sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
02762789b685c9245c0a4a9a6a50d25a156cdf1b616394393fcfb0ef17386846 | MATLAB | 3,202 | 115 | function ea_fsl_apply_normalization(varargin)
% Wrapper for FSL applywarp used for reapplying normalization (non-linear
% registration)
options = varargin{1};
useinverse = 0;
if nargin > 1 % manual application
input = varargin{2};
output = varargin{3};
useinverse = varargin{4};
end
if nargin >= 5
re... |
8f3cf6c4b1683f0c5fd784bda4684c4b1d98103651b7f24083c1916d454ee786 | MATLAB | 3,202 | 74 | %%
% get max of flight intensity values for each mic in each experiment for each fly
% normalize flight intensity values to the range
% calculate changes in flight intensity
% threshold changes in flight intensity to grab 'accel' and 'decel' timestamps
% grab 6 seconds of neural activity data around accel/decel po... |
760d237c3ecba7a1659bd1f3837a3893df3f9dee227309008e525acdc2897346 | MATLAB | 3,203 | 79 | %% PaCER/EXAMPLE_1_2.m - Example file for using PaCER - Precise and Convenient Electrode Reconstruction
% to reconstruct precise curved electrode trajectories
% and contact locations from post operative CT imaging
% of DBS electrodes
%
% Andreas Husch
% ... |
c692a987a21b33aed855b327428571c2092803212e58184ec033908ebe56ec68 | MATLAB | 3,203 | 79 | %% oor - optimal opliptimal oblique sampling along a given polynonimal
%
% Returns: improvedSkeleton - skeleton gained along the polynomial by
% resampling and intensity weithed centroid calculation
% medIntensity - median intensity profile along the polynoial
%
% Andreas Husch
... |
7917c66a63ccde9e95b05d6aba20c35d8a6986318ec8753068c3aabec92d862c | MATLAB | 3,204 | 94 | function table = palm_strcsvread(varargin)
% Read a CSV file containing non-numeric fields (strings) and
% return a cell array. Numbers are converted to double and, if contiguous,
% can be easily converted to arrays with cell2mat. The remaining
% are left as strings.
%
% Usage:
% table = palm_strcsvread(filename,delimi... |
9127c7d8b4348951d4c07c3ea4753d068a9631d38feb2dee82b19b46b76ecd05 | MATLAB | 3,205 | 102 | %%*******************************************************************
%% schurmat_qblk: compute schur matrix corresponding to SOCP blocks.
%%
%% HKM direction: output = schur + Ax*Ae' + Ae*Ax' - Ad*Ad'
%% NT direction: output = schur + Ae*Ae' - Ad*Ad'
%%
%% where schur = A*D*A', and Ad is the modification to ADA'
%% s... |
2933f89dc913332ada04134fe0679924f79b539a7ec19f817d872cece10959b8 | MATLAB | 3,208 | 104 | function x = eyeK(K)
% eyeK Identity w.r.t. symmetric cone.
%
% x = eyeK(K) produces the identity solution w.r.t. the symmetric cone,
% that is described by the structure K. This is the vector for which
% eigK(x) is the all-1 vector.
%
% See also eigK.
% Complete rewrite for SeDuMi 1.3 by Michael C. Grant... |
2a0cead925c2e19234d136158d44769864fff2609a1fd399e6c19c1833dd8148 | MATLAB | 3,208 | 77 | function []=v2structDemo2()
% V2STRUCTDEMO2 is a usage example demo function for the function V2STRUCT. This demo
% shows a suggestion for how to use v2struct in managing input to other functions with
% improved usability.
%
%% Last update:
% 30.06.2011, Adi N.
fprintf(['Running usage demo function for v... |
59212443ccf4f18c5ffc99631ab62be21dcec973c39c4678ed1621d905a4275d | MATLAB | 3,208 | 92 | signatures_to_plot = {'NPS' 'NPSpos' 'NPSneg'}; % NPS, VPS, SIIPS, etc., etc.
myscaling = 'raw'; % 'raw' or 'scaled'
mymetric = 'dotproduct'; % 'dotproduct' or 'cosine_sim'
% Controlling for group admin order covariate (mean-centered by default)
group = [];
if isfield(DAT, 'BETWEENPERSON') && isfiel... |
aae123442e8e3f788b001053f3986c96a83f2c4e89168c8db85d3ffb221d4b01 | MATLAB | 3,216 | 63 |
% this script takes anatomical files specified in DAT structure and warps
% them to MNI space (using IXI template from CAT toolbox and SPM's
% segmentation routine). This script assumes functional and anatomical data
% are coregistered.
anat_path=fullfile(datadir, DAT.structural_folder, DAT.structural_wildcard);
ana... |
3d15d1a6e02a6571768d4102ffc44da7ab5a5faa5de7107b450cfe58901ba43d | MATLAB | 3,218 | 104 | function out=validate_aes(aes)
%Generate useable aes structures: empty fields are replaced with arrays of
%ones of the correct size. The size of the other fields are checked for
%consistency. Handle special case of size parameter that can be set by the
%user
%Old matlab test for iscategorical absent from pre 2013b
per... |
b9f09a35d2cd33585badc92ecad3010e0741022d9eed094764c9ecd1e5ff572b | MATLAB | 3,218 | 72 | % 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... |
d11ad94a95b6aa4fa125d0673f29f7ffcc7364cff65d2a33ee629e553fb39e53 | MATLAB | 3,218 | 97 | clc
clear
% -------------------------------------------------------------------------
% Script description:
% This script compares neural activity values at different time point
% combinations against a baseline time point, and calculates the number of
% neurons whose activity exceeds baseline for each combination.
... |
2c6444fd8144fe3990c6c45f97529f0ebb3c0e3b3a6bd18d2c36a7ba41dca910 | MATLAB | 3,219 | 106 | %firws() - Designs windowed sinc type I linear phase FIR filter
%
% Usage:
% >> b = firws(m, f);
% >> b = firws(m, f, w);
% >> b = firws(m, f, t);
% >> b = firws(m, f, t, w);
%
% Inputs:
% m - filter order (mandatory even)
% f - vector or scalar of cutoff frequency/ies (-6 dB;
% pi rad / sample)
%
% O... |
8abbe028f762c00b3a6367e0f44731f7ee1c7195404ecd8393c92f29599c18eb | MATLAB | 3,219 | 97 | function P = chi2Tests(X, method)
% Chi-square tests of homogeneity and independence
% Computes the P-value for IxJ-table row/col independence.
% Program by Steinar Thorvaldsen, steinar.thorvaldsen@uit.no, Dec. 2004.
% Ref.: DeltaProt toolbox at http://services.cbu.uib.no/software/deltaprot/
% Last change... |
7ce233cad42bdb8216de2435c4d488ad932e9e3cbdd446953a0f3be6be686910 | MATLAB | 3,220 | 68 | % Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
% convert vbm and behavior to doc
CBIG_CODE_DIR = getenv('CBIG_CODE_DIR');
proj_dir = [CBIG_CODE_DIR '/stable_projects/disorder_subtypes/Sun2019_ADJointFactors'];
addpath([proj_dir '/step2_MMLDA'])
addpath(... |
82c871be1774a055812166541eea3d81f1fa73bf51ea8b632393a27631c29e77 | MATLAB | 3,222 | 92 | function ea_cvshowvatfmri(resultfig,pX,directory,filesare,handles,pV,selectedparc,mod,options)
%mV=pV; % duplicate labeling handle
%mX=pX; % duplicate labeling data
stims=get(handles.vatseed,'String');
stim=stims{get(handles.vatseed,'Value')};
% check out which vats to use
[usevat,dimensionality,currentseed,sides]=ea_... |
b18f8c8b285cbbca04f05a8b3c7c95edea2fa19c30727e7a258ef92b612f677b | MATLAB | 3,222 | 102 | function run_pRF_V7(SubID)
% pRF analysis script using SPM12 and SamSrf V7.13
% Adjusted for Ubuntu server setup (15/06/2025)
% Created : "2015-03-16 14:42:38 TDekker"
test = false;
if test
disp('Just a test, no calculations done...');
return;
end
%% Set defaults
nRuns = '3';
WhichFolder = 'retinotopy';
Sc... |
c0a870ae5a21b23729e4c672523f82c260f5b63d7f7ac24fd6c5efdcfd58b933 | MATLAB | 3,222 | 88 | % correctfit() - correct fit using observed p-values. Use this function
% if for some reason, the distribution of p values is
% not uniform between 0 and 1
%
% Usage:
% >> [p phat pci zerofreq] = correctfit(pval, 'key', 'val');
%
% Inputs:
% pval - input p value
%
% Optional inputs... |
bcf4b9a901df6e4421aee4bdcc764b985245f3694dda02536255a7792d974036 | MATLAB | 3,225 | 102 | function [res, typeNameStr, errStr]= dtdstruct_istype(dtdStruct)
%function [res, typeNameStr, errStr]dtdstruct_istype(arg)
%
% function determines if arg is a valid dtdStruct. If this is the case,
% also the type name is returned as the second return value.
%
% arg: arbitary data .. may be a dtdStruct
... |
eafb6ee3286389068161314131ca2aa0a98fe499d5916ad627e74f0f09bca571 | MATLAB | 3,229 | 97 | function varargout = mat2xml(matfile, xmlfile)
%MAT2XML Convert a MAT-file into an XML file
% MAT2XML(MATFILE, XMLFILE) loads MAT-file MATFILE and converts it
% into an XML file saved in XMLFILE.
% T = MAT2XML(MATFILE) also converts the MAT-file MATFILE to XML
% but returns it instead as an XMLTree object T.
... |
2c5662d72a126549e46b58eb29efa5209e5ef74e4b28ef5784bedd8638c0edab | MATLAB | 3,230 | 85 | function ClusNum = VLSM_clusterPermutation(voxdir)
A = load([voxdir,filesep,'ForPerm.mat']);
permnum = 1000;
Dind = full(A.Dind);
GROUP1 = A.GROUP1;
GROUP2 = A.GROUP2;
COVterm = A.COVterm;
VALt = A.VALt;
indexs = A.indexs;
V = A.V;
tic
for iperm = 1:permnum
ord = round(rand(1,size(Dind,2))*size(Dind,2));
or... |
94a795cab2c959fe4511f80e20753d22787a2435fce467cad02e7af7a31b754c | MATLAB | 3,231 | 74 | function correctManifestFile(manifest_file, attributes_file)
% Some manifest files, created by syntalos (especially the ones that were
% created between 2021-05-18 and 2021-06-15), have false timestamp indices (data_aux.parts).
% This function serves as to correct these errors.
manifest_struct = read(manifest_file);
... |
5027bb52857f2fa1e8b084d417b7b6a5897887b11b430b02d837d018f2db8602 | MATLAB | 3,234 | 74 | function [redo, options]=ea_prepare_dti(options)
% general DTI preprocessing goes here
redo = 0; % Initialize return value
directory=[options.root,options.patientname,filesep];
% BIDS: If DWI files don't exist, copy from rawdata with BIDS-compliant names
if ~exist([directory, options.prefs.dti], 'file')
options ... |
dd4ead13afbdc3f3d1502c31e4ed0d17be15197f2591bee4ec90225c877b05ad | MATLAB | 3,237 | 69 | function spindleSummary = spindlesum(spindles, srate, samples)
% Summarize sleep spindle features. Calculates spindle density
% (spindles/min) and gets average value of spindle features on each channel
%
% Required inputs:
%
% spindles: A structure containing spindle data (output of
% fun_sleep_spindles)
%
% srate: The... |
57ff8b9650ad4e9c6e62014da981f09ad551937bc7cb0a6230ec479d158e76e2 | MATLAB | 3,238 | 155 | % Example 6.4: Regressor selection problem
% Section 6.3.1, Figure 6.7
% Original by Lieven Vandenberghe
% Adapted for CVX Argyris Zymnis - 10/2005
%
% Solves
% minimize ||A*x-b||_2
% subject to card(x) <= k
%
% where card(x) denotes the number of nonzero elements in x,
% by first solving (for some valu... |
cbe9e6fe9bdddf034a19a5963ce5cf65941e3bba01d308f1fb67204869e54184 | MATLAB | 3,239 | 59 | function ea_dispbn(varargin)
vnum=['v',ea_getvsn('local')];
if nargin>0
if strcmp(varargin{1},'ee')
for space=1:100
spstr=repmat(' ',1,space);
% display banner..
disp(' Welcome to ');
disp(' ... |
3b1f6ebfca2c8434d2e5e05de853038f00ba2c67636516db0fec3ca7ea0d785f | MATLAB | 3,242 | 111 | % corrcoef_cell() - compute pairwise correlations using arrays and
% cell array inputs.
%
% Usage:
% >> c = corrcoef_cell( data );
% >> c = corrcoef_cell( data );
%
% Inputs:
% data - [cell array] data consisting of PAIRED arrays to be compared.
% The last dimension of e... |
3c9d7e4905081c0f96477eec96187eafbb8c92311f4809dbd27065e8863566f5 | MATLAB | 3,244 | 59 | fprintf(1,'Executing %s at %s:\n',mfilename(),datestr(now));
ver,
try,
if isempty(which('spm')),
throw(MException('SPMCheck:NotFound', 'SPM not in matlab path'));
end
[name, version] = spm('ver');
fprintf('SPM version: %s Release: %s\n',name, version);
fprintf('SPM p... |
6680accb7758c23b90933782f2c689bdc4c2edc33aede4c9226cb6b061fab1bd | MATLAB | 3,246 | 149 | function [baseline, decline] = CBIG_hypoTest_2t(stats)
% [baseline, decline] = CBIG_hypoTest_2t(stats)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
beta = stats.Bhat;
betaCov = stats.CovBhat;
baseline = zeros(3, 3);
decline = zeros(3, 3);
%% --------------... |
748b3bd67317717661eb3ee72216f9ad0c4b3d835ce2725929760457b3103c3d | MATLAB | 3,251 | 108 | % plotchans3d() - Plots the 3-D configuration from a Polhemus ELP
% file. The axes of the Cartesian coordinate system are
% plotted. The nose is plotted as a bold red segment.
% Usage:
% >> plotchans3d( elpfile, zs);
% >> plotchans3d( [X,Y,Z], elecnames, zs);
%
% Inputs:... |
10ea266ea955851eeadc626087a2ebcb86c319c7eab3edf644fff0943bef5e9c | MATLAB | 3,252 | 97 | function[S,tau,tc] = staogram(data_spk,data_lfp,smp,plt,Tc,Tinc,Tw,w,D)
%
% staogram : calculates a moving window spike triggered ave %
% Usage:[S,tau,tc] = staogram(data_spk,data_lfp,smp,plt,Tc,Tinc,Tw,w,D)
%
% ******** INPUT *********
% Note that all times have to be consistent.... |
4bf6d12127fe826baba87b6148dfea65259fefd1e13f2318f98cd6c8c6db59fd | MATLAB | 3,252 | 95 | function [cn rt] = core_numbers(A,varargin)
% CORE_NUMBERS Compute the core numbers of the vertices in the graph.
%
% [cn rt] = core_numbers(A) returns the core number (cn) of each vertex.
% The core number is the largest integer c such
% that vertex v exists in a graph where all vertices have degree >= c.
% The vecto... |
eb5cd718ecc5aa3fce5ae78d4e8ac5497a303668b5e6f3eab5ae5cf1d8c2b720 | MATLAB | 3,254 | 96 | function data = AFOFdata_struct7(inputdata, filenames)
% USE THIS FOR EXP7 (CEM)
% how it works:
% fly = AFOFdata_struct7(data,filenames) where data and filenames are
% inputdata and filenames from AF_OF_importer()
for e = 1:length(inputdata)
for t = 1:size(inputdata{e}{1},1)
trial.filename = filen... |
eb3f602f11525fdf0bfda58185abf7141f519c57c8116fbef5e49e8e51dc39e3 | MATLAB | 3,256 | 80 | function ClincFreq_CalWeiCent(outdirCent,OutWeiCentdir,SetUpPara,Para,AtlasTempU,dbmask)
% [V0,D0,namelist] = Dynamic_read_dir_NIFTI_sparse(INDIR);
% D0(isnan(D0)) = 0;
% D0(isinf(D0)) = 0;
% D0 = D0>0;
%
% Dvol = sum(D0)';
% Dvole = sum(D0,2);
% IgV = Para.IgP;
% indexs = find(Dvole>=(size(D0,2)*IgV/100));
... |
0c0a52d62aa92d976a4b4dac96e09528f3f7371dca6e1d011bd9d2234ecacc1d | MATLAB | 3,257 | 49 | %% Get peaks respectivly center points at threshold below the peaks from 1D
% intensity profile. Expected peakWaveCenter number == 4 for now (needs update to support electrodes with more ring contacts)!
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg ... |
87a1ab865125c38f5415ceb45cb08c7b5b996d51fc72264c1526469499d21eba | MATLAB | 3,258 | 149 | function [baseline, decline] = CBIG_hypoTest_2t(stats)
% [baseline, decline] = CBIG_hypoTest_2t(stats)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
beta = stats.Bhat;
betaCov = stats.CovBhat;
baseline = zeros(3, 3);
decline = zeros(3, 3);
%% --------------... |
fbb8ecb89f77282fd6437e34e5e781d9fff3db68e2b516f1a5bccd983a977b46 | MATLAB | 3,258 | 102 | %% figure S7
% TE tuning selectivity is independent of signal power and SNR.
% (A) TE magnitude violin plot: awake vs anesthesia
% (B) LMM bar chart: power-controlled SI difference from M5
% (C) LMM bar chart: SNR-controlled SI difference from M5
load('figureS7_data')
addpath('functions');
set(0, 'DefaultAxesFontNa... |
4e2bcb7018d4c25339fad7298c145747d667fe5f04d09abece0d5b2989a5c88b | MATLAB | 3,261 | 90 | % readbdf() - Loads selected Records of an EDF or BDF File (European Data Format
% for Biosignals) into MATLAB. This function is outdate
% Use the functions sopen() and sread() instead
%
% This program is deprecated (obsolete). Use the sopen() and sread()
% function instead
% Version 2.11
%... |
f6b82f236faf15074bb207f94c4c77694f0dac97ee5978266607509828194ea0 | MATLAB | 3,262 | 95 | % Figure 8.15: Linear placement problem
% Section 8.7.3, Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 10/24/05
% (a figure is generated)
%
% Placement problem with 6 free points, 8 fixed points and 27 links.
% The coordinates of the free points minimize ... |
e83494656942538296abdb375286fb81f5a1f79b5f063de39862ceddcb614c13 | MATLAB | 3,263 | 86 | function [coords_mm,trajectory,markers] = ea_runtraccore(options)
if isfile(options.subj.recon.recon)
options.native = 0; % Load MNI reco
[coords_mm,trajectory,markers] = ea_load_reconstruction(options);
end
if isempty(options.sides)
return
end
% build lfile
fis={[ea_space,'bb.nii']};
switch options.subj... |
314bc40cc43dff511f2f625be88050deb0ffeabd12373ec3e2ea0e009fe9bc49 | MATLAB | 3,264 | 80 | function p_all = CBIG_MMLDA_association_atrophy_behavior_wrapper(out_dir)
% CBIG_MMLDA_association_atrophy_behavior_wrapper(out_dir)
%
% Wrapper function to use GLM to investigate association between atrophy and behavior
%
% Input:
% - out_dir : output directory
%
% Output:
% - p_all : all pairwise p values
%... |
92cdcdc27cdf9d5e346262da44e9948227611aa4fb53d249cff4151b88c61d0d | MATLAB | 3,265 | 104 | function pairs = MatchPairs(list1,list2,varargin)
%MatchPairs - Pair nearest values in two lists.
%
% USAGE
%
% pairs = MatchPairs(list1,list2,<options>)
%
% list1 first list
% list2 second list
% <options> optional list of property-value pairs (see table below)
%
% =============... |
c2cda154146ca3b65d3b16051a26f7da8119fd00f53b362eb4d4e93e93309096 | MATLAB | 3,265 | 98 | classdef GeneralWaveform < handle
%GENERALWAVEFORM implements a class for the any type of signals. This
%class should convert to the discrete or continuous waveform the input
%signals.
% Detailed explanation goes here
properties (SetAccess = 'protected')
SamplingFreq (1,1) double = 2e... |
0a5aaef05d7a033d58b447e8f43982ef86d6c1ca47e0416a3a7aaddf92900a14 | MATLAB | 3,266 | 98 | function [z, r, tp] = fsLR2roizmat(gL, gR, roiL, roiR)
% DESCRIPTION:
% Extract ROI time series from 32k by 32k fsLR and save as correlation
% matrix (r), fisher-z-transfromed correlation matrix (z), or
% roi-by-timepoint matrix (tp).
% ROI needs to formatted where each column represents a separate ROI,
% w... |
b2d743c2e750ddf42d594d0e07253d997d029ff25230e33cd7335e9ef813fd47 | MATLAB | 3,267 | 96 | function calllochist(Dendrite_CrossSess, spine_evolve, handles)
binvalue = handles.thresh*2;
dendID = table2array(Dendrite_CrossSess(:,1));
dendID(dendID==0) = [];
dendID(isnan(dendID)) = [];
targetID = dendID(1);
DendLoc = table2array(Dendrite_CrossSess);
SpineLoc = table2array(spi... |
f1228c92db64e5a524ec996ce3dd6ceec54828bbcbf7c2363f7be2f3472fd0d7 | MATLAB | 3,270 | 94 | function [T F]=DelaunayInside3D(V,F,Options)
%
% [T Fr]=DelaunayInside3D(V,F,Options)
%
% inputs,
% V : Vertex List N x 3, with x,y,z positions
% F : Face List M x 3, with vertex indices
% options : Struct with options
% options.verbose : if true, show information
%
% outputs,
% T : Tetrahed... |
3b256d19e210d91c88ebd8563fe54b19338c1cd3f8e3dda914bfdc764b828a0b | MATLAB | 3,274 | 79 | function [dx,dy,dz,dy0, err] = sddir(L,Lden,Lsd,pv,...
d,v,vfrm,At,DAt,dense, R,K,y,y0,b, pars,pMode) %#ok
% [dx,dy,dz,dy0, err] = sddir(L,Lden,Lsd,p,d,v,vfrm,At,DAt,dense, R,K,y,y0,b, pars)
%
% SDDIR Direction decomposition for Ye-Todd-Mizuno self-dual embedding.
% Here, p is the direction p = dx+dz. If p=[], t... |
2f8a6e3d1689ad685b3105d03f23d3f2b28ff7356359e196c5604c1b96b1c474 | MATLAB | 3,275 | 93 | ccc;
%%
dataP1 = load("..\MAT Data\figure data\Prediction CC.mat");
dataP2 = load("..\MAT Data\figure data\Prediction XX.mat");
dataPE1 = load("..\MAT Data\figure data\PE CC.mat");
dataPE2 = load("..\MAT Data\figure data\PE XX.mat");
%%
run("private\plotConfig.m");
colors = {'#84348C', '#4FB352'}; % AC, PFC
scal... |
fab975067d6c8ded5ab72effb586fc84ee0e76f2005a7d13842ddf02982c917d | MATLAB | 3,276 | 119 | function y = psdscale(ud,x,K,transp)
% y = psdscale(ud,x,K [,transp])
%
% PSDSCALE Computes length lenud (=sum(K.s.^2)) vector y.
% !transp (default) then y[k] = vec(Ldk' * Xk * Ldk)
% transp == 1 then y[k] = vec(Udk' * Xk * Udk)
% Uses pivot ordering ud.perm if available and nonempty.
%
% ********** INTERNAL F... |
166c98b169ba713fbc560552153cc7df108455c6810cc55d725e70d03e11157c | MATLAB | 3,277 | 97 | % Example 6.8: Spline fitting
% Section 6.5.3, Figure 6.20
% Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 10/03/05
% (a figure is generated)
%
% Given data u_1,...,u_m and v_1,...,v_m in R, the goal is to fit to the
% data piecewise polynomials with maxi... |
9ef10508004066b66a5018290a0f467c0b07ae1c91e00db5fdfdca802d03fd58 | MATLAB | 3,279 | 108 | function [maxsize,clstat,sizes] = palm_clustere(X,y,thr,opts,plm,varargin)
% Compute cluster extent statistics, for volume or surface
% data (vertexwise or facewise).
%
% Usage:
% [maxsize,clstat,sizes] = palm_clustere(X,y,thr,opts,plm)
%
% Inputs:
% - X : Statistical map.
% - y : Modality index (of those store... |
c1b2afe7f1f3f9c571304baa22c46926f22816112f23254ef90fc5f3b6682497 | MATLAB | 3,281 | 100 | function obj=stat_fit(obj,varargin)
% stat_fit() Display a custom fit of the data
%
% Example syntax gramm_object.stat_fit('fun',@(alpha,beta,x)alpha*cos(x-beta),'disp_fit',true)
%
% This fuction uses the curve fitting toolbox function fit() to
% fit a provided anonymous function with arguments
% (param1,param2,...para... |
23c69234f630f6a36470409d290509b41357d1ca400a6ad06414161f100ddb9c | MATLAB | 3,282 | 80 |
% The canlab_dataset object is a way of collecting behavioral data
% and/or meta-data about fMRI (and other) studies in a standardized format.
% It has entries for experiment description, Subject-level
% variables, Event-level variables (e.g., for fMRI events or trials in a
% behavioral experiment) and other fields fo... |
4d28d3e152f7aabd0ab656b73e506b68eae4833f1d411ddc2d5501d48ff8a94d | MATLAB | 3,283 | 95 | % written by Yiyuan Han, Essex BCI-NE Lab, 04/03/2020
% Build the binary clssifiers using the CFC as features
function [sFeatures,fWeights,perfMat] = binaryClassCFC(class1,class2,blockTagsAC,CFCdata,mode,folderpath,featureNum)
%% Extract the data in specific conditions
indices = find(char(blockTagsAC(:,2))==class... |
acf5202f26e86f6973b6a08b77ce2cabb6d4eca13ae3b8644de21ed1b5b1149b | MATLAB | 3,284 | 78 | function ex_ftrstruct_Curves2dx = impexp_cfg_ftrstruct_Curves2dx
% 'Export Mori to DX' - MATLABBATCH configuration
% This MATLABBATCH configuration file has been generated automatically
% by MATLABBATCH using ConfGUI. It describes menu structure, validity
% constraints and links to run time code.
% Changes to this file... |
11ece020ab0fd9b4cc248d8378304dcf1a66d6516e09efb87f2e06cc95bb349e | MATLAB | 3,285 | 115 | function [pointset_resources] = populate_point_resource_str(points, colors, n_resources)
%
% See also VERBATIM.
%
% File: populate_point_resource_str.m
% Author: Ioannis Filippidis, jfilippidis@gmail.com
% Date: 2012.06.14 -
% Language: MATLAB R2012a
% Purpose: point resource strings
% Copyrig... |
0788e5c63b47271715c3c03ac2a5754333f1eb42949302da73ce253a4b82dc6a | MATLAB | 3,287 | 108 | function compile(varargin)
%% History
% 2008-04-01: Added check for pre Matlab 2006b for non-large dim
% sparse matrices.
%%
debug = 0; if strmatch('-debug',varargin), debug=1; end
verbose = 0; if strmatch('-verbose',varargin), verbose=1; end
clear mex
mbglfiles = {'astar_search_mex.c', 'bfs_mex.c', 'd... |
28b9a58d08cfa434a5d05d5c76d30b703c345b91e87c57c811dec13494200b7c | MATLAB | 3,287 | 77 | function obj=stat_glm(obj,varargin)
% stat_glm Display a generalized linear model fit of the data
%
% Example syntax (default arguments): gramm_object.stat_glm('distribution','normal','geom','lines','fullrange','false')
% This will fit a generalized linear model to the data, display
% the fit results with 95% confidenc... |
3be11e049b3435a036733c7866bddefc073b62fa28a5ebd8906aaf80636a518b | MATLAB | 3,287 | 102 | % icavar() - project ICA component activations through the ICA weight matrices
% to reconstitute the observed data using selected ICA components.
% Returns time course of variance on scalp for each component.
%
% Usage: >> [srcvar] = icavar(data,weights,sphere,compnums);
%
% Inputs:
% data ... |
7efcc7440f97937f8fa2964e0fc05235c0295d27df7bf01785d3cee7ed152549 | MATLAB | 3,291 | 85 | % Name: Robert Kim
% Date: 03-18-2024
% Email: robert.f.kim@gmail.com
% plot_timeconstant.m
% Description: Script to plot the synaptic decay time constants of inhibitory vs excitatory units across trained RNN models. The script can be used for both one-modality and two-modality models by changing the model_dir variable... |
58b804ad4e56653e5882d61d89bf7431d0cb7a4687763eeae959c352b4cbcfab | MATLAB | 3,292 | 131 | function [h,p] = ConcentrationTest(angles,group,alpha,nRandomizations)
%ConcentrationTest - Test homogeneity of concentration parameters.
%
% Test whether the concentration parameters for N groups of circular data are equal.
% The data are assumed to have Von Mises distributions. If the median concentration
% is infer... |
ac41e41664777d8a4c7489d9914cffe6402a2222c31942e67749e1a332d01cc3 | MATLAB | 3,292 | 101 | function [fid, sens, label] = read_polhemus_fil(Fname_pol,skip)
% Reads Polhemus files:
% either sensor file or headshape file or both
%
% FORMAT [fid, sens, label] = read_polhemus_fil(Fname_pol,skip)
% Input:
% Fname_pol - Polhemus ASCII file containing sensor locations (cm)
% (headshape can also be con... |
226a0133d53b76829c837b7df5ab05b9f9cb4ebbed256fae0233dee0432a9fa0 | MATLAB | 3,294 | 79 | function [dims, isndarray, maxlevel, count] = nestbracket2dim(str,brackets,testndarray)
%
% [dims, isndarray, maxlevel, count] = nestbracket2dim(str,brackets)
%
% Extracting the dimension vector of a JSON string formatted array
% by analyzing the pairs of opening/closing bracket tokenss; this function
% only returns v... |
94cec96d9d0284f8736043531dc9c1d15ae1bca2b133165a19c2cd07fe38ac84 | MATLAB | 3,295 | 96 | function X = build_concat_design(Fs, block_T, nBlocks, baseline_sec, block_sec, aux, varargin)
%BUILD_CONCAT_DESIGN Design matrix for concatenated epochs via glmproc.make_design.
% X = variance.build_concat_design(Fs, block_T, nBlocks, baseline_sec, block_sec, aux, ...)
%
% Positional inputs:
% Fs ... |
574e4592f627400acc63f7368ee40f22645673b4e93414558da65060769b4065 | MATLAB | 3,297 | 100 | function [P, beta] = x2p(X, u, tol)
%X2P Identifies appropriate sigma's to get kk NNs up to some tolerance
%
% [P, beta] = x2p(xx, kk, tol)
%
% Identifies the required precision (= 1 / variance^2) to obtain a Gaussian
% kernel with a certain uncertainty for every datapoint. The desired
% uncertainty can be specifie... |
23607e37a49adab722f458899ed5df5055ad707de5f225b0756ef4a857b60bf6 | MATLAB | 3,298 | 78 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%% CPC METACOGNITION TUTORIAL 2019: PLOT TYPE2ROC %%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Function to plot type2 ROC curve from observed ± estimated data fit
%%%%%%%%%%%%%%%%%%%%... |
bd92c5d574375731d95cb8b8f6676e0d1d0d1ce7fc4416313e015efc63243682 | MATLAB | 3,298 | 89 | function separatePausedNSx(varargin)
% separatePausedNsx Saves paused data segments from a single NSx file
% as individual NSx files
%
% separatePausedNSx(FILENAME) where FILENAME has N paused segments
% will create N individual files with the same extension named
% FILENAME-1,... |
d3debdd4bf84cce47c553bfad1f79184d6a5cf91bb1634262e229ec102494b5b | MATLAB | 3,299 | 104 | %% figure S8
% TE tuning selectivity is robust to the choice of time lag (tau).
% (A) Overall TE tuning curves for tau = 5, 10, 15, 20 ms (awake & anesthesia)
% (B) Selectivity index vs tau for each motif
load('figureS8_data')
addpath('functions');
set(0, 'DefaultAxesFontName', 'Arial');
set(0, 'DefaultTextFontName... |
d81a4bb907037a42999acb83c20d8ad25b2678b8cb09df72d8ccae45b06d3746 | MATLAB | 3,299 | 106 | %%*****************************************************************************
%% HSDsqlpmisc:
%% produce infeasibility certificates if appropriate
%%
%% Input: X,y,Z are the original variables, not the HSD variables.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modifi... |
e6580472a12afceb625f66fcea468882a9065788db341085399275c6c8dd549e | MATLAB | 3,301 | 100 | % REPR TOML representation of a MATLAB object
%
% REPR(obj) returns the TOML representation of `obj`.
function str = repr_syntalos(obj, parent, grandparent)
if ispc
newline = sprintf('\r\n');
else
newline = sprintf('\n');
end
switch class(obj)
% strings
case 'char'
% A Syntalos error o... |
a425a5d1d452beac6cda651aa21ba630f1763b2f5da24e99cf19bdedc4cd6e16 | MATLAB | 3,303 | 98 | %% Publishing reports
%% Why?
%
% Publishing reports of your data analysis is a great way to save code and
% results.
%
% If you're doing a paper, you can save a record of what you did in the
% report, and what the results were.
%
% You can save figures in your report, and stats and tables too ...
% And even interpret... |
27264733cf07f7d76b03b0d892e14a4c2c92cdc3e2faccbc9dbabf9c5abf99d4 | MATLAB | 3,305 | 76 | function [sv,sp,fm] = spsvd(data,params,mdkp)
% Space frequency SVD of input data - continuous processes
% Usage: [sv,sp,fm] = spsvd(data,params,mdkp)
% Inputs:
% data (data matrix in timexchannels form)-required
% params structure containing parameters - params has the
% following fields: tapers... |
2570e582d04ddff542ca0cebdcd8f787b10c9ce1a76b77c48cec04f37bf9b147 | MATLAB | 3,306 | 115 | % CLIP_NII: Clip the NIfTI volume from any of the 6 sides
%
% Usage: nii = clip_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be cut from which side.
%
% option.cut_from_L = ( number of voxel )
% option.cut_from_R = ( number of voxel )
% option.cut_from_P ... |
a662bde9844c3b5bd47edca16c8c6816d551374a5282b450ec042a6d8278664a | MATLAB | 3,307 | 90 | function proc = process_NSC_frac_data(data, k, alpha)
% Process NSC counts and fraction data
% Automatically scales, filters, computes mean/std using filterLognormalGaussian,
% and stores both raw and filtered full-time vectors for plotting.
% ---------- NSC TOTAL ----------
nsc_times = []; % mean per... |
3e626d7386c9d5ae1853a5eb01676cb2db39e9c4ab19b620dbd09e893c7c60a0 | MATLAB | 3,308 | 89 | function dpvl = palm_vtxlabel(dpv,fac)
% Label a DPV file (vertexwise data).
%
% Usage:
% dpvl = palm_vtxlabel(dpv,fac)
%
% - dpv : Binary data per vertex to be labelled. The non-zero
% regions receive an unique identifier.
% - fac : Face indices (see palm_srfread for details).
% - dpvl : Labelled data per... |
fe0d1f1c5fef42d6e0f0e8e46912761fdee31e0a23d867ceafdbe028ca60ebb0 | MATLAB | 3,310 | 96 | % Figure 8.16: Quadratic placement problem
% Section 8.7.3, Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 10/24/05
% (a figure is generated)
%
% Placement problem with 6 free points, 8 fixed points and 27 links.
% The coordinates of the free points minimi... |
4ecfa945eaff124aaa3763c1fff0b87a2bb99466ac9aa641cc95ef5aebf3c45f | MATLAB | 3,311 | 94 | function ea_newseg(files,dartel,del,force)
% SPM NewSegment
% we cannot generate the TPM from the SPM TPM anymore since
% we use the enhanced TPM by Lorio / Draganski:
% http://unil.ch/lren/home/menuinst/data--utilities.html
% keep the 'y_*' and 'iy_*' file by default
if ~exist('del', 'var')
del = 0;
end
if ~exist... |
2c1d3fa56e38b69ff389110ddc4c7f31b736310e3031860fb338af05e525db8e | MATLAB | 3,312 | 108 | function [sel1, sel2] = LeG_match_str(a, b, fullout)
% MATCH_STR looks for matching labels in two lists of strings
% and returns the indices into both the 1st and 2nd list of the matches.
% They will be ordered according to the first input argument.
%
% Use as
% [sel1, sel2] = match_str(strlist1, strlist2)
%
% The s... |
5712f2c5ec8e9bae9ad2c31679243f048cd5bd9298be5dd215f906f16a452146 | MATLAB | 3,312 | 75 | function [RegPara, ds_val_threshold] = Call_initialReg(RegPara, handles, k, fext, imageinfo, Nbatch)
RegPara.Corr_initial = 0;
if RegPara.NimgFirstRegistration >= 20
ini_iter = 1; Corr_initial = 0;
t0 = ceil(RegPara.Imagelength(1)*0.1);
while Corr_initial < RegPara.MinCorr_initial && ini_iter <= RegPara.in... |
0116b4c7bb4ecfed680ae0428f79a6496d9072a4a179a835c4d36a6e1a311205 | MATLAB | 3,313 | 110 | function [maxsize,clstat,sizes] = palm_clustert(X,y,thr,opts,plm,varargin)
% Compute cluster Tippett statistics, for volume or surface
% data (vertexwise or facewise).
%
% Usage:
% [maxsize,clstat,sizes] = palm_clustert(X,y,thr,opts,plm)
%
% Inputs:
% - X : Statistical map.
% - y : Modality index (of those stor... |
76edb66a6e07088a46f0b6571ea9c6d65a5d5c66f19fe10d550017e0b4c27a6b | MATLAB | 3,315 | 98 | function [Sc,Cmat,Ctot,Cvec,Cent,f]=CrossSpecMat(data,win,params)
%
%
% Multi-taper cross-spectral matrix - another routine, this one allows for multiple trials and channels
% but does not do confidence intervals. Also this routine always averages over trials - continuous process
%
% Usage:
%
% [Sc,Cmat,Ctot,Cvec,Cent... |
259d4c695ce84994fee38c45d8f4481e0ed8cd39fd6b29b6c96646161b1a5e43 | MATLAB | 3,317 | 80 | function Obj = SOFAconvertBTDEI2SOFA(BTDEI)
% OBJ=SOFAconvertBTDEI2SOFA(BTDEI) converts the HRTFs described in BT-DEI
% to a SOFA object.
%
% BTDEI format is used by Michele Geronazzo, University of Padova.
%
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences;
% Licensed und... |
e3d5b9514c10eb1e773722f4ae0a14042a125faa5e57283d5666723d8bb3ca24 | MATLAB | 3,317 | 84 | % 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... |
ff2e61a950d519da44c93773cb84d71ce29cfe098f4afea3c641b780f21c33b1 | MATLAB | 3,318 | 90 |
%Produces high pass filtered versions of background subtracted LFP data to
%use in single unit analysis.
%Specifically needed to find waveforms that correspond to spike times
%identified by kilosort/phy.
%Doing this ahead of time makes single unit analysis code run much faster
%and saving this data removes the... |
006460bcb4e6f3ae642d165a31c5230d1fd16c73de008f4a26c9566fdbc1e785 | MATLAB | 3,319 | 103 | function plotEBC(root,out,fign, fig_row)
%
% Downloaded from the Github of Hasselmo's lab
% Modified by Yanbo Lian for the purpose of displaying figures
% %% occupancy circular
% figure(fign); subplot(1,4,1);
% % the +pi/2 brings "forwards" to "up"
% [t2, r2] = meshgrid(wrapTo2Pi(out.params.thetaBins+p... |
6909ff10c55e5e1f94278fcd467f89eedfdafc849d741effab8065c9c533fad8 | MATLAB | 3,319 | 94 | % Figure 8.17: Fourth-order placement problem
% Section 8.7.3, Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 10/24/05
% (a figure is generated)
%
% Placement problem with 6 free points, 8 fixed points and 27 links.
% The coordinates of the free points min... |
e34d7600704e7c94e886ac54318b24c046339fae754b342f2b8f8908176ea922 | MATLAB | 3,320 | 77 | function ea_predict_leave_nothing_out(uipatdirs,stimname,typemap,regressor,fdmri,dowhat)
if size(regressor,1)<size(regressor,2)
regressor=regressor';
end
if ~exist('fdmri','var')
fdmri.do='both'; % can be fmri, dmri or both
end
for pat=1:length(uipatdirs)
[~, subPrefix] = fileparts([uipatdir{pt}, '_']);
... |
6d2d6d2ca6a5ec0e4ec7da2d858f5afefda79e0df591358d4b5d6718b8bafe15 | MATLAB | 3,324 | 59 | function unitClassif = classifyCells(ephysProperties, paramEP, region)
% classify striatal, GPe and cortical cells
unitClassif = cell(size(ephysProperties,1),1);
if ismember(region, {'CP', 'STR', 'Striatum', 'DMS', 'DLS', 'PS'}) %striatum, classification as in Peters et al., Nature, 2021
unitClassif(ephysProperti... |
478956a4c1a54b089fac0d70d11ec14e7a7ceb9525e0414a3eaf0c0e5d307dc7 | MATLAB | 3,326 | 80 | % configure file for calculation of tensors
% DTI Configuration file
% BATCH system (Volkmar Glauche)
%
% File created by Susanne Schnell
function tensor = dti_cfg_tensor
% ---------------------------------------------------------------------
% filename Input raw data filename
% -------------------------------------... |
3e9043a82a6bb3981302f349d0364151d6150a0e40682cc4c98e52521110340c | MATLAB | 3,329 | 111 | function [maxsize,clstat,sizes] = palm_clusterm(X,y,thr,opts,plm,varargin)
% Compute cluster mass statistics, for volume or surface
% data (vertexwise or facewise).
%
% Usage:
% [maxmass,clstat,masses] = palm_clusterm(X,y,thr,opts,plm)
%
% Inputs:
% - X : Statistical map.
% - y : Modality index (of those stored... |
5062c339112fb438cd8c787943e19da373799dfed1b1ca090b8a2a3192f148d4 | MATLAB | 3,329 | 103 | %% Red-Black Ordering with MatlabBGL
% In this example, we will use the MatlabBGL library to compute the
% red-black ordering of a matrix. For certain matrices, the red-black
% ordering does not exist, but if a red-black ordering exists, then this
% algorithm will find it.
%
% A matrix has a red-black ordering if t... |
20a13f88f9fd77a18999f33b58bc46bcc7219e6290a3336e9da0fa302e84261e | MATLAB | 3,330 | 99 | % axcopy() - Copy a Matlab figure axis and its graphic objects to a new pop-up window
% using the left mouse button.
%
% Usage: >> axcopy
% >> axcopy(fig)
% >> axcopy('noticks')
% >> axcopy(fig, command)
%
% Notes:
% 1) Clicking the left mouse button on a Matlab figure axis copies... |
ec9ef00c267f143875eeb375a69f185f33333c4a28c45084866035a29f094a2e | MATLAB | 3,330 | 115 | % plotAverageWaveforms
%
% Plots average waveforms for all channels and specified units across the
% array. It will prompt for a CMP file to map each channel to its electrode
% representation.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Use plotAverageWaveforms(NEV, units)
%... |
9cc5296133ac8257193309a64db208fd97217c1192f2f6a706754a9d7d02d755 | MATLAB | 3,331 | 90 | % sph2spm() - compute homogenous transformation matrix from
% BESA spherical coordinates to SPM 3-D coordinate
%
% Usage:
% >> trans = sph2spm;
%
% Outputs:
% trans - homogenous transformation matrix
%
% Note: head radius for spherical model is assumed to be 85 mm.
%
% Author: Robert Oostenveld, SMI/FC... |
905a0c7057ec90112fca7acd024e3bc05dc095c114e79980e66e0d12c2421d65 | MATLAB | 3,333 | 123 | function cvx_optpnt = lorentz( sx, dim, iscplx )
%LORENTZ Real second-order cone.
% LORENTZ(N), where N is a positive integer, creates a column
% variable of length N and a scalar variable, and constrains them
% to lie in a second-order cone. That is, given the declaration
% variables x(n) y
% the cons... |
bdfd018e3ee3e1577e92e3b6b198fd7a640af73143bbf2730c2bc1fe4c0527cb | MATLAB | 3,339 | 94 | % sph2topo() - Convert from a 3-column headplot file in spherical coordinates
% to 3-column topoplot() locs file in polar (not cylindrical) coords.
% Used for topoplot() and other 2-D topographic plotting programs.
% Assumes a spherical coordinate system in which horizontal angles... |
e2b80705fba0a5855c156becbc0e8c79f0b8a9b5f6ec18885a16b02ec12cdcb3 | MATLAB | 3,339 | 89 | function imData=read_file(path_to_file,sframe,num2read,options,im_info)
% Reads uncompressed multipage .tiff, .hdf5, .avi or .raw files
% Usage: my_data=read_file('path_to_data_file, start frame, num to read);
% INPUTS:
% path_to_file: location of file to be read
% sframe: first frame to read (optiona... |
64c810bb32268cb5974681ae53863a3a9de7b672fa4d4c15452eae2e9d206857 | MATLAB | 3,340 | 98 | function [TermLabels] = PIDTermLabels(N)
%PIDTermLabels creates a list of the term labels to ease interpretation of
%the PID output.
% [TermLabels] = PIDTermLabels(N) is a cellular array that contains the
% term labels for the output of the PID function. It follows the notation
% of Williams and Beer.
%
% P. L.... |
c8a79e1e597fccf3a4e2d8475969aa94d7998ca3553da72f770e33ba3f29ad8d | MATLAB | 3,341 | 99 | function signal = simulate_noisy_model_signal(SANDIinput, model_params)
% Builds the dataset for supervised training of the machine learning models
% for SANDI fitting.
%
% Author:
% Dr. Marco Palombo
% Cardiff University Brain Research Imaging Centre (CUBRIC)
% Cardiff University, UK
% 4th August 2022
% Email: palomb... |
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