sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e1915ac31394038606c7a4f28ff8fc95fa8ccaf7c2679307e56af75906647da0 | MATLAB | 2,975 | 79 | function plot_footprint(PATH, cfg, fieldNames)
% Plot the previously calculated gait artifact footprint proposed by Jacobsen et al.,2020
% The group-average footprint will be plottdt across the raw data and five
% different artifact attenuation strategies in one spider plot
% download toolbox at
% https://de.mat... |
479c11493216d39df117a0e58dd4caabdf336c3dcee4572acc6b546a372b0619 | MATLAB | 2,976 | 80 | function [alpha, beta, r2] = CharnessRabinModel(Thap)
% function [alpha, beta, r2] = CharnessRabinModel(Thap)
%
% Fits the Charness & Rabin (2002) inequality model to the happiness data.
% Input is table, with happiness and outcome values; outputs are the
% best-fitting parameters (grid search).
%
% In this analysis, I... |
7b92bbf36f05e93f4bdc1adb35bf8eb406116a3f7755316edd9d14b3d6890f46 | MATLAB | 2,976 | 78 | function [selCh_all, selCh_groups] = ch2roi_selCh_atlasRoi(params, nCh, useOnlySignif)
% TBD (now=Oct23)
% returns all selected channels 'selCh_all' & channel groups 'selCh_groups'
% returns channel indices 'ch' indexing the selected channels: selCh_H(ch)
% specified in: params.connectivity.selectedChnls
% based on atl... |
8cc8e88b72991259e8399d55daad5503e56861f70b37dfaf7fb5a0d8924a4fdb | MATLAB | 2,977 | 119 | function [movie_trim]=trimMovieEdges(h5Path,varargin)
% [movie_trim]=trimMovieEdges(h5Path)
% trimMovieEdges(h5Path)
%
% h5Path can also be a local workspace variable.
% Variable input arguments:
% options.timeChunk=false;
% options.saveData=true;
% options.verbose=1;
% options.dataset='mov';
% options.windowSize=5000... |
383a7a4b4ee6bb16926eed22fcc89c60039986e6eee8d944a516dca60933302c | MATLAB | 2,978 | 125 | function sero_pulseq_plotMechSpectrum(seq, n, mode, fInterval, tRes, ascData)
% function sero_pulseq_plotMechSpectrum(seq, n, mode, fInterval, tRes, ascData)
%
% Function to plot the mechanical spectrum from seq based on the Matlab
% function "pspectrum".
% n is 1x2 index vector that defines start and end index.
% mode... |
d976ae48e4d9b3a68aad1cd3f8f0067c8266f95e8783f6d54acaf63d726d935f | MATLAB | 2,978 | 82 | function [simControl, simMuscimol] = simDynamics(ratList, behaviorDataPath, ...
simType, twin, binSize, smoothfactor)
%Simulate wait times and wait time dynamics around block transitions using different
%versions of the behavioral model. SSS 08/2023
%INPUTS:
% ratList = matfile containing a list of rat names to ... |
1090c3d1bdddfec6bcedd2159249fec60c85aa463e60f91342b9ecb9f0edcd48 | MATLAB | 2,980 | 78 | % REALPROBA - compute the effective probability of the value
% in the sample.
%
% Usage:
% >> [probaMap, probaDist ] = realproba( data, discret);
%
% Inputs:
% data - the data onto which compute the probability
% discret - discretisation factor (default: (size of data)/5)
% ... |
c98a4d1bb1473f196ed834b6182824daf71f73ac1b61d1df2fffdc09b8ec467c | MATLAB | 2,982 | 54 | function preprocess_nsd_SWI(subjix)
% function preprocess_nsd_SWI(subjix)
%
% <subjix> is 1-8
%
% Use ANTS to use a BSplineSyN to match the SWI magnitude image (gradunwarped)
% to the EPI 1.0-mm resolution. We use some carefully crafted parameters.
%
% We then create a final 0.5-mm SWI image and some other resolution... |
48601b6ad6d1c3c8429a09f6d7d8c6f0b1dddf6834d146ff694b62d51ad89e71 | MATLAB | 2,984 | 83 | % Expects subjix to be defined.
% Creates a number of variables in the workspace (does not include the data).
% define
hemis = {'lh' 'rh'};
datanames = {'lh' 'rh' 'subcortex' 'func1pt8mm' 'cerebellum'};
imageres = 50; % resolution for the prf model (8.4/50 = 0.168 deg)
pxtodeg = 8.4/imageres;
% calc
fsdir = sprintf(... |
a5b98cb0d0690c760278fdacaca81c9a7236eb894be1d00907e855a6e4b15c30 | MATLAB | 2,984 | 84 | function data = osp_import_Tarquin_fit_ouput(filename, startRow, endRow)
%IMPORTFILE Import numeric data from a text file as a matrix.
% data = IMPORTFILE(FILENAME) Reads data from text file
% FILENAME for the default selection.
%
% data = IMPORTFILE(FILENAME, STARTROW, ENDROW) Reads
% data from rows STARTROW t... |
01014f5af3f3a559d3a99d68cf418e83bdee5f2e619371c7875b610b12c50673 | MATLAB | 2,985 | 77 | %% Main Simulation Functions Suite
% Refactored spiking neural network simulation code
% Author: Deying Song
% Date: Aug 15th, 2025
% Version: 2.0
%% ========================================================================
% MAIN SIMULATION WRAPPER
%% ==================================================================... |
29c7ec0e71bafe32dcc5ad6ba52ce8864c5ce1783ef1635a36c46a4e93eb15cd | MATLAB | 2,987 | 86 | lossless_marks = load('derivatives/EEG-IP-L/code/scripts/lossless_marks.mat');
timeOrdering = {'manual','init_ind','ch_sd','low_r','mark_gap','logl_init', ...
'ic_sd1','logl_A','logl_B','logl_C','ic_sd2','ic_dt','ic_a','ic_b','ic_lg','ic_hg'};
for mark=1:length(lossless_marks.extra.chan_info)
id = 0;
for ... |
d0cf5a754a4cd58a252b90265832d0e812cae87e818f4ba0ec109e296698761f | MATLAB | 2,987 | 118 | function showVoxObj(mapORcoords, figI, subplotTriple, adjustMargin, axisLabels, materialDef)
% USAGE
% showVoxObj(mapORcoords[, figI, subplotTriple, adjustMargin, axisLabels])
%
% FUNCTION
% to display a binary voxel object defined by mapORcoords
%
% ARGUMENTS
% mapORcoords
% this can be a 3D binar... |
709a08c6e9522df429a7d67cc3312802d0c0e54a767fcf07d9de0114a5d404fb | MATLAB | 2,988 | 89 | % firfiltsplit() - Split data at discontinuities and forward to dc padded
% filter function
%
% Usage:
% >> EEG = firfiltsplit(EEG, b);
% >> EEG = firfiltsplit(EEG, b, causal);
% >> EEG = firfiltsplit(EEG, b, causal, usefftfilt);
%
% Inputs:
% EEG - EEGLAB EEG structure
% b ... |
5619ec87058c13022db2a1254b3367ae67ca2205f991faca3e87368fb0e33a57 | MATLAB | 2,989 | 108 | function [Out] = GetRMSError(sn)
Azimuths = [-75:15:75];
for idx = 1:length(Azimuths)
TargetAzimuth = Azimuths(idx);
% --- lp
ResponseAzimuths = sn.lp_Azi(:,idx);
nTrials = length(ResponseAzimuths);
nTrialsHalf = nTrials * 0.5;
n1 = nTrials/2; % last idx of first half of trials
n2 = ... |
bac1a5f84b5f31fb2b242a3afb2e6781b3c6e411d7b1ec0c295384b2e7801c08 | MATLAB | 2,989 | 76 | function task_gaitERSP_IC(sii, PATH, cfg, fieldName)
% perform spectral PCA à la Seeber
% - sii: vector of subject IDs to be processed
% - PATH: structure with all paths leading to diff processing steps
% generated in naj_neurCorGait_paths
% - cfg: structure with all processing variables generated in naj_neur... |
74213877d31aff853be5f08881fc73cbac7fd67a9dc1f897dc28f51336a6e604 | MATLAB | 2,990 | 97 | function FCMap = WMMultiSeedFC(FunDir,SeedDirS,MaskDir,OutDir)
% SeedDir is a structure
% SeedDir={'a/s.nii';'d/ss.nii'}
if nargin==3
OutDir=[];
end
[funhead fundata] = TMSReadNii(FunDir) ;
dim1 = funhead(1,1).dim(1); dim2=funhead(1,1).dim(2); dim3=funhead(1,1).dim(3);
if iscell(SeedDirS)
... |
da3df1dcaaf5534300750d3c2432d1e5414643fd090705e634c579114bce79db | MATLAB | 2,990 | 67 | function y = BF_TieBreakNoise(y, seed)
% BF_TieBreakNoise Adds tiny, reproducible jitter to break exact ties in y.
%
% Returns y unchanged unless it has a high proportion of repeated values
% (< 90% unique), in which case Gaussian noise with standard deviation
% 1e-10 x std(y) is added: small enough to leave any well-... |
f5d7a085364dac96f8d938c67044df297f1fd05de4bd3f8549adaf814d39feee | MATLAB | 2,990 | 72 | % script to find potential conflict between Matlab functions in the current
% path
%
% A. Delorme, May 25th, 2012
% Copyright (C) A. Delorme, May 25th, 2012
%
% 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 wit... |
62e37e003e9a322eaae05b44eb6d49e8ed6b2c7d7979105c4846179587f92439 | MATLAB | 2,991 | 97 | function [dat dt t0] = loadHWS(fn,group,waveform)
% Function for loading data written by HWS from NI Labview
dat = [];
fid = H5F.open(fn,0,0);
gid = H5G.open(fid,'/');
% iterate through all the wfm_group
for i = 0 : H5G.get_num_objs(gid)-1
% check the name attribute of the wfm_group/id group
id_group = ... |
a329e0311a21a43248427e7552b4f13962618b2f7c740723bd5dfdd0d3a1a27c | MATLAB | 2,991 | 116 | function conmask = xyz2density(XYZmm,mask,V,str,radius,studyweight,varargin)
% conmask = xyz2density(XYZmm,mask,V,str,radius,studyweight,[enter vox xyz flag] AND [no write image])
%
% Take a list of xyz mm coordinates and turn it into a density mask
% with spherical convolution.
%
% XYZmm: n x 3, mask = zeros of corr... |
c44b9a42d1e4c8cb1ab9dd9b504d04e6a4ce877b37326f810fff0b43d8cce9e2 | MATLAB | 2,992 | 103 | function [SH3D,Residuals,b] = spherical_harmonic_shimming(img,mask,order)
dim = size(img);
%% for volume fitting
% find non-zero elements
Indices = find(mask(:,:,:));
% get Cartesian coordinate of the non-zero elements
[x1,y1,z1] = ind2sub(size(img(:,:,:)),Indices);
% solutions of the linear operation
R = img(Indices... |
c2b5934a87c1553abd9f94bfce856bfca24526bb3708f156fc510565143c8451 | MATLAB | 2,994 | 87 | % fit_sortBasisSet.m
% Helge Zoellner, Johns Hopkins University 2020.
%
% USAGE:
% basisSetOut = fit_sortBasisSet(basisSetIn)
%
% DESCRIPTION:
% This function sorts an external basis set according to the conventions
% used in Osprey
%
% OUTPUTS:
% basisSetOut = FID-A basis set container that only contains the basis
%... |
26441006bda41dae89543660e3d7fd196277dd814df23c98aaf4edfe37a71e7d | MATLAB | 2,996 | 68 | %% cluster based rois
% follow the methods here to manually find and save your clusters
% marsbar and spm save a .mat file
% this script reads the .mat file and the base space image that you select
% manually to create rois, based on the resolution of the image you cretaed
% step 1:
% we can open marsbar and choose th... |
3ed592d43397926aa3b8fd23228750b8f8ad838d0d7c6204cf091fe3aa6901d0 | MATLAB | 2,996 | 74 | function out = EN_LZComplexity(y, n, preProc)
% EN_LZComplexity Lempel-Ziv complexity of a n-bit encoding of a time series
%
% ---INPUTS:
% y, the input time series
% n, the (integer) number of bits to encode the data into
% preProc [opt], first apply a given preProcessing to the time series. For now,
% j... |
6fce54d8a0d33b06289bd3123a9b869b21d38ee10a1236c06b243447225897fa | MATLAB | 2,996 | 117 | function result = GKclust(data,param)
%checking the parameters given
f0=param.c;
X=data.X;
[N,n] = size(X);
[Nf0,nf0] = size(f0);
X1 = ones(N,1);
%default parameters
if exist('param.m')==1, m = param.m;else m = 2;end;
if exist('param.e')==1, e = param.m;else e = 1e-4;end;
if exist('param.ro')==1, rho=param.ro;
else
... |
e2986f071ec59b59c5080dad29fb2877863b6576c2dad359afd1be76e9cec37b | MATLAB | 2,996 | 60 | function [Nens,ensId,centInd,delta,rho,templates,predbounds,pcs,bincor] = ensembles_pca(raster,minSpk,prctdata,isHalo,thrMet,npcs,filename)
%
% [Nens,ensId,delta,rho,Ts,sampCent,templates] = subSample_ensembles(raster,minSpk,sampFac,kernel,prctdata,thrMet,savemem,isGpu)
%
% Find ensemble on several subsamples of the ra... |
f4cc13d77fd9831dedeab0215e3c0220d689d2cce6e3fcd3def5779f5b98b27d | MATLAB | 2,996 | 79 | function physio = tapas_physio_fill_empty_parameters(physio)
%fills empty values with default parameters, typically derived from other
%parameters, e.g. time_slice_to_slice from TR and Nslices
%
% NOTE: for real default values that do not depend on other input
% parameters, set them in tapas_physio_new directly!
%
% p... |
1e4d81f87cc69cc45a5630abb6cf329534b4ea3478e3026560f4d22335885112 | MATLAB | 2,998 | 84 | function this = MrAffineTransformation_load_from_file(this, testFile)
% Unit test for MrAffineTransformation Constructor from file
%
% Y = MrUnitTest()
% run(Y, 'MrAffineTransformation_load_from_file')
%
% This is a method of class MrUnitTest.
%
% IN
%
% OUT
%
% EXAMPLE
% MrAffineTransformation_load_from_file
%
%... |
1f401ed04803d590ae0b90f58272d94068e55bd50fbd501ef5062f5830efd609 | MATLAB | 2,998 | 118 | function [x,err,it] = perform_conjugate_gradient(A,y,options)
% perform_conjugate_gradient - perform conjugate gradient
%
% [x,err,k] = perform_conjugate_gradient(A,y,options);
%
% Solves for A*x=y.
% Works both for vector x,y and matrix x,y (parralel soving of many
% linear equations).
%
% Works only for... |
d9e215703cb50f2b881358d0de655b280ca1d372e54b7e45a5924b5bc85ee4c4 | MATLAB | 2,998 | 78 | function [Data, Header] = y_Read(FileName, VolumeIndex)
%function [Data, Header] = y_Read(FileName, VolumeIndex)
% Read NIfTI file Based on SPM's nifti
% ------------------------------------------------------------------------
% Input:
% FileName - the path and filename of the image file (*.img, *.hdr, *.nii, *.nii.gz)... |
16c2855a731c43ed3f72bc40ab7801cc0e8f908576d9d68b342c7bf8dc8b0cb1 | MATLAB | 2,999 | 84 | % logging_fcallstack() - Return the current stack trace as a string
% formatted with the provided format string and
% starting with the preamble
% Usage:
% >> output = logging_fcallstack(message, formatstr, unroll, stack)
%
% Inputs:
% message - The message to print ... |
9895449c93b499b27f48bca949217a43115f7945572da4b3059528660f1ebac9 | MATLAB | 2,999 | 89 | % GAUSS2D - generate a 2-dimensional gaussian matrix
%
% Usage:
% >> [ gaussmatrix ] = gauss2d( rows, columns, ...
% sigmaR, sigmaC, peakR, peakC, mask)
%
% Example:
% >> imagesc(gauss2d(50, 50)); % image a size (50,50) 2-D gaussian matrix
%
% Inputs:
% rows - number of rows in mat... |
c8ddd0f9fd7ec3eba312fadf14879f8c9db2d545785927cbbf2e01e143a3345b | MATLAB | 2,999 | 53 | function [photoFrames,photo_duration,photoOff_duration,photo_subsession,photo_durations] = get_photostim_times(T,session_idx, num_subsession_frames,Fs)
% read photostim times from excel
% num_subsession_frames are the frames within minutes of interests
photo_start_times = []; photo_end_times = []; photo_durations = ... |
307eaf9b68f8004caaa647a10fce5783d7c6acb17c7ba96761078e7080f75107 | MATLAB | 3,000 | 94 | function HalfViolinPlot(data, pos, colour, width, kdeWidthForOnePoint)
% Parameters
% -----------
% data :
% pos : float
% center position on the x axis
% color :
% width : has nothing to do with kde computation, just the plotting (ie.
% not to be confused with bandwidth)
% kdeWidthForOnePoint :
% created May 20... |
32e2c06f70689f219440dd311717912367f5433fedf8e74885d845bbc470f040 | MATLAB | 3,000 | 74 | %{
# pixelwise responses to full-field directional stimuli
-> tuning.OriDesignMatrix
-> preprocess.PrepareGalvo
-> preprocess.Slice
---
regr_coef_maps : longblob # regression coefficients, width x height x nConds
r2_map : longblob # pixelwise r... |
793a5109cb33a60522760b3b0a2fc33c6b7e015fed1e6201ea838905f7ec1e7f | MATLAB | 3,000 | 82 | function simulationOptions = simulationOptions_demo_SL()
%
% simulationOptions_demo
%
% This function is used to make a simulationOptions struct for use in the
% simulation part of the demo. The options should be set to personal
% preference.
%
% Cai Wingfield 7-2010
%__________________________________________________... |
e09ac6ec4b6a13cc75ec71b7bead6c133053f0310551741b9059abfd644eaff2 | MATLAB | 3,000 | 68 | function [] = start_NBSPredict(varargin)
% start_NBSPredict shows welcome message to user and run NBSPredict
% toolbox. It bypasses and immediately starts analyzing the data if a
% configuration file is provided (please check MANUAL to see how to create
% a configuration file). If any configuration file provided,
% sta... |
7081fe66e53ed0d3b62cfb887de8c85d9cf38c85a1699cf6fd3a16c74f5252cf | MATLAB | 3,001 | 93 | % Using Phantom 100x100 example, look at conductance maps interactively
% Author: Aina Frau-Pascual
% Input image
im = phantom(100);
% Change compute_connmatrix flag to true if you want to compute conductance matrix
compute_connmatrix = false;
% Construct mesh structure
Lx = size(im, 1); % domain le... |
b7033afc80185c525f9e3b3537688e4cc8511fb751738d1f9f68b6101ae00127 | MATLAB | 3,001 | 92 | function [score,in,out]=clusterquality(f,S,partition)
%function [score,in,out]=clusterquality(f,S,partition)
%
%PURPOSE
%
%To compute a simple quality (compactness) index for the given
%clusters. The more dense and isolated a cluster is the bigger
%value the index gets; however, if there is only one item in a
%cluster ... |
78accc45ecc7804a62bdfd55647e5e442e624ed158ca41a8b268cefdaa8180cd | MATLAB | 3,004 | 123 | function [pos, mom, ampl, time] = read_asa_dip(fn)
% READ_ASA_DIP reads the dipole position, moment and amplitude
% This importer is designed for fixed-dipole models and only supports
% a limited number of the options that ASA has.
%
% Use as
% [pos, mom, ampl, time] = read_asa_dip(filename)
%
% See also READ_ASA_V... |
06b01d4eee07272bb45d67e6b70f37a5245b1eab85148e6adcf8e3b0f9c76c94 | MATLAB | 3,006 | 120 | function fear_amyHFOtrigReact(basename,varargin)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
% basename='~/data/Fear/triple/booyah180430/booyah180430';
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
%%
param.binSiz... |
c3dd1f7451b0dafb1d584e6ee96526d1723745c0f42eb1fae31af623574c8767 | MATLAB | 3,006 | 98 | function tapas_rdcm_plot_pred(Ep, Y, X, region_id)
% tapas_rdcm_plot_pred(Ep, Y, X, region_id)
%
% Plots Yd_fft vs the linear combination of the 'true' (according to the
% given model) regressors and parameter values for region_id (if it is
% specified) in frequency (separate real and imaginary) and time domain.
%
%... |
483dc18051753f3f75b1629e678021b56438efe65a66f3d6287f05237a9e3599 | MATLAB | 3,007 | 108 | function OUT = tor_knn(data,clas,k)
% OUT = tor_knn(data,clas,k)
%
% tor wager
%
% k nearest neighbor classification of T. Denoeux
% with cross-validation
%
%
% Example:
% Create a fake dataset and test
% x = randn(100,3); y = repmat((1:4)',25,1);
%x(find(y==1),1) = x(find(y==1),1) + 2; % add some discriminability to... |
5bf4025b053efa15740e913c1d581764ae352bac381218641ac04ba65719e2d8 | MATLAB | 3,008 | 81 | % RUNPCA - perform principal component analysis (PCA) using singular value
% decomposition (SVD) using Matlab SVD or SVDS
% >> inv(eigvec)*data = pc;
% Usage:
% >> [pc,eigvec,sv] = runpca(data);
% >> [pc,eigvec,sv] = runpca(data,num,norm)
%
% Inputs:
% data - input data ma... |
61ad991789b4ddf4214c3609149413ea8ebc45fb30dcd0c86deba4e4c03c5191 | MATLAB | 3,008 | 112 | function Test_EDM()
% function test_EDM()
%
% Low-rank Euclidean distance matrix completion
% This test file is related to the paper,
%
% B. Mishra, G. Meyer and R. Sepulchre,
% "Low-rank optimization for distance matrix completion",
% IEEE CDC, 2011
%
% Paper link: http://www.montefiore.ulg.ac.be/~mishra/papers/1112.p... |
1115c71ab31823ea3424f3e8040d2bc30fffc406e12d2160c9d8b5306808dcb0 | MATLAB | 3,009 | 104 | function fear_getAvarageNremWaveletPow(basename,varargin)
% basename='~/data/Fear/triple/karmeliet190901/karmeliet190901';
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName);
%%
param.lfp=basicMetaData.lfp;
param.Ch=[basicMetaData.Ch.hpcTheta,... |
ad0d65e97a04cdd71421892b51d8d96a9e000c0eb281ba0eb32b8eef6e687731 | MATLAB | 3,009 | 107 | function hhh=tapas_uniqc_vline(x,in1,in2)
% function h=tapas_uniqc_vline(x, linetype, label)
%
% Draws a vertical line on the current axes at the location specified by 'x'. Optional arguments are
% 'linetype' (default is 'r:') and 'label', which applies a text label to the graph near the line. The
% label appears in... |
b1d26962d46edd5aa148712dc58673a69251072b304266b61c97ff609d4f450b | MATLAB | 3,009 | 126 | function varargout= flatColorMap(n,L,r,pos,useCenter)
% colormap=flatColorMap(n,L,r,pos,useCenter)
% make color maps with similar brightness
%
% default values
% n (8): number of color;
% L (60): brightness (L in Lab color, 0 - 100)
% r (0.9): radius on a-b plane (0-1), regulates color saturation
% pos ('octagon'... |
2f1ef6dee1b920503e222bcf56016b1947942c217a60c3eeb94e17a3be42de37 | MATLAB | 3,010 | 72 | function task_GA_footprint(PATH, cfg, fieldNames)
% Calculated the gait artifact footprint proposed by Jacobsen et al.,2020
% Since data from the best cluster after independent component clustering
% is included, of which not every subject is part of, only the footprint of
% the group-averaged data will be calculated
%... |
79d0c98aae52dc72a552161ab7c487b0fd00a0c8327220c8f520e7a44c3ae828 | MATLAB | 3,011 | 111 | function cell_sig = CellsortApplyFilter(fn, ica_segments, flims, movm, subtractmean)
% cell_sig = CellsortApplyFilter(fn, ica_segments, flims, movm, subtractmean)
%
%CellsortApplyFilter
% Read in movie data and output signals corresponding to specified spatial
% filters
%
% Inputs:
% fn - file name of TIFF movie fi... |
5c12ce67ed14fd5ca5ad1a8abeb0934a54e1e1ce57bd6422541b3835da01ea34 | MATLAB | 3,012 | 82 | function out = IN_MutualInfo(y1, y2, estMethod, extraParam)
% IN_MutualInfo Mutual information of two data vectors.
%
% Uses the information dynamics toolkit implementation.
%
% ---INPUTS:
%
% y1: input time series 1
% y2: input time series 2
%
% estMethod: the estimation method used to compute the mutual informati... |
107951860e7f9ffc7c6d1c1f0786ff72c7a984f9146d988b4fd862eb45b6c2e5 | MATLAB | 3,014 | 85 | classdef convertIntegrationTest < matlab.unittest.TestCase
%CONVERTINTEGRATIONTEST End-to-end smoke test for petraToCT.convert.
%
% DESCRIPTION:
% Runs the full debias -> segment -> normalise -> HU map pipeline
% on the small PETRA fixture and checks that the output
% pseudo-CT file ... |
edae1f5af21fc7cfbe4ebf9ca26683c7cb56161a78a87b6284f044c8d19be916 | MATLAB | 3,014 | 116 | function afni_fig_interface(src, evnt)
cf = gcf;
figure(src);
% evnt
ud = get(src,'UserData');
if (isempty(ud) | ~isfield(ud,'axes_lock')),
ud = default_ud();
set(src,'UserData',ud);
end
if ( lower(evnt.Character) == 'l' ),
ud.axes_lock = ~ud.axes_lock;
set (src,'UserData... |
042d0aba8929c047c554a63d97fbffefdb161d64ff155100ce26079ef7c1f43d | MATLAB | 3,016 | 85 | function [cs,index] = sort_nat(c,mode)
%sort_nat: Natural order sort of cell array of strings.
% usage: [S,INDEX] = sort_nat(C)
%
% where,
% C is a cell array (vector) of strings to be sorted.
% S is C, sorted in natural order.
% INDEX is the sort order such that S = C(INDEX);
%
% Natural order sorting sorts ... |
7b0338d955da218d1b602a9a750b69234bf6b63e0519adb2de643c6f83e0013a | MATLAB | 3,016 | 96 | function this = add_dims(this, iDim, varargin)
% Adds additional dimensions to existing dimInfo
%
% Y = MrDimInfo()
% Y.add_dims(iDims, varargin)
%
% This is a method of class MrDimInfo.
%
% IN
% iDim (vector of) dimension indices to be added (e.g. 3 for 3rd
% dimension)
% o... |
a25bcc958875d2c5b8588d9a19e01d6a1c87d7bd3490588e1546302a1beac3f0 | MATLAB | 3,017 | 64 | function out = SY_DriftingMeanCUSUM(y)
% SY_DriftingMeanCUSUM Parameter-free CUSUM test for a drifting mean.
%
% SY_StatAv and SY_DriftingMean both test for a drifting mean by splitting the
% time series into segments -- requiring a choice of segment length or number
% of segments. This is the analogous test with no f... |
36e8dd51fcfeb83d4fe140b83ec95483dc0e519aac5bd9b561d63262d5832bca | MATLAB | 3,019 | 93 | % LOADELEC - Load electrode names file for EEGPLOT
%
% Usage: >> labelmatrix = loadelec('elec_file');
%
% Author: Colin Humprhies, CNL / Salk Institute, 1996
%
% See also: EEGPLOT
% Copyright (C) Colin Humphries, CNL / Salk Institute, Aug, 1996
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the docu... |
055b90a39d90c462186858ceab0f6ddc31956eb61a11a6c1ab2139959b2cfe71 | MATLAB | 3,020 | 85 | %{
# masks created manually
-> meso.Segmentation
%}
classdef SegmentationManual < dj.Computed
properties
popRel = meso.SummaryImagesAverage
end
methods(Access=protected)
function makeTuples(self, key)
images = ne7.mat.normalize(fetch1(meso.SummaryImagesAverage & key,... |
c85ee482bde10f9373707e844836460e999ee3d2e8d796a561102faa4e458999 | MATLAB | 3,021 | 82 | function DataSegmentation( BASEdir )
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Wrote by David André Barrière 09th September 2022
% This function permit to create and launch Normalization and Segmentation
% processing using SPM8 function.
% Usage : set BASEdir variable with your ... |
7d318a40fdcf9c6cb846f7970130a72cfe920126530ac223696b0396169db6bc | MATLAB | 3,022 | 76 | % EEG_URLATENCY - find the original (ur) latency of a time point in
% the original continuous data.
%
% Usage:
% >> lat_out = eeg_urlatency( event, lat_in );
%
% Inputs:
% event - event structure. If this structure contain boundary
% events, the length of these events is added... |
8023c777acb1afe486d95067b1f5d9891db74c423241789c42e6833b7f2f10bc | MATLAB | 3,023 | 108 | function status = Hide(parameter1,parameter2)
%Hide - Hide (or show) existing or future figures, e.g. to speed up batch processing.
%
% USAGE
%
% Hide(figures,'on') % hide these figures
% Hide(figures,'off') % un-hide this figure
% Hide('all') % hide all existing figures
% Hide('none') ... |
c2775d571ad8c3766c185ce545612ca17184cfe0b22292df264d9e19f458b8b0 | MATLAB | 3,023 | 118 | function [LatOpt, LatMdl, BlkInf, RPE, Belief, Kappa] =...
GenerateLatencyData_Bayes_subopt_onlylambda(params, ratTrial,...
gen_arg, noise_arg, noise_params)
%%Similar to GenerateSynthData_Bayes, but with two new parameters: lambda
%%(prior weighting) and lapse rate. cmc 8/19/21.
%% Pull Parameters
H0 = 1/40;
... |
ef86dc893797732b21a679b3736d4a359ecca59562bac890f8aa4199ef108505 | MATLAB | 3,024 | 87 | function [dyn_wc, mean_wc] = dyn_wavcoh_pleakage(data, options)
% Computes the wavelet coherence (WC) with pairwise
% leakage correction/pairwise orthogonalisation
% Tewarie et al., 2019 Tracking dynamic brain networks using high temporal
% resolution MEG measures of functional connectivity
... |
0205cc05ae9e61217b5947b89d964a924b5cd0e910f4e88c5b1e86e6a8e5c1ae | MATLAB | 3,025 | 89 | function verbose = tapas_physio_plot_raw_physdata(ons_secs, verbose)
% plots raw data from physiological logfile(s) to check whether read-in worked
%
% fh = tapas_physio_plot_raw_physdata(ons_secs)
%
% IN
% ons_secs structure with the following fields
% .t [Nsamples, 1] time onsets vector (in seconds... |
0f260c4e734ba842a426a43100107cf6e9eda5868d5202df5a6f737ef69bf36a | MATLAB | 3,026 | 123 | function coactPaper_tableS07()
labelWeight=true;
labelCase=true;
labelSize=9;
letGapX=5;
letGapY=5;
fontsize=6;
close all
fh=initFig('width',18.6,'height',2.3,'font','Arial','fontsize',fontsize);
x=1;y=1;
panel_01(x,y,7);
drawnow();
print(fh,sprintf('~/Dropbox/FearAnalyses/paper/figure/tableS07_%s.pdf',datestr(now,... |
dcf4da307f95a233f42738505217c73ce0d9b44460d10f350fa6a5be22dfd17f | MATLAB | 3,026 | 87 | function [COEFF, SCORE, LATENT, EXPLAINED, MU] = tapas_physio_pca( timeseries, method )
% Performes the Principal Component Analysis (PCA)
%
% [COEFF, SCORE, LATENT, EXPLAINED, MU] = tapas_physio_pca( timeseries )
%
% IN
% timeserie (nVoxels x nVolumes)
% method 'svd' or 'stats-... |
fe25d39e9e7e931695d04bd62a59b1145d43d8b7615cb2a6db7fc85944d12e0d | MATLAB | 3,027 | 90 | % LAPLAC2D - generate a 2 dimensional laplacian matrice
%
% Usage :
% >> [ gaussmatrix ] = laplac2d( rows, columns, sigma, ...
% meanR, meanC, cut)
%
% Example :
% >> laplac2d( 5, 5)
%
% Inputs:
% rows - number of rows
% columns - number of columns
% sigma - stand... |
aa7037c121f1f07361d8550632de92a9581a33aa310c9b36fdb6c877f98f691b | MATLAB | 3,030 | 124 | function tnet = vl_simplenn_tidy(net)
%VL_SIMPLENN_TIDY Fix an incomplete or outdated SimpleNN network.
% NET = VL_SIMPLENN_TIDY(NET) takes the NET object and upgrades
% it to the current version of MatConvNet. This is necessary in
% order to allow MatConvNet to evolve, while maintaining the NET
% objects clea... |
ae703c182978a430270f5cd347d7c8a6055c1a47da240296b2a9ec65d6059405 | MATLAB | 3,030 | 84 | function [newx, newkey, info, hooked] = applyHook(problem, x, storedb, key, options, info, last)
% Apply the hook function to possibly replace the current x (for solvers).
%
% function [newx, newkey, info, hooked] =
% applyHook(problem, x, storedb, key, options, info, last)
%
% Applies the options.hoo... |
e25a8e6acc28db6f2ff4c2fdff89f174099806398bc50bbfe5ec39ba1aa17134 | MATLAB | 3,030 | 86 | %% Figure 5 main
YOURDATAPATH = '';
savePath = [YOURDATAPATH '/' 'models' '/'];
%% Load model outputs
load(sprintf('%sall_regression,M1,angles,radrates', savePath), 'outputsM1_rr')
load(sprintf('%sall_regression,S1,angles,radrates', savePath), 'outputsS1_rr')
%% Panel A and B:
% RADICaL decoding for mouse 1
plotVE(ou... |
72f908ed5709e55a339a5e4b402535efa8748cb9de3d9e8d966cc30e88c161cf | MATLAB | 3,033 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {''};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-control01_task-YOURTASK_run-1';
matlabbatch{1}.spm.tools.physio.log_files.vendor ... |
250083728499fd1c70bfa0acb0a78441c0157bcee62f5b2ed210b616a8d73acf | MATLAB | 3,034 | 81 | function roi_statistics()
% Correlate ROI values with self-construal and TAS-20 scores.
%% USER SETTINGS
roiValuesFile = 'D:\path\to\roi_values.csv';
selfConstrualFile = 'D:\path\to\SC_Collectivism_forMRI.csv';
tasFile = 'D:\path\to\TAS20_with_demographics_N40_z.csv';
outputDir = 'D:\path\to\roi_statistics';
expectedN... |
fc9825569d3f0ce17036a558600649527343892c7cca2d0d25c247f46551ef70 | MATLAB | 3,034 | 76 | function create_volume_meshes(input_img, maxvoxelvolume, input_coordsys, ...
output_coordsys)
%
% Input: input_img <string> fullpath to folder, where the results of
% mysegment.m are stored
% maxvoxelvolume <float> desired maximal volum... |
4285555dddf072e520af2ef44cb7278da3ac3a1b925c986ceec51cd7b35a4371 | MATLAB | 3,035 | 84 | function [cpx_file, Ref, img_array, img_body ,noise_array, noise_body] = loadRefScan(cpx_file)
%% [cpx_file ,Ref, img_array, img_body, noise_array, noise_body] = loadRefScan(cpx_file)
% Loads a Philips coil reference scan (*.cpx format).
%
% Input:
% cpx_file Coil sensitivity scan (*.cpx).
%
% Output:
% ... |
e9d2ed2fc469307491c8343e3aae175faf6123e24d7a6f24b8ef10a062d88bbe | MATLAB | 3,036 | 81 | function [hasSPM,OspreyVersion] = osp_CheckRunPreviousModule(MRSCont, module)
%% osp_CheckRunPreviousModule(MRSCont, module)
% This function checks that all required modules have been run prior to
% executing the module name that is passed as an argument to this
% function.
%
% There is no output, the function ... |
4c50dd99141cd8ac32b4f46cf38d1a8669ee4a8099cb02662babe237b3778776 | MATLAB | 3,038 | 91 | function [indx, label, blockindx, blocklabel] = labelcmb2indx(labelcmb, label)
% LABELCMB2INDX computes an array with indices, corresponding to the order
% in a list of labels, for an Nx2 list of label combinations
%
% Use as
% [indx] = labelcmb2indx(labelcmb, label)
% or
% [indx] = labelcmb2indx(labelcmb)
%
% Lab... |
8151281196b823720ce39e6ae21f8d73d6ade4658f32369498bf3f4702e59208 | MATLAB | 3,038 | 77 | function test_suite = test_expDesign %#ok<*STOUT>
try % assignment of 'localfunctions' is necessary in Matlab >= 2016
test_functions = localfunctions(); %#ok<*NASGU>
catch % no problem; early Matlab versions can use initTestSuite fine
end
initTestSuite;
end
function test_exDesignBasic()
in... |
125ee4ea60f8bf872c3f0c1a5f19efdb192a5522eb6312c3c6b5600b3effea88 | MATLAB | 3,039 | 102 | function [y, pst] = tapas_ceode_gen_erp(P, M, U)
% [y, pst] = tapas_ceode_gen_erp(P, M, U)
%
% Compute predicted data based on a specified DCM, with variable integrator
% specification.
%
% Adapted from spm_gen_erp.m (original function lincense below).
%
%
% INPUT
% P struct parameter structure
%... |
9798d881f8858b5a8d4f8d3a454fdb853f7214c2b7ba9574afb101407bf6ef1d | MATLAB | 3,039 | 101 | function [tracedtensor] = diagsum(tensor1, d1, d2)
% C = DIAGSUM(A, d1, d2) Performs the trace
% C(i[1],...,i[d1-1],i[d1+1],...,i[d2-1],i[d2+1],...i[n]) =
% A(i[1],...,i[d1-1],k,i[d1+1],...,i[d2-1],k,i[d2+1],...,i[n])
% (Sum on k).
%
% C = DIAGSUM(A, d1, d2) traces A along the diagonal formed by dimensions... |
2825a0ad32c429401c9fa106e65f0ded3649ceef79e199bbc688bb9d73633cfd | MATLAB | 3,041 | 88 | function fear_swrTrigIcaReac(basename,varargin)
% basename='~/data/Fear/triple/achel180320/achel180320';
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
load([basename '.basicMetaData.mat']);
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
%%
param.tWindow=2... |
2f0362c432869b790f5a0b8d2b2d1a2459f6f7a4a1c4456527e531d7c4702bef | MATLAB | 3,041 | 105 | function this = plot_stat_images(this, varargin)
% plots statistical images (mean/snr/sd/diffLastFirst) in comprehensive
% plot for several slices
%
% Y = MrSeries()
% Y.plot_stat_images('ParameterName', ParameterValue)
%
% This is a method of class MrSeries.
%
% IN
% 'ParameterName'
% 'selectedSlices [1, n... |
70388e452d202cba65fa4c667d2b6f2399ad781de2012924f0b54050a1bae4e7 | MATLAB | 3,042 | 64 | function osp_OverviewTabChangedFcn(src,~,gui)
%% osp_OverviewTabChangedFcn
% This function is triggered when the overview tab is changed. It refreshes
% the figure.
%
%
% USAGE:
% osp_OverviewTabChangedFcn(src,~,gui);
%
% INPUT: src = handle of the fit tabs
% gui = gui class containi... |
845a8b8bac470a13076638a8738622e933898f297d80c59a3388fa65361d2ed8 | MATLAB | 3,042 | 90 | % fit_runFit.m
% Georg Oeltzschner, Johns Hopkins University 2019.
%
% USAGE:
% [fitParams, resBasisSet] = fit_runFit(dataToFit, basisSet, fitModel, fitOpts);
%
% DESCRIPTION:
% This function performs spectral fitting of the data in dataToFit, using
% the basis set in basisSet, using a set of options defined in fitOpts... |
bd6e7960849fb755a079ce959f9555c8ea7d3be6dd104bba2568343ea1961303 | MATLAB | 3,042 | 106 | function [output_file] = Intarpolate_and_align_AP(name, data_file, Blender_file, channels, start_point, end_point)
% input:
% name: string, name of subject
% data_file: full path to ap.bin file
% Blender_file: full path to mat file with blender output
% channels: a vector with all cha... |
10751c5f6a4d5303236f6e6ace49689825dde3bd18f1fdba31e4c318eb9fe8d9 | MATLAB | 3,044 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {''};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-s999_task-random_run-99';
matlabbatch{1}.spm.tools.physio.log_files.vendor = 'BID... |
226f892d52b454fa11e2dfd88b1ca445971a51c2d39ce68a5749c97c9f4e134a | MATLAB | 3,045 | 71 | function export_in_set(app, openfilename)
% export an input eegfile into a .set
events = ''; % In case no events in input file
nOutFiles = 1; % FREQ files will yield 1 file per frequence, other formats: just 1
% Load file
[~,FileName,FileExtension] = fileparts(openfilename);
if strcmpi(FileExtensi... |
e8ab7d40a6164c6d1d3a972a0e4e29f45224a34443ee6f9110dc8aeeeb407f79 | MATLAB | 3,045 | 97 | function H = decode_nifti1(blob)
% DECODE_NIFTI1 is a helper function for real-time processing of MRI data
%
% Use as
% H = decode_nifti1(blob)
%
% Decodes a NIFTI-1 header given as raw 348 bytes (uint8) into a Matlab structure
% that matches the C struct defined in nifti1.h, with the only difference that the
% vari... |
09c879b9d18981479b0f49215ed8a696cf3be8b8fe49a1099f99b92ffee3649e | MATLAB | 3,046 | 84 | function plotSingleChannel_stackedTrials(params, spectra, spectralData)
% plot single stracked single trials for all freq. bands (ch-by-ch)
% spectra =
% data: [129×85×57×188 double] = 4D: [freq x time x chnl x trials]
% freq: [1×129 double]
% time: [85×1 double]
% labels: [1×188 double]
... |
7ca628ff8c8e4be3d265ca03d8ffcb6a39a9068dfa236ecbe939c91fd2f9c141 | MATLAB | 3,046 | 95 | function output = poolVar(matFileName,varargin)
% poolVar(matFileName,varargin)
% poolVar(matFileName,'presetType',varargin)
%
% For each session, load
% [rootDir]/[sessionName]/[subDir]/[[sessionName] [delimiter] [matFileName]]
% as output.(sessionName)
%
% when presetType is set as 'base', defalut option is follow... |
e6bd43e7ac705e858bef7970fe491742b64c7f7698cebaccf812e1ae8b69d335 | MATLAB | 3,046 | 80 | function useCh = ch2roi_getSignificance(groupInfo, signif_criteria, ch_hVals, ch_xVals, method)
% determines if to use the channel based on 'signif_criteria'
% if the channel is significantly activated for longer than a threshold
% value, useCh = true (else false)
if nargin < 5
method = 'contEpochs';
end
%% selec... |
aa0c48ce53d54650be2007a044d7792828aeb573d32bfce9e84edaa3fa8b6015 | MATLAB | 3,047 | 73 | % (C) Copyright 2020 CPP visual motion localizer developpers
%direction matrix has motion directions in sequential order
%one block: 0 180 0 180 0 180...
%another block: 90 270 90 270
%targets introduced at the positins of fixation targets (repeation of
%either of the direction chosed with equal probability
function ... |
b70fc9902e98d2ff9b6e94e8138710dce65700b86a564d19665bbbe51dda05ff | MATLAB | 3,047 | 107 | function [Cstar, gamma, T] = clsutil_shrinkage(X, opt)
%CLSUTIL_SHRINKAGE - Shrinkage of covariance matrix with 'optimal' parameter
%
%Synopsis:
% [CSTAR, GAMMA, T]= clsutil_shrinkage(X, OPT);
%
%Arguments:
% X: DOUBLE [NxM] - Data matrix, with N feature dimensions, and M training points/examples.
% OPT: PROPLIST -... |
1aa5bc1513a02cdd47d36d2ebdb5cf490e3b792e6d2bc099c2b220c80d7b7143 | MATLAB | 3,048 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 3;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-control01_task-YOURTASK_run-1';
matlabbatch{1}.spm.tools.physio.log_fil... |
8499a1f2a849e4840a7df652f1e8d535059808da1c7c3b4c36e8f792457b75fb | MATLAB | 3,048 | 87 | function pred = knnpred2(Xtest,X,class,class_exp,K,dist_type,pret_type)
% prediction of new samples with calculated model
%
% pred = knnpred(Xtest,X,class,K,dist_type,pret_type)
%
% ------------ INPUT ---------------------------------------------------
% Xtest: dataset to be predicted [n_test x p] n objects, p ... |
d566b6c71b49a5e3e5745530968edc8fb9436c8c231a9a12858008c1ab6196cc | MATLAB | 3,048 | 90 | %% h = sepia_handle_panel_qsm_NDI(hParent,h,position)
%
% Input
% --------------
% hParent : parent handle of this panel
% h : global structure contains all handles
% position : position of this panel
%
% Output
% --------------
% h : global structure contains all new and other handle... |
0578123a19b4ac318e42435829caf9499f409e24d0c26ca34c594bc13248482a | MATLAB | 3,049 | 92 | function [gradf, err] = tapas_riddersgradient(f, x, varargin)
% Calculates the gradient of the function f at point x according to Ridders' method:
%
% Ridders, CJF. (1982). Accurate computation of F'(x) and F'(x) F''(x). Advances in Engineering
% Software, 4(2), 75-6.
%
% INPUT:
% f Function handle o... |
87f7d4a16580ac601798c8acbe11801a0c45a92678c9f0f3c4fe58ff410fbaf1 | MATLAB | 3,049 | 79 | % GENERATE_NLS_DATA Solve the Nonlinear Schrödinger (NLS) equation
% using a split-step Fourier method via ode45.
%
% Equation: i*psi_t + (1/2)*psi_xx + |psi|^2 * psi = 0
% Initial condition: psi(x, 0) = 2*sech(x) (2-soliton solution)
%
% This script generates the spatiotemporal data (psi_... |
d0f15ecf00bc48c92e004aa13ebb9bc2380c3038f7f51e56713aff5dbfa4cef9 | MATLAB | 3,049 | 117 | function far = far_for_threshold(th,hsi,det_img,filt,params)
% far = far_for_threshold(th,hsi,det_img,filt,params)
%
% finds the false alarm rate for a given threshold in the detector output image (det_img)
%
% 5/7/2013 - Taylor Glenn - tcg@cise.ufl.edu
if ~exist('params','var') || isempty(params)
params = Bullw... |
6acf6213cc483cc40a7119c648023101e198394d45ad68a66355b331afe07ba8 | MATLAB | 3,050 | 91 | function map = osp_generateMRSImap(MRSCont, kk, nominator_spec,denominator_spec, nominator, denominator)
%% map = osp_generateMRSImap(MRSCont, kk, nominator_spec,denominator_spec, nominator, denominator, figTitle)
% Creates a matrix with the corresponding metabolite map
%
% USAGE:
% out = osp_plotFit(MRSCont,... |
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