sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
e606ac0e756b4078c36a497ea19db00e9ce5d68b45cd5522c4012eccf243a64e | MATLAB | 11,330 | 428 | function [x,fval,exitflag,output]=fminsearchcon(fun,x0,LB,UB,A,b,nonlcon,options,varargin)
% FMINSEARCHCON: Extension of FMINSEARCHBND with general inequality constraints
% usage: x=FMINSEARCHCON(fun,x0)
% usage: x=FMINSEARCHCON(fun,x0,LB)
% usage: x=FMINSEARCHCON(fun,x0,LB,UB)
% usage: x=FMINSEARCHCON(fun,x0,LB,UB,A,b... |
8cdf56496338afe3d1bfac30a4fb5821970bf9c308de5cc29546d44df4628bfa | MATLAB | 11,335 | 468 | % hungarian() - Solve the assignment problem using the Hungarian method.
%
% Usage: >> [C,T]=hungarian(A)
%
% Inputs:
% A - a square (correlation/distance/cost) matrix.
% C - the optimal assignment (closest row/col pairs)
% T - the total (minimized) cost of the optimal assignment.
%
% Author: Niclas Borlin, 199... |
202bf97e0bf01393a4c9de8717479ae76084e92088da89105b5bf3dafbf4af4e | MATLAB | 11,339 | 235 | function options = NoRMCorreSetParms(varargin)
% Struct for setting the NoRMCorre algorithm parameters. Any parameter that is
% not set gets a default value
% Author: Eftychios A. Pnevmatikakis
% Simons Foundation, 2016
Names = [
% dataset info
'd1 ' % number of rows
'd2 ... |
edfc152b06adbff0511a664268b0ac739d68a955a7517a937f79dfd711c2d064 | MATLAB | 11,362 | 246 | %% set up main variables for analyses
a = spm_read_vols(spm_vol('SPECT_output_group_loading_coeff_.nii'));
size(a); %tells you the dimensions of a, in this case it's a subject ...
% by component matrix of 213 x 53
%you can save it as a txt file as follows:
save("loadings.txt","a","-ascii")
%we c... |
21a350ab7f6340402855bd6128f07c9297c85f7180fcc341c41d336cbb44d2e6 | MATLAB | 11,375 | 241 | %This script takes output from coherence calculation function and exports
%into a table that can be imported in R
%Inputs: Cell array of animal IDs, cell array of filter names, cell array
%of run states (options: 'runall' 'runthresh' 'nonrun' 'all'
%'diff_runVSnon' 'diff_threshVSnon'), seg (= to size of bins used... |
195641303e8bddcfd95ceb3e3b35e58e00a5d299919ab0a6760ced535f5a29a5 | MATLAB | 11,377 | 216 | function bz_PlotRippleStats(maps,data,stats,varargin)
%bz_PlotRippleStats - Plot descriptive stats for ripples (100~200Hz oscillations).
%
% USAGE
%
% bz_PlotRippleStats(maps,data,stats,<options>)
%
% Use the ouputs of <a href="matlab:help RippleStats">RippleStats</a> as input parameters. Using cell arrays of
%... |
50beb0e4a612284b2406dfe72b81a134f848836f50ed3ac8c9c9035be77e0143 | MATLAB | 11,390 | 269 | % pop_rejkurt() - rejection of artifact in a dataset using kurtosis
% of activity (i.e. to detect peaky distribution of
% activity).
%
% Usage:
% >> pop_rejkurt( INEEG, typerej) % pop-up interative window mode
% >> [OUTEEG, locthresh, globthresh, nrej] = ...
% = pop_rejkurt( INEEG,... |
d7010aead7c12c10822dd945000c1e68ec0d136bff567952ca528e907646a667 | MATLAB | 11,398 | 337 | function V = run_variance(subject_ids, paths, mesh_path, nirsmodel_path, layout_mat, opts)
%RUN_VARIANCE Estimate within-subject GLM beta variability using block-resampling.
%
% V = fnirspower.pipeline.run_variance( ...
% subject_ids, paths, mesh_path, nirsmodel_path, layout_mat, ...)
%
% Description
% -... |
7a32b8f6fb3093b8aa000557a30936db439d4ba372694863f9cf733835411f85 | MATLAB | 11,400 | 245 | function spectralevents_vis(specEv_struct, timeseries, TFRs, tVec, fVec)
% SPECTRALEVENTS_VIS Conducts basic analysis for the purpose of
% visualizing dataset spectral event features and generates spectrogram
% and probability histogram plots.
%
% SPECTRALEVENTS_VIS(specEv_struct,timeseries,TFRs,tVec,fVec)
%
% In... |
43c3b32cf1c97613b4762c79764b8eefd23e0526785f2ee1f8020f4c9b3958fb | MATLAB | 11,407 | 289 | function varargout = channel_ar_gui(varargin)
% CHANNEL_AR_GUI MATLAB code for channel_ar_gui.fig
% CHANNEL_AR_GUI, by itself, creates a new CHANNEL_AR_GUI or raises the existing
% singleton*.
%
% H = CHANNEL_AR_GUI returns the handle to a new CHANNEL_AR_GUI or the handle to
% the existing singleton... |
84fc13a524156ce0182bf03f3b4b2b0b16dd57172343708622831b8a36df3403 | MATLAB | 11,413 | 341 | function [map,stats] = Map(v,z,varargin)
%Map - Map z on (x,y) where x, y and z are time-varying variables (samples).
%
% Compute a continuous map, where one time-varying variable z is represented
% as a function of one or two time-varying variables x and y. The variable z
% can either be a point process (typically... |
e33a8f3cbce2760f9ccb72225c06bebd00b67375c46a00d4cc94942edbf51409 | MATLAB | 11,413 | 233 | function [belowThreshFlag3D, fractionFlagMat3D, avgPval, coefMat4D] = explainIndCellsMvrgWithRand(testResults, spekLabelBase, smLabelBase, sigThreshInput)
%EXPLAININDCELLSMVRGWITHRAND calculate significances for multivariate regression results of randomized data of individual cells
%
%SYNOPSIS: [belowThreshFlag3D, fra... |
b35f204a250b2a6993431e68c097c10697c8e1b204769951550a3c9353a93dc5 | MATLAB | 11,426 | 312 | % ====================================
%% Help
% ====================================
%
% CBIG_language_prediction
%
% This script generates full (all-run) individual-specific brain parcellations
% for NIH subjects with known language task laterality (L/B/R), then computes
% the language laterality index (LI) for each ... |
0ceca20eebeda33c3292ba54a99c039d2806a49975a2285f8128e4fb529886ab | MATLAB | 11,427 | 276 | function varargout = ea_vatsettings_dembek(varargin)
% EA_VATSETTINGS_DEMBEK MATLAB code for ea_vatsettings_dembek.fig
% EA_VATSETTINGS_DEMBEK, by itself, creates a new EA_VATSETTINGS_DEMBEK or raises the existing
% singleton*.
%
% H = EA_VATSETTINGS_DEMBEK returns the handle to a new EA_VATSETTINGS_DEMB... |
d0748a2936e867459ec2beffbf533f85d527e57a58237b6ba689798d4f433e36 | MATLAB | 11,432 | 266 | function CFA_CheckData
% uiwait(msgbox({'Currently, it only used for two conditions:',...
% '1. Data after regrouped but before normalization.',...
% '2. Data after normalization.'}))
PG = uigetdir(pwd,'Check Data');
% PGout = uigetdir(pwd,'Result Picture directory');
[pth nam ext] = fileparts(PG);
PGout = [pth... |
b41b8517eaf316c541743b5a19b2eaf1eef3c444fc5b4755fe15e0f699809c0f | MATLAB | 11,435 | 314 | function ea_create_tpm_darteltemplate(mute)
if exist([ea_space,'TPM.nii'],'file') && ~ea_checktpmresolution && exist([ea_space,'.tpm'],'file')
return
end
if ~exist('mute','var')
answ=questdlg('Lead Neuroimaging Suite needs to generate some files needed for the process. This only needs to be done once but will ... |
fb099b8f931e997fed8d261fee45fe3de64d0b8391aac581a560c982413640e9 | MATLAB | 11,440 | 233 | function options = NoRMCorreSetParms(varargin)
% Struct for setting the NoRMCorre algorithm parameters. Any parameter that is
% not set gets a default value
% Author: Eftychios A. Pnevmatikakis
% Simons Foundation, 2016
Names = [
% dataset info
'd1 ' % number of rows
... |
32d9bdf00f8884bb4867eaca94052d52f663075161415e63ba2178728ebe94c5 | MATLAB | 11,455 | 325 | % jader() - blind separation of real signals using JADE (v1.5, Dec. 1997).
%
% Usage:
% >> B = jader(X);
% >> B = jader(X,m);
%
% Notes:
% 1) If X is an nxT data matrix (n sensors, T samples) then
% B=jader(X) is a nxn separating matrix such that S=B*X is an nxT
% matrix of estimated source signals.
% 2)... |
d2c262fb2f302a5d092be68aa18b5c31fb61189b5f6e1cf1d1641c593701f9b9 | MATLAB | 11,458 | 265 | function ClincFreq_ClinWeiLocationStat(INDIR,OutWeiLocdir,SetUpPara,Para,VolLab,ClincWei)
[V,D,namelist] = Dynamic_read_dir_NIFTI_sparse(INDIR);
D(isnan(D)) = 0;
D(isinf(D)) = 0;
D = D>0;
Dvol = sum(D)';
Dvole = sum(D,2);
IgV = Para.IgP;
indexs = find(Dvole>=(size(D,2)*IgV/100));
Dmasked = zeros(V.dim);
Dmasked(index... |
a26189c7981c22ce6db5c30955e71eaef21f7c2f9b225f0dccf3fa56ca16496d | MATLAB | 11,460 | 297 | function [EMGFromLFP] = bz_EMGFromLFP(basePath,varargin)
% USAGE
% [EMGCorr] = bz_EMGCorrFromLFP(basePath)
%
% INPUTS
% basePath - string combination of basepath and basename of recording
% example: '/animal/recording/recording01'
%
% (Optional)
% 'restrict' ... |
fdef93abe9ad8bb79e727c9f4260c30a76dbb5246be5708877b3344d603ebbb1 | MATLAB | 11,473 | 333 | function [specslope,spec] = bz_PowerSpectrumSlope(lfp,winsize,dt,varargin)
%[specslope] = bz_PowerSpectrumSlope(lfp,winsize,dt) calculates the
%slope of the power spectrum, a metric of cortical state and E/I balance
%see Gao, Peterson, Voytek 2016; Waston, Ding, Buzsaki 2017
%
%INPUTS
% lfp a buzcode-formatt... |
e81d2755f1c36dd89e78f8334ea4c479c9ddb2b2b19063fd9fd07b8f0a9128b6 | MATLAB | 11,485 | 239 | function vw = videoWriter(url, varargin)
% videoWriter class constructor
% Creates a object that writes video files. We use a plugin
% architecture in the backend to do the actual writing. For example,
% on Windows, DirectShow will typically be used and on Linux, the
% ffmpeg library is often used.
%... |
43215141b13cb31b2409b9f65c4735a04d3fc942daacfee1f2cdf28c1a0eff14 | MATLAB | 11,493 | 253 | function [Cmn,Phimn,Smn,Smm,f,ConfC,PhiStd,Cerr] = coherencyc_unequal_length_trials( data, movingwin, params, sMarkers )
% This routine computes the average multi-taper coherence for a given set of unequal length segments. It is
% based on modifications to the Chronux routines. The segments are continuously structu... |
10c024244f93cbd6feb9feda6dc43e4986479e342d57f5f02c4a3992de9dfe4d | MATLAB | 11,505 | 283 | function [output, Greg] = dftregistration_min_max(buf1ft,buf2ft,usfac,min_shift,max_shift,phase_flag)
% function [output Greg] = dftregistration(buf1ft,buf2ft,usfac);
% Efficient subpixel image registration by crosscorrelation. This code
% gives the same precision as the FFT upsampled cross correlation in a
% small fra... |
828807356ab1a9da046083cae465eb2b975ddafd72ecc7e23cf12b015c5b5f1b | MATLAB | 11,506 | 323 | %%*****************************************************************************
%% sqlp: solve an semidefinite-quadratic-linear program
%% by infeasible path-following method.
%%
%% [obj,X,y,Z,info,runhist] = sqlp(blk,At,C,b,OPTIONS,X0,y0,Z0);
%%
%% Input: blk: a cell array describing the block diagonal structu... |
55f20514883c4272e78459091c96de5ab99953d54404b62a035ab29a18c657f4 | MATLAB | 11,510 | 249 | classdef KTUEAImpedanceFile
% Plots a graphical representation of the impedance data collected by
% Cerebus and saved in a text file.
%
% Usage:
%
% plotImpedances(mapfile)
%
% WHERE:
%
% mapfile: Is the mapfile structure obtained with mapfileLoader
% function that maps the electrode... |
80093b1a0ef4ae4443b50ad923583e45214a831669882fc3489e9a8a883bc81c | MATLAB | 11,526 | 396 | function [VertPos, CellList] = make_voronoi_pbc_fast(cx, cy)
% MAKE_VORONOI_PBC_FAST Build a periodic Voronoi tessellation from a set
% of cell-center seed points, to use as the initial vertex-model geometry.
%
% [VertPos, CellList] = MAKE_VORONOI_PBC_FAST(cx, cy) computes the
% Voronoi diagram of the seed points ... |
44aa4cff512e16521a337d6a174e44f674dfb50c3543413cdf9c8777ca5e0993 | MATLAB | 11,529 | 269 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% demo_eigenmode_analysis.m
%%%
%%% MATLAB script to demonstrate how to use surface eigenmodes to analyze
%%% fMRI data. In particular, the script demonstrates how to
%%% (1) reconstruct a task fMRI spatial map,
%%% (2) reconstruct a resting... |
f96c2ba52b7261f95aade541df90cbae5876606006e93f691eccbc1b6d50ad91 | MATLAB | 11,532 | 383 | function stackview(hr,showfun)
if nargin == 1,
showfun = @(x) imagesc(x,[0 1]);
end;
[ds.maps cmap] = compMesoParams(hr);
ds.img = ds.maps(:,:,:,4);
ds.hr = hr;
dirs = load('dwidirections');
ds.dirs256 = [dirs.dirs256 -dirs.dirs256];
ds.modelstruc = evalin('base','modelstruc');
proto.ten = hr.user.bTensor;
pr... |
915c34e3e00921f575da9f14968babcedf7ea2ffdf285a43ef180b0782e932c0 | MATLAB | 11,548 | 358 | %%******************************************************************
%% ops:
%%
%% Z = ops(X,operand,Y,alpha);
%%
%% INPUT: X = a matrix or a scalar
%% or a CELL ARRAY consisting only of matrices
%% operand = sym, transpose, triu, tril,
%% real, imag, sqrt, abs, ... |
ceb77f9a2d01130690b9f5d4cd0b20ffb43a2b424d58a1a7fd3338f60c82865c | MATLAB | 11,554 | 267 | function [probMotionType,motionChar,errFlag] = summarizeDiffAnRes(tracks,...
minTrackLen,probDim,diffAnalysisRes,extractType)
%SUMMARIZEDIFFANRES calculates motion type probabilities and motion characteristics from diffusion analysis
%
%SYNOPSIS [probMotionType,motionChar,errFlag] = summarizeDiffAnRes(tracks,...
% ... |
580c69d531f8f4c99a1144464f1cbde005e61c8373c25882e7e2d8f7505cb54e | MATLAB | 11,563 | 277 | classdef KTUEAMapFile
% UEAMAPFILE -- Defines a class that contains information on a UEA
% electrode array using CMP files provided by Blackrock Microsystems.
%
% To load a CMP file type 'MapName = UEAMapFile' where MapName is the name
% of the variable that will be created and will contain the map class.
%
% ... |
78e0e25e7957dd98dd21c78c60d6260dd4c170cad9beaaf715d7a4b7009a236e | MATLAB | 11,582 | 346 | function [map,stats] = Map(v,z,varargin)
%Map - Map z on (x,y) where x, y and z are time-varying variables (samples).
%
% Compute a continuous map, where one time-varying variable z is represented
% as a function of one or two time-varying variables x and y. The variable z
% can either be a point process (typically... |
c14b918a842d27d41ede050dcbb7f5a36522c03bea8357ac109ae9ed1b2e8c0a | MATLAB | 11,608 | 232 | function HispeedTrials = assignTrialsToVideos(videoDir)
% Check if the correct directory was chosen
% The user has to pick the overall 'videos' folder, not a hispeed folder
if ~exist(videoDir,'dir')
error('The given folder doesn''t exist.')
elseif ~endsWith(videoDir,'videos')
error('Incorrect directory. \n%s'... |
c3d792be74c98c07f1333c310fb20f56f69ea4d9d8d411a8f75a47a16ec5917f | MATLAB | 11,612 | 356 | function [c, s, kernel, iter] = deconvCa(y, kernel, smin, fit_gt, debug_on, sn, maxIter, theta, lambda)
%% deconvolve calcium traces to infer spike counts
%% inputs:
% y: 1*T vector, observed calcium traces
% kernel: struct variable with two fields {'fhandle', 'pars', nMax}. kernel
% deterines the convolution ke... |
3e961141a5cd5bc78153a3b67f0438d951744981d9e2017304ee3d2cc5fb059b | MATLAB | 11,627 | 348 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
addpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
%% ======================= step 1 for disposal all data
%% input data
step05_retest_00_init;
step01_CBFandCCSImaps_00_init;
%% compute cosine si... |
46e3836275aee650b1887bcea2b376909acf5293e49601a188ddf835b3eb5922 | MATLAB | 11,643 | 301 | %% Simulate geometric and hybrid response, optimal stimulus
% hybrid connectivity has one FNP
clear; clc;
% Load model parameters
loadparam;
% Optimal stimulation (stimulus placed at source of FNP)
stim.stimR = hetparam_het.a;
% Compute timestep and grid spacing
dx = topology.L / topology.Nx;
dt = topology.T / topol... |
74e349ffd087a1e1a7c9d09aa2e444a97160a28489d33766c389394dbd618e57 | MATLAB | 11,644 | 280 | function [a, r2, out_a, out_l] = dfa(ts, n_min, n_max, n_length, plotOption)
% [a, r2, n_bp, n, n10, F,F10, F_fit, n_fit, Xave, Yave, logF_fit] = dfa20200727(ts, n_min, n_max, n_length, plotOption)
% Inputs - ts, input time series
% n_min, minimum box size (default n_min = 10)
% n_max, maximum box ... |
3635b6957717fe017c3d62ec986f3d2f490ef81496e0b415207f05f7598ff620 | MATLAB | 11,654 | 276 | function [parameters] = LoadParameters(filename)
%LoadParameters - Load parameters from an XML file.
%
% USAGE
%
% parameters = LoadParameters(filename)
%
% filename parameter file name
% -or-
% basePath where the parameter file baseName.xml lives
% Copyright (C) 2004-2011 by Mic... |
bf8567e826aba54c26f7e05a137bc2fbe5477d102c4e5e94002ad109cd11092d | MATLAB | 11,662 | 221 | function PlotRippleStats(r,m,d,s,varargin)
%PlotRippleStats - Plot descriptive stats for ripples (100~200Hz oscillations).
%
% USAGE
%
% PlotRippleStats(ripples,maps,data,stats,<options>)
%
% Use the ouputs of <a href="matlab:help RippleStats">RippleStats</a> as input parameters. Using cell arrays of
% repea... |
c8a873117b5494b7aa2718cfce084a03229334a3dd991a3022af9640a546a1b4 | MATLAB | 11,688 | 320 | % function testscript(pname,direction,movingwin,segave,params,fscorr)
%
% This script runs a sequence of analysis steps using the test
% data contained in data. The data consists of a single tetrode
% recording from macaque area LIP during a memory saccade experiment
% a la Pesaran et al (2002). The data is already sep... |
b6086796be32c4010a55f919a5d98f533462739d57bcecfa10c08fa8cf4d782a | MATLAB | 11,705 | 375 | function [ cvx_optpnt, mode ] = geo_mean_cone( sx, dim, w, mode )
%GEO_MEAN_CONE Cones involving the geometric mean.
% GEO_MEAN_CONE(N), where N is a positive integer, creates a column vector
% variable X of length N and a scalar variable Y, and constrains them to
% satisfy GEO_MEAN(X) >= Y and X >= 0. That i... |
6d95c999e1a89a917fc104c880d14865e8b82def04cd540fbb5ffebe4df1021a | MATLAB | 11,729 | 219 | %% refitElec - refits a previously extracted corse electrode model using
% ptimal oblique samplingto increase accuracy and enable
% automatic contact localisation. Intital refitting
% ("2nd pass" is followed by a final "3rd pass" to
% calibrate the point of origin... |
16897bc28957f205c3e16967ff2f596ea6d90ee9f949343e54a83412d9fedb4b | MATLAB | 11,743 | 265 | function movieData = condColocPt2Pt2BlobWrapper(movieData, paramsIn)
%CONDCOLOCPT2PT2BLOBWRAPPER applies colocalization method described in condColocPt2Pt2Blob to a MovieData file
%
% movieData = condColocPt2Pt2BlobWrapper(movieData, paramsIn)
%
% Applies colocalization method described in condColocPt2Pt2Blob to three... |
0fa324bb76eff9d1352d6358575b73a89d223ab5406f078ef8fa58cecd53fa23 | MATLAB | 11,752 | 367 | function runstim_THINGS(T_Trl)
global Par %global parameters
Par.Mouserun = 0;
dasusemouse( 0 );
preloaded_pics = 40;
ncount = 4;
monkey = 'monkeyF';
% cogstd('sPriority','high')
LOG.fn = 'runstim_THINGS';
DateString = datestr(now,'yyyymmddHHMMSS'); % get date-timestamp
ds_yyyymmdd = DateString(1:8)... |
671d8d911f2f32b4e9db69721ee2d5513d8b3f65d6302b925714632aca05bb3e | MATLAB | 11,755 | 367 | function runstim_THINGS(T_Trl)
global Par %global parameters
Par.Mouserun = 0;
dasusemouse( 0 );
preloaded_pics = 40;
ncount = 4;
monkey = 'monkeyN';
% cogstd('sPriority','high')
LOG.fn = 'runstim_THINGS';
DateString = datestr(now,'yyyymmddHHMMSS'); % get date-timestamp
ds_yyyymmdd = DateString(1:8)... |
4646484dcd0001b46060cd2959815e2a2b3e7a120dda6dd3cd76eae09a183e5e | MATLAB | 11,756 | 315 | % eeg_getepochevent() - Return dataset event field values for all events
% of one or more specified types
% Usage:
% >> epochval = eeg_getepochevent( EEG );
% >> epochval = eeg_getepochevent( EEG, 'key', 'val');
%
% Inputs:
% EEG - Input dataset
%
% Optional inputs:
%... |
cfaa04a3c8620f9bf42aa863a846c6dc198d48be5e58c7c4af01da86503e3903 | MATLAB | 11,759 | 367 | function runstim_THINGS(T_Trl)
global Par %global parameters
Par.Mouserun = 0;
dasusemouse( 0 );
preloaded_pics = 40;
ncount = 4;
monkey = 'monkeyN';
% cogstd('sPriority','high')
LOG.fn = 'runstim_THINGS';
DateString = datestr(now,'yyyymmddHHMMSS'); % get date-timestamp
ds_yyyymmdd = DateString(1:8)... |
b310bb22b22bbd884006eea0b61ebb49eb9ae5615e3b3947fd66bc67f98617f3 | MATLAB | 11,769 | 316 | %% prep_4_apply_signatures_and_save.m
%
%
% *USAGE*
%
% This script
%
% # calls a_set_up_paths_always_run_first, then loads DAT/DATA_OBJ*/DATA_OBJ_CON*
% from image_names_and_setup.mat/data_objects*.mat/contrast_data_objects.mat
% if not already in the workspace
% # calculates selected CANlab signature responses fo... |
6ad3b84f69d4fd9fa98776e7ba42b69c8c3ba8a4fc8982cccca0243ba45d5fb9 | MATLAB | 11,772 | 228 | function [fibsvalBin_proj, fibsvalSum_proj, fibsvalMean_proj, fibsvalPeak_proj, fibsval5Peak_proj, fibcell_proj, connFiberInd_proj,fibsvalBin_magn, fibsvalSum_magn, fibsvalMean_magn, fibsvalPeak_magn, fibsval5Peak_magn, fibcell_magn, connFiberInd_magn, totalFibers] = ea_discfibers_native_calcvals(vatlist, cfile, space,... |
57381e012ee54e3704390f450e8b235b8d782c22707a6bbf2ad94db0a6c84668 | MATLAB | 11,773 | 314 | % ====================================
%% Help
% ====================================
%
% CBIG_test_MSHBM_esfmri_inhomo
%
% This script replicates the electrostimulation-evoked network inhomogeneity
% analysis from Lim 2026. Network labels are iterated directly as 1:15.
%
% PREREQUISITES:
% Run CBIG_test_MSHBM_esfmri... |
bfccd7cb76594a39b213d250f7e1ff90600a1e0bb852152928b68fbded7b5524 | MATLAB | 11,779 | 328 | function bz_MakeXMLFromProbeMaps(probemaplist, basepath,basename,plugorder,defaults)
%MakeXMLFromProbeMaps - Generate a .xml file to accompany .dat files for a
%recording in the neuroscope/klusters/ndmanager system. Uses a library of
%probe map layouts.
%
% USAGE
%
% MakeXMLFromProbeMaps(basepath,basename,ProbeFil... |
1bc21c0dfa44639e64fe05d91b65bd97618fd1db8873cede051ba5a27a9cfad2 | MATLAB | 11,787 | 283 | function [output, Greg] = dftregistration_min_max(buf1ft,buf2ft,usfac,min_shift,max_shift,phase_flag)
% function [output Greg] = dftregistration(buf1ft,buf2ft,usfac);
% Efficient subpixel image registration by crosscorrelation. This code
% gives the same precision as the FFT upsampled cross correlation in a
% small... |
ac58c2628b6b51f06cc45da315f1aafe0802064c9464a254cf50c13a5d9c8957 | MATLAB | 11,813 | 301 | function tracksReform = groupSegmentsComptracksAfterReformation( tracksIn)
%groupSegmentsComptracksAfterReformation will rearrange compTracks to
%have only the segments that interact
%
% SYNOPSIS tracksReform = groupSegmentsComptracksAfterReformation( tracksIn)
%
% INPUT
% tracksIn : compTracks af... |
39bc2a930e91182f1849121a86734c83a7db17fa7c96f00c62ca41f61a9403e6 | MATLAB | 11,836 | 394 | function [c,lags] = ea_xcorr(x,varargin)
%XCORR Cross-correlation function estimates.
% C = XCORR(A,B), where A and B are length M vectors (M>1), returns
% the length 2*M-1 cross-correlation sequence C. If A and B are of
% different length, the shortest one is zero-padded. C will be a
% row vector if A is a ro... |
be383da42883ec32f447d45a392c879136e0fb56091ecaad906f280c15f43762 | MATLAB | 11,840 | 253 | function [I,Ihat,cvs,val_struct]=ea_unifiedmapping_crossval(viz,explorer,strategy,iterations,posthoccorrect,customconfig)
if ~exist('customconfig','var')
customconfig=[];
end
switch explorer.multitractmode
case 'Split & Color By Group'
if ismember(strategy(1:6),{'Custom','Import'})
ea_erro... |
bf679bd000dd4387dbd40425652ba2d7151901b4a9c22bf3eaf3f4425b9c3b8d | MATLAB | 11,852 | 228 | function [fibsvalBin_proj, fibsvalSum_proj, fibsvalMean_proj, fibsvalPeak_proj, fibsval5Peak_proj, fibcell_proj, connFiberInd_proj,fibsvalBin_magn, fibsvalSum_magn, fibsvalMean_magn, fibsvalPeak_magn, fibsval5Peak_magn, fibcell_magn, connFiberInd_magn, totalFibers] = ea_unifiedmapping_native_calcvals(vatlist, cfile, sp... |
752456f9df8752125d7cd82bfc6fd02fe528480bffe88e5585de2a633caf14be | MATLAB | 11,856 | 273 | % pop_jointprob() - reject artifacts in an EEG dataset using joint
% probability of the recorded electrode or component
% activities observed at each time point. e.g., Observing
% large absoluate values at most electrodes or components
% is im... |
c85323246075a3dbfcae5c1d7b5bb12f243c20e568fb579138d3b36df2c1ce96 | MATLAB | 11,860 | 339 | %%*****************************************************************************
%% HSDsqlp: solve an semidefinite-quadratic-linear program
%% by infeasible path-following method on the homogeneous self-dual model.
%%
%% [obj,X,y,Z,info,runhist] =
%% HSDsqlp(blk,At,C,b,OPTIONS,X0,y0,Z0);
%%
%% Input: blk: a cel... |
98a04130b420f983b3d8cc27494c4e3dc37343b98d6e97b4ae1e757877455daa | MATLAB | 11,874 | 278 | function ea_perform_lc(options)
% This function is the main execution function of LEAD-DBS Connectome.
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn
% BIDS fix: Ensure options.prefs ha... |
537d6f7b01cce88da8aec5ce9ac3c67d4dbbe029c9a60fb7e84d3de9b0921696 | MATLAB | 11,877 | 212 |
close all
%% NK1R Figures
%
tmpfix=zeros(size(dyn1l1p0a_nk1r_bioall.tt)); tmpfix(502:901)=1;
tmpfixS=zeros(size(dyn1l1p0aS_nk1r_bioall.tt)); tmpfixS(502:601)=1;
tmpfixL=zeros(size(dyn1l1p0bL_nk1r_bioall.tt)); tmpfixL(502:1501)=1;
figure(1), clf,
subplot(231),
plotmsd4(dyn1l1p0a_nk1r_bioall.tt,mean(dy... |
0cfcab17839192057b78b81d730ab137cb5aa7488b30db9d3859a1fa6619b40c | MATLAB | 11,884 | 197 | function [signal, ref_section] = RFT_clean_asr(signal,cutoff,windowlen,stepsize,maxdims,ref_maxbadchannels,ref_tolerances,ref_wndlen,usegpu,useriemannian,maxmem)
% Run the ASR method on some high-pass filtered recording.
% Signal = clean_asr(Signal,StandardDevCutoff,WindowLength,BlockSize,MaxDimensions,ReferenceMaxBadC... |
93f0b2df5c896a638cb4efb533c9c22a2eccb5f3eca98ec8749fc8c07d095b15 | MATLAB | 11,928 | 317 | %% LaBGAScore_mrs_run_osprey_GE.m
%
%
% *USAGE*
%
% This script runs Osprey analysis of mrs data organized according to
% standard LaBGAS file organization by calling, for each voxel, that
% study's own renamed copy of the Osprey jobfile template
% (LaBGAScore_mrs_osprey_jobfile_GE.m or, if nr_sess = 1,
% LaBGAScore_mr... |
659d330a641fefcaedd23bbcc79560ae373fdfe57085b100b924ff8465e63656 | MATLAB | 11,948 | 321 | classdef Grid < uix.Box
%uix.Grid Grid
%
% b = uix.Grid(p1,v1,p2,v2,...) constructs a grid and sets parameter
% p1 to value v1, etc.
%
% A grid lays out contents from top to bottom and left to right.
%
% See also: uix.HBox, uix.VBox, uix.GridFlex
% Copyright 2009-2016 The ... |
0d7b4bc1da607d437ab5eb833081b3e0eb078870303d83cfb001ba2a30ad6982 | MATLAB | 11,951 | 391 | function uTest_FilterM(doSpeed)
% Unit test: FilterM
% This is a routine for automatic testing. It is not needed for processing and
% can be deleted or moved to a folder, where it does not bother.
%
% uTest_FilterM(doSpeed)
% INPUT:
% doSpeed: If ANY(doSpeed) is TRUE, the speed is measured. Optional.
% OUTPUT:
% On... |
6f9634ab922c1b9304bde5f4003a16dee37dbbe12b6be3b0d57f31f0f6fdfd0d | MATLAB | 11,957 | 317 | %% LaBGAScore_mrs_run_osprey_Philips.m
%
%
% *USAGE*
%
% This script runs Osprey analysis of mrs data organized according to
% standard LaBGAS file organization by calling, for each voxel, that
% study's own renamed copy of the Osprey jobfile template
% (LaBGAScore_mrs_osprey_jobfile_Philips.m or, if nr_sess = 1,
% LaB... |
569dc242a698d1a3876ddbaf951ae9fd6a5a6427c644eba587dd4853b0f2fa49 | MATLAB | 11,976 | 278 | % std_figtitle() - Generate plotting figure titles in a cell array
%
% Usage:
% >> celltxt = std_figtitle(key1, val1, key2, val2);
%
% Inputs:
% 'subject' - [string] Subject name
% 'datatype' - [string] data type (For example 'erp')
% 'chanlabels' - [cell array or string] channel names
% 'compnames'... |
1e574a3ebd969519b01241b752de62b6f5390a30f9998ec00b9a47404df15181 | MATLAB | 11,982 | 340 | % run combineFlies.m first to get 'leftall', 'leftmeans', 'rightall',
% 'rightmeans'
for n= 1:8
fn = fieldnames(leftall{n});
for f = 1:numel(fn)
summarymeanL(f,n) = mean(mean(leftall{n}.(fn{f})(:,27:52)));
summarymeanR(f,n) = mean(mean(rightall{n}.(fn{f})(:,27:52)));
% summarym... |
7cd780b2d103f1a71e9e5794ec7bf7fc46a522ede76c40952280f07a59a9f3cf | MATLAB | 11,985 | 470 | function z = xmltools( arg, out_file, varargin)
% XMLTOOLS - tools for managing xml data sets
% - if arg is a string : arg is an XML file to convert into MATLAB struct
% - if arg is a variable : it is a MATLAB struct to write into XML, to stdout if out_file is not given
% use :
% z = xmltools('filename.xml')... |
91c1f89352997a733c7717c3f3027d414c62ef304f740578123a5868600cccd3 | MATLAB | 11,992 | 438 | function [varargout] = rdir(rootdir,varargin)
% RDIR - Recursive directory listing
%
% D = rdir(ROOT)
% D = rdir(ROOT, TEST)
% D = rdir(ROOT, TEST, RMPATH)
% D = rdir(ROOT, TEST, 1)
% D = rdir(ROOT, '', ...)
% [D, P] = rdir(...)
% rdir(...)
%
%
% *Inputs*
%
% * ROOT
%
% rdir(ROOT) lists the specified files.
% RO... |
fa69b579f7cf533cf3eb53f19bc629b3d58362ae93bd3fb8c5c09a4c72882d5b | MATLAB | 12,008 | 320 | % function testscript(pname,direction,movingwin,segave,params,fscorr)
%
% This script runs a sequence of analysis steps using the test
% data contained in data. The data consists of a single tetrode
% recording from macaque area LIP during a memory saccade experiment
% a la Pesaran et al (2002). The data is alread... |
6969edd57f09ca998cdda57a4717858a5c0a27de43b596a4f021507cb8268f1c | MATLAB | 12,015 | 331 | function File = GetFullPath(File, Style)
% GetFullPath - Get absolute canonical path of a file or folder
% Absolute path names are safer than relative paths, when e.g. a GUI or TIMER
% callback changes the current directory. Only canonical paths without "." and
% ".." can be recognized uniquely.
% Long path names (>259... |
68e93adca9be7dba1dde039054a14004c85c00973ac7b44d7a80d218281d6617 | MATLAB | 12,024 | 290 | function varargout = ea_subcorticalrefine(varargin)
% EA_SUBCORTICALREFINE MATLAB code for ea_subcorticalrefine.fig
% EA_SUBCORTICALREFINE, by itself, creates a new EA_SUBCORTICALREFINE or raises the existing
% singleton*.
%
% H = EA_SUBCORTICALREFINE returns the handle to a new EA_SUBCORTICALREFINE or t... |
c61be55588d4af9648d2dcfe953df288b1438d126e30ffb238ad549016497d6d | MATLAB | 12,031 | 355 | function [x, y] = lap(cc, NONLINK_MARKER, extendedTesting, augmentCC, noLinkCost)
%LAP solves the linear assignment problem for a given cost matrix
%
% A linear assignment tries to establish links between points in two sets.
% One point in set A can only link to one point in set B and vice versa.
% The cost associ... |
59ea4f8d00244231582f0f5991f53879f946e367e07fecc89cb9c4067f8c6dad | MATLAB | 12,037 | 321 | % eeg_getdatact() - get EEG data from a specified dataset or
% component activity
%
% Usage:
% >> signal = eeg_getdatact( EEG );
% >> signal = eeg_getdatact( EEG, 'key', 'val');
%
% Inputs:
% EEG - Input dataset
%
% Optional input:
% 'channel' - [integer array] read only specifi... |
1b1b67e3f4785fe9f0e24e03aef806d83d196625900bfad49446d1fde97dafa9 | MATLAB | 12,041 | 334 | function hcb=colorbarf(cout,H,loc)
% COLORBARF Display color bar for a filled contour plot.
% =========================================================================
% colorbarf Version 1.5 19-Feb-2001
%
% Usage:
% colorbarf(cout,H,[loc])
%
% Example: [cout,H,cf]=contourf(peaks);
% colorbarf... |
645697d2226560ac9a771e86f3ed99687ca1b3d6819aef2c5b17e93844b2c93f | MATLAB | 12,065 | 268 | ccc;
RAWDATAPATHs = dir("..\MAT Data\raw\**\7-10Freq Active\**\*.mat");
% Date filter
DATESTRs = {'cc20220520', 'cc20220706', 'cc20220801', 'cc20221014', 'cc20221015', ...
'xx20220711', 'xx20220812', 'xx20220820', 'xx20220822', 'xx20220913'};
RAWDATAPATHs = RAWDATAPATHs(contains({RAWDATAPATHs.name}, DATE... |
2e0fcdf9f8d26bec277916e281698cabea9ff3e5a3812d9fab679a2231e62966 | MATLAB | 12,075 | 308 | function mixtures = generateMixtures(targets,interferers,varargin)
%GENERATEMIXTURES Generate arrays of mixtures from targets and interferers.
%
% MIXTURES = IOSR.BSS.GENERATEMIXTURES(TARGETS,INTERFERERS) generates an
% array of MIXTURE objects using SOURCE objects TARGETS and INTERFERERS.
% Each mixture object ... |
6f961ee56b00528084db619a0b0e1e3e471c9585b54a23dbd4e15dffce91a8ea | MATLAB | 12,094 | 238 | % std_clustread() - this function has been replaced by std_readdata() for
% consistency. Please use std_readdata() instead.
% load one or more requested measures
% ['erp'|'spec'|'ersp'|'itc'|'dipole'|'map']
% for all components of a specified clus... |
33ab0b86a505b897c5d7dd35ef7bdfea7eb09d6486e896fb56c5b491e795fb63 | MATLAB | 12,150 | 414 | %% Create and plot design matrices
%%
% Create and plot your own design matrix easily using CANlab tools!
% Note: This also requires SPM software functions
%
% These functions are useful for design simulations. They use the following
% core functions, which may also be useful to use separately if you are
% doing simul... |
f2d8c86085d4c0bb1b9b61628e2750ac434fa131b2f891af4c1f605ba67abc01 | MATLAB | 12,164 | 297 | %% Create raster_data.mat files for The Neural Decoding Toolbox
% For each unit the code depends on a particular file, with three
% variables: raster_data, raster_labels, and raster_site_info
% raster_data: matrix as [num_trials x num_time_points]
% time points could be bins of milliseconds with either a spike (= 1) or... |
5861afa8853acfa7a93ae7352708d45891432826cef9ff21b221ef7f4374819d | MATLAB | 12,184 | 387 | % envproj() - plot envelopes of projections of selected ICA component
% projections against envelope of the original data
%
% Usage: >> [envdata] = envproj(data,weights,compnums);
% >> [envdata] = envproj(data,weights,compnums, ...
% title,limits,chanlist,compn... |
4093c82e5cf1b8868cad4a290fc4c55505b051bba835d175c0fd720fef6ea572 | MATLAB | 12,186 | 279 | % mtimesx does a matrix multiply of two inputs (single, double, or sparse)
%******************************************************************************
%
% MATLAB (R) is a trademark of The Mathworks (R) Corporation
%
% Function: mtimesx
% Filename: mtimesx.m
% Programmer: James Tursa
% Version: 1.1... |
05bfd20ebb222ae1b5487d5fac630ce5aa6319fc46c8f5226ce8ed5ea6258c2b | MATLAB | 12,206 | 381 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
if ~contains(path, '/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
addpath(genpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab'));
end
%% ======================= step 1 ... |
61ece73e909536fd0c92573eab9822b88c03d9fc7bc15721e9652568720f24d3 | MATLAB | 12,226 | 331 | %% Calculate Cross SCF of p over ensemble of hybrid connectivities
clear; clc;
% Load model parameters
loadparam;
dx = topology.L / topology.Nx;
dt = topology.T / topology.Nt;
N = 100;
num_connectomes = 10;
% Create bins of dr and dt
dist_bin_array = 0:0.02:0.2;
delay_bin_array = 0:0.002:0.02;
num_... |
a133d087169eb5072e089a25ca657d13df651b0f42aa65fd8cc9fedb126bad8e | MATLAB | 12,246 | 348 | % Name: Robert Kim
% Date: 04-04-2026
% Email: robert.f.kim@gmail.com
% S6.m
% Description: Script to analyze the weights of the trained models to understand the effect of lesioning. Used for Fig. S6 in the paper.
clear; clc;
% Add parent folder to MATLAB path for any helper functions used by this script
addpath(ful... |
fd0797cc6b0f76530cb49820fb00226dfe5781895471d54ae0e14c9eaed804b0 | MATLAB | 12,246 | 275 | % F04_B.m
% Manuscript Fig 4b: MB task-specific functional correspondence.
% Input tables are read from manuscript_figure_source_data/data/main_text_source_data.xlsx.
clear all
ROI={"Dorsal", "Lateral","Ventral"}
%% read dataTables
Fig4b=read_main_text_source_table("fig4b_points");
Fig4b_noiseCeiling=read_main_text_so... |
70e367a031ccc10687e72c6800064beb6a8a2b21cff08ad6bddbf927ee26c292 | MATLAB | 12,259 | 304 | classdef fastBSpline
%fastBSpline - A fast, lightweight class that implements
%non-uniform B splines of any order
%
%Matlab's spline functions are very general. This generality comes at
%the price of speed. For large-scale applications, including model
%fitting where some components of the mode... |
f33b276b5061ef68337fbb8c60bf0c1227db2bfab3d23fedba76e3c332a3f351 | MATLAB | 12,275 | 396 | function editor(tree)
%XMLTREE/EDITOR A Graphical User Interface for an XML tree
% EDITOR(TREE) opens a new figure displaying the xmltree object TREE.
% H = EDITOR(TREE) also returns the figure handle H.
%
% See also XMLTREE
if ~isempty(getfilename(tree))
title = getfilename(tree);
elseif ~isempty(inputname(1)... |
29c2c0819ca0196f8fc6583b6db89fdf7ab419b30ee9758e7f31fba6693a94fe | MATLAB | 12,293 | 175 | function [hessian_mat, sorted_eigenvalues, sorted_eigenvectors] = get_qvm_hessian(V,C,KP,P0,KA,A0,strain)
% GET_QVM_HESSIAN Build the vertex-model energy Hessian and return its
% eigen-decomposition, under Lees-Edwards (sheared) periodic boundary
% conditions.
%
% [hessian_mat, sorted_eigenvalues, sorted_eigenvector... |
70c3e53c6f085f8526cb4ca0d6bb56d0e10599d6f5981fa4643867e37dd43b28 | MATLAB | 12,304 | 304 | function res = saveastiff(data, path, options)
% options.color
% : true or FALSE
% : If this is true, third dimension should be 3 and the data is saved as a color image.
% options.compress
% : 'no', 'lzw', 'jpeg' or 'adobe'.
% Compression type.
% 'no' : Uncompressed(Default)
% 'lzw' :... |
f775a52578e0b9fd2f4d5409e57eeb79c8ba88638f038245a8f532e6b6407530 | MATLAB | 12,314 | 324 | function [label_matched, table_matched] = ...
CBIG_gwMRF_match_yeo2011(alex_annot, yeosplit_annot, hemi, network_name, k, p, reorder_idx)
% [label_matched, table_matched] = ...
% CBIG_gwMRF_match_yeo2011(alex_annot, yeosplit_annot, hemi, network_name, k, p, reorder_idx)
%
% This function match the Schaefer20... |
88a81d873687d267b984d4f1851039771f9e688a9ee81405f8b1a3c8621200a0 | MATLAB | 12,328 | 282 | % pop_editoptions() - Edit memory-saving eeglab() options. These are stored in
% a file 'eeg_options.m'. With no argument, pop up a window
% to allow the user to set/unset these options. Store
% user choices in a new 'eeg_options.m' file in the
% ... |
f80c2b65abb4b290e80c9953608d84301ed54681c671d2764f8698d01d81a1db | MATLAB | 12,328 | 392 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [img,hdr] = load_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('Usage: [img,hdr] = ... |
df91007486a3e700fa35ddb3dc4f42db7ecf766001ac26ac34494dff5170f59b | MATLAB | 12,340 | 401 | function options=ea_handles2options(handles)
% main function converting GUI handles to options struct used in
% ea_autocoord & ea_write (i.e. the main lead batch functions).
%% some manual options that can be set:
options.endtolerance=10; % how many slices to use with zero signal until end of electrode estimate.
optio... |
8d2ecae1cbf67a51cb100648e37a3b67fca4b21116c781c8b4282f6fda456fc0 | MATLAB | 12,376 | 311 | % trtyps = {'OFneg90';'OFneg45';'OFzero';'OFpos45';'OFpos90';
% 'AFneg90';'AFneg45';'AFzero';'AFpos45';'AFpos90';
% 'OFAFneg90';'OFAFneg45';'OFAFzero';'OFAFpos45';'OFAFpos90'};
% trtyps = {'one';'two';'three';'four';'five';'six';'seven';'eight';'nine';'ten';'eleven';'twelve';...
% 'thirteen';'fourteen';'f... |
04e47f142b0252cd3b9956bc9154f78cf9bdced8845494ae0a2b775c28b0773b | MATLAB | 12,415 | 177 | function dE2_mat = get_dE2_mat_vm_LE(V,newC,K_A,K_P,A0,P0,strain)
% GET_DE2_MAT_VM_LE Assemble the full Hessian (second derivative) matrix
% of the vertex-model energy with respect to vertex positions, under
% Lees-Edwards (sheared) periodic boundary conditions.
%
% dE2_mat = GET_DE2_MAT_VM_LE(V, newC, K_A, K_P, A0,... |
38ff5ecca84dbdc2f8175803bd10a05f056963087c9bd9313373bf071d3e43d9 | MATLAB | 12,418 | 401 | function editor(tree)
%XMLTREE/EDITOR A Graphical User Interface for an XML tree
% EDITOR(TREE) opens a new figure displaying the xmltree object TREE.
% H = EDITOR(TREE) also returns the figure handle H.
%
% This is a beta version of <xmltree/view> successor
%
% See also XMLTREE
%___________________________________... |
8c20da63c91534e883a614d799c8be93ac11c46fe9f465950873e46ba2105661 | MATLAB | 12,430 | 278 | % F04_A.m
% Manuscript Fig 4a: MB task-to-stream assignment.
% Input tables are read from manuscript_figure_source_data/data/main_text_source_data.xlsx.
clear all
close all
ROI={"Dorsal", "Lateral","Ventral"}
%% read dataTables
Fig4a=read_main_text_source_table("fig4a_points");
Fig4a_noiseCeiling=read_main_text_source... |
228fbf51eb90100cb420a12fc8ffa4ddfe0c74452b2e82b737b99a191b59c900 | MATLAB | 12,460 | 467 | function z = xmltools_ss( arg, out_file, varargin)
% xmltools_ss - tools for managing xml data sets
% - if arg is a string : arg is an XML file to convert into MATLAB struct
% - if arg is a variable : it is a MATLAB struct to write into XML, to stdout if out_file is not given
% use :
% z = xmltools_ss('... |
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