sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
659fbc10d1e421c199954210d4cd84f011dffc62000fb3467f62e556a272dbd2 | MATLAB | 4,940 | 139 | % THIS SCRIPT RUNS lassoPCR models for WITHIN-PERSON CONTRASTS it will
% exclude conditions which have contrast values of 0 and contrasts that are binary (1/-1)
%
% Contrasts are pecified in DAT.contrasts
%
% This script makes sense to run if you have contrasts that are not simple
% A vs. B (1 -1) comparisons. e.g., if... |
296c7dcb19ab34076ca5459ec0670d8675e5d45dd38834655c78b49ca0d8f08a | MATLAB | 4,942 | 137 | function handles = dan_data_check(handles)
% Checks that the score and ar files are the same dimensions as
% the data
%%
% Authors: Dan Denis
% Date: 2021-07-14
%%
% Check the sleep stages
stageFields= fieldnames(handles.psg.stages);
stageFields(cellfun(@isempty, regexp(stageFields, 's\d', 'match'))) = [];
for... |
7620e4bd55ad0fd9ebca328b5471c5857f1c821f60bed776c4a4d2a5fa7561b2 | MATLAB | 4,942 | 144 | function ts = run_init_cstminput_periodic(topology,homparam,hetparam,stiminput,init)
% RUN with Initial Conditions, or zero trivial conditions if init = NaN;
% Input is specified by user
% Periodic boundary conditions
% Takes in input of model parameters, timesteps and lengthsteps.
% Returns timeseries at each point.
... |
bd8f696690b7e01fe20a2d0086f397e64ded5b28b36d39fa5ab8f863fd2f1fc6 | MATLAB | 4,944 | 145 | function [warped]= individual2sn(P, input)
% INDIVIDUAL2SN warps the input coordinates (defined as Nx3 matrix) from
% individual headspace coordinates into normalised MNI coordinates, using the
% (inverse of the) warp parameters defined in the structure spmparams.
%
% this is code inspired by nutmeg and spm: nut_mri2m... |
c904d654a095856fe5f32d8d58659460c77747ea49c8cdcfcaba04918c808556 | MATLAB | 4,949 | 111 | function [ROC_AUC_val roc_curve] = get_AUC(target_present_vals, target_absent_vals)
% This helper function calculate the area under an ROC curve based on a vector of values
% when a target was present and a vector of values when a target was absent.
%
% Input params:
% target_present_vals: column vector of va... |
fd2d3b5b2afc94e8eb19c2e86ef4ca2c2a4bb6565d11911d94e9dbc3cda3395c | MATLAB | 4,954 | 81 | % Specialized analyses for FMAToolbox.
%
% Firing map and curves, etc. (place cells, grid cells, head direction cells).
%
% FiringCurve - Compute spatial firing curve (e.g. for a head direction cell).
% FiringMap - Compute spatial firing map (e.g. for a place cell).
% PhaseCurve ... |
d1f67332b2deeff40e2d9628851b0f4864e3ec6a97c0b5d006fd575b71591126 | MATLAB | 4,955 | 131 | function f=readPrairie2(froot,cycle,label,chno,imno)
% Usage ... f=readPrairie2(froot,cycle,label,chno,imno)
%
% PrairieView data reader
% This function will read individual images if the froot name includes the
% file extension. If froot ends in a slash to indicate a folder, it will
% read all images within cycles, la... |
3cc8a889a450ebf44f5b01f415497ae70d623d6cdb3f63af6ea965bddafb4e2d | MATLAB | 4,957 | 119 | function outdir = LaBGAScore_export_scaled_contrasts(resultsdir, conidx, outdir, varargin)
% Write the second-level contrast images to disk, one .nii per subject.
%
% :Usage:
% ::
% outdir = LaBGAScore_export_scaled_contrasts(resultsdir, conidx, outdir, ...)
%
% WHY THIS EXISTS. The decoding wrapper points cfg.files... |
191d7ec95c7a3e0c24c38734134dd6760fdbf37a442083487dc95c0edba4b71c | MATLAB | 4,958 | 155 | % Section 7.4.3: Probability bounds example with Voronoi diagram
% Boyd & Vandenberghe "Convex Optimization"
% Original version by Lieven Vandenberghe
% Adapted for CVX by Michael Grant, 2005/12/19
% Generates figures 7.5-7.8
% The constellation points. Feel free to change them, but they must
% produce a valid Voronoi... |
0a62f41fddd6537ec1dd6e41580cf4347f1465284539f71196303dfd0178df92 | MATLAB | 4,963 | 83 | classdef Detrender < uint8
enumeration
HIGHPASS (1) % highpass filter
BUTTER_HIGH (2) % butterworth highpass filter
MOVMEDIAN (3) % movmedian subtraction
MOVNTHPRCT (4) % movmin subtraction
... |
4632f86e1acd70339cfccb5e39e120b90f166bc20aa87ef51187035a656148d4 | MATLAB | 4,964 | 140 | function [dist,binned,stats] = CircularDistribution(angles,varargin)
%CircularDistribution - Compute circular distribution and statistics.
%
% USAGE
%
% [dist,binned,stats] = CircularDistribution(angles,<options>)
%
% angles angles in radians
% <options> optional list of property-value pairs (se... |
ab551dac78f6644a448da4cd01e79c2ec24c0aa9408e355a452c5385633219fd | MATLAB | 4,964 | 117 | % written by Yiyuan Han, Essex BCI-NE Lab, 10/01/2020
% Multi-class classifiers for each participant
%% Only remain the participants with complete data in all of 4 classes
classes = ['O' 'H' 'W' 'S'];
classNum = length(classes);
parIndices = find((ismember(blockTagsAC(:,1),validParticipants))&(ismember(blockTa... |
ac6ccda13b767be01418f92db7fc9d8e7ab514a3a053fbb424bbbae65e1efd62 | MATLAB | 4,964 | 145 | function [Y0,design_names,nDesignScores] = myPLS_getY(behavMode,...
behaviorData,grouping,group_names,behav_names)
% Number and IDs of groups
groupIDs = unique(grouping);
nGroups = length(groupIDs);
% Number of behavior scores
nBehav = size(behaviorData,2);
% Number of subjects
nSubj = size(behaviorData,1);
% ... |
8b5778eab9094e1e98c950d5b2041a7ec146e1023318b274fc197bd96206c269 | MATLAB | 4,968 | 58 | % configure file for DTI tools
% BATCH system (Volkmar Glauche)
%
% File created by Susanne Schnell
%%
function dtijobs = dti_cfg
%_______________________________________________________________________
% dtijobs DTI tools
%_______________________________________________________________________
dtijobs = cfg_c... |
f9466c6db56437a8aed996dfb424e97352f2ba67e0d1f60d560f77cfe695a4a0 | MATLAB | 4,970 | 116 | % imagescloglog() - make an imagesc(0) plot with log y-axis and
% x-axis values
%
% Usage: >> imagescloglog(times,freqs,data);
% Usage: >> imagescloglog(times,freqs,data,clim,xticks,yticks,'key','val',...);
%
% Inputs:
% times = vector of x-axis values (LOG spaced)
% freqs = vector of y-axis val... |
7498fc3d11c9dd9f03e2ff2300229217e68809161f33e67e7277fb3ae100acd3 | MATLAB | 4,972 | 130 | function [lh_labels, rh_labels, LI_lang] = CBIG_MSHBM_Epilepsy_LI(params)
% ====================================
%% Help
% ====================================
%
% CBIG_MSHBM_Epilepsy_LI
%
% Estimates an individual-specific 15-network cortical parcellation for a
% patient with drug-resistant epilepsy using the NIH 34-s... |
68ced3bfd24fbf5d23f6da25d2144e11f49695b0eeb7e630c656155777f7f50c | MATLAB | 4,975 | 139 | function [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave,numsp1,numsp2)
% Function to compute lower and upper confidence intervals on the coherency
% given the tapered fourier transforms, errchk, trialave.
%
% Usage: [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave,numsp1,numsp2)
% Inputs:
% C - coherence
% ... |
14e7f0487aff24bf207aff3634ac381a896f190bb208dac1a99e28e62847d4cd | MATLAB | 4,978 | 120 | % std_readtopoclust() - Compute and return cluster component scalp maps.
% Automatically inverts the polarity of component scalp maps
% to best match the polarity of the cluster mean scalp map.
% Usage:
% >> [STUDY clsstruct] = std_readtopoclust(STUDY, ALLEEG, cluste... |
4500af0ca40bb6125a944e6916d3d91d474e92adb315e4b385067fdb72450fc3 | MATLAB | 4,979 | 158 | % eeg_laplac() - gives the laplacian for the data contained in EEG
% for the values 1:stepl:end with electrodes position gived by EEG.chanlocs.
% Step must be a number betwen 1 and length(EEG.data)
% The metod used for computig the laplacian is the described by Perrin et al.
% 1989 using a spline interpolation betwee... |
9154a0c48c01dc586e2172319da54900ce880c08024a4b73ad1be8f526a2d9cd | MATLAB | 4,979 | 130 | % dipfit_nonlinear() - perform nonlinear dipole fit on one of the components
% to improve the initial dipole model. Only selected dipoles
% will be fitted.
%
% Usage:
% >> EEGOUT = dipfit_nonlinear( EEGIN, optarg)
%
% Inputs:
% ...
%
% Optional inputs are specified in key/value ... |
330ad0346d53e794159412eaccaf2c8829aefe480b69c9940facb879a12c32fe | MATLAB | 4,984 | 139 | % pop_eventstat() - Computes and plots statistical characteristics of an EEG event,
% including the data histogram, a fitted normal distribution,
% a normal ditribution fitted on trimmed data, a boxplot, and
% the QQ-plot. The estimates value are printed in a panel ... |
ee5c7cf43b158edef0713b08e82022e6e723a2877de082c7b3bceb66cbd1facf | MATLAB | 4,990 | 121 | function [left right] = getPFNdata(allflies,trialtypes,flies,datatype,roi_idx)
% This function produces summary data structures for the left and right
% halves of the PB for PFN intensity data.
% Be sure to clear the values of 'left' and 'right' before running the
% function.
% roi_idx should be
% [1,2] for ... |
06af2199bfdb28439eb16a9907c0715d5a43a21c704d1d0b7352aa8d30e4cd9f | MATLAB | 4,992 | 145 | function imwrite2tif(varargin)
% IMWRITE2TIF Write image to tif file with specified datatype.
% IMWRITE2TIF(IMGDATA,HEADER,IMFILE,DATATYPE) exports IMGDATA with HEADER
% to TIF file named IMFILE. HEADER is usally obtained by IMFINFO from
% original image file, and it can also be left empty. String DATATYPE
% ... |
1681acce6f5ba302061052920ada4fedbf69746d4e8419acde51dff76c0ad5ce | MATLAB | 4,992 | 165 | function [fig, varargout] = draw_surface_parcellation_dull(surface_to_plot, parc, hemisphere, medial_wall, with_medial, cmap)
% draw_surface_parcellation_dull.m
%
% Draw parcellation on surface using a defined colormap with dull plot lighting
%
% Inputs: surface_to_plot : surface structure with fields
% ... |
6145b4c151163df14fcc8fd44a9b56f4da6a0bf6723a839e405e402ee426f2aa | MATLAB | 4,993 | 130 | function ProcessFluordata(flydata,name,per)
matfiles = dir('*f*.mat');
for f = 1:length(matfiles)
load(matfiles(f).name)
if matfiles(f).name>10
if matfiles(f).name(11)=='1'
disp('yes')
flydata = res1;
elseif matfiles(f).name(11)=='2'
flydata = res... |
91ded70b0cf24f141a7850d73335628064586f4cff0490851d5ccd42ac9796b1 | MATLAB | 4,993 | 86 | function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencysegc(data1,data2,win,params)
% Multi-taper coherency, cross-spectrum and individual spectra with segmenting - continuous process
% computed by segmenting two univariate time series into chunks
%
% Usage:
% [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencysegc... |
bc7a7eb0f40d2743ca30146d2fe2b4b9f6e607e1961ceb5e3b5ea5992a100990 | MATLAB | 4,996 | 130 | function [firingMaps] = bz_firingMap1D(varargin)
% USAGE
% [firingMaps] = bz_firingMap1D(spikes,behavior,lfp,tau)
%
% INPUTS
%
% spikes - buzcode format .cellinfo. struct with the following fields
% .times
%
% behavior - buzcode format behavior struct
%
%
% tau - desired smoothing window
... |
77828046275c299e6bef8d829825310018c63787b2823ed16ae17a8dd688c00a | MATLAB | 4,999 | 151 | classdef ea_conda_env
properties
name;
yml;
path;
python;
end
properties (Dependent)
is_created;
installed_version;
latest_version;
end
properties (Access = private, Constant)
mamba_path = ea_conda.mamba_path;
end
methods
... |
cf25a73b81801ffb2115a3b53cbf33524a47ab00e42105eb8af154ec800e7f2d | MATLAB | 5,000 | 171 | function [y,x,g] = tab2box(Xin,Yin,Gin)
%TAB2BOX Prepare tabular data for boxPlot function
%
% Y = IOSR.STATISTICS.TAB2BOX(XIN,YIN) prepares data, in tabular form,
% for use in the BOX_PLOT function. Specifically, XIN and YIN are vectors
% (for example column vectors from a results table). Y is an N-by-P
% num... |
67acb7778cb5c9ece25fbd66a1fcbf542a804a229a8fbb4e4e7d6589690070bb | MATLAB | 5,003 | 148 | function matrixToNSx(varargin)
% matrixToNSx
%
% Converts a MATLAB data matrix (channels as rows, samples as columns) into
% a NSx file.
%
% Use matrixToNSx(inputData, samplingFreq, inputUnits, savedDataPath)
%
% All input arguments are optional.
%
% inputData: data matrix (channels as rows, samples as columns... |
ccaa42188b7bfeb302d4f25b80609907e12d9645a1c9ce8a4ab0ca83a2590fdb | MATLAB | 5,003 | 137 | %% LaBGAScore_pet_prep_4_apply_signatures_and_save.m
%
%
% *USAGE*
%
% This script
% 1) calculates selected signature responses for PET images
% included in DAT, and saves them to new fields in DAT.
% 2) calculates responses per NPS subregion if NPS is selected, can/should
% later be expanded to all signatu... |
48547853fb1f1e2ad1a927768d11d0fceaf82bcc25965d28b8aae86fde61efe3 | MATLAB | 5,004 | 142 | function varargout = palm_quickperms(varargin)
% Create a set of permutations that is left in the Octave/Matlab workspace
% for later use, or to be exported to other programs.
%
% [Pset,VG] = palm_quickperms(M,EB,P,EE,ISE,CMCx,CMCp)
%
% Inputs (to skip an argument, use an empty array, []):
% M : Design matrix. It... |
aef727396be7542908d360b2269ffdeefda01fe78fa7b7c71818501d1d21f132 | MATLAB | 5,011 | 183 | function [vertices, edges, colors] = u3d_pre_contourgroup(ax)
%U3D_PRE_CONTOURGROUP Preprocess contour output to u3d.
%
% usage
% [vertices, edges, colors] = U3D_PRE_CONTOURGROUP
% [vertices, edges, colors] = U3D_PRE_CONTOURGROUP(ax)
%
% input
% ax = axes object handle
%
% output
% vertices = posit... |
02338b21dacd4f069ecf9b18472ac501f1d820fe69263fb04f505eef168fd0f3 | MATLAB | 5,014 | 131 | %
% KTNEVComments
%
% This is a class that deals with comments saved in a NEV file. The user
% can read the comments, get their timestamp information and even add
% comments to the NEV file and then save it as a new file.
%
%
% addComment: Allows the user to add a new comment to the
% ... |
d355a5fe58166aa63d486728b061f9c5aa91c0a12ea43786a8e4e100677bdf84 | MATLAB | 5,014 | 132 | %%***********************************************************************
%% nzlist: find the combined list of non-zero elements
%% of Aj, j = 1:k, for each k,
%% assuming that the Aj's are permuted such that
%% A1 has the fewest nonzero elements, followed by A2, and so on.
%%
%% [isspA,nzlistA,... |
efa86f3ffcd796f1a3ff497969f39739bebf932e004eba65a80e0d2f7f39fc24 | MATLAB | 5,015 | 139 | function splitNSxNTrode
% splitNSxNTrode
%
% Opens and splits an NSx file based on its NTrode groups. It depends on
% openCCF file.
%
% Use splitNSxNTrode
%
% This function does not take any inputs.
%
% Example 1:
% splitNSxNTrode;
%
% In the example above, the user will be prompted to select a CCF file
% f... |
783ad076dd70a518ca57cf8d0ba31dd3f8ace643475c31f6f90bdaa4143c6b19 | MATLAB | 5,024 | 158 | function session = invivoImport(varargin)
% invivoImport(collectionFolder,overwrite,rat_folders,prefixes)
% Takes in dacq files and creates a CMBobject out of them.
%
% base_path is folder containing rat folders
% overwrite =1 to overwrite existing files, default is 0
% set "folders" to only look in certain... |
2fc43a7160bd4d89c213808e20122985cd06038f109eac75ae4c58eb948839d0 | MATLAB | 5,025 | 143 | %% Make polar wedge plots for signatures
% This example shows how to load several signatures and plot their cosine
% similarities with a set of resting-state networks, to interpret the
% signatures in terms of networks.
%
%% General instructions
%
% Before you start, the CANlab_Core_Tools must be added to your path w... |
4aa35efd5d070d8e256d9d692497b2fce4abd869315b57a7e106a102faf0756b | MATLAB | 5,029 | 143 | function anonymize_dicm(src, rst, subID)
% Replace PatientName in dicom header with an ID without altering ANYTHING else.
%
% anonymize_dicm('sourceFolder', 'anonymizedFolder', 3) % 'sub003' as ID
%
% All three input argument are optional:
% 1. A dicom file name or a folder containing dicom files to anonymize.
% 2... |
40caa594ec8323d745f23130f65513391db99a5fa0e86e0dbe3c0b6e7aafe6b0 | MATLAB | 5,030 | 121 | function varargout = ea_normsettings_schoenecker(varargin)
% EA_NORMSETTINGS_SCHOENECKER MATLAB code for ea_normsettings_schoenecker.fig
% EA_NORMSETTINGS_SCHOENECKER, by itself, creates a new EA_NORMSETTINGS_SCHOENECKER or raises the existing
% singleton*.
%
% H = EA_NORMSETTINGS_SCHOENECKER returns the... |
0cc66e954e766229b104ae6397076bf856185d3351bc1d11ba66c12a4ac67ded | MATLAB | 5,035 | 137 | %% Align MINFLUX localisations of PIEZO trimers to a reference PIEZO trimer using the iterative closest point algorithm to generate a superparticle for presentation purposes
% – Sep 11th 2024, Stefan G. Lechner (s.lechner@uke.de) –
% Uses the 'AllTrimerCoord' array created by AFLA_analysis_finalOPT as the input
% The ... |
a6939f2319e8bdf8e44801de488f2e7393ed89780f141fca1e12a8342a4b0c5e | MATLAB | 5,037 | 129 | %extracts spikes from raw signal
%applies band-pass filtering to raw signal before doing so.
%
%params.nrNoiseTraces: 0 if no noise should be estimated
% >0 : # of noise traces to be used to estimate autocorr of
% noise, returned in variable autocorr
%
%
%params.detectionMethod: 1 ->... |
ca09db2f9590fb1b840f17595ebd0b783ea3e0d5afd95686b4dd05bb22e03e39 | MATLAB | 5,038 | 105 | function [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpb(data,win,params,segave,fscorr)
% Multi-taper segmented spectrum for a univariate binned point process
%
% Usage:
%
% [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpb(data,win,params,segave,fscorr)
% Input:
% Note units have to be consistent. See chronux.m for more informat... |
1945783770d2c6df361ba2e4a2b9e794caf9b2b180b6784237e39dea71360456 | MATLAB | 5,039 | 170 | function CBIG_pMFM_step2_STDFCD_permutation_correlation_desikan()
% This function is the second step of the permutation test of SWSTD-FCD
% correlation. In this step, 10000 permuted SWSTD FCD correlation will be
% generated and store for further use.
%
% Written by Kong Xiaolu and CBIG under MIT license: https://gith... |
ea0faf9b296416a04c7139eecd7cc508b55cada165172d93912adf60c78d1a1a | MATLAB | 5,041 | 164 | %%*********************************************************************
%% gdcomp: Compute gd = 1/td in Equation (15) of the paper:
%%
%% R.M. Freund, F. Ordonez, and K.C. Toh,
%% Behavioral measures and their correlation with IPM iteration counts
%% on semi-definite programming problems,
%% Mathematical Programm... |
2b7c84d8256b5943f8f093f937da430803533459d4366f1d88f5e2b837cfb694 | MATLAB | 5,042 | 143 | % bz_CCH_CONV predictor and p-values for CCH using convolution
%
% CALL [ PVALS, PRED, QVALS ] = CCH_CONV( CCH, W )
%
% GETS CCH vector (a single CCH) or matrix (CCHs in columns)
% has to be non-negative integer... |
9619f2be6131a293a3e0c3444bbbd86dc21ec0f1e56ed4595e8e4b3536404f23 | MATLAB | 5,043 | 136 | % eeg_insertbound() - insert boundary event in an EEG event structure.
%
% Usage:
% >> [eventout indnew] = eeg_insertbound( eventin, pnts, ...
% abslatency, duration);
% Required Inputs:
% eventin - EEGLAB event structure (EEG.event)
% pnts - data points... |
4db5273361b32ca1ab222a59f7fdea3895076fe9734a7159b9de2a7118b0f031 | MATLAB | 5,044 | 146 | %PCI State Transitions (Comolatti et al, Brain Stimulation 2019)
%
%function [pci,dNST,parameters]=PCIst(signal_evk,times,parameters)
%
%Please cite this paper if you use this code:
%Comolatti R et al., "A fast and general method to empirically estimate the
%complexity of brain responses to transcranial and intracrania... |
aa55fde97993d8b1883d672536019268fe792e69f316ef97cfabbe2189393c6e | MATLAB | 5,045 | 134 | function varargout = ea_methodsdisp(varargin)
% EA_METHODSDISP MATLAB code for ea_methodsdisp.fig
% This will show the method window.
% Requires a c formatted string (printf) as input, within a cell array
% String passed requires to be terminated with '\n'
% Text before the 5th character will be ignored
% Example: {'\n... |
88a9bd0f7f2a7702ca130a101f4ac7645e9358010808bb2da1d076bc45d259d4 | MATLAB | 5,046 | 142 | %%% Figure 1C: behavior result example
ccc;
%% Load behavior data
temp = dir("..\MAT Data\pre\**\cc20220520\Behavior.mat");
data = load(fullfile(temp.folder, temp.name));
mu.parsestruct(data);
%% Plot settings
colors = {[35 71 153], [244 179 179], [240 133 25], [233 90 111], [230 33 41]};
colors = cellfun(@(x) x / 2... |
2aa8134a19e755d0dbac1f03119cb57f9e3a54850319ddedf02e09709571d91d | MATLAB | 5,051 | 110 | function utrackPackPaths = getUtrackPackPaths(qfsmPackPaths)
%GETUTRACKPACKPATHS returns the corresponding paths to results of u-track analysis of single-molecules movies for each FSM movie path
%
%SYNOPSIS: utrackPackPaths = getUtrackPackPaths(qfsmPackPaths)
%
%INPUT qfsmPackPaths: (n x 1 cell array) containing p... |
6f87789a71bfc8918b9c07282e4cee1e8246545c11491dfc3ca0560b548466ae | MATLAB | 5,051 | 141 | % Maximize stopband attenuation of a lowpass IIR filter
% "Linear Programming Design of IIR Digital Filters with Arbitrary
% Magnitude Functions" by L.R. Rabiner, N.Y. Graham, and H.D. Helms
% (figures are generated)
%
% Designs a lowpass IIR filter using spectral factorization method where we:
% - minimize maximum st... |
14f921b087596876001319ec225ae575907b302091b8a66f829fb8351f39c391 | MATLAB | 5,052 | 160 | function [tau, curve, info] = ami_histogram(x, L, opts)
%AMI_HISTOGRAM Average mutual information versus lag, histogram estimator.
% TAU = AMI_HISTOGRAM(X,L) returns the lag of the first local minimum of
% the average mutual information of X with itself over lags 0:L, using an
% equal-width joint histogram.
%
% ... |
fe62b8581d9d08a39abfbfaec2622f7c3dbda4f28fe16b721ebab3235b086cb3 | MATLAB | 5,056 | 156 | function draw = draw_funcs
draw.maE= @maE;
draw.revise=@revise;
draw.single = @single;
draw.binary = @binary;
draw.multi = @multi;
draw.xozline=@xozline;
draw.hor_ver=@hor_ver;
draw.mesh = @mesh;
end
function [Ex,Ey,Emax] = maE(x1,x2,y1,y2,E)
Emax = 0;
for i =... |
60f39a38002687d949c5f45095113bfb694abe9256c6a59ab4a99b7c7109e77f | MATLAB | 5,058 | 185 | % Figures 6.11-6.14: Total variation reconstruction
% Section 6.3.3
% Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX Argyris Zymnis - 10/2005
%
% Suppose we have a signal x, which is mostly smooth, but has several
% rapid variations (or jumps). If we apply quadratic smooth... |
f3e2fcbd50656f75a3f1538c6ff81d067dcb4532d08a57e6bc65761cd4e51ea8 | MATLAB | 5,061 | 173 | function [str,cur_line] = struct2str(s,units,max_width,max_struct_elem, ident_str,total_ident_len,str,cur_line)
%
% AF 11/6/01
if (exist('units','var') ~= 1)
units = struct([]);
end
if (exist('max_width','var') ~= 1)
max_width = Inf;
end
if (exist('max_struct_elem','var') ~= 1)
max_struct_elem =... |
98eb13f571d77380f470f5d235d8c0a104f9e64b050c567a2016a07c117519ac | MATLAB | 5,062 | 158 | function myOISscr2g(fname,nk,idname)
% Usage ... myOISscr2g(fname,nk,idname)
%
% This function writes masks onto pre-processed mat files to
% define ROIs for further analysis
% Setting a value of nk furhter defines ROIs using k-clustering
% If nk is replaced with fname2, masks are remapped
%
% Ex. myOISscr2g(''... |
0cd6573e847db73eb7fcd38a026222be6cc68befd32f154d736a30b375302100 | MATLAB | 5,065 | 175 | % FDLA and FMMC solutions for a 50-node, 200-edge graph
% S. Boyd, et. al., "Convex Optimization of Graph Laplacian Eigenvalues"
% ICM'06 talk examples (www.stanford.edu/~boyd/cvx_opt_graph_lapl_eigs.html)
% Written for CVX by Almir Mutapcic 08/29/06
% (figures are generated)
%
% In this example we consider a graph des... |
dd4491fdd02d18f14ec8afb0d302c509e8aac9aff590f5bd4941687c12551c4f | MATLAB | 5,066 | 86 | function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencysegc(data1,data2,win,params)
% Multi-taper coherency, cross-spectrum and individual spectra with segmenting - continuous process
% computed by segmenting two univariate time series into chunks
%
% Usage:
% [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencysegc... |
442286c5337a201848d358d16eeb61ec92d6aed8ce68e2d5f0529febdbdf466f | MATLAB | 5,067 | 170 | function CBIG_pMFM_step2_STDFCD_permutation_correlation()
% This function is the second step of the permutation test of SWSTD-FCD
% correlation. In this step, 10000 permuted SWSTD FCD correlation will be
% generated and store for further use.
%
% Written by Kong Xiaolu and CBIG under MIT license: https://github.com/T... |
93d34723e545f18aeb700d935297c4c5dcb92f89bcb05a157579218967c59066 | MATLAB | 5,069 | 114 | function [SS,tau]=mtspectrum_of_spectrumc(data,win,tapers2spec,params)
% Multi-taper segmented, second spectrum (spectrum of the log spectrum) for a continuous process
% This routine computes the second spectrum by explicitly evaluating the
% Fourier transform (since the spectrum is symmetric in frequency, it uses
% a ... |
367c7c43f0e1b3f4e563de651fcf2eb0ae656e65c4f7c25e843884e666cc9754 | MATLAB | 5,072 | 153 | function A = catstruct(varargin)
% CATSTRUCT Concatenate or merge structures with different fieldnames
% X = CATSTRUCT(S1,S2,S3,...) merges the structures S1, S2, S3 ...
% into one new structure X. X contains all fields present in the various
% structures. An example:
%
% A.name = 'Me' ;
% B.inco... |
5af040e8ef24542edd25ece16fe423c5026daaf07e440f2b30b1cec50aa0c39d | MATLAB | 5,073 | 213 | %% Batch script to run Constrained NeuroMark ICA on SBM (or PET)
% using external template
% Enter the values for the variables required for the ICA analysis.
% Variables are on the left and the values are on the right.
% Characters must be enterd in single quotes
%
% After entering the parameters, use icatb_batch_fil... |
b46a6c79ff6205925399c48f1567170b36a728661de393758e57865488683345 | MATLAB | 5,074 | 161 | %% New features in MatlabBGL version 3.0
% Although MatlabBGL 3.0 was never officially released, here are some of
% it's key features.
%% Better performance
% We redid the backend interface to the BGL routines. This optimization
% gave a considerable performance increase.
%%
% test_benchmark on MatlabBGL 2.1
%
% 20... |
fca40f0d71d441baa613420f192d9f4080f7052884f8b1988c5bf06f65f97084 | MATLAB | 5,076 | 156 | function Ihat=ea_ihat_databaselookup_netmap(obj,vals,connval,patientsel,test,training,usemask)
% set up the fingerprint to predict and the variable of interest
fp_topredict=connval(patientsel(test),usemask)';
I_test=obj.responsevar(patientsel(test));
vizz=0; % visualisation of sharpening. 0 = turned off, 1 = turned... |
56a53999043ad40b09c04bf085a97a858d64219abeca2f0f52a9778b73bfb8aa | MATLAB | 5,079 | 161 | classdef GridFlex < uix.GridFlex
%uiextras.GridFlex Container with contents arranged in a resizable grid
%
% obj = uiextras.GridFlex() creates a new new grid layout with
% draggable dividers between elements. The number of rows and columns
% to use is determined from the number of elements in... |
6c1962615adb98496aa681262d247d6a16c02a77208945c2a5b17d1c2324d7b4 | MATLAB | 5,079 | 146 | % pop_signalstat() - Computes and plots statistical characteristics of a signal,
% including the data histogram, a fitted normal distribution,
% a normal ditribution fitted on trimmed data, a boxplot, and
% the QQ-plot. The estimates value are printed in a panel ... |
970df4f66d1be3820fb657c7d442bf82f3c8947c9031359dd48fc145d1635fc0 | MATLAB | 5,080 | 145 | % written by Yiyuan Han, Essex BCI-NE Lab, 13/12/2019
% binary classification between two specific conditions
function perfMat = binaryClassTest(class1,class2,blockTagsAC,features,folderpath,nameTag)
%% Extract the data in specific conditions
% These two classes should be modified according to each requirement
indices... |
a4bcbbbaec7128276647b4175cf2252e8abf8cb6db02d58b5a1a17c028ae235d | MATLAB | 5,081 | 184 | function[s,t,E] = sta(data_spk,data_lfp,smp,plt,w,T,D,err)
% Spike Triggered Average
% Usage: [s,t,E] = sta(data_spk,data_lfp,smp,plt,w,T,D,err)
%
% Inputs
%
% Note that all times have ... |
eed0465429a929ae7ad7374163f9c834d4023e9ad01c86ba30b8d112852429e7 | MATLAB | 5,081 | 135 | clear;
clc;
close all;
addpath(genpath('../functions/'));
SUBINFO_FILE = '../../subInfo/rid_sex_mDoB_yDoB_mExam_yExam_ageExam_dx_icv_bl.csv';
GMICV_FILE = '../../vbm_810bl/gmVolAndICV/rid_gmVol_icv_bl.csv';
%% Subjects
% All these info is baseline info
[RID_dx, ~, ~, ~, ~, ~] = get_data(SUBINFO_FILE, GMICV_FILE, 2)... |
f6cc8cbf5ccd2d20ac374e792d30766579fb496ce381ba77d1a34171fad57ef9 | MATLAB | 5,081 | 129 | function ea_fnirt(varargin)
% Wrapper for FSL FNIRT nonlinear registration
fixedimage = varargin{1};
movingimage = varargin{2};
outputimage = varargin{3};
% Set output dir
volumedir = [fileparts(ea_niifileparts(outputimage)), filesep];
% Do linear registration first, generate the affine matrix 'fslaffine*.mat'
movPa... |
6a008e989b3174d188de51e6b1cf0cff92688b7fff899ed0bf71b8cc2553c305 | MATLAB | 5,085 | 134 | function data = TDTdigitalfilter(data, STREAM, FC, varargin)
%TDTDIGITALFILTER applies a digital filter to continuous data
% data = TDTdigitalfilter(DATA, STREAM, FC, 'parameter', 'value', ... ),
% where DATA is the output of TDTbin2mat, STREAM is the name of the
% stream store to filter, FC is the cutoff fr... |
0c15330c15133c116acab3865a465bc702d80dbd66efd757d052bef016f98bb2 | MATLAB | 5,086 | 131 | function f=readPrairie2(froot,cycle,label,chno,imno)
% Usage ... f=readPrairie2(froot,cycle,label,chno,imno)
%
% PrairieView data reader
% This function will read individual images if the froot name includes the
% file extension. If froot ends in a slash to indicate a folder, it will
% read all images within cycl... |
148da6cb60b6f35a4287a8d25348cd3b7853e455abd834cce5c4b49e20140f3f | MATLAB | 5,086 | 151 | function [dv, corrval, regdata] = registration_offsets_modified(data, ops, removeMean)
% modified by Yiyi Yu
%% Parameters
[ly, lx, nFrames] = size(data);
refImg = ops.mimg;
subpixel = getOr(ops, {'subPixel' 'SubPixel'}, 1); % subpixel factor
usFac = getOr(ops, 'registrationUpsample', 1); % factor to upsample
phaseCor... |
49160ad77895d6c0286b00d6c6a1c59b1dcc34170bf233d3ce3ee073dc15b42f | MATLAB | 5,088 | 188 | function test_main
%% Implement a test suite for matlab_bgl
% Call this function to test the MatlabBGL package.
%% Setup some parameters
msgid = 'matlab_bgl:test_main';
%%
fprintf('testing trivial input...\n');
test_trivial
%%
fprintf('testing code examples...\n');
test_examples
%%
fprintf('testing old test scrip... |
58a844d8d2f83c004a065019a45fc33fc171f1bc63b4dc8795fdc30f0a2f1b78 | MATLAB | 5,088 | 134 | % eeg_matchchans() - find closest channels in a larger EEGLAB chanlocs structure
% to channels in a smaller chanlocs structure
% Usage:
% >> [selchans,distances,selocs] = eeg_matchchans(BIGlocs,smalllocs,'noplot');
% Inputs:
% BIGlocs - larger (or equal-sized) EEG.chanlocs structur... |
2a586778fa1f2011f7be596e1634fe2676d8981ec80ee153879e078548a9a68a | MATLAB | 5,090 | 139 | function segmentLocMaxWrapper(movieData, varargin)
%DETECTMOVIETHRESHLOCMAX compiles detection data from movie frames
%% ----------- Input ----------- %%
%Check input
ip = inputParser;
ip.CaseSensitive = false;
ip.addRequired('movieData', @(x) isa(x,'MovieData'));
ip.addOptional('paramsIn',[], @isstruct);
ip.parse(mo... |
747bdb31c95f70834f4ef15fe853dd88f9b5cceaac5f8977886bbd11a333e4b7 | MATLAB | 5,092 | 144 | function [regularizer_global,Theta_global,Theta_mean]=...
inf_regularization_based_inference(~,F,t,ID,U,F_prime,X,mesh,...
k,o_keep_all_trajectory,o_force_constraint,constraint_algorithm,...
o_use_initial_guess,nCores,rep,magnitude)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamica... |
5ff9a4bc18966b92133594d0c47c54fb39eb814aaca9347fceeb00afc7f508b4 | MATLAB | 5,093 | 121 | function PSTH = calc_PSTH(event,spikes,varargin)
% This is a generalized way for creating a PSTH for units for various events
%
% INPUTS
% event : event times formatted according to the Cell Explorer's convention
% spikes : spikes formatted according to the Cell Explorer's convention
%
% OUTPUT
% psth
%
% Dependenc... |
e4a1af3c902e171c76cb8cb3d93e8e8e1402c2eb89a14ee77a24ee33b0e524b7 | MATLAB | 5,094 | 173 | % sobi() - Second Order Blind Identification (SOBI) by joint diagonalization of
% correlation matrices. THIS CODE ASSUMES TEMPORALLY CORRELATED SIGNALS,
% and uses correlations across times in performing the signal separation.
% Thus, estimated time delayed covariance matrices must be nonsi... |
058c6c88a64a27863247e10e9ff902aa0fb0abb56f2d9e5e50646f0c98510097 | MATLAB | 5,095 | 156 | function plotCondColocPvalues(savePlot,valueRange,fileToLoad,saveResPath)
%PLOTCONDCOLOCPVALUES plots the pvalues from condColocStatTest for each colocalization measure on heatmap
%
%Synopsis: plotCondColocPvalues(savePlot,valueRange)
% Function takes the output of condColocStatTest and plots the biggest
% pvalue among... |
c994adaa62bb17305094baddd7dc970bbd2ceebf33319fdbb3bda54e3f98b7fa | MATLAB | 5,095 | 135 | %% Script to get the variance decomposition for bmrk4 based on overall aversion pattern and modality-specific patterns
clear all
close all
clc
load bmrk4_pain_specific_PTV_overall.mat
load bmrk4_taste_specific_PTV_overall.mat
load bmrk4_vision_specific_PTV_overall.mat
% PTV = pain, taste, vision (observed pain). Run... |
f9a23f1a4f3d32b64a5f36da7cfaa15db40d6726bab0a2118b739509b85b7901 | MATLAB | 5,099 | 132 | function [A, strucCorr_score, B, U, V, R, Rp, pVal, Ncca] = CBIG_ASDf_CCA_factorBehavior(ind_scores,...
id_keep, reg, PAPset, path_subInfo, path_behav_scores, path_factorLoading, factor_order,...
factor_idx)
% [A, strucCorr_score, B, U, V, R, Rp, pVal, Ncca] =
% CBIG_ASDf_CCA_factorBehavior(ind_scores, id_keep,... |
9962fdf47b712910f9bd9c1b3be7ec7073af4d3efcf35f0ee421758645301e82 | MATLAB | 5,100 | 176 | function Process_ConvertOptitrack2Pos(fbasename,varargin)
% USAGE
%
% Process_ConvertOptitrack2Pos(fbasename,varargin)
%
%
%
% fbasename basename of the video file (should be filebasenmae.avi)
% <options> optional list of property-value pairs (see table below)
%
% ==============================... |
1ec34d58f1eb5bce2bb5b9d8b66eaff19a68f470b520a58a1cb73d745d0f291b | MATLAB | 5,101 | 113 | function [corr_brainMap, corr_factorComp] = CBIG_ASDf_factorHierarchy(k, inputDir, r_k, r_kplus)
% [corr_brainMap, corr_factorComp] = CBIG_ASDf_factorHierarchy(k, inputDir, r_k, r_kplus)
%
% This function quantifies the nested hierarchy of factors in terms of both
% E(RSFC patterns|Factor) and Pr(Factor|Participant).... |
ee72cbcd75ccba90f640416681e8e8862c36dfcab97331da3c4ebfe68a85d49c | MATLAB | 5,101 | 206 | function [mr,b0idx,finames] = ea_build_DTD(bvalue,dirname,dtif,DTDf,HARDIf,bvalf,bvecf)
% converts the dti.nii and dti.bval/.bvec files to Freiburg DTD and raw
% HARDI-formats.
V=spm_vol([dirname,dtif]);
for fi=1:length(V)
finames{fi}=[dirname,dtif,',',num2str(fi)];
end
%% change into mrstruct format
mr = ... |
3b71e89bae6ee34c38c6f8a9130180c369412bbc6887f3e94d4587a8b9374f06 | MATLAB | 5,108 | 146 | % acsobiro() - A. Chickocki's robust Second-Order Blind Identification (SOBI)
% by joint diagonalization of the time-delayed covariance matrices.
% NOTE: THIS CODE ASSUMES TEMPORALLY CORRELATED SIGNALS.
% Thus, the estimated time-delayed covariance matrices
% for a... |
2749bbbb90d1284dafedd91f5b55361babb488671f15d6f48ee1a5d974c14f8a | MATLAB | 5,109 | 127 | %% Step 1 Tiny Dancers: Load EEG and preprocess
% Steps are Bandpass filtering, Bad channel rejection, ASR,
% Automatic ICA, Bad channel rejection part 2 and interpolation, followed
% by rereferencing to the average
% Trinh Nov 22
%% initialise fieldtrip
clc
clear all
close all
addpath('E:/MUSICOM_TinyDanc... |
f4836f408b3d2f17a5f92acfb72eaa09004a90fb728349420509eafcccf51096 | MATLAB | 5,109 | 142 | function [vertices, faces] = freesurfer_read_surf(fname)
% freesurfer_read_surf - FreeSurfer I/O function to read a surface file
%
% [vertices, faces] = freesurfer_read_surf(fname)
%
% Reads the vertex coordinates (mm) and face lists from a surface file.
%
% Surface files are stored as either triangulations or quad... |
8ebc5a165cbe9531747ecef9e2cc545aba2ae9742ddf376d94efd03cb7ec4f55 | MATLAB | 5,110 | 150 | function DBAddFigure(f,eid,name,comments,parameters,mfiles,varargin)
%DBAddFigure - Save figure in current database.
%
% Save figure as MATLAB fig and PNG image. Also save code used to generate it
% (although not required, installing <a href="http://sites.google.com/site/oliverwoodford/software/export_fig">export_fig<... |
79395ea6a72f14cffbec4802d839f2180e0f88e3f5414b6f61c2ba7c20467134 | MATLAB | 5,113 | 150 | % 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... |
34ba92a01a99d33c41b2d3381dedbd618a5a02ebfaaca17e8b0172ea8db104ab | MATLAB | 5,114 | 135 | function varargout = save(tree, filename)
% XMLTREE/SAVE Save an XML tree in an XML file
% FORMAT varargout = save(tree,filename)
%
% tree - XMLTree
% filename - XML output filename
% varargout - XML string
%__________________________________________________________________________
%
% Convert an XML tree into a ... |
9afc41eeecaab11297592fdf7b856b3a11d733d267b24d16f84f454d604b04e7 | MATLAB | 5,118 | 133 | % std_maketrialinfo() - create trial information structure using the
% .epoch structure of EEGLAB datasets
%
% Usage:
% >> STUDY = std_maketrialinfo(STUDY, ALLEEG);
%
% Inputs:
% STUDY - EEGLAB STUDY set
% ALLEEG - vector of the EEG datasets included in the STUDY structure
%
% ... |
76a29f5ec060d89348a665888f6493c192e72f0fde5521a924421d1b3f9d97a3 | MATLAB | 5,120 | 174 | % Example 6.9: Bounding consumer preference
% Section 6.5.5, Figures 6.25-6.26
% Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX Argyris Zymnis - 11/30/2005
%
% We are given a set of consumer preference data for bundles
% of two goods x_1 and x_2. These points are generated... |
5ff5b0fd6f94e9048e724444cce2f9ca81cd1e165602e4b20bd1ccd68919d86a | MATLAB | 5,124 | 118 | function OUT = run_glm_beta_resampling_epoched(E, iter_blocks, n_iter, bad_channels, concat_baseline_sec)
%RUN_GLM_BETA_RESAMPLING_EPOCHED Resample GLM betas from pre-epoched Hb.
%
% OUT = RUN_GLM_BETA_RESAMPLING_EPOCHED(E, iter_blocks, n_iter, bad_channels, concat_baseline_sec)
%
% Purpose
% -------
% Esti... |
a90b30236f2a0ecdadb0496e2870c6e547650e1a5081ab53ccbabcb9f906c88e | MATLAB | 5,127 | 125 | % Bayesian model used for parameter recovery simulation
clear; clc;
%% Setup
% task data location
path_root = getenv('DECIDENET_PATH');
path_beh = fullfile(path_root, 'data/main_fmri_study/sourcedata/behavioral');
path_out = fullfile(path_root, 'data/main_fmri_study/derivatives/jags');
path_resp_artif = fullfile(path_... |
7698dd76819192298156122eb0ec88abaf41fc4488b89761b6031a482a74fb22 | MATLAB | 5,128 | 148 | function T=Mesh2Tetra(V,F,options)
% This function MESH2TETRA converts a triangulated surface mesh into a
% tetrahedron volume mesh.
%
% Main advantage above existing constrained 3D Delaunay is that it
% will never add new boundary points, (usefull for active appearance models)
% Disadvantage, some highly non... |
2ac6018ee473d00ffd9e3174d323aa38d13f77b61e83dff8178b2a24a667ba9e | MATLAB | 5,130 | 118 | function [likelihood, results, label, params, tau] = CBIG_hMRF_adapt_c(params, label, i, full_corr_mat, lh_mask,...
rh_mask, avg_mesh, Smooth_cost, tau, Neighborhood_lh, Neighborhood_rh, Neighborhood_lh_rh)
% [likelihood, results, label, params, tau] = CBIG_hMRF_adapt_c(params, label, i, full_corr_mat, lh_mask,..... |
4618a83971bfb8bd987dc7653f1a07111cfecca75b5ae0383aa735acf67154f2 | MATLAB | 5,131 | 159 |
%% 1. Create strings listing where the toolbox and the tutoral data directories are and add the toolbox to Matlab's path
toolbox_dir = '../../ndt.1.0.0/';
raster_file_directory_name = 'Zhang_Desimone_7objects_raster_data/';
addpath(toolbox_dir)
add_ndt_paths_and_init_rand_generator
%% 2. Bin the data usi... |
a4317108ed5275a1cf7d867f7a3c1704527df8e98127960ef37c74074a55161f | MATLAB | 5,131 | 109 | % This version was derived from the original version by Pestilli and Caiafa.
% Copyright (2015), Franco Pestilli (Indiana Univ.) - Cesar F. Caiafa (CONICET)
% email: pestillifranco@gmail.com and ccaiafa@gmail.com
% https://github.com/francopestilli/life available under
% https://github.com/francopestilli/life/blob/mast... |
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