sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
56ddc4af4bf8bcb7d278742f7a94b273ab57eb7544da497fcc63c117030e204d | MATLAB | 7,451 | 191 | function [hx, hy, hz] = ft_plot_ortho(dat, varargin)
% FT_PLOT_ORTHO plots 3 orthographic cuts through a 3-D volume and interpolates if needed
%
% Use as
% ft_plot_ortho(dat, ...)
% or
% ft_plot_ortho(dat, mask, ...)
% where dat and mask are equal-sized 3-D arrays.
%
% Additional options should be specified in key... |
e0f10f99b4b911c3730b7af2b9ba74ccbd269d0de3f3f9230edf192abf3a3230 | MATLAB | 7,453 | 128 | %% 共空间模式 | common spatial patterns (CSP) 不可在main中调用，仅可单独使用
%% one vs rest Multiclass or two-classes 目标函数法
% how：N个类别得到N个投影矩阵，对每个投影矩阵取最佳的2m个方向（前后各m个），特征矩阵为2m*N维
% 优点：N类需要计算N个投影矩阵，即使N很大，计算量也不会很大
% 缺点：由于rest类别是混合类别，内部特征并不统一，因此很难找出最优的投影方向，即结果可能并不是最优的
% 注意：在计算CSP投影矩阵时，并非使用整个trial，而是将trial划分出若干segments，
% 对每个segments提取CS... |
bd2e8829c7d6a3c0ba971b0c63bea37b98fc071146854d3a4e8fb58c8b4e793d | MATLAB | 7,457 | 240 | function [Mean_MMT_Elbow_Wrist] = Muscle_Moment_G5(x)
% MATLAB code provided by Seyed Mohammad Ali Rahmati
% Affiliation: Biomechanics and Motor Control Lab, Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA.
% This script computes the maximum muscle moment averaged over the cycle as a fu... |
948f9a663f5f3bc789ae42c06b3665b1707f511d3baf3cde7d6673a130fa31ce | MATLAB | 7,458 | 291 | function draw_figure3ABC_S1C(p,decRes)
%
% This code is for drawing figure 3ABC and S1C
%
%
%% settings
compPairs = {'category','dimension'};
% roi parameters
hcpIdx = ~cellfun(@isempty,strfind(p.roiDescrip,'hcp180'));
subIdx = ismember(p.roiDescrip,{'thalamus','hyppocampus','hypothalamus','pallidum','brainstem','caud... |
c5edc88358f775e213e153c0f5cdb7971a7adf3cddf924cc2e516b2a2da1d4f5 | MATLAB | 7,458 | 191 | function [ReHoBrain_AllWindow, GHeader] = y_reho_Surf_Window(WindowSize, WindowStep, WindowType,InFile, NNeighbor, AMaskFilename, AResultFilename, SurfFile, IsNeedDetrend, CUTNUMBER)
% Calculate dynamic regional homogeneity (i.e. ReHo) from the 2D surface brain
% FORMAT [ReHoBrain_AllWindow, GHeader] = y_reho_Sur... |
0e247e5803381571b3c020211a64d340cd941e6c39d4d0e80b8a72d0014f4045 | MATLAB | 7,460 | 175 | function h_finalizeSpineAssigment3(handles)
global h_img3;
[currentInd2, handles2, currentStruct2, currentStructName2] = h_getCurrendInd3(handles);% "2" is "Current"
structNames = fieldnames(h_img3);
for i = 1:length(structNames)
if ~strcmpi(structNames{i}, currentStructName2) && ~strcmpi(structNames{i... |
dc17a83528728c6a2b83e13649f9e1c6d10d23c155382fdb163f2d269ad93b8d | MATLAB | 7,460 | 143 | classdef CBIG_AuthorTopicEM_unit_test < matlab.unittest.TestCase
% CBIG_AuthorTopicEM_UnitTest
%
% Wrapper function to unit-test a coordinate-based meta-analysis with
% the author-topic model and expectation-maximization (EM) algorithm.
% The inference was performed with the following hard-coded hyperparamete... |
5b0da1afa3193be184a4feb355416b47d2e8a996887eddf37440d2d0fe9a39e8 | MATLAB | 7,465 | 136 | function [stat, cfg] = ft_statistics_analytic(cfg, dat, design)
% FT_STATISTICS_ANALYTIC performs a parametric statistical test on the
% data, based on a known (i.e. analytic) distribution of the test
% statistic. This function should not be called directly, instead
% you should call the function that is associated wi... |
819ee3b752098fa0055753f49f13c729f60e64d8211094f6435499f08a59e174 | MATLAB | 7,467 | 189 | classdef ImarisReader < matlab.mixin.SetGet & dynamicprops
% ImarisReader Imaris ims file reader class
%
% Syntax
% ------
% obj = ImarisReader(filepath)
%
% Description
% -----------
% obj = ImarisReader(filepath) creates an ImarisReader object obj to
% r... |
65049661bc392f0c88ac481cb9b0a0cf2f4464ae8dddca6aba3f8afd13b36ae8 | MATLAB | 7,470 | 230 | % DELCODE-SAME, Figure "FADE SAME ApoE"
% _
% original paper: Soch*, Richter* et al., HBM, 2022
% Figure S3: Analysis of FADE scores as a function of ApoE genotype
%
% DELCODE paper: Soch et al., medRxiv, 2023
% Figure 4: FADE and SAME scores by diagnostic group and ApoE genotype
%
% written by Joram Soch <Joram.So... |
094aaabf5eec750501d741f50a7513284248a5461bc29d4034b58d552faf0d06 | MATLAB | 7,475 | 202 | function ft_plot_montage(dat, varargin)
% FT_PLOT_MONTAGE makes a montage of a 3-D array by selecting slices at regular distances
% and combining them in one large 2-D image. Note that the montage of MRI slices is not to
% be confused with the EEG montage, which is a way of specifying the reference scheme
% between e... |
6fd54f621727b50f2ecc76a30cf3432aa2c9b2676b710a02fb46f4bb110d99f2 | MATLAB | 7,475 | 296 | function [hfigs,savenames,errprctiles] = PlotPerLandmarkErrorPrctilesOverX(varargin)
[errprctiles,gtdata,nets,legendnames,colors,colorfracprcs,exptype,...
n_train,...
conddata,labeltypes,datatypes,...
maxerr,prcs,...
pttypes,...
hfigs,figpos,savedir,savenames,dosavefig,xl,savekey] = myparse(varargin,'errprct... |
e5f0ca70966f8452e7a62abe903dba2444fa469ef48d7371ab26968c182c886c | MATLAB | 7,476 | 196 | function [] = makeProbeMap(folder,varargin)
%% this function takes an xml file with spike groups already assigned and
%% generates *.prb files for each shank for spike detection/masking/clustering
%% IMPORTANT: this function ASSUMES that the order of the channels for each shank
%% in the spike groups map onto a specif... |
f7adff7b607fc080e92b63def54cb78b81cfe1b2dda07d71da0750f32f36cb7f | MATLAB | 7,476 | 164 | %% Light Level Calibration Workflow Example (https://elifesciences.org/reviewed-preprints/93795v2)
% IMPORTANT NOTE: This script is an example of the workflow for
% and isomerization rate calculation. You will need to modify certain values
% (especially calibration values and file paths) based on your own devices,
... |
83246f6ea545f97e55f0ac85606639937df09fb8840494bdabc07d0f38b3f0d5 | MATLAB | 7,480 | 213 | %% Enrichment and Mcnemar
% This code runs enrichment on 2 independent groups.
% McNemar chi-square is used to compare network pairs between groups.
%% Load data
% load IM structure
load('filepath to IM structure');
% load connectivity data
group1fc = load('filepath to group 1 fc data');
group2fc = load... |
86b84117d289b0130969db0660f9c57d73e3a12560a397a7d59aea0abb70fd7d | MATLAB | 7,480 | 178 | function [Allobject_container, SHGMask_container, CellMask_container, PixelRatio8o7, Overlapped8o7, ...
Cell755, Cell860] = generate_masks_SeparateMasks(roi_names, ...
file_identifiers, image_array, filtersize, prctile_thr, Masks)
if nargin < 6
Masks = 0;
elseif nargin < 4
Masks = 0;
prctile_thr = ... |
b0b433037eb262bb439ff9a2d4ba34933fd7dcd270c43b341e5dc9a2863370f5 | MATLAB | 7,484 | 232 | function varargout = montage2( IS, prm )
% Used to display collections of images and videos.
%
% Improved version of montage, with more control over display.
% NOTE: Can convert between MxNxT and MxNx3xT image stack via:
% I = repmat( I, [1,1,1,3] ); I = permute(I, [1,2,4,3] );
%
% USAGE
% varargout = montage2( IS, ... |
f02ee6709268533a4880feac7bdd043bfff0c7f9bed086a50fa94b0dce331847 | MATLAB | 7,486 | 349 | function [pdf,pdd] = mpbdv(v,x)
%% Parabolic cylinder function
% =========================================================
% Purpose: This program computes the parabolic cylinder
% functions Dv(x) and their derivatives using
% subroutine PBDV
% Input: x --- Argument of ... |
fc0335c05f8d5128952cb286fcb9ae5d7e4b03e62e1ad365241118443318e2a7 | MATLAB | 7,486 | 142 | function parallel_BSC_LSS_FIR(stat_path,sots_path,exp_folder,N,TR,model,q_level,ground_truth)
% ========================================================================
% Ruslan Masharipov, October, 2023
% email: ruslan.s.masharipov@gmail.com
% ========================================================================
... |
e57bf8ba53e5de3dd65dc98ffec9982d3f3d8e658dbfb04a173cbdd86ad913b4 | MATLAB | 7,488 | 162 | function GonzalezPereyra_etal_Fig_05
load ([pwd '/Data_GonzalezPereyra_etal_Fig_05.mat']) %#ok<*LOAD>
I500Colors=[55 170 200]./255;
I200Colors=[255 153 85]./255;
Color_300=[100 100 100]./255;
Color_500=[255 153 85]./255;
[SortedMatrix_Train,maxIndex_FromTrain]=SortThisMatrix_Mean(ZscoresTrain,1000,1290,[]); %#ok<*... |
61259e216882ca1dc7364b4b84d212fff696d62b7622ed66f5119e586665196b | MATLAB | 7,505 | 219 | function [pos, tri] = headsurface(headmodel, sens, varargin)
% HEADSURFACE constructs a triangulated description of the skin or brain
% surface from a volume conduction model, from a set of electrodes or
% gradiometers, or from a combination of the two. It returns a closed
% surface.
%
% Use as
% [pos, tri] = headsu... |
bb56d3d79633b29e142be573ba2e1741f72fff4960b943b5d593ba6a5eb5fe59 | MATLAB | 7,507 | 150 | function [res, rand_diffs] = bootTestDiffSeeds(paths, bootcfg)
% This function performs permutation-based significance testing (via
% t-test for 2 groups or f-test for >2 groups using the max procedure)
% to build a null distribution and control for Type 1 error.
% INPUTS---------------------------------------------... |
be28c7032eeec56a4a14d878d7c2b783e16e3b0b6c511bdbf8e8a4db59971359 | MATLAB | 7,515 | 198 | classdef VideoPanel < TempoPanel
properties (SetAccess = private)
video
showFrameNum = true
end
properties (Access = private, Transient)
currentFrameImage
currentFrameNum
imageHandle
frameNumHandle
lastDrawNowUpdate
en... |
21ea328e4b678356100e3b0dee584ebb3e1356c5d8bc48fa82c85d2a597c2a8e | MATLAB | 7,517 | 120 | function ActiveDur(MATPATH, FIGPATH, params)
%% Parameter setting
params.processFcn = @NoveltySU.preprocess.ActiveProcess_3_6Dur;
NoveltySU.utils.parseStruct(params);
temp = string(strsplit(MATPATH, "\"));
protStr = temp(end - 2);
DATAPATH = MATPATH;
FIGPATH = strcat(FIGPATH, "\");
S... |
f86c46ed5bc703c554046b52ad1529649484f4a47f08b86526f7a4d6644196da | MATLAB | 7,517 | 195 | function [mri] = align_neuromag2acpc(mri, method, template)
% ALIGN_NEUROMAG2ACPC performs an approximate alignment of the anatomical
% volume from NEUROMAG towards ACPC coordinates. Only the homogenous transformation
% matrix is modified and the coordsys-field is updated.
%
% Use as
% mri = align_neuromag2acpc(mri)... |
ff334edeef82e0ca8136f1fb23b34a9a2f919d92c21fde5a24430665ef04cefa | MATLAB | 7,517 | 224 | function [Tlocal,Dlocal]=bspline_trans_points_double(O_trans,Spacing,X,check)
% If Spacing and points are not an integer, we can not use fast look up tables,
% but have to calculate the bspline coefficients for every point
if(nargin<4)
check = any(mod(Spacing,1)>0)|any(mod(X(:),1)>0);
end
switch size(X,2)
... |
7048435ddb5a677d6b15692145e84e0d55f7e2cae37ae33865ea3f67a2d3d64b | MATLAB | 7,522 | 176 |
if exist("IdProcedure")==0
IdProcedure = 99 ;
end
%% INITIALIZE
clear ami* rand* adjust* mean_quantization_error legend_entries scDim
% clc
% Cell arrays per salvare i risultati
results_ami = cell(size(som_dims, 1), length(epoch_values));
results_ari = cell(size(som_dims, 1), length(epoch_values));
... |
3c5ff626ac4ca08b666d3c161792acc8cada1b07833673676d35774e25656ab5 | MATLAB | 7,528 | 230 | function Perm_2group_Ttest_1tp_Figs2(dataOut,IM,params)
% This function is the same as Perm_2group_Ttest_1tp_Figs2 except
% that it does not plot the block-wise FPR values.
% Also, it plots the FPR-p-vals for both
% Chi-squared and HG to see dynamic range
Pth=0.05/params.B;
PthMcN=0.05;
[NNidx,Tidx,TNidx]=IM2idx_HS... |
5b2c5454e30d7174537296871f3ca0885274cc6f59a7415cf2a75958fe0912db | MATLAB | 7,534 | 214 | function [Class, FileDataset] = opencls(Dataset, Original, Verbose)
% Class = opencls(Dataset, Original, Verbose)
%
% Generates a data structure array from ClassFile.cls in Dataset. Each
% element of the array (each trial class) contains the fields: Name, Id,
% Count, Trials. Trials is a vector of trial ... |
b675c5d08ef8d1429638bf732d4249bc3708b3edc951c04e46444157cb3218fd | MATLAB | 7,534 | 205 | function names = scnlab_filter_fmri_data(imgs, mvmt, mask, tr, spersess, hp)
% Outlier and artifact removal for one subject
% Writes new output images for timeseries
%
% :Usage:
% ::
%
% names = scnlab_filter_fmri_data(imgs, mvmt, mask, tr, spersess, hp)
%
% :Examples:
% ::
%
% OUT = mean_image(imgs, 'mean_ravol... |
e648b9a821f39aa33867efb0d361d2506958955e7a6fee2589df5cad779fc1e9 | MATLAB | 7,537 | 189 | function PopulationAnalysisThroughTime(config,varargin)
%%
if strcmp(mfilename,'') || nargin==0
opts=Analyze.Libet.Config_BasicLinearModel;
else
opts=feval(config,varargin{:});
end
if ~isfield(opts,'WindowType')
opts.WindowType='windowStarts';
end
if strcmp(opts.WindowType,'windowStartsTR'... |
cd421c572bf85be37d1b66c032f979e32e3712027a2400952075b7d0692f22af | MATLAB | 7,547 | 201 | %%FindEvents
function [posevents,negevents]=FindEvents(data,posspikes,negspikes,psn,nsn,psw,nsw,fs,Settings,DoDisplay)
% Use the peak information (locations and size) to find events, as defined
% in the 'Settings'. Positive events and Negative events are considered
% separately and both returned. Optionally, can d... |
76315d15f1d874b7651086a0e2d3b49aa18da119961d396cac0ff9b0f70e2ace | MATLAB | 7,550 | 209 | % 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 performs k-means clustering on maximum muscle moments and compares it with function-based grouping.
% I... |
900fd3e63987bf36f09a642f853e8d340468533a6f6dfa3a040434a25479ba95 | MATLAB | 7,554 | 183 | function [parcellation] = ft_datatype_parcellation(parcellation, varargin)
% FT_DATATYPE_PARCELLATION describes the FieldTrip MATLAB structure for parcellated
% cortex-based data and atlases. A parcellation can either be indexed or probabilistic
% (see below).
%
% A parcellation describes the tissue types for each of ... |
9217cc8eceb2804fb67cfe5be714a04f038066404b0cfe670fb0d6349fb0b7dc | MATLAB | 7,555 | 183 | function [parcellation] = ft_datatype_parcellation(parcellation, varargin)
% FT_DATATYPE_PARCELLATION describes the FieldTrip MATLAB structure for parcellated
% cortex-based data and atlases. A parcellation can either be indexed or probabilistic
% (see below).
%
% A parcellation describes the tissue types for each of ... |
3a879411395f24118ee450f4bfbd847e677c4630d964574bf2a68b28574bca82 | MATLAB | 7,559 | 190 | load(fullfile(dipole_folder, strcat(patno,'_',model_name,'_',dipole_name, ...
'_output_charge_solution')));
%% XY transverse cross section
% Prepare plane data
planeABCD = [0 0 1 -Z]; % Equation of the plane of the cross-section (Ax + By + Cz + D = 0)(meters) for neighbor triangle search acceleration
... |
9de3a8f7b2c9ae7139a5c9d069635e3367612aac7e046072c8f3c6903eff3a9f | MATLAB | 7,559 | 273 | function [ newevents avglongestprobe avgendtotal convergefrac ] = ...
wlProc_doEvAnnealAllWave( ...
oldevents, samprate, wavedata, ...
comparefunc, maxprobes, maxtotal)
% function [ newevents avglongestprobe avgendtotal convergefrac ] = ...
% wlProc_doEvAnnealAllWave( ...
% oldevents, samprate, wavedat... |
2e7faf0e600a1457a64f6bcf63fff8ad00073312418830010fe5d582c172babb | MATLAB | 7,570 | 266 | %SPTENMAT
%
%SPTENMAT Methods:
% aatx - Implicitly compute A * A' * x for sptenmat.
% disp - Command window display of a sptenmat.
% display - Command window display of a sptenmat.
% double - Convert a sptenmat to a sparse matrix.
% end - Last index of indexing expression for sptenmat.
% ful... |
1dae47272dd76e489ecd468b23dacb9cf5e42a5f825ba129a8d62890626cb20c | MATLAB | 7,578 | 189 | % Second-kind integral equation on the unit sphere, Laplace double-layer.
%
% This is essentially the 3D version of IE_CIRCLE, where now the geometry is the
% unit sphere represented using flat triangles. The system is discretized via
% collocation with tensor-product Gauss-Legendre integration for the near-field
% pan... |
7cf5c8474b463b8655f18d8c10689f18303406999325095d72a83598a3841beb | MATLAB | 7,578 | 188 | function h_f = plotCuboidSurfaces(nFig,model,simFluorescence)
lambdatext = [955 ' [nm]']; % The 955 is the unicode number for the lambda character. Because the editors of MATLAB versions prior to 2020a do not support unicode, we have to make the lambda in this sneaky way.
x = model.G.x;
y = model.G.y;
z = mo... |
94da2f1e04d49413a1185c89ef18dba69b2653d9bac5cb3e88d66022ab3e2df6 | MATLAB | 7,578 | 267 | function [x,iter,resids] = fgmres(A, b, tol, varargin)
% Flexible GMRES method
% [x,iter] = fgmres(A, b, tol, varargin)
%
% Tries to solve a linear system Ax=b via the flexible GMRES
%
% A should be given as a function handle @(x)A(x), which computes the
% Matrix-Vector product A*x.
%
% A and b can be passed as regul... |
fa6b39981b1c84a89746206824e08b55c652d2bd4fa89514cc4fa0a2d510e851 | MATLAB | 7,578 | 318 | function xy = PolyDraw(varargin)
%% PolyDraw.m USAGE NOTES AND CREDITS
%
% Syntax
% -----------------------------------------------------
% PolyDraw()
% PolyDraw(ax)
% PolyDraw(...,2)
% PolyDraw(...,...,sec)
% xy = PolyDraw(__)
%
%
% Description
% --------------------------------------------------... |
37687947c542d9775a3d8a3710f7039c41dee8bbc5fbe2fe524ac0e03477a358 | MATLAB | 7,579 | 201 | %PRINT_PDF Prints cropped figures to pdf with fonts embedded
%
% Examples:
% print_pdf filename
% print_pdf(filename, fig_handle)
%
% This function saves a figure as a pdf nicely, without the need to specify
% multiple options. It improves on MATLAB's print command (using default
% options) in several ways:
% - ... |
69548ce6094a898049f87af91deaf358e971b1daf480fd725a0701250c0f7ba9 | MATLAB | 7,581 | 202 | classdef TopologicalSpace < handle_light
% Collection of sets on which maps such as chart and embedding are
% defined.
% Roughly corresponds to the concept of a topological space but really
% just a bookkeeping device to keep track of domains in the surface on
% which maps can be defined.
... |
4c7fd57ae267f2f5723a5f2bba434f16348ce362dc5a7e334c8cc0fad991e446 | MATLAB | 7,586 | 178 | function [varargout] = read_plexon_nex(filename, varargin)
% READ_PLEXON_NEX reads header or data from a Plexon *.nex file, which
% is a file containing action-potential (spike) timestamps and waveforms
% (spike channels), event timestamps (event channels), and continuous
% variable data (continuous A/D channels).
%
%... |
5074f8c84220ee6c63ab6a2472a6bcd4036d4ad04699b53de640e71bfb64b081 | MATLAB | 7,600 | 157 | function results = predict_featsets(datadir, kerneldir, resultsdir, HMM_name, varN, iterN, Fn, Kn, FSn)
% results = predict_featsets(datadir, kerneldir, resultsdir, HMM_name, varN, iterN, Fn, Kn, FSn)
%
% runs kernel ridge regression to predict behavioural variables (here age
% and intelligence in HCP dataset) using di... |
c2449fb990a20f346e11702edaf334904f029f9844520ad0577e30bdf5b3d7d5 | MATLAB | 7,601 | 210 | function [freq] = ft_freqbaseline(cfg, freq)
% FT_FREQBASELINE performs baseline normalization for time-frequency data
%
% Use as
% [freq] = ft_freqbaseline(cfg, freq)
% where the freq data comes from FT_FREQANALYSIS and the configuration
% should contain
% cfg.baseline = [begin end] (default = 'no'), alterna... |
7aab0cb3f561fb7c14589822000249e0c86247d6669ba7ee2c4c9b6de5ba25c3 | MATLAB | 7,603 | 206 | %PRINT2EPS Prints figures to eps with improved line styles
%
% Examples:
% print2eps filename
% print2eps(filename, fig_handle)
% print2eps(filename, fig_handle, options)
%
% This function saves a figure as an eps file, with two improvements over
% MATLAB's print command. First, it improves the line style, makin... |
daf47858eccd1cff06fcae24597973e504fbaa6e6cb16973116f78441f624170 | MATLAB | 7,610 | 269 | function datasetId = h5datacreate(h5file,varname,varargin)
%H5datacreate Create HDF5 dataset.
%
% H5DATACREATE(HFILE,VARNAME,parameter,value,...) creates a dataset
% named VARNAME. HFILE may be either a path to the HDF5 file or a file
% ID to an already opened file.
%
% If VARNAME is a full pathname, all
... |
a8614ec371d3d977579946b6b2ea938dc0a7912e3eb8a7184219bdac7a9bd6ac | MATLAB | 7,619 | 187 | %% This script performs repeated-decodings of a given simulation with varied decode parameters
% varyDecodeParam.m
%
% run_grid_decode.m performs decoding across a parameter grid.
% It calls run_param_decode to decode each parameter, and this calls
% run_net_decode.m to decode each network.
%
% Outline:
% - Loa... |
9d40bce640de2eea68828290b2a7b97c8c7ec9a2cde061c665eda31f1377bf60 | MATLAB | 7,623 | 168 | function homo_with_weight = CBIG_MSHBM_parameters_validation(project_dir,mesh,num_sess,num_clusters,subid,w,c)
% homo_with_weight = CBIG_MSHBM_parameters_validation(project_dir,mesh,num_sess,num_clusters,subid,w,c)
%
% This script will estimate the individual-level parcellation for the
% validation subjects with num_c... |
2eeb7fede490a1ee64764598c778fc54a84bf39ad3b751f7ccf2bfb7624fba32 | MATLAB | 7,624 | 129 | %% Description
% Here, we demonstrate calculation and plotting of the far field angular
% distribution of the "escaped" photons, both for excitation light and for
% fluorescence light. It is enabled by specifying the optional
% "farFieldRes" parameter, which serves also to specify the resolution you
% want of the far f... |
7557180342feac161b5a7b2ec36d14e14ba42e34ef2083b5c9e7556af623740c | MATLAB | 7,625 | 211 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
function [amp, lat, snr] = get_mergedData(condition, srmr_nr, subjects, has_allsubj)
%% set variables
loadpath_ga = getenv('GADIR');
% get condition info
[cond_info] = get_conditionInfo(condition, srmr_nr);
cond_name = cond_info.cond_name;
nerve = cond_info.nerve;
str_st... |
d3280a87fbba409a711482754cc37e8d6480e9dd23f148ea60da6a4c5ea0cb78 | MATLAB | 7,629 | 200 | function [obj] = ft_convert_units(obj, target, varargin)
% FT_CONVERT_UNITS changes the geometrical dimension to the specified SI unit.
% The units of the input object is determined from the structure field
% object.unit, or is estimated based on the spatial extend of the structure,
% e.g. a volume conduction model of... |
138be4761ada742cd5d31b9d271b918320186330bdedfbbb2294ddaa7a12b252 | MATLAB | 7,630 | 243 | classdef TrxVisualizer < handle
% shows a trx/centroid marker, text label, trajectory traces
properties
parent_ % scalar LabelerController
lObj % scalar Labeler, derived from parent_.labeler_
hTraj; % nTrx x 1 vector of line handles
hTrx; % nTrx x 1 vecto... |
6e6bf35ca1aae5a13b95cbbff26b2b5e4ebbb3f1cdaeec1093ba55ef978d2d76 | MATLAB | 7,630 | 281 | %%cell count
clear all
close all
for i = 1:2
for f = 1:2
cd Example_images/
filename1 = ['220311_5050_1_cs' num2str(f) '_20X_' num2str(i) '_DAPI.tif'];
filename = extractBefore(filename1,'DAPI');
dapi = imread(filename1);
[px, py] = size(dapi);
% figure
% su... |
f9a5f915932dc827e1698d48f61ff3fa951c5d832580aa08bea05cd901246e18 | MATLAB | 7,632 | 283 | function hh = errorbar_h(varargin)
%ERRORBAR Error bar plot.
% ERRORBAR(X,Y,L,U) plots the graph of vector X vs. vector Y with
% error bars specified by the vectors L and U. L and U contain the
% lower and upper error ranges for each point in Y. Each error bar
% is L(i) + U(i) long and is drawn a distance of ... |
3e9067e50c0abb4153acf1d5d12b310336b5ebdbe77aee7c52349eb2fc0b82be | MATLAB | 7,633 | 205 | function [dipout] = ft_eloreta(dip, grad, headmodel, dat, Cf, varargin)
%
% Use as
% [dipout] = ft_eloreta(dipin, grad, headmodel, dat, cov, varargin)
% where
% dipin is the input dipole model
% grad is the gradiometer definition
% headmodel is the volume conductor definition
% dat is t... |
e6bcd007dc46477f29ea7b285d988300c70e2f240eed92755cb5e0c12a5b9f18 | MATLAB | 7,633 | 198 | function varargout = DPABISurf_FieldMap(varargin)
% DPABISURF_FIELDMAP MATLAB code for DPABISurf_FieldMap.fig
% DPABISURF_FIELDMAP, by itself, creates a new DPABISURF_FIELDMAP or raises the existing
% singleton*.
%
% H = DPABISURF_FIELDMAP returns the handle to a new DPABISURF_FIELDMAP or the handle to
%... |
2cda83a58d918dd94ccbf29453a92d0e305d5618efd00e4f026bba0b7dd6fb50 | MATLAB | 7,635 | 184 | function [Objects] = f_imageAnalysis(Label, chHoechst, chMAP2, chFOXA2, chTH, PreviewPath, MetaTable)
%vol(chHoechst, 0, 1000)
%vol(chMAP2, 0, 2000)
%vol(chTH, 0, 2000)
%vol(chFOXA2, 0, 1000)
%% Organoid segmentation
chOrganoid = imlincomb(0.25, chHoechst, 0.25, chMAP2, 0.25, chFOXA2,... |
e94fd31b6a0c2f8b01a84f75668a55f817f8995e8fc247d68bd46fdf7d8bfe10 | MATLAB | 7,636 | 192 | % rectify_stereo_pair.m
%
% Script file that rectifies a set of stereo images after stereo calibration
% This script loads the stereo calibration file Calib_Results_stereo generated by calib_stereo.m
% Therefore, type help calib_stereo for more information.
if ~exist('fc_right')|~exist('cc_right')|~exist('kc_right')|... |
6ef834a4e6a7d642a8e3f006c9f3bc891c3c3ea83a119e757e537f861d1a696e | MATLAB | 7,639 | 205 | function [dipout] = ft_eloreta(dip, grad, headmodel, dat, Cf, varargin)
%
% Use as
% [dipout] = ft_eloreta(dipin, grad, headmodel, dat, cov, varargin)
% where
% dipin is the input dipole model
% grad is the gradiometer definition
% headmodel is the volume conductor definition
% dat is t... |
8f23730e9c18d6511d1e0c6e5d819baafb3a309cc4bbed4b1f08f414077a7d8b | MATLAB | 7,644 | 231 | % onsetsim
corepath = pwd;
addpath([corepath,'/functions'])
ath = 0.05; % arbitrary threshold value for ttest
pth = 1 - ath; % permutation threshold
Nperm = 2000;
%% Make template
% true onset = 160 ms, F=81, max at F=126
true_onset = 160;
Xf = 0:2:500; % 500 Hz
Nf = length(Xf);
temp1 = zeros(1,Nf);
erp = normpdf(li... |
040b11dac17c959fc7a7a74575824bc6976ada0635449a0ea8d05bb0bfab3729 | MATLAB | 7,645 | 312 | %load data: contact lead author
%% MEAN DFOF
i=find(nRuns(:,1)>1);
allAverageDfofsUse=allAverageDfofs(i);
ddAO = cat(2, allAverageDfofsUse{:});
% ddAO=ddAO(iUse);
ddAO = ddAO(aoCellIdx);
ddVS = cat(2, allAverageDfofsUse{:});
% ddVS=ddVS(iUse);
ddVS = ddVS(vsCellIdx);
figure; hold on
a=ddAO';
b=ddVS... |
0ab5e44c70613dc20809418f4fe75d5f56e135bb4d742b7c88de0da44bdc4c04 | MATLAB | 7,649 | 190 | function varargout = w_SurfClusterSize(varargin)
% W_SURFCLUSTERSIZE MATLAB code for w_SurfClusterSize.fig
% W_SURFCLUSTERSIZE, by itself, creates a new W_SURFCLUSTERSIZE or raises the existing
% singleton*.
%
% H = W_SURFCLUSTERSIZE returns the handle to a new W_SURFCLUSTERSIZE or the handle to
% t... |
07d28330b209b0d70fa8b2b043ce57e085eeaf19292edfed0722f9537fdfd294 | MATLAB | 7,651 | 185 | %% Description
% This example shows how to import a shape from an STL file (sample.stl)
% and optionally apply scaling (unit conversion), rotation and mirroring on
% the mesh before using a function to voxelise the mesh.
%
% Importing is done inside the geometry function at the end of the model
% file (this file). The ... |
bdcbc985b4c8a7455ef45a9ac0077fe1e2a6f27ffc333182d353d28011c2a6d7 | MATLAB | 7,661 | 169 | function [VMHCBrain, Header] = y_VMHC(AllVolume, OutputName, MaskData, IsNeedDetrend, Band, TR, TemporalMask, ScrubbingMethod, ScrubbingTiming, Header)
% [VMHCBrain, Header] = y_VMHC(AllVolume, OutputName, MaskData, IsNeedDetrend, Band, TR, TemporalMask, ScrubbingMethod, ScrubbingTiming, Header)
% Calculate VMHC
% Ref:... |
22fded8e52328deebb075fac860bd23c87758e61ca37636553033fe66a7c6969 | MATLAB | 7,664 | 238 | function [newpupil] = blink_regressout(pupildata, fsample, blinksmp, saccsmp, plotme, addBackSlowDrift)
% method by Knapen, de Gee et al. (2016)
% http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155574
% estimate canonical responses to blinks and saccades, then take those out
% of the pupil timecours... |
67d6a95d369547bd1414eb0378931e26c582387a4627d5b8bdb6de4b69294de9 | MATLAB | 7,671 | 233 | function hfig = tightfig(hfig)
% tightfig: Alters a figure so that it has the minimum size necessary to
% enclose all axes in the figure without excess space around them.
%
% Note that tightfig will expand the figure to completely encompass all
% axes if necessary. If any 3D axes are present which have been zoome... |
e7020289cd3c53cc7d077b84bcce5bf74070019000540b44f3389e9eb2d6bbe6 | MATLAB | 7,676 | 217 | function [dat] = ft_fetch_data(data, varargin)
% FT_FETCH_DATA mimics the behaviour of FT_READ_DATA, but for a FieldTrip
% raw data structure instead of a file on disk.
%
% Use as
% [dat] = ft_fetch_data(data, ...)
%
% See also FT_READ_DATA, FT_FETCH_HEADER, FT_FETCH_EVENT
% Copyright (C) 2009-2013, Jan-Mathijs Sch... |
e94a7dd6fab7ac57fd524de8c5b39affda6d5b9e856628b403641123f33fb2bf | MATLAB | 7,676 | 231 | % Rob Campbell (2023). raacampbell/shadedErrorBar
% (https://github.com/raacampbell/shadedErrorBar), GitHub. Retrieved
% July 18, 2023.
function varargout=shadedErrorBar(x,y,errBar,varargin)
% generate continuous error bar area around a line plot
%
% function H=shadedErrorBar(x,y,errBar, ...)
%
% Purpose
% Makes a ... |
27445b9f938d4de4e1c73d8dc70f3ba40695c6abb89b5c4c68fa09246e3b348b | MATLAB | 7,680 | 187 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% n0_sample_dipole_positions.m -- Uniform sample (without repetition) %%%
%%% of random dipoles, perpendicular to the grey matter shell %%%
%%% of the patient. %%%
%%%%%%%%%%%%%%... |
ac9b8a702e5f48d7c0ee254046577d72c2aab2bb55bde6c8b4e9aafcbe88372e | MATLAB | 7,681 | 269 | function CBIG_DrawSurfaceMapsWithBoundaryInteract(lh_data, rh_data, ...
lh_labels, rh_labels, mesh_name, surf_type, min_thresh, max_thresh, colors)
% CBIG_DrawSurfaceMapsWithBoundaryInteract(lh_data, rh_data, ...
% lh_labels, rh_labels, mesh_name, surf_type, min_thresh, max_thresh, colors)
%
% This function is... |
f7731c5e3ba604c0bd470eaaad457e596b8352fa4b05c5376c9f62eaf30f4feb | MATLAB | 7,681 | 214 | function [dataout] = ft_heartrate(cfg, datain)
% FT_HEARTRATE estimates the heart rate from a continuous PPG or ECG channel. It
% returns a new data structure with a continuous representation of the heartrate in
% beats per minute.
%
% Use as
% dataout = ft_heartrate(cfg, data)
% where the input data is a structure ... |
7136e2c0af5c31cc61dd726676615760c007c1a3b9f4859af0e3941dcbc50be0 | MATLAB | 7,688 | 188 | function [PBEstruct] = detect_PBE(spikes, modelParam, varargin)
% detect_PBE.m
%
% Detects population burst events. Assumes 'spikes' only includes cells
% that you want to include in burst detection (e.g. E-cells only).
%
% Inputs:
% - opS: logical spike matrix, opS(ithCell,ithTimeBin,ithTraj,ithTrial)
% - modelPar... |
8263bf981f69b0e067bb18be523a487ae624c167feed02e3c9d4ddd6ffbc5f5c | MATLAB | 7,690 | 238 | function ft_write_headshape(filename, bnd, varargin)
% FT_WRITE_HEADSHAPE writes a head surface, cortical sheet or
% geometrical descrition of the volume conduction model or source
% model to a file for further processing in external software.
%
% Use as
% ft_write_headshape(filename, bnd, ...)
% or
% ft_write_hea... |
6daaddf1ff922670b7c01d8a3935b8285fafc1f27a3bf9dfb4b358bbbf0fcc07 | MATLAB | 7,694 | 243 | function [X_train, Y_train, X_test, Y_test] = makeCrabs()
% Crabs data set from http://www.stats.ox.ac.uk/pub/PRNN/
% Xtrain: 80 * 5
% Y_train in {1,2} for male, female
% Xtest: 120*5
% Ytest in {1,2}
%
% First column: true label
% 0 = Blue male
% 1 = Blue female
% 2 = Orange Male
% 3 = Orange Female
%
c... |
78c796fbcb5129553307d3684470954584f5f1ef95f218ef1b206aeae14890be | MATLAB | 7,694 | 214 | function [dataout] = ft_heartrate(cfg, datain)
% FT_HEARTRATE estimates the heart rate from a continuous PPG or ECG channel. It
% returns a new data structure with a continuous representation of the heartrate in
% beats per minute.
%
% Use as
% dataout = ft_heartrate(cfg, data)
% where the input data is a structure ... |
d3f4f76c2d207b4f204c48cb546c6e00f63421de4cf0f38a96a0ac5b95db3884 | MATLAB | 7,695 | 215 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
%% SRMR2_03_esg_analysis
clear; clc
delete(gcp('nocreate')) % clear parallel pool
%% variables that need to be changed
% step
step_number = 1;
% sampling rate
sampling_rate = 1000;
% subjects
subjects = 1:24;
%% define variables and paths
% experiment
srmr_nr = 2;
% c... |
9fe83dfcb051c95a1fbf207956f8fba47ea420ee6b2ea04ebd773da49bc6fc4a | MATLAB | 7,696 | 209 | function varargout = ReorientThreQC(varargin)
% REORIENTTHREQC MATLAB code for ReorientThreQC.fig
% REORIENTTHREQC, by itself, creates a new REORIENTTHREQC or raises the existing
% singleton*.
%
% H = REORIENTTHREQC returns the handle to a new REORIENTTHREQC or the handle to
% the existing singleton... |
9f8271fa8e9eca367215159ded18525856dac398d0a9989e35fb95e3edc6dd37 | MATLAB | 7,702 | 172 | function [Obj,modified] = SOFAupgradeConventions(Obj)
%SOFAcompatibility
% [Obj,modified] = SOFAupgradeConventions(Obj) upgrades the Obj to the next higher
% version if required. MODIFIED is 1 when an upgrade was required.
% In order to obtain the most recent version, SOFAupgradeConventions
% should be proces... |
cda07c20a827fd3b556802b946892b885448665cb885c5c70999b04f5b98b86f | MATLAB | 7,713 | 280 |
outDir = '/nrs/branson/mayank/jay/out/';
trkDir = '/nrs/branson/mayank/jay/tracks/';
dd = dir(fullfile(outDir,'*.h5'));
%%
params = singleViewTrackingDefaultParams;
parfor ndx = 1:numel(dd)
curIn = fullfile(outDir,dd(ndx).name);
curOut = fullfile(trkDir,dd(ndx).name);
if ~exist(curOut,'file')
trackSingleVie... |
4b5f96a75b68dace9037d26920c16043a89b3a504fa0b8abad60209d4a25b53e | MATLAB | 7,714 | 249 | function [handles] = VBA_spm_uitab(hparent,labels,callbacks,...
tag,active,height,tab_height)
% Create tabs in the SPM Graphics window
% FORMAT [handles] = spm_uitab(hfig,labels,callbacks,...
% tag,active,height,tab_height)
% This function creates tabs in the SPM graphics window.
% These tabs may be associated w... |
fccb02fb3fa12ef7a0fc1013217edb84b65d9d20d7020aff462cf16d4a36678b | MATLAB | 7,716 | 222 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% File : GetOMEData.m
% Version : 1.3
% Author : czsrh
% Date : 13.09.2019
% Insitution : Carl Zeiss Microscopy GmbH
%
% Simple script to get "some" not, but not all metainformation using
% the MATLAB wrapper for the BioFormats... |
a618d2032fbf89fd8a9b740c454a28ca5e06634ad742857ed277e8d7f143f281 | MATLAB | 7,728 | 200 | %% ============== Statistical Analaysis ===================== %%
%% load data and directories
clear
fundir = pwd;%[maindir 'TMS_code/'];
datadir = pwd;%[maindir 'TMS_code/'];
savedir = pwd;%[maindir];
addpath(fundir);
cd(fundir);
defaultPlotParameters
sub = load_TMS_v1([datadir '/TMSanalysis_1... |
3f72ee5d97d9cbec0335b34416dcd2b0d76524877ff24e6ccb65ac229e6f836f | MATLAB | 7,740 | 139 | %% Description
% This example shows how to execute MC simulations in a for loop, in this
% case simulating a pencil beam incident on a slab of "standard tissue"
% with variable (parametrically sweeped) thickness. The slab thickness is
% passed in as a part of the GeomFuncParams field and used in the geometry
% function... |
cef201de59687f7d64ae98094eaa61f6fb8dd058e37e2c9cf6ef0e6860b3cc14 | MATLAB | 7,742 | 283 | % latencia.m
%
% v.0.5.2 fix 26.11.2009
%
% Genera LAN.time
% para luego poder epoquira LAN.data continuo
% res = % code of event mark of epoch
% parametres = [1 2 ; 4 8] % eventos
% % si es 'no' solo bustca los res.
% names = % nombre de tipos de vento [ {control} {t... |
8316742060bab4ef9e140e70896e06ed531dd63a1024f8388b886ddf5ff4e3be | MATLAB | 7,743 | 178 |
function [] = GroupDataToRegions (parameters)
mice_all = parameters.mice_all;
periods_all = parameters.periods_all;
dir_groups = parameters.dir_in_groups;
groups_file_name = parameters.file_name_groups;
groups_variable_name = parameters.groups_variable_name;
dir_input_base = parameters.d... |
e0d0e75daa2be9002a9c8faad1b02ef8ee75d14a28de4d5612432f28335a4811 | MATLAB | 7,746 | 175 | function [place_fields,t,replay_time,replay_spikes,ground_truth_replay]=generate_linear_replay_events(number_of_place_cells,no_of_events)
% This code is used to generate place fields and then simulate linear replay trajectory and generate place
% cell spiking (Possion process)
%
% Masahiro Takigawa 2023
% First cr... |
b4eecdaf9b847fe145b8c9ab647d81663963b93e1b402a1fb7473a66bbfb54b4 | MATLAB | 7,749 | 205 | %% for passive touch, finds the onset of the first peak, late wave, and also the peak times
clear
close all
Fs = 2500;
%paths to the relevant data sets for Figure 2
dataPaths{1} = 'D:\InVivo\Baclofen\2022-04-19_Baclofen\3-baseline_220419_104537';
dataPaths{2} = 'D:\InVivo\Baclofen\2022-04-21_Baclofen-Attem... |
692c5f1a2b12fbd10e010f98c07d9c025bf2c055aa877ecbbf6c63e026b2718a | MATLAB | 7,751 | 270 |
function cluster_visual_(GLAN,clus_ind,stat_ind, data_ind,para)
%GLAN = MODEL_l
%
if nargin <5
para=[0 .1 4 10 1 50];
end
tt1=para(1);
tt2=para(2);
ff1=para(3);
ff2=para(4);
th1=para(5);
th2=para(6);
if nargin<4
stat_ind=1;
end
if nargin<3 | isempty(data_ind)
d... |
d391e5fc7fca2f619d4f26753aaa20cfda1c34f37ca2e0c20c002496d6993c3b | MATLAB | 7,752 | 336 | clear all
close all
clc
% Use this script to generate figures similar to those in Figure 3A of:
%Luna, R., Li, J., Bauer, R., & van Leeuwen, C. (2023). Retinal waves in adaptive
%rewiring networks orchestrate convergence and divergence in the visual system.
%Network Neuroscience
cd '..\scripts\Output'
... |
3b9c6ce2db3e6b4f060808029b46113096cd78a5755f1387098540a41fde447c | MATLAB | 7,763 | 227 | function varargout=shadedErrorBar(x,y,errBar,varargin)
% generate continuous error bar area around a line plot
%
% function H=shadedErrorBar(x,y,errBar, ...)
%
% Purpose
% Makes a 2-d line plot with a pretty shaded error bar made
% using patch. Error bar color is chosen automatically.
%
%
% Inputs (required)... |
38d021a755d52f163d16ca11160e7569bd300f03ab34f4c0a3a9f46b895c74a6 | MATLAB | 7,764 | 244 | classdef AxisHUD < handle
% Axis heads-up display
%
% Contains:
% * Series of text labels like Tgt: 3
% * handedness indicator
% TODO: Refactor for extensibility, just have structs/dicts instead of
% hardcoding state/meths for tgt vs lblpoint vs susp etc.
properties (Constant)
txtXoff = 10
txtHgt = 17
... |
31af221dfe40ef682d44f37ae3b09077bf4e7e370821d1c8923d166c1c0243bc | MATLAB | 7,766 | 173 | function [ALFFBrain_AllWindow, fALFFBrain_AllWindow, GHeader] = y_alff_falff_Surf_Window(WindowSize, WindowStep, WindowType,InFile,ASamplePeriod, HighCutoff, LowCutoff, AMaskFilename, AResultFilename, CUTNUMBER)
% Use dynamic ALFF method to compute the brain and return a ALFF brain map which reflects the "energy" of t... |
203b0392901c49ba31939155ce1a68c00cd54a2abc61dc8af1e6b95bc7bcf934 | MATLAB | 7,768 | 229 | function CBIG_Plot17NetworksRearrCorrMat_WhiteGrid(lh2lhcorrmat, ...
lh2rhcorrmat, rh2rhcorrmat, scalelim, filename_prefix)
% CBIG_Plot17NetworksRearrCorrMat_WhiteGrid(lh2lhcorrmat, ...
% lh2rhcorrmat, rh2rhcorrmat, scalelim, filename_prefix)
% Example : CBIG_Plot17NetworksRearrCorrMat_WhiteGrid(lhlh, lhrh, rh... |
5e42f3d73373e678e88cfe71604a36eea8f7602375a19934d268e3ad16192cef | MATLAB | 7,768 | 267 | function [C,time,g,s,k, phi, sta, stb] = minTimeGradientRV(C,g0, gfin, gmax, smax,T, ds, show)
% [C,time,g,s,k] = minTimeGradient(C, g0, gfin, gmax, smax,T,ds, show)
%
% This function computes the rotationally variant solution to the time
% optimal gradient design.
%
% C - The Curve in k-space given in a... |
dafb72d1e9e94b6380191d6ae67c4f6ce39f4e601f3be7935aa94c0f17c385ef | MATLAB | 7,772 | 260 | classdef LabelCoreSeqModel < LabelCoreModel
% Sequential labeling model
%
% Label mode 1 (Sequential)
%
% There are two labeling states: 'label' and 'accepted'.
%
% During the labeling state, points are being clicked in order. This
% includes the state where there are zero points clicked (fresh image).
%
% Once all poi... |
882e3c2d3d2494422a0c52991c9000ae201bd5aee144b5253cb73309f252a6d5 | MATLAB | 7,778 | 235 | function freezeColors(varargin)
% freezeColors Lock colors of plot, enabling multiple colormaps per figure. (v2.3)
%
% Problem: There is only one colormap per figure. This function provides
% an easy solution when plots using different colomaps are desired
% in the same figure.
%
% freezeColors freezes the co... |
92854b3360adc358e0ad4c212c9e87f2e3f3a5aba2614fad8954723d29cbc82f | MATLAB | 7,778 | 264 | function [model, loglikHist] = mixGaussBayesFit(X, K, varargin)
% Variational Bayes for fitting mixture of K gaussians
% data(i,:) is i'th case
% See Bishop sec 10.2 for details
%
%PMTKauthor Emtiyaz Khan, Cody Severinski, Kevin Murphy
% This file is from pmtk3.googlecode.com
[maxIter, thresh, plotFn, verbose, alpha0... |
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