sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
99c3c16d7facf6528c0cfe2762fc22ccc08dac5be2a77217e14e8f880e108eec | MATLAB | 3,088 | 77 | % run the inputmapping to get handles
function SelectfeatureForVisual(handles)
figure(1), clf('reset')
hold on
%%%% display rois and traces
if ~isempty(handles.im_norm)
%%%% show spine rois
handles = get_spineROImask(handles);
roi_mask = handles.roi_mask;
% roi_mask = zeros(size(handles.roi_mask));
... |
e5fb98230225e52c729ade3e3b403dca9510c49f9450b44c418c0ea873413ad0 | MATLAB | 3,091 | 98 | classdef ( Hidden, Sealed ) FigureObserver < handle
%uix.FigureObserver Figure observer
%
% A figure observer raises an event FigureChanged when the figure
% ancestor of a subject changes.
% Copyright 2014-2015 The MathWorks, Inc.
% $Revision: 1435 $ $Date: 2016-11-17 17:50:34 +0000 (T... |
7e10c9eeeae0c7ca60866abe4fea7b14d627297e3cac2bbd17b5b687a6f9a8ee | MATLAB | 3,092 | 71 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
c9fdbe989017dea6ea7841c29b7e670e2800a97831b3cc8298fb52388f9d28ff | MATLAB | 3,092 | 97 | %% Add all folders to path
addpath(genpath(pwd));
%% Load raw data
data = data_WT_raw(); % or data_IFNAGRKO_raw()
k = 1000; % scaling factor
alpha = 0.01; % filtering parameter
%% Process all NSC counts and fractions
proc = process_NSC_frac_data(data, k, alpha);
%% Define scenari... |
d7074605e3a37f6aece2b8ee861b06ed9f3d0465a1527dfe9ca5ac0f59306ade | MATLAB | 3,092 | 63 | function info = getinfo(vr)
%INFO=GETINFO(VR)
% Returns a structure whose fields contain information about the opened
% video object. The (minimum) set of fields in the INFO structure is
% shown below:
% url String specifying the data source, in the format preferred
% by the plugin being use... |
2c97c2bf255cafb37e07e54c586797c818292d0d1d7686406fd8892472627e39 | MATLAB | 3,093 | 98 | function PlotShortTimeCCG(data,varargin)
%PlotShortTimeCCG - Plot time-varying auto/cross-correlograms of point processes.
%
% USAGE
%
% PlotShortTimeCCG(data,<options1>,<options2>)
%
% data data obtained using <a href="matlab:help ShortTimeCCG">ShortTimeCCG</a>
% <options1> optional list of pr... |
d064c87b38f519a4ff712cc2aa274c738607d44251419d76dc0db3469cc8806e | MATLAB | 3,095 | 90 | % data = Doric.load(filename)
% Load Doric's hdf5 datafiles (.doric) using typical dataset locations
% corresponding to time, and demodulated signals 1 and 2.
%
% datasets = {'01-LockIn/Time', '01-LockIn/Values', '02-LockIn/Values'};
% data = Doric.load(filename, datasets)
% Same as before but provide the name o... |
5e615b1ad299296cfa6cf62e862bda25c8f50c4974310d7ab9378e118fba90ac | MATLAB | 3,097 | 90 | function l = IsExtremum(samples,varargin)
%IsExtremum - Identify local maxima or minima.
%
% Find the maxima (resp. minima) in a signal by smoothing the signal and then
% finding the points where the derivative goes from positive to negative (resp.
% from negative to positive).
%
% USAGE
%
% status = IsExtremum(sa... |
b1a538197212b59550709624d329154c3a1e6175a871c51ed0bfb3064109c74d | MATLAB | 3,099 | 90 | %%***************************************************************************
%% sqlpu2lblk: decide whether to convert ublk to lblk
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 10 Jul 2007
%%*********************************************************************... |
2acde59d5420367bc584befb3a237c88960164b740117275a4cca342292b215e | MATLAB | 3,101 | 86 | % mtimesx_sparse does sparse matrix multiply of two inputs
%******************************************************************************
%
% MATLAB (R) is a trademark of The Mathworks (R) Corporation
%
% Function: mtimesx_sparse
% Filename: mtimesx_sparse.m
% Programmer: James Tursa
% Version: ... |
aa8a2afadc6e31039ef2bd172c5498077527d2b3a2cd7b6ce03cf45be6d699af | MATLAB | 3,101 | 75 | function postprocess_write_file_for_trajectories(filename_prefix,traj,traj_high,...
traj_low,traj_time,taxa_names,o_write_original_data, concentrations, c_times)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome ti... |
e6bea04164598eb39dcceebb6400366d1ccd8164b5d424513636c4f9bcccb435 | MATLAB | 3,101 | 106 | function X = make_design(time, Fs, stimvec, acc_reg, extra_regs, varargin)
%MAKE_DESIGN Build GLM design matrix consistent with the main pipeline.
% X = glmproc.make_design(time, Fs, stimvec, acc_reg, extra_regs, ...)
%
% Positional inputs:
% time : T×1 (seconds). Pass [] to auto-construct from Fs.
% ... |
d0061beedb42fa3d150701830e9ce6e684437e6939b9e746afda411eaa4b1888 | MATLAB | 3,102 | 82 | function [dist] = warp_error(M, input, target, varargin);
% WARP_ERROR computes the mean distance after linear or non-linear warping
% and can be used as the goalfunction in a 3D warping minimalisation
%
% Use as
% [dist] = warp_error(M, input, target, 'method')
%
% It returns the mean Euclidian distance (residu) wh... |
ae4f6707fd08c334f052830d955360accb7210d15a6f5db75a7fd7475eb1efdc | MATLAB | 3,103 | 80 | %% Recording algorithm behavior with MatlabBGL
% In this example, we will write a simple visitor that outputs an
% algorithm's behavior. The algorithm we will examine is dijkstra_sp. To
% examine the runtime behavior we will use a visitor which outputs a string
% every time a function is called.
%% Setup
% ... |
42fd4b71e75c37e0c85647d1e130c00553e26f7e8150976663bb200fd1dec31d | MATLAB | 3,105 | 86 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
89e4493fad50a236e7657e41a5b7b32c38ec26ec263159623eba909007861614 | MATLAB | 3,105 | 71 | function ubj=saveubjson(rootname,obj,varargin)
%
% ubj=saveubjson(obj)
% or
% ubj=saveubjson(rootname,obj,filename)
% ubj=saveubjson(rootname,obj,opt)
% ubj=saveubjson(rootname,obj,'param1',value1,'param2',value2,...)
%
% Convert a MATLAB object (cell, struct, array, table, map, handles ...)
% into a Universal Bin... |
09fedc6f48d3aa7208a78f116e4eec976d0e062a76ce086201780bb69e07ba9d | MATLAB | 3,107 | 97 | % ttest_cell() - compute paired t-test. Allow fast computation of
% multiple t-test using matrix manipulation.
%
% Usage:
% >> [F df] = ttest_cell( { a b } );
% >> [F df] = ttest_cell(a, b);
%
% Inputs:
% a,b = data consisting of PAIRED arrays to be compared. The last
% dime... |
179d7a691831417c4c08206cf3efaf91053b534e18e7c24475e3f827ea1074ed | MATLAB | 3,108 | 73 | function ApparentPositionVector = SOFAcalculateAPV(Obj)
%SOFAcalculateAPV
% APV = SOFAcalculateAPV(Obj) calculates the apparent position vector
% (APV) which represents the position of the source relative to the
% listener's position and view. APV is in the format [azi ele radius]
% with units [deg deg m]... |
4155e853915ea51e0f763b065e57d93178bf0e4d473b2e1045fb6b7890d6b803 | MATLAB | 3,109 | 101 | function importCellMaskOO(processOrMovieData,varargin)
%importCellMask imports a previously-defined cell mask to movieData
%
%Khuloud Jaqaman, March 2015
%
% Copyright (C) 2021, Jaqaman Lab - UTSouthwestern
%
% This file is part of conditionalColoc.
%
% conditionalColoc is free software: you can redistribute it and/o... |
83e919fd48d164d26516816215eb56bb0005259c40a8444f7bbd973636c20b96 | MATLAB | 3,109 | 61 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
f05302fdf0229f1de6dbcc0a0607d6e2bbbb0d2190708740afac762054158d6c | MATLAB | 3,110 | 76 | function [C, lags] = pxcorr(x, varargin)
%PXCORR Efficient cross-correlation for point process data.
% C = PXCORR(A,B,Fs) returns the cross-correlation between A and B at
% sampling rate Fs for the point process whose times are given in the
% length N(>1) vector A and the length M (>1) vector B. C wil... |
0f15ca8be89d25280783f89be5d0d797c93da8c544383118d7f7bf9dadc325da | MATLAB | 3,112 | 122 | function AUC = bootstrapOOB_PLSDA(X, Y, C, opts)
% bootstrapOOB_PLSDA Out-of-bag bootstrap AUC for one resample.
%
% AUC = bootstrapOOB_PLSDA(X, Y, C, opts)
%
% Draws one bootstrap sample of subjects WITH replacement, trains on it, and
% evaluates on the out-of-bag subjects. Repeated by the caller nBoot times to... |
f10861b1d631d3ec5e3c307c84d12abfae872d24676f3bdc584dbf6441a8d0b6 | MATLAB | 3,112 | 77 | function ea_plot_fiber_state(varargin)
% example
% ea_plot_fiber_state('/home/forel/Documents/data/TWEEDMiniset/derivatives/leaddbs/sub-TWEED02/stimulations/MNI152NLin2009bAsym/tst/subthalamopallidal/PAM/sub-TWEED02_sim-fiberActivation_model-ossdbs_hemi-R_tract-gpe2stn_ass_right.mat')
fiberActivationProb... |
0b446a4ae44477293f7a3ade6daf86b430ba97e721a89840e0c782628546a564 | MATLAB | 3,113 | 118 | function [pval, k, K] = circ_kuipertest(alpha1, alpha2, res, vis_on)
% [pval, k, K] = circ_kuipertest(sample1, sample2, res, vis_on)
%
% The Kuiper two-sample test tests whether the two samples differ
% significantly.The difference can be in any property, such as mean
% location and dispersion. It is a circula... |
de913004cf0b7847cf3043d344502be8b376a23f10344375b2517874c9c6864b | MATLAB | 3,114 | 102 | function H=subindex_extended(method, side)
%SUBINDEX Label subplots with an index (e.g. a,b,c)
% SUBINDEX labels subplots in the current figure with an index in
% the top left corner.
%
% SUBINDEX(METHOD) labels subplots with an index defined by METHOD.
% Options are:
% METHOD = 'letter' : a, b, c, etc. (defa... |
83544f74e7279bdcda5e60817db41ea8b8e628c85321b94b6cbf58313a90c203 | MATLAB | 3,115 | 74 | function ea_postprocess_multisource_axonstates(axonStateFolder,options,settings)
% Merge multisource axon states using logical disjunction.
% IMPORTANT:this is a special case for multisource prob. PAM
% By Butenko, konstantinmgtu@gmail.com
arguments
axonStateFolder % folder where axons states across samples a... |
c1dfb535f90f9f104a85da7504f98ebdb046cf2df2ed97a26977109383ac3f02 | MATLAB | 3,115 | 74 | function CBIG_MMLDA_brain_to_zscore_create_refpara(vol4D_bl, mask, ind_CN_bl_brain, regressor_bl_brain, zscore_method, output)
% CBIG_MMLDA_brain_to_zscore_create_refpara(vol4D_bl, mask, ind_CN_bl_brain, regressor_bl_brain, zscore_method, output)
%
% Create a mat file which contains reference parameters for CBIG_MMLDA_... |
fd4c2a4ef13ffe6047b707145c1a90c5bbef814a6a3071576f3ede58e6178f43 | MATLAB | 3,115 | 62 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modific... |
27ef62ad59829232afe47bb4f39031a1b185a85214977598a13a2f52f5a58820 | MATLAB | 3,116 | 117 | %% NAVIGATE TO `IMAGING METADATA` FOLDER
clear
alldates = {'250909','250911','250916','250917','250919'};
% alldates = {'250929','250930'};
% alldates = {'251017','251020'};
cd(alldates{5})
%%
listing = dir('f1*');
%%
alldata.expID = [];
alldata.expdate = [];
alldata.trial = [];
alldata.leftstacks = [];... |
a4662184215478253217dddb44fe7d2d1eabffc1734ce1149d63bc80a6602412 | MATLAB | 3,116 | 100 | % Name: Robert Kim
% Date: 05-10-2026
% export_instr_lesion_results_to_excel.m
% Description: Export one-layer instruction lesion-result .mat files into a
% single Excel workbook with one sheet per lesion file. Each sheet contains
% three columns:
% 1) trained model filename
% 2) anti performance
% 3) pro perform... |
fee81fc8fcaa0b0031fd09a66bfe34e6d6fc2f7094bad95696ce5310d09b980c | MATLAB | 3,117 | 110 | function [x, V, VV, loglik] = kalman_filter(y, A, C, Q, R, init_x, init_V, varargin)
% Kalman filter.
% [x, V, VV, loglik] = kalman_filter(y, A, C, Q, R, init_x, init_V, ...)
%
% INPUTS:
% y(:,t) - the observation at time t
% A - the system matrix
% C - the observation matrix
% Q - the system covariance
% R - the o... |
ac678c41ddec165435ce9c84cfd1f95b28c47f9ee2bb4944ac7d447df5fee557 | MATLAB | 3,118 | 91 | % eeg_point2lat() - convert latency in data points to latency in ms relative
% to the time locking. Used in eeglab().
% Usage:
% >> [newlat ] = eeg_point2lat( lat_array, [], srate);
% >> [newlat ] = eeg_point2lat( lat_array, epoch_array,...
% srate, timelimi... |
00fc19124c48a78e89a3ec48ad654696a17376bbc297f80c052d9315be3128da | MATLAB | 3,120 | 37 | function SANDIinput = InitializeSANDIinput(ProjectMainFolder, Delta, smalldelta, SNR)
SANDIinput = struct; % Initialize the variable containing all the SANDI analysis info
%%%%%%%%%%%%%%%%%%%%%%%%%%% USER DEFINED INFO %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
SANDIinput.StudyMainFolder = ProjectMainFolder; % <---- USER DE... |
25bec72b929a04f6808d2814f609258c76725e8b573c3c02dc33655d2534b19a | MATLAB | 3,122 | 116 | % Figures 6.21-6.23: Basis pursuit using Gabor functions
% Section 6.5.4
% Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Argyris Zymnis - 11/27/2005
%
% Here we find a sparse basis for a signal y out of
% a set of Gabor functions. We do this by solving
% minimize... |
3c75abc33389e0c29d1362e8dae3f7ff58d4ce62aeb9d58714bbd91c11c27c2b | MATLAB | 3,122 | 117 | function browsePETHs(peths, grid, tPts)
% browsePETHs - GUI for paging through batches of PETH plots
%
% Usage:
% browsePETHs(peths, [rows, cols])
if nargin < 2
grid = [5, 8]; % default grid if not specified
end
batchSize = prod(grid);
nPeths = length(peths);
nPages = ceil(nPeths / b... |
6cd80e3a9d299798ec3d68e09e1b8bbb60eb32a319231f60fb388e88f298ad4c | MATLAB | 3,122 | 95 | % std_uniformfiles() - Check uniform channel distribution accross data files
%
% Usage:
% >> boolval = std_uniformfiles(STUDY, ALLEEG);
%
% Inputs:
% STUDY - EEGLAB STUDY
%
% Outputs:
% boolval - [-1|0|1] 0 if non uniform, 1 if uniform, -1 if error
%
% Authors: Arnaud Delorme, SCCN/UCSD, CERCO/CN... |
a59bf43a26e4ca6c8650a6b4fe65f308e5b378b257939b9f15d2b76b3d750e7f | MATLAB | 3,122 | 79 | function ea_postprocess_multisource_pam(options,settings,side)
% Merge multisource PAMs using logical disjunction.
% IMPORTANT:fiberActivations here have the same pre-filtering with
% Phi_vector_max. That is why they contain the same fibers and can be
% merged directly
% By Butenko, konstantinmgtu@gmail.com
arguments... |
4a1e50737a31bc82960a20eaf998ceb9c33dee8f7d3de539bd463cd174c6b8c0 | MATLAB | 3,125 | 99 | % compute empirical p-vals under the null hypothesis that observed samples
% come from a given surrogate distribution. P-values for Type I error in
% rejecting the null hypothesis are obtained by finding the proportion of
% samples in the distribution that
% (a) are larger than the observed sample (one-sided test)
% (b... |
d696920d8ba1e7a47d13661f650beef391d2b80f2fb2ec65e72f3867819534f2 | MATLAB | 3,126 | 86 | function smoothed = smooth3f(data, filt, sz, arg)
%SMOOTH3F Smooth 3D data (fast version).
% W = SMOOTH3F(V) smoothes input data V with a Gaussian kernel. The
% smoothed data is returned in W.
%
% W = SMOOTH3F(V, 'filter') Filter can be 'gaussian' or 'box' (default)
% and determines the convolution... |
c8bb98e2bc9d888aaf0c9e0c8e6a76c2de3d9d86744e4a34d2d34ec5fd9619b4 | MATLAB | 3,127 | 87 | function [scalingFactor_uV, channelMapImro, probeType] = readSpikeGLXMetaFile(param)
% JF
% read spikeGLX meta file and calculate scaling factor value to convert raw data to
% microvolts
% ------
% Inputs
% ------
% metaFile: string, full path to meta file (should be a structure.oebin file)
% ------
% Outputs
% ------
... |
f767b55e03971574e5bc895690d1a492d85dc7bb3a037f6be1bba611eb3556e4 | MATLAB | 3,127 | 102 | function cdata = loadIcon( filename, bgcol )
%loadIcon Load an icon and set the transparent color
%
% cdata = uix.loadIcon(filename) loads the icon from the specified
% filename. For PNG files with transparency, the transparent pixels are
% set to NaN. For other files, pixels that are pure green are set to
% ... |
09b426d1bc51322c64e0b30ffe084a002362fe7455da6f837a3d0480610db670 | MATLAB | 3,128 | 76 | function [weights, anglebins] = anglehist(Z, bins)
%ANGLEHIST Magnitude-weighted angle histogram of polar data.
% WEIGHTS = ANGLEHIST(Z) histograms the angles of complex data Z into 10
% equally spaced bins around 2*pi, with each element in Z contributing
% an amount equal to its magnitude to its correspo... |
34876f5fc099207d0734e887f1cfe9c481fa77650678106c015b6b63534ee8c6 | MATLAB | 3,128 | 90 | function ClincFreq_D2V(INDIR,OutD2Vdir,voxelsize,Ventricledir,Ventriclematdir)
[Vven,Dven] = Dynamic_read_dir_NIFTI(Ventricledir);
[V,D,namelist] = Dynamic_read_dir_NIFTI_sparse(INDIR);
D(isnan(D)) = 0;
D(isinf(D)) = 0;
D = D>0;
load(Ventriclematdir);
Dvens = reshape(Dven,Vven.dim);
for i = 1:size(ROItab,1)
indexs ... |
0809205c135538b47ac556b3d740dfd4cfd919d79793a21872699ba4522ecb02 | MATLAB | 3,130 | 75 | function [node,elem,face,regions]=vol2mesh(img,ix,iy,iz,opt,maxvol,dofix,method,isovalues)
%
% [node,elem,face,regions]=vol2mesh(img,ix,iy,iz,opt,maxvol,dofix,method,isovalues)
%
% convert a binary (or multi-valued) volume to tetrahedral mesh
%
% author: Qianqian Fang (fangq <at> nmr.mgh.harvard.edu)
%
% input:
% img:... |
4e86d0f7bccadbbb7660949f674832b376d01e7675149383a4d01059d1dbc7d3 | MATLAB | 3,130 | 97 | function data = AFOFdata_struct10(inputdata, filenames)
% USE THIS FOR EXP1+5 (CEM)
% how it works:
% fly = AFOFdata_struct(data,filenames) where data and filenames are
% outputs from rotoball_importer()
for e = 1:length(inputdata)
for t = 1:size(inputdata{e}{1},1)
trial.filename = filenames{e};
... |
88df462d85570514066a535fff6d18b83222f2e077c5050b31d833598f8b1537 | MATLAB | 3,130 | 97 | function [strmodelshading, strfaces_colors, strfaceshading, strcolors,...
nface_vertex_data_unique] = mesh_diffuse_colors(faces, points, face_vertex_data)
% File: mesh_diffuse_colors.m
% Author: Ioannis Filippidis, jfilippidis@gmail.com
% Date: 2012.06.10- 2012.06.24
% Language: MATLAB R201... |
b6071c071fcd56ae5a53e9aa4ffb2a21a3823f9d39a102eaed5849f25682408b | MATLAB | 3,132 | 77 | function []=v2structDemo2()
% V2STRUCTDEMO2 is a usage example demo function for the function V2STRUCT. This demo
% shows a suggestion for how to use v2struct in managing input to other functions with
% improved usability.
%
%% Last update:
% 30.06.2011, Adi N.
fprintf(['Running usage demo function for vs2truct ... |
24ff4350ba4d4821882b823bc82a8016b6916a44caa8266a6f18e286425fff2d | MATLAB | 3,133 | 91 | % questdlg2() - questdlg function clone with coloring and help for
% eeglab().
%
% Usage: same as questdlg()
%
% Warning:
% Case of button text and result might be changed by the function
%
% Author: Arnaud Delorme, CNL / Salk Institute, La Jolla, 11 August 2002
%
% See also: inputdlg2(), errordlg2(), s... |
8576906c1d67f0014567069773b2f86985c315e3b72aa0e9c35cba3aa59d5636 | MATLAB | 3,135 | 80 | function options = ea_prepare_dti_bids(options)
% Copy DWI files from BIDS rawdata to derivatives with BIDS-compliant names
directory = [options.root, options.patientname, filesep];
% Create preprocessing/dwi directory if needed
derivDwiDir = fullfile(directory, 'preprocessing', 'dwi');
if ~isfolder(derivDwiDir)
... |
e610aa59778df5208b94067d6366e6df0610832654b9b5c65c68f3a01ac2abaa | MATLAB | 3,136 | 103 | function data = balldata_struct(inputdata, filenames)
% how it works:
% fly = balldata_struct(data,filenames) where data and filenames are
% outputs from rotoball_importer()
for t = 1:length(inputdata{1})
trial.filename = filenames{1}{t};
trial.fps = round(1/mean(diff(inputdata{1}{t}(:,1))));
trial.wind_s... |
0493b9fd78b54b5fef92c901b7b6c6c7250f00e9970259b6250ace20cb507c7a | MATLAB | 3,138 | 77 | %% a2_plot_TF
% Plot time frequency
% C. baratin, J. bastin, G. Becq 20260603
rois = ["PFCvm", "aIns"];
for iroi = 1: 2
plot_roi(rois(iroi))
end
function plot_roi(roi)
T1 = readtable(roi + "_h.csv");
T2 = readtable(roi + "_TF.csv");
T3 = readtable(roi + "_p.csv");
temp = table2arra... |
0d9bb709fdc9ea4d09972d16d9fd50422c473debdc549c8fe67e5c08ae2a9522 | MATLAB | 3,139 | 70 | function [proportionImg, imgMask, xBounds, yBounds] = makeProportionMap(binaryVals, valPositions, gridRes, xLimits, yLimits, smoothSD)
% Computes a binned and smoothed image of bin proportions for
% spatial location data with binary memberships
%
% This function bins the ROI cell positions, computes the ratio of
% logi... |
75958a864a1498eca313b12e4ad7ccb60155ecb50f36149e75ba4c4997f2d105 | MATLAB | 3,143 | 86 | function [VD,error] = LCN_LOGAN(MIDSCANTIMES,C_MEASURED,CA_TIMES,CA,logan_start_time,figure_nr)
% LCN_LOGAN.m
%
% calculates the slope of the Logan plot. The slope is the distribution
% volume VD
%
% FORMAT [VD,error] = LCN_LOGAN(MIDSCANTIMES,C_MEASURED,CA_TIMES,CA,logan_start_time);
%
% INPUT VARIABLES
%-------------... |
a6950cce605b7ce3452f15b1f897d86cc8b1e4d959d261e3388116ad5dbdd5fb | MATLAB | 3,143 | 96 | function varargout = ea_explorer_stats_2sampleweightedlinreg(varargin)
% Function to estimate a certain mass univariate test (see below) as used
% in explorer apps.
% - Expects valsin as V x N matrix where
% V is the number of
% voxels/streamlines... |
f3a75561cb325d913c1cfc9b820565f37debb13ccdfcf901f4f2348d7b300732 | MATLAB | 3,145 | 97 | % pop_firpmord() - Estimate Parks-McClellan filter order and weights
%
% Usage:
% >> [m, wtpass, wtstop] = pop_firpmord(f, a); % pop-up window mode
% >> [m, wtpass, wtstop] = pop_firpmord(f, a, dev);
% >> [m, wtpass, wtstop] = pop_firpmord(f, a, dev, fs);
%
% Inputs:
% f - vector frequency band edges
% ... |
0f284f51d94a61ee2e76bf6354117a340dcd3c9bad79246f9dde2e5ce090d7da | MATLAB | 3,149 | 51 | %-----------------------------------------------------------------------
% Job saved on 11-Apr-2016 11:51:36 by cfg_util (rev $Rev: 6460 $)
% spm SPM - SPM12 (6470)
% Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
%-------------------------------------------... |
b66c8ceb57d6bcad12a36a5aad6d1480df3d39a295aabb78ae53f30b876e7223 | MATLAB | 3,149 | 51 | %-----------------------------------------------------------------------
% Job saved on 22-Apr-2016 17:56:02 by cfg_util (rev $Rev: 6460 $)
% spm SPM - SPM12 (6470)
% Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
%-------------------------------------------... |
a71c30b1e12a13160c00bfb8418a04248908638e685ec909a428b89196b1d121 | MATLAB | 3,150 | 66 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
41c8e8c39edf3d2608661f512f3533270a99940741ded2117d690544acd89da5 | MATLAB | 3,151 | 100 | % strmultiline() - format a long string as a multi-line string.
%
% Usage:
% >> strout = strmultiline( strin, maxlen, delimiter);
%
% Inputs:
% strin - one-line or several-line string
% maxlen - maximum line length
% delimiter - enter 10 here to separate lines with character 10. Default is
% ... |
df119dfcd2011b37c0fdf2e8940f712aceebf49228dc438ce79fd64186bbfc69 | MATLAB | 3,151 | 109 | function varargout = palm_lowrank(varargin)
% Do various tasks related to lowrank matrix completion.
%
% Usage:
% U = palm_lowrank(G)
% [Grec,mom] = palm_lowrank(G,U,nsel)
% Grec = palm_lowrank(G,U,ysel)
%
% _____________________________________
% Anderson M. Winkler
% FMRIB / University of Oxford
% May/... |
6267f0d582337fa82eaf3abfc9ce35e4f477bbce0a9298857586eba0b4b5fbca | MATLAB | 3,153 | 58 | function [corr_lasso,corr_select,corr_L2,rms_lasso,rms_select,rms_L2] = computeCdiffTrialTrajectories(T,trials,data_counts,BMD,intervene_matrix,intervene_matrix_filtered_merge,keep_species,experimentBlocks)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers ... |
a44237f951e50419d4e66987ea18c9d795f4a715f6fa51aa6c3dee07c864df1a | MATLAB | 3,154 | 77 | %% Step 2 Tiny Dancers: Epoching and artefact rejection
clear all
clc
addpath 'C:\Users\tnguyen\OneDrive - Fondazione Istituto Italiano Tecnologia\Documenti\MATLAB\functions'
addpath 'D:\MUSICOM_EEG/onsets'
addpath('D:\MUSICOM_EEG/EEG/')
addpath('C:/Users/tnguyen/OneDrive - Fondazione Istituto Italiano Tecnolog... |
adf43f558723383d2ab8a8e7b2ed8aaed7aa93c100cc52fd656e47d2b9253cdd | MATLAB | 3,154 | 77 | function ea_gentargetreport(M)
thresh = inputdlg('Please enter threshold in mm:','Enter threshold...',1,{'0.5'});
if isempty(thresh)
return
end
thresh=str2double(thresh{1});
conInd = arrayfun(@num2str, 1:max(M.S.numContacts), 'Uni', 0);
rnames = [strcat('k', conInd, 'R'), strcat('k', conInd, 'L')];
for thr=0:1
... |
a3edd3fd8dcc0c1af3fae02949fe63b2a8edab2939b394dd17d61fc3f817a3f4 | MATLAB | 3,155 | 63 | function info = getinfo(vr)
%INFO=GETINFO(VR)
% Returns a structure whose fields contain information about the opened
% video object. The (minimum) set of fields in the INFO structure is
% shown below:
% url String specifying the data source, in the format preferred
% by the plugin bei... |
b5678ffaa3ef79ab801dcb8a0505f7404dcb69f8caeb7353fecc914f4af1d324 | MATLAB | 3,155 | 94 | function [P, beta] = d2p(D, u, tol)
%D2P Identifies appropriate sigma's to get kk NNs up to some tolerance
%
% [P, beta] = d2p(D, kk, tol)
%
% Identifies the required precision (= 1 / variance^2) to obtain a Gaussian
% kernel with a certain uncertainty for every datapoint. The desired
% uncertainty can be specified... |
9a15a8eb69444e49a69d43855bdf8a17c99bfbe4b359df3ea91100ee449a9bff | MATLAB | 3,156 | 88 | % std_selcomp() - Helper function for std_erpplot(), std_specplot()
% and std_erspplot() to select specific
% components prior to plotting.
% Usage:
% >> std_selcomp( STUDY, data, cluster, setinds, compinds, comps)
%
% Inputs:
% STUDY - EEGLAB STUDY structure.
% data -... |
e7ea9fe7c840dd07c0b0e58a3c8b7704c1ba5edd3ea5bb5084655a3e62455914 | MATLAB | 3,157 | 107 | function [baseline, pVals] = CBIG_ASDf_hypoTest(betas, stats, numReg, k)
% [baseline, pVals] = CBIG_ASDf_hypoTest(betas, stats, numReg, k)
%
% This function performs hypothesis test for GLM for two-, three- and
% four-factor estimates.
%
% Input:
% - betas:
% betas output from MATLAB glmfit.m function
%... |
9f9baadc308013330edd8d5b8d2da2e0193aeadffef9a17e88e242ad278b8882 | MATLAB | 3,159 | 74 | % eeglab_error() - generate an eeglab error.
%
% Usage: >> eeglab_error;
%
% Inputs: none, simply capture the last error generated.
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, 2006-
%
% see also: eeglab()
% Copyright (C) 2006 Arnaud Delorme, Salk Institute, arno@salk.edu
%
% This program is free software; you can re... |
bef97e58fca6ddf9b407642b8752157d539d8f04efff4f9ec5ede7256fca00bd | MATLAB | 3,159 | 80 | function yi = interp1qr(x,y,xi)
%% Quicker 1D linear interpolation
% Performs 1D linear interpolation of 'xi' points using 'x' and 'y',
% resulting in 'yi', following the formula yi = y1 + (y2-y1)/(x2-x1)*(xi-x1).
% Returns NaN for values of 'xi' out of range of 'x', and when 'xi' is NaN.
%
% 'x' is column vecto... |
569b3b5f8473b311f0e4e350eee03359295e47e5bb168f532babb091be8eabf6 | MATLAB | 3,161 | 129 | function sm_data = G_Smooth( data, dim, N, method)
% Smooth along any dimension for N-d matrix
%
% Usage
% data = G_SmoothD( data, dim, N);
% data = G_SmoothD( vector, [], N);
% data = G_SmoothD( data, dim, N, method);
%
% Input
% data, N-d matrix, If data is a vector, the dim will omitted.
% dim, alon... |
60202f8f58d5d966545f38d0fd407588a65b65e604d108ab352f7fa6b04c5f68 | MATLAB | 3,164 | 108 | function [ch] = getchannels_drift(animal, shank, set)
%Get channel-brain region assignments depending on time period of recording - this is
%done to help account for drift
%Inputs = animal ID string, shank number (1-8), set
%Other files needed within Matlab file path - 3 mat files with different sets of chan... |
6c83353ce31263238f6641588ae806885771c56ce53d216dd93180ea6e23997b | MATLAB | 3,166 | 131 | function [nz, nan_count, off_set] = determine_rois_with_minimumNZ(CN_a2, bl_dir, n, Sa, t_result_dir)
% Author: Betty Tijms 19.01.11
%% Extract the regions of interest according to 'template' bl_ind.
% CN_a2 - list of the directories of the bl_ind --> the bl_ind with different off_sets
% n - the dimensions of the cube... |
23e1643f8fa584ec645b450368fa5381108b0de1cd199a4e02ee760aecef8800 | MATLAB | 3,169 | 87 | % erpregout() - regress out the ERP from the data
%
% Usage:
% newdata = erpregout(data);
% [newdata erp factors] = erpregout(data, tlim, reglim);
%
% Inputs:
% data - [float] 2-D data (times x trials) or 3-D data
% (channels x times x trials).
%
% Optional inputs:
% tlim - [min max... |
6e12e936f928d0653c1012f33bc3fab057f1e025d0f669808d22c370e8a5c108 | MATLAB | 3,169 | 89 | % floatwrite() - Write data matrix to float file.
%
% Usage: >> floatwrite(data,filename, 'format')
%
% Inputs:
% data - write matrix data to specified file as four-byte floating point numbers.
% filename - name of the file
% 'format' - The option FORMAT argument specifies the storage format as
% ... |
0e72b53a7bf846f9a6864a57fd6f25bf9476dc4e301ba55a9cb7f98f0fe251e1 | MATLAB | 3,170 | 72 | function Obj=SOFAconvertTUBerlinBRIR2SOFA(irs)
% OBJ=SOFAconvertTUBerlin2SOFA(irs) converts the HRTFs described in irs
% (see TU-Berlin HRTF format) to a SOFA object, using the MultiSpeakerBRIR
% Convention.
%
% SOFA API - demo script
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of ... |
07964b38ca7207169d0cb44ce00d0fb6a40b0d68d4460ecd6fb48fa91935cd7f | MATLAB | 3,172 | 61 | function checkAndConvertRawWaveforms(savePath, spikeTemplates, spikeClusters)
rawWaveformFolderNew = dir(fullfile(savePath, 'templates._bc_rawWaveforms_kilosort_format.npy'));
rawWaveformFolderOld = dir(fullfile(savePath, 'templates._bc_rawWaveforms.npy'));
% Check if need to convert to new format. old format was alw... |
6525cf718bec769f29d6b6f9260a46e876e3139ace0e6586aca38ac5768e5016 | MATLAB | 3,172 | 92 | % eeglab
%foldername = 'C:\Users\yh19218\OneDrive - University of Essex\PG Research\3_Data\Rename';%For Windows
foldername = '/Users/yiyuan/OneDrive - University of Essex/PG Research/3_Data/Rename';%For MacOS
fileDetail = dir(foldername);
filename = {};
% Read al file names conteined in the targeted folder
for r = 3:si... |
fb94b18040ee83dd87069211b2d4a2f93fccee32c968a82abd0056150d647fa0 | MATLAB | 3,172 | 92 | function plotgraph(A,xy,weights)
% Plots a graph with each edge width proportional to its weight.
%
% Edges with positive weights are drawn in blue; negative weights in red.
%
% Input parameters:
% A --- incidence matrix of the graph (size is n x m)
% (n is the number of nodes and m is the number of e... |
1808fbc849fded0163b2c0bf68324d49301d9f593b30d29afff61951b4da6f63 | MATLAB | 3,174 | 87 | % Construct spherical harmonics basis matrix at specified points.
%
% SYNTAX: [basis] = construct_SH_basis(degree, sphere_points, dl, real_or_complex);
%
% INPUTS:
%
% degree - maximum degree of spherical harmonics;
% sphere_points - n sample points on sphere; [nx3]
% dl ... |
9c1af197b1bb405f027608422a49df060a3fa2a0cd0c17fcca0ccb67c92c701c | MATLAB | 3,176 | 136 | function dacq_posSwitch(fname)
%[root.scaleFactor, root.ts, root.x, root.y, root.headdir, root.epoch] =
%dacq_pos(dataPath,prefix)
%
% Finds video file with the prefix "prefix" in folder "dataPath", and
% returns relevant spatial information for a CMBobject
% Bill 2012.06.20
%file information
%file = strcat(prefix,'.... |
fad99ccdb6d8400d6dd4137e23b6d57a43d84d084a61d095f9e59ccea4721609 | MATLAB | 3,177 | 86 | function [node,elem]=meshcheckrepair(node,elem,opt,varargin)
%
% [node,elem]=meshcheckrepair(node,elem,opt)
%
% check and repair a surface mesh
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2008/10/10
%
% input/output:
% node: input/output, surface node list, dimension (nn,3)
% elem: input/output, su... |
21d21b82d5b4dd7ea028d722c454b5e33f68afc451f895a087fb0e2879988150 | MATLAB | 3,178 | 83 | function distance = Distance(positions,reference,varargin)
%Distance - Compute instantaneous distance to a reference point.
%
% USAGE
%
% distance = Distance(positions,reference,<options>)
%
% positions a list of position samples
% reference reference point (same coordinates as positions)
% <opt... |
9d609a8d8114c0e9943f54c5532a64e736325e69516e248d19bf800ac957908c | MATLAB | 3,178 | 114 | function CFAT
% clinic frequency analysis main function
% Version 1: fisrt build in 02 Dec. 2021
% Updata on 11 Mar. 2022
% Qiang Xu,
% Department of Radiology, Jinling hospital
% Medical School of Nanjing University
% fmrixuq@126.com
%%=========================================================================
% part ... |
9cc258c691898cc75e408544b8362303c93d13f2e80c32c16d1c5f5057c47ac1 | MATLAB | 3,181 | 84 | %%******************************************************************
%% dwd: distance weighted discrimination.
%%
%% [w,beta,residp,residn,totalviolation,X,y,Z] = ...
%% dwd(Ap,An,penalty);
%%
%% You're given two matrices, A+ and A-, whose columns
%% give points in R^n you want to separate "nicely" to allo... |
abf8cfe8803624046ce1ea322bda3c6d30241208b3bd9894446f0a4ed10ff6a7 | MATLAB | 3,182 | 105 | %% INVERSEFNOISE - generates 1/f^alpha noise
% Generates noise with 1/f^alpha spectral power density over a specified
% range of frequencies.
%
% Syntax: [noise] = inverseFNoise(n, alpha, Fs, varargin)
%
% Input:
% n (integer) - the number of desired data points in the sample.
% alpha (double) - the exponent of th... |
b5cfd9ebf3a5b573b9a845eb32b81ddf940042296542780526da17a7c78ec754 | MATLAB | 3,182 | 79 | % readneurodat() - read neuroscan location file (.dat)
%
% Usage:
% >> [ CHANLOCS labels theta theta ] = readneurodat( filename );
%
% Inputs:
% filename - file name or matlab cell array { names x_coord y_coord }
%
% Outputs:
% CHANLOCS - [structure] EEGLAB channel location data structure. See
% ... |
1863cbda1fab6549e9dba1333a030b61d5b391548c2047f5554abb7c83682c89 | MATLAB | 3,185 | 102 | % Digital circuit sizing
% Boyd, Kim, Vandenberghe, and Hassibi, "A Tutorial on Geometric Programming"
% Written for CVX by Almir Mutapcic 02/08/06
% (a figure is generated)
%
% Solves the problem of choosing gate scale factors x_i to give
% minimum ckt delay, subject to limits on the total area and power.
%
% minimi... |
4bac23b917cec7dbcf3c29579dc74d012a1208ae287dfabb66fd2686765dfcb6 | MATLAB | 3,185 | 93 | function ea_lg_exportstats(M, output)
if ischar(M)
if isfolder(M) % M is the group folder
load(ea_getGroupAnalysisFile(M), 'M');
elseif isfile(M) % M is the path of the lead group file
load(M, 'M');
end
end
if ~exist('output', 'var')
output = strrep(ea_getGroupAnalysisFile(M.root), '.m... |
751e1b324dae622a7e593c420d716a36add8c5e55e827809b84a5ae6f8e672d0 | MATLAB | 3,186 | 59 | function [data_out,trial_count] = Trinh_automaticartefactdetect(data_in, method, sliding, threshold, window, channels,reject_method)
%% function to automatically detect artefacts according to a sliding window approach
% can be used for range or standard deviation
% method is then either 'range' or 'stddev'
% slidi... |
f21b04b36c603818d4277dd30661d74858d88b8a0dc3724f9374245e3393b935 | MATLAB | 3,187 | 64 | function CBIG_ArealMSHBM_generate_ini_params_Schaefer(seed_mesh, targ_mesh, resolution, out_dir)
% CBIG_ArealMSHBM_generate_ini_params_Schaefer(seed_mesh, targ_mesh, resolution, out_dir)
%
% This script will generate initialization parameters which are initialized by Schaefer2018
% parcellations in a given surface sp... |
8b2e170ae27a3bfeb8d6fd79ba3f29728f47d7e8d5454f54dacbcd2a44ea9fab | MATLAB | 3,188 | 81 | function EXPORT_SUCCESS = prairieView_ExportCoordFile(coord_path, xyz_loc)
% SYNTAX: EXPORT_SUCCESS = prairieView_ExportCoordFile(coord_path, xyz_loc)
%
% METHOD: exports xyz coordinates to filesystem in format that can be
% loaded by prairie view.
%
% INPUT:
% coord_path [r, path]: string of full file path wh... |
be0c5f9e43fab5507c305c0299dbbf334526bcc83d76f60e40ad2386ce47efa8 | MATLAB | 3,188 | 87 | function str = mean2str(m,s,n,varargin)
%mean2str - Convert mean or median and SEM (or confidence interval) to string.
%
% USAGE
%
% s = mean2str(m,s,n,<options>)
%
% m mean or median
% s standard error (see <a href="matlab:help sem">sem</a> or <a href="matlab:help semedian">semedia... |
6b29f08d873f30ac2e780a84e262ef1ca685d908b75fa7476da3b29bd252c173 | MATLAB | 3,191 | 83 | function ea_get_native_Eproj(tractset,stim_ID)
% Comptute E-field metrics on fibers warped into native space.
% The results are stored as
% patient_folder/miscellaneous/connnectomeName/stim_ID/E_peak.mat (values for all fibers in the connectome!)
% By Butenko and Roediger, konstantinmgtu@gmail.com
arguments
tracts... |
c750478b947aca3945171763b2a3eb9d2378f01938a7821f4799445f11da4738 | MATLAB | 3,193 | 135 | function [adfreq, n, ts, fn, ad] = plx_ad(filename, ch)
% plx_ad(filename, channel): Read a/d data from a .plx file
%
% [adfreq, n, ts, fn, ad] = plx_ad(filename, ch)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% channel - 0 - based channel number
%
% a/d data come in fragments. Eac... |
f0284734077b9b8037ae7e63ce5d42ab2bbbf16ed7aa1e11517296cc3dd07ece | MATLAB | 3,194 | 78 | function labels = validateAtlasLabels(atlasData, p, caller)
% validateAtlasLabels Check that atlas label i really is feature i.
%
% labels = validateAtlasLabels(atlasData, p, caller)
%
% The three diagnostic plotters paint results into a NIfTI with
%
% for i = 1:p
% mask = atlasData == i;
% ... |
91c007c0f705c50f45c9db1625f59e921a5c4b3328fd1a39a87b5dd6b9cf36f1 | MATLAB | 3,195 | 105 | function compile(varargin)
%% History
% 2008-04-01: Added check for pre Matlab 2006b for non-large dim
% sparse matrices.
%%
debug = 0; if strmatch('-debug',varargin), debug=1; end
verbose = 0; if strmatch('-verbose',varargin), verbose=1; end
clear mex
mbglfiles = {'astar_search_mex.c', 'bfs_mex.c', 'd... |
f774d25ac7e6239185b267e924cbaa0e2843f1506363dced261830b9f1b29e8b | MATLAB | 3,195 | 85 | function Vout = LCN12_write_image(img,outputfilename,description,datatype,Vref)
% LCN12_write_image
%
% this script will read an image in matlab.
%
% syntax: Vout = LCN12_write_image(img,outputfilename,description,datatype,Vref)
%
% INPUT
% img = 3D or 4D matrix of an image
% outputfilename = name o... |
33a8889b9c9376cd015c318d27bf1e5a9dae4c5e59203e3657b910a207bba222 | MATLAB | 3,196 | 97 | function ref = ea_create_union_ref_nii(outPath, inFiles, voxSize)
% CREATE_UNION_REF_NII Build an empty reference NIfTI covering the union
% of multiple inputs, at a chosen voxel size.
%
% outPath : output .nii or .nii.gz for the reference
% inFiles : char or cellstr of input NIfTI paths
% voxSize : [vx vy vz] in mm (... |
ef4bd41a5bdc734e207e4b11d51cfba996701941c4f6d71b867e01fedee4c3d0 | MATLAB | 3,197 | 105 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
f8d1e95d43cda3a3672e4bd870911dbba895ffcfddd87962c80ddfc35e0311e8 | MATLAB | 3,197 | 88 | function [coef, X] = llsFitSH(dirs, y, order)
% Author: Jelle Veraart and Santiago Coelho (jelle.veraart@nyulangone.org)
% copyright NYU School of Medicine, 2022
%X = getSH(order, dirs, 0);
X = getSH(order, dirs);
coef = X\y;
end
% function Y = getSH (Lmax, dirs, CS_phase)
%
% % Ylm_n ... |
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