
% filename: path to file
%
%
% Outputs:
%
% data: either an array continuous samples (in micro... |
92530378a18d6b17ea4e312471a30b1c8c391058798e130e23ef1f15e9211dc5 | MATLAB | 6,261 | 136 | %{
vis.Trippy (manual) # randomized curvy dynamic gratings
-> vis.Condition
---
version : tinyint # trippy version
rng_seed : double # random number generate seed
packed_phase_movie : longblob # phase movie... |
334efb064017d990cc8a2251edb74e21030d327469bc09b4ddccf95813f1a5a8 | MATLAB | 6,264 | 161 | %% plot tactile beta
% from the mask fo indivudual ms ROi
%%
%settings for plots
shape='.';
%%set the size of the shape
sz=50;
%%set the width of the edge of the markers
LineWidthMarkers=1.5;
%%set the width of the edge of the mean line
LineWidthMean=4;
%%set the length of the mean line
LineLength=0.4; %the actual l... |
639715b0ff1781fba0d330995954e66021a6b002ea8494b76df9a4f568299a98 | MATLAB | 6,264 | 146 | function [map,stats] = FiringMap(positions,spikes,varargin)
%FiringMap - Compute firing map (e.g. for a place cell, head direction cell, etc.)
%
% Compute firing map (e.g. for a place cell), as well as occupancy and spike
% count maps. Optionally, field statistics can also be computed, including
% in-field peak and... |
e9fc698cd55c3da6b15dfae383196f277e928a13714cb5f33560ce12a32815a5 | MATLAB | 6,266 | 209 | function [ subject, backup ] = nmri_backup_cleaning_marking(subject, params)
%[ subject, backup ] = nmri_backup_cleaning_marking(subject, params)
%
% This function will create a backup file of the cleaning, marking and vigilance
% scoring from one subject
% Will use the dws-filt and cleaned/ICA-cleaned file to extra... |
82b59be200079df772f59e82ebda3325129d06e87e9d05fef15ea0ca79639264 | MATLAB | 6,267 | 168 | function res = hlp_varargin2struct(args, varargin)
% Convert a list of name-value pairs into a struct with values assigned to names.
% struct = hlp_varargin2struct(Varargin, Defaults)
%
% In:
% Varargin : cell array of name-value pairs and/or structs (with values assigned to names)
%
% Defaults : optional list of n... |
68bddc3be8a42c37bf9900173f5344bc2ad1420b8e2ae5547b0d5391198bc325 | MATLAB | 6,271 | 165 | %% Use predetermined crop ROI parameters to crop a single image of the
% calibration lframe We will use these
% cropped images to determine view extrinsic parameters.
clear
% Load in the crop params
basedir = 'D:\20191030\mouse9\calibration\';
numCams = 6;
numPoints = 5;
ext = '.tiff';
% Input the physical (x,y,z) dim... |
82bddf12cecb81077941b5590cf15d91e089afc9b1cc9ab3e73f6640f6977d6c | MATLAB | 6,271 | 149 | %% DEMO4_RSAsearchlight_sim
% simulates fMRI data for a number of subjects and runs searchlight
% analysis using RSA, computes the similarity maps for each subject
% and does group level inference.
% demo of the searchlight analysis
%%%%%%%%%%%%%%%%%%%%
%% Initialisation %%
%%%%%%%%%%%%%%%%%%%%
clear;clc
returnHere = ... |
94ecd0bae90e096a5dd5e7756af27e0968ff6a62ce17f0e15efb58319eb04db6 | MATLAB | 6,273 | 198 | %PRINT2ARRAY Exports a figure to an image array
%
% Examples:
% A = print2array
% A = print2array(figure_handle)
% A = print2array(figure_handle, resolution)
% A = print2array(figure_handle, resolution, renderer)
% [A bcol] = print2array(...)
%
% This function outputs a bitmap image of the given figure, at t... |
b60a1081ea2f81387a673943698555c2f136d22e18f3299f0c9edc914935d251 | MATLAB | 6,275 | 180 | function this = MrDataNd_shift_timeseries(this, verboseLevel)
%Tests shift_timeseries using synthetic data (sine waves of different frequency
% per slice)
%
% Y = MrUnitTest()
% run(Y, 'MrDataNd_shift_timeseries')
%
% This is a method of class MrUnitTest.
% It creates sine waves of different frequencies per slice... |
689f6dc07f6a58917a82d8b322bb69d6820c6196913618d522215c02e7d342ec | MATLAB | 6,278 | 108 | function plot_communication_subspace_similarity
close all
clear all
clc
% Plot communication subspace similarity.
% Select a folder containing data.
folder_name = uigetdir;
cd(folder_name)
% Control.
load('population_regression_control.mat')
mean_similarity_animal_session_control = population_regression_control.simi... |
9fa33ce3296ca3e55aee7a162d11a07913372f12e64da8aa3f09136ef35c1f87 | MATLAB | 6,285 | 168 | function varargout = TMSsphereROI_GUI(varargin)
% TMSSPHEREROI_GUI M-file for TMSsphereROI_GUI.fig
% TMSSPHEREROI_GUI, by itself, creates a new TMSSPHEREROI_GUI or raises the existing
% singleton*.
%
% H = TMSSPHEREROI_GUI returns the handle to a new TMSSPHEREROI_GUI or the handle to
% the existing ... |
d0c2c76a563f3bffc9b7a1b51692ea5fbaa17fa480c0c5858e5bee3cda58d792 | MATLAB | 6,285 | 132 | % dipfitdefs() - default settings and filenames for dipolefitting
% to source in the ICA/ERP package functions.
% Insert local dir reference below.
%
% Note: Edit this file to change local directories under Unix and Windows
%
% Author: Robert Oostenveld, SMI/FCDC, Nijmegen 2003
% SMI, ... |
860b480a528455fa2f0f8d436b3125f82dead0a37ac0a8a5fdd1e22399ebb614 | MATLAB | 6,287 | 194 | % POP_COMMENTS - edit comments
%
% Usage:
% >> EEG = pop_comments( EEG);
% >> newcomments = pop_comments( oldcomments);
% >> newcomments = pop_comments( oldcomments, title, newcomments, concat);
%
% Inputs:
% EEG - EEGLAB structure
% oldcomments - old comments (string or cell array of strings)
% tit... |
8541cb7bd4d985b018b10317fcb17f7df5d7eef74e03ef7d1a394de75fa44c56 | MATLAB | 6,290 | 191 | % Morphology Enabled Dipole Inversion (MEDI)
% [x, cost_reg_history, cost_data_history] = MEDI_L1(varargin)
%
% output
% x - the susceptibility distribution
% cost_reg_history - the cost of the regularization term
% cost_data_history - the cost of the data fidelity term
%
% input
% RDF.mat has to be i... |
c948523a2c9b972147e361f44f7bc533850868c49c56a9d71ccbd4ee3283ce98 | MATLAB | 6,291 | 251 | function [pval table] = circ_hktest(alpha, idp, idq, inter, fn)
%
% [pval, stats] = circ_hktest(alpha, idp, idq, inter, fn)
% Parametric two-way ANOVA for circular data with interations.
%
% Input:
% alpha angles in radians
% idp indicates the level of factor 1 (1:p)
% idq indicates the level... |
41e26738699d1a4fcf63b19c30feed90faf9f8f0c77b4e223064f86e3eb93344 | MATLAB | 6,301 | 171 | function bpa = tapas_bayesian_parameter_average(varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This function calculates the Bayesian parameter average for the individual estimates handed to
% it.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
9972c66e5417d70fab82b2e584dcba28ec911359353e9f6cf15ce36bc55d6c89 | MATLAB | 6,301 | 172 | function out = MF_armax(y, orders, pTrain, numSteps)
% MF_armax Statistics on a fitted ARMA model.
%
% Uses the functions iddata, armax, aic, and predict from Matlab's System
% Identification Toolbox
%
% ---INPUTS:
%
% y, the input time series
%
% orders, a two-vector for p and q, the AR and MA components of the model... |
c13b961ba74a6836c9f2c997d985999cb70e48ddd9235c6062f4ee6f79c6954d | MATLAB | 6,306 | 153 | % plugin_getweb - support function to get plugin information from the web
% Copyright (C) 2012- Arnaud Delorme
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided th... |
253bfc839a01708e2e3db24b3b5f969d8099e137a18159bee72adeab7065350b | MATLAB | 6,307 | 168 | function [w, A, C, sbc, fpe, th]=ARFIT_arfit(v, pmin, pmax, selector, no_const)
%ARFIT Stepwise least squares estimation of multivariate AR model.
%
% [w,A,C,SBC,FPE,th]=ARFIT(v,pmin,pmax) produces estimates of the
% parameters of an m-variate AR model of order p,
%
% v(k,:)' = w' + A1*v(k-1,:)' +...+ Ap*v(k-p,:... |
57414df4b739fa7d4f0aff2e7b765351668ca24df19f39ab254bbf51f1f65008 | MATLAB | 6,307 | 176 | % Main script for super-resolution reconstruction of diffusion MRI data using T1w guidance
%
% Reference:
% Lee H, ..., Huang S, Communications Biology, 2026
%
% Requirements:
% - FreeSurfer installed and configured
% - FreeSurfer recon-all completed for each subject
% - FSL (flirt, fslmaths, convert_xfm)
% - MRtrix3 (... |
317d2c24cc80bd0b12a8f03ffe5d7bfa545b2aa087f5e22a241b0211d16060a9 | MATLAB | 6,309 | 209 | function [ltom, htom, mtol, mtoh,...
ltom_incong, htom_incong, sems, outmat] =...
block_dynamics_latency(A, twin, smoothfactor, z_arg, varargin)
%plot how latency changes around block transitions. cmc 7/16/21
%inputs: A struct- If given S struct, will convert it to A.
% twin- ntrials around block transit... |
fc632c25bd015a78dab4db313260feb32f8aa806a131e5c9f550bdc3ae848b66 | MATLAB | 6,312 | 217 | %% Part 1 : Single Neuron
close all
clear all
rng(1)
% load('Z:\CLOOSE_benchmark_tests\Spine_imaging\DF_gcampspinebci04_000_006.mat');
% load('Z:\BCI\glusnfr_spine_bci\glusnfrbci4\Baseline\baselineMask_1.mat')
% load('Z:\CLOOSE_benchmark_tests\Spine_imaging\ROIS_gcampspinebci04_000_006.mat')
load('Z:\CLOOSE_benchmar... |
73021efea23987b8f01f23521a1212d121af5c733b3673f57bb7430ccd698b6e | MATLAB | 6,315 | 162 | %**************************************************************************
%
% This is a simple extension of the bar plot to include error bars. It
% is called in exactly the same way as bar but with an extra input
% parameter "errors" passed first.
%
% Parameters:
% errors - the errors to be plotted (extra... |
4530da012f301c2384544c6100b5c01e65c6beaa5ff417965fc769859f0f3a9e | MATLAB | 6,316 | 163 | %% plot tactile beta
% from the mask fo indivudual ms ROi
%%
%settings for plots
shape='.';
%%set the size of the shape
sz=50;
%%set the width of the edge of the markers
LineWidthMarkers=1.5;
%%set the width of the edge of the mean line
LineWidthMean=4;
%%set the length of the mean line
LineLength=0.4; %the actual l... |
d36e1914cc1af039f2b6559563010d80fc14e467f9bd2b68bc6d2d9a3e87ec36 | MATLAB | 6,316 | 190 | % Bang et al (2020) Private-public mappings in human prefrontal cortex
%
% Reproduces Figure 4-figure supplement 1
%
% "Private confidence" is computed by training multinomial regression on
% data from prescan session and then applying weights to data from fMRI
% session while setting context weights to zero
%
% Visual... |
5f97d06ee6a1180a8c100bcaa2a4720d1caed9aa0f8599438faaf0e9b3a35bda | MATLAB | 6,319 | 196 | % POPHELP - Same as matlab HTHELP but does not crash under windows.
%
% Usage: >> pophelp( function );
% >> pophelp( function, nonmatlab );
%
% Inputs:
% function - string for a Matlab function name
% (with or without the '.m' extension).
% nonmatlab - [0|1], 1 the file is not a Matlab file
%... |
a0cb0e2c97fc7bd60e111095a3c2cc3a7e4dd18a2e31da50874055c16848a89a | MATLAB | 6,319 | 194 | function M = multinomialfactory(n, m)
% Manifold of n-by-m column-stochastic matrices with positive entries.
%
% function M = multinomialfactory(n)
% function M = multinomialfactory(n, m)
%
% The returned structure M is a Manopt manifold structure to optimize over
% the set of n-by-m matrices with (strictly) positive e... |
dce150a153a1cc73402a272c7a48de94fcd012faad008646b79a5dbb9a1686e9 | MATLAB | 6,320 | 177 | function [ obj ] = mh_init( obj )
% Initialize Markov chain state for Metropolized Gibbs sampling.
% Requires obj.dcm and obj.prior to be intialized.
%
% This is a protected method of the tapas_Huge class. It cannot be called
% from outside the class.
%
% fMRI forward model
obj.options.fncBold = @bold_gen;
%% prio... |
66e97fea1f8f2be5850cdbda5a712c0c9eb86b5af521c1fc7e7494436a2b1bc9 | MATLAB | 6,323 | 216 | %% h = sepia_handle_panel_swi(hParent,h,position)
%
% Input
% --------------
% hParent : parent handle of this panel
% hFig : handle of the GUI
% h : global structure contains all handles
% position : position of this panel
%
% Output
% --------------
% h : global structure c... |
cc0fe1077cdbdff974b5f2145e84ba15a3018b5c3b96918915e78bc4359883aa | MATLAB | 6,325 | 141 | classdef circularGraph < handle
% CIRCULARGRAPH Plot an interactive circular graph to illustrate connections in a network.
%
%% Syntax
% circularGraph(X)
% circularGraph(X,'PropertyName',propertyvalue,...)
% h = circularGraph(...)
%
%% Description
% A 'circular graph' is a v... |
6913c0b7f731f9f56e829d215c3ddf73f82eefa17d7445aa373a2838d7b02c7a | MATLAB | 6,328 | 159 | % DFTFILT2 - discrete complex wavelet filters
%
% Usage:
% >> wavelet = dftfilt2( freqs, cycles, srate, cyclefact)
%
% Inputs:
% freqs - frequency array
% cycles - cycles array. If one value is given, all wavelets have
% the same number of cycles. If two values are given, the
% two ... |
9a0b2dfcd85c5321dbb835fdc0a225f8ceafe9a1584a70da16d738d09c04574e | MATLAB | 6,328 | 185 | % fit_makeSplineBasis.m
% Georg Oeltzschner, Johns Hopkins University 2020.
%
% USAGE:
% [splineArray] = fit_makeSplineBasis(dataToFit, fitRangePPM, dkntmn);
%
% DESCRIPTION:
% This function creates an array of cubic baseline spline functions, which
% serve as a basis set for the LCModel baseline computation.
%
% The ... |
83f09582be5df7effd604bf40097b1ee775ab96ef79a5d1a92b0344366b3a4c2 | MATLAB | 6,329 | 170 | function [y, lambda, info] = hessianextreme(problem, x, side, y0, options, storedb, key)
% Compute an extreme eigenvector / eigenvalue of the Hessian of a problem.
%
% [u, lambda, info] = hessianextreme(problem, x)
% [u, lambda, info] = hessianextreme(problem, x, side)
% [u, lambda, info] = hessianextreme(problem, x, s... |
e5e9c473ff960b944cb6c0665f1be3b5e5e1aac8865acfc60ba3d745cc2c9e4e | MATLAB | 6,329 | 117 | % POP_DIPPARAMS - Set plotting parameters for dipoles.
%
% Usage:
% >> STUDY = pop_dipparams(STUDY, 'key', 'val');
%
% Inputs:
% STUDY - EEGLAB STUDY set
%
% Optional inputs:
% 'axistight' - ['on'|'off'] Plot closest MRI slide. Default is 'off'.
% 'projimg' - ['on'|'off'] lot dipoles projections... |
c697c58f15d9ac0237a99ecb5d3509236d2370630e39ca28376331616f312828 | MATLAB | 6,333 | 198 | function run_permuttest_examples
%RUN_PERMUTTEST_EXAMPLES Run paired permutation t-test examples.
% Generates random multivariate data for 2 "dependent" samples X and Y.
% Each sample has 20 variables, each with a mean value of 0, except for
% the first 10 variables of Y which have a mean value of -1. Each
% v... |
366fc28594cf20d1f908146cba13613bca7e472791e58c2b89d21ced08dc035f | MATLAB | 6,334 | 208 | function [BCMatrix, BCRHS] = boundaryCondition3D(BC)
% It creates the matrix of coefficient based on the BC structureprovided
% by the user. It also generates the right hand side vector of the linear
% system of equations
%
% SYNOPSIS:
% [BCMatrix, BCRHS] = boundaryCondition3D(BC)
%
% PARAMETERS:
%
%
% RETURNS:
%
%
%... |
863daef4f6428d9d5a50ccef28f417a69e280fadc7ee72015aea914811e50dd3 | MATLAB | 6,334 | 127 | %% ============================================================
% Main burst analysis script
% ============================================================
clear all; close all; clc;
%% ============================================================
% Set parameters and import data
% ==============================... |
cf7f76decfd66bf4bb506be910e5cbac10b93a2affe0955bd6dd761cd9c85252 | MATLAB | 6,334 | 189 | function M = grassmanncomplexfactory(n, p, k)
% Returns a manifold struct to optimize over the set of subspaces in C^n.
%
% function M = grassmanncomplexfactory(n, p)
% function M = grassmanncomplexfactory(n, p, k)
%
% Complex Grassmann manifold: each point on this manifold is a collection
% of k vector subspaces of di... |
7208b0b4ec00dc84d9c6799ecabd009df12513fe716440e2d043207465737c5b | MATLAB | 6,335 | 167 | function ISInTh = getISInTh(SpikeTimes, N, Steps, plotFig)
%GETISINTH Returns the threshold to use for BurstDetectISIn.m
% Tim Sit 2018
% Based on HistogramISIn.m by Douglas Bakkum, 2013, but automatically
% returns the result rather than having to eyeball it, and uses a freely
% available (and perhaps m... |
6f76021be9973199db840078c6bb7034dca1adbd973b72f08e2c10757ae66009 | MATLAB | 6,339 | 155 | function G = crossvalIPMraw(Y,SPM,conditionVec,varargin)
% function dist=rsa.spm.crossvalIPMraw(Y,SPM,conditionVec,varargin);
% First, gets the regression coefficent from the SPM, and prewhitens them.
% Prewhiten can be controlled using different methods (run-wise or overall).
% The same code is used in rsa.spm.noiseNo... |
acdf282eb5bb367bdb0f4eecd51b91532e4bd5fe80f17a834e3e6158812ac165 | MATLAB | 6,339 | 160 | function plot(segStream,cfg,varargin)
% Plot the contents of a McsSegmentStream object with spike cutouts.
%
% function plot(segStream,cfg,varargin)
%
% Produces for each segment a 3D plot of trials x samples and a time series
% plot which overlays all trials.
%
% Input:
%
% segStream - A McsSegmentSt... |
455caeff4dfb16cbbc9ca15acc5e2a0f1eb3d1e50cde830f050539b6dadb54ce | MATLAB | 6,341 | 163 | function out = PH_ForcePotential(y, whatPotential, params)
% PH_ForcePotential Couples the values of the time series to a dynamical system
%
% The input time series forces a particle in the given potential well.
%
% The time series contributes to a forcing term on a simulated particle in a:
%
% (i) Quartic double-wel... |
ed2e237204a8055784a58944fe6aa72dd7aebb3a65384a8ed6e8b6260958ad7d | MATLAB | 6,341 | 174 | function [rpulset, verbose] = tapas_physio_filter_respiratory(...
rpulset, rsampint, cutoff_freqs, despike, normalize, verbose)
% Preprocesses respiratory data
%
% Key steps
% + Remove NaNs and outliers
% + Optional: Despike with sliding-window median filter
% + Detrend at `cutoff_freqs(1)` Hz
% + Remove no... |
ff7d74ae84a99b0d11897008aa97f85503445334452d359944bff42a02e95dd0 | MATLAB | 6,344 | 226 | function plotFigureS1_rawWTexperts(processedBehaviorPath)
%Plot figure S1 - raw wait time block transition dynamics for expert rats
% and inference model predictions
% YOU MUST RUN processBehaviorData BEFORE RUNNING THIS FUNCTION
%INPUTS:
% processedBehaviorPath = path to where you have saved the outputs from
% ... |
bad747e7c99d7e7156ee7eb97ca666126a4f63a1947b6430110f02d0d1aa371c | MATLAB | 6,345 | 133 | function [STA, coherenceCurve, STA_shuff_mean, STA_shuff_SD, coherence_shuff_mean, coherence_shuff_SD] = HI_calc_coherence(spkTimes, inputSignal, Fs, windowSize, iterations, plotFlag, varargin)
switch nargin
case 8
minFreq = varargin{1};
maxFreq = varargin{2};
case 7
error('Only one inp... |
9354bab55ba259283d6f9fdc86bb79c56ad52e30538e74257a64d56a43e25cf5 | MATLAB | 6,350 | 157 | function [dWU] = Template_building(DATA,ops)
[NT, Nchan ,Nbatch] = size(DATA);
Nfilt = ops.Nfilt;
% Deleted the option to choose from data or not, now only fromdata.
% thus, the initiale template will always be calculated from the data.
if(ops.template =='Y')
% dWU0 = load(ops.template_file);
load(ops.tem... |
0d4841f36227942fac5ab0c4b865966d2c79fe7bf3422cd292de7a3b9521a9ab | MATLAB | 6,353 | 141 | %{
vis.Matisse2 (manual) # conditions for the moving matisse stimulus
-> vis.Condition
---
-> vis.Matisse2Cache
pre_blank_period : decimal(5,3) # (seconds)
duration : decimal(5,3) # (seconds)
pattern_width : smallint # pi... |
6a84e528aa384dfbee9c19dfa7ddb7978c11f2fd102806200506ec9802605744 | MATLAB | 6,353 | 141 | % CORRECT_MC - compute an upper limit for the number of independent
% time-frequency estimate in a given time-frequency image.
% This number can be used to correct for multiple comparisons.
%
% Usage:
% [ncorrect array] = correct_mc( EEG, cycles, maxfreq, timesout);
%
% Inputs:
% E... |
b0aca9a73820c721d7d698f0edd46ae208cee5d49d0029d99b0ce0646a78175b | MATLAB | 6,356 | 156 | function out = CO_TranslateShape(y, shape, d, howToMove)
% CO_TranslateShape Statistics on datapoints inside geometric shapes across
% the time series.
%
% Inputs specify a shape and its size, and a method for moving this shape
% through the time domain.
%
% This is usually more informative in an em... |
c2c6fd06f1ef5c76b8b690329b0618d2906b8dd6069e551ed09393aa3c98a128 | MATLAB | 6,356 | 148 | function [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)
% Multi-taper time-frequency spectrum - point process times
%
% Usage:
%
% [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)
% Input:
% data (structure array of spike times with dimension channels/trials;
% also ... |
57827f58c476c33de81fe2543c07f2a82b69dcc05bf8f795d6fd6eba61d0e8e1 | MATLAB | 6,361 | 204 | function [x, E, s, lambdamax] = ML_l1pwc(y, lambda, display, stoptol, maxiter)
% Performs discrete total variation denoising (TVD) using a primal-dual
% interior-point solver. It minimizes the following discrete functional:
%
% E=(1/2)||y-x||_2^2+lambda*||Dx||_1,
%
% over the variable x, given the input signal y, acco... |
c3a8d8c2ef11725a14f90aba3daabd6b06c85ef0d89548554f463fb68f614ba9 | MATLAB | 6,362 | 186 | function [headmodel] = ft_read_headmodel(filename, varargin)
% FT_READ_HEADMODEL reads a head model (or volume conduction model of the head) from
% various manufacturer specific files. Currently supported are ASA, CTF, Neuromag,
% MBFYS, MATLAB and SimNIBS. The volume conduction model is represented as a
% structure w... |
4d486dc2f975b26c14982699fb73a521684e9dfec88b1052d706533e7d89b4a3 | MATLAB | 6,363 | 111 | %% Plot the beta parameters from a ROI
% spherical functional roi
% use subject masks - lS1, lPC, rPC, lMTt, rMTt, lhMT, rhMT
% from TACTILE MOTION LOCALIZER
% take the avg of beta values from the roi
% example (1)lS1- motion_beta and (2) rS1 -static_beta
% across two runs
%% extract beta estimates from TML task a... |
9873110e2ac43345b56445b9202815a5b231d8a30ca96c491ca4331fcbc7b3ef | MATLAB | 6,363 | 201 | function [h,a] = PlotDistribution2(var1,var2,varargin)
%PlotDistribution2 - Plot bivariate data along with respective distributions.
%
% USAGE
%
% [h,a] = PlotDistribution2(var1,var2,<options>)
%
% Using cell arrays will overlay variable pairs.
%
% var1 variable 1
% var2 variable 2
% ... |
876862481ce6ae78eeea05e9fafd63a33284b7c012e0509f3740e869cc3a5ad7 | MATLAB | 6,371 | 155 | % EEG_SELECTSEGMENT - Select a data segment
%
% Usage:
% OUTEEG = eeg_selectsegment(INEEG, 'key', val)
%
% Input:
% INEEG - input EEG dataset structure
%
% Optional inputs:
% 'timeoffset' - [2x float array] beginning and end in seconds. For example
% 'timeoffset' of [0 1800] selects the fi... |
b7bd389e6e5f12f0cc4f13fa4118ea19394a4bd730fedf7a5d25e1ac8e5fdeec | MATLAB | 6,371 | 156 | function firstlevel_main()
% Representative Figure 3 first-level model for sub-001.
% Edit USER SETTINGS, then run this function.
%% USER SETTINGS
rootDir = 'D:\path\to\MRI_project';
behRoot = 'D:\path\to\behavioral_results';
spmDir = 'C:\path\to\spm';
subName = 'sub-001';
emID = 'em0001';
nRuns = 4;
TR = 0.8;
deri... |
45712402d3aa5378b92e34c7f659982bf8e948d14fc6706613444265242dd798 | MATLAB | 6,372 | 197 | function styleOptions = setPlotStyle(styleName, varargin)
% SETPLOTSTYLE Set consistent plot styling for different publication types
%
% Syntax:
% opts = setPlotStyle(styleName)
% opts = setPlotStyle(styleName, 'Name', Value, ...)
%
% Description:
% Configure plot styling for different publication formats.
%
% In... |
6a33bed5098701e79c0d2ef81fc1ddd06f338a7d615de920f24fa2e0901b1417 | MATLAB | 6,372 | 180 | %% SetupForceSettings.m 08/12/2020 Julia Becker
% This script creates .force-settings files for the JPK software which
% allow to automatically read in and/or alter AFM measurement settings
% during an AFM experiment.
% CAVE! You need to have calibrated your cantilever before running this
% scrip... |
ec54f79f651c836449e2e5422be4edf9d737789ee1b2a309de7ba94c8c540f6b | MATLAB | 6,373 | 187 | function fear_icaCoactTrigLFPaverageHighThreshold_shuffle(basename,varargin)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115'
% basename='~/data/Fear/triple/karmeliet190901/karmeliet190901';
load([basename '.basicMetaData.mat'])
fprintf('\n%s start %s with data of %s\n',datestr(now),mfilename,basicMe... |
066abf5955e239fa1352e4416a04859ec345fcf24b34f92d21e1450c9a677d94 | MATLAB | 6,382 | 208 | function [p,F] = CircularANOVA(angles,factors,method)
%CircularANOVA - One or two-way ANOVA on circular data.
%
% Circular ANOVA can be performed using one of three methods with different
% assumptions and limitations:
%
% 1) Watson & Williams (1956)
% The data are drawn from von Mises distributions with ... |
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