sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1f6f4fb1704bf0a572a158682c612b91ccc5d755e9fd32e4dc2c0993874c9511 | MATLAB | 2,152 | 71 | function [S, W, B] = segregation(M, Ci, varargin)
% DESCRIPTION:
% The degree to which edges are more dense within communites and more
% sparse between communities, which quantifies the segregation of a
% weighted network (Chan et al. 2014).
%
% USAGE:
% S = segregation(M,Ci)
% [S, W, B] = segregation(M,... |
3c723c5bd54a2a5a348bafc7cb6a6691f9482e9bda6cb7146c4cb9519ebe379a | MATLAB | 2,152 | 57 | function [C_calc] = LCN_calc2_model_2T4k(params, midscantimes, frameduration, CA_FINETIMES,FINETIMES,calc_option,STEP)
%
% calculates the output value for the model_2T4k_Vbfixed (with parameters params)
%
% params: values for [K1,k2,k3,k4]
% midscantimes = list of midscan times of each frame (in min p.i.).
% framedura... |
5b92d211eddd32a061d540b2922cb37db014dc6ac787a738b3568aeca12a874b | MATLAB | 2,152 | 57 | function dist = ComputeDistBetweenLabels(surface, orig_surface, label1, label2)
% e.g. ComputeDistBetweenLabels('<SUBJECTS_DIR>/<SUBJECT>/surf/lh.sphere', '<SUBJECTS_DIR>/<SUBJECT>/surf/lh.white', 'lateraloccipital_gt', 'lateraloccipital')
% e.g. ComputeDistBetweenLabels('<SUBJECTS_DIR>/<SUBJECT>/surf/lh.sphere', '<SU... |
667f5921aef29d2b98b5e3efd4e11b98b5b3e6f50f39a3f07de56c92a63dde2b | MATLAB | 2,153 | 64 | function [lh_cov_mat, rh_cov_mat, dim] = CBIG_hMRF_build_prod_matrix(lh_input_file, rh_input_file,...
lh_output_file, rh_output_file)
% CBIG_hMRF_build_prod_matrix(lh_input_file, rh_input_file, lh_output_file, rh_output_file)
%
% This function generates the premultiplied matrix with the input concatenated time seri... |
833bcb6e1fb298421290b6f31eb98564aa9fdf237ecf4958f4e9974e3e6ee586 | MATLAB | 2,153 | 48 | % Read time data and reorganize them
% Reorganize the data to fit the catplot function
folder = ("C:\Users\yh19218\OneDrive - University of Essex\OneDrive - University of Essex\PG Research\0A_Journal\202004_unknown Journal_Probability Score\1_Results\0_Final Results\TimeNew\");
classes = ['OvsC';'HvsW';'OvsH';'OvsW';'... |
af0de78a969e99b94316cf7c609473b55909bea99ec21389ed4fa25f384cda7b | MATLAB | 2,153 | 64 | function [Serrp,Serrj]=uispecerr(S,J,err,trialave,numsp)
% Function to compute lower and upper confidence intervals on the spectrum
% Usage: [Serrp,Serrj]=uispecerr(S,J,err,trialave,numsp)
% Outputs: Serrp (Serrp(1,...) - lower confidence level, Serrp(2,...) upper
% confidence level), similarly for Serrj
%
% Inputs:
%... |
12afe91986a29bddafb546679f516869447f55480a8a710c877fd1bc7d624793 | MATLAB | 2,156 | 64 | % FDLA and FMMC solutions for a 64-node, 95-edge cut-grid 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 g... |
f9d017262e3793d02b36f280c056e0ea1e6be4910a38a38ac244e0eba25b0abb | MATLAB | 2,156 | 44 | function ea_get_prob_fiber_states_for_multisource(options,settings,outputPaths,axonStateFolder,resultfig)
% convert PAM samples from multiple sources to prob. PAM
% IMPORTANT:this is a special case for multisource prob. PAM
% By Butenko, konstantinmgtu@gmail.com
arguments
options % Lead-DBS options fo... |
91379cebb2ceb7d01d4fb760e63b365de7788df49617984c28aa1fbf50803d88 | MATLAB | 2,157 | 44 | % 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... |
1d9fb0a1fb7ad63e1df1d481deec7035febb7d22e64092d6e490b00010d4e7ae | MATLAB | 2,159 | 58 | function m_full = getFullMask(m,frame_d,delay,kernel)
%GETFULLMASK Convert frame rate mask to a sample-by-sample mask
%
% M_FULL = IOSR.BSS.GETFULLMASK(M,FRAME_D) expands the time-frequency
% mask M, which has one unit for each frequency channel and frame of
% length FRAME_D (in samples), to a sample-by-sample m... |
48820fe3aa2f0f029e1ad9c0c96fe951ec370e5e5b2b0e55f404fe71b7e66eef | MATLAB | 2,159 | 57 | function [img,V] = LCN12_read_image(filename,Vref)
% LCN12_read_image
%
% this script will read an image in matlab.
%
% INPUT
% filename = name of the file (either full path or name if you
% are in the correct directory). If the file is a 4D
% file, you have to specif... |
0dbc690d905f3c4a32979af998801ef4f59e8d65b500193ba483c671058acaeb | MATLAB | 2,160 | 44 | %% readLabels - read ITK-Snap label file
%
% Florian Bernard, Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% mail@andreashusch.de, husch.andreas@chl.lu
function [labelNames, rgbColors, labelId]=readLabe... |
6f7f54554fb2a54475af563d2f28df28dcc28fd508309fead86ea1fe80a27a26 | MATLAB | 2,161 | 49 | function Z = CORE_pxcorr(x,y,maxlag)
%CORE_PXCORR Core computational routine for PXCORR.
% Z = CORE_PXCORR(X,Y,MAXLAG), where X and Y are length M and N
% vectors respectively, returns the length (2*MAXLAG+1) vector
% Z such that Z(i) = #(X(j)-Y(k) == i), |i| <= MAXLAG.
%
% CONDITIONS (including requireme... |
f246f42e1295b2c1f2cda421cfc9817b6ee5067f0b8600fa44fc556366b2d09a | MATLAB | 2,162 | 59 | function ea_save_networkmapping_model(obj, ExternalModelFile)
% this function is called from the GUI
% we want to define the model outside of cross-validation
if ~exist('patsel','var') % patsel can be supplied directly (in this case, obj.patientselection is ignored), e.g. for cross-validations.
pa... |
fde0cef67c5c6fd0d70ea3d09021881abbdf94b29067aae36c1b245bdb279b2a | MATLAB | 2,162 | 62 | %% Detection of novel (reconfigured) sequences
load('result_reconfigured.mat'); % load actual and reconfigured dataset
%% Figures
% ordered probability matrix
subplot(3,6,9);
x_sum_col = sum(x2_pMat_LR);
[sum_sort,idx_col] = sort(x_sum_col,'descend');
x2_pMat_sort = zeros(100);
for i_ne = 1:100
for j_n... |
0d84f480d99c87d49884446e1303b225c8679270443219984b060d043f2d614c | MATLAB | 2,163 | 53 | function str = hyperlink(url, label, msg)
%HYPERLINK create a string that is displayable as hyperlink in Matlab console
%
% Usage examples:
% fprintf('Search on %s\n', hyperlink('http://google.com','Google'));
% fprintf(hyperlink('http://google.com','Google','Search on Google\n'));
%
% HYPERLINK converts the speci... |
32e14b3b2f226ac99a0111e776f1c3e2ddf131d02b785ee025510728b28e62c8 | MATLAB | 2,165 | 73 | function self = FixPos(self, max_allowed_flips)
% Fixes large jumps in position and interpolates missing values
%
% Takes all 0,0s and large jumps in position (greater than
% jitter_threshold=15 pixels/sample) that persist for less than
% max_allowed_flips (default = 5) and linearly interpolates the missing
% data. Smo... |
900d6382d774a53d530de6f79842704308c1bc7c6316f22a6d731799cd715378 | MATLAB | 2,165 | 60 | function CBIG_MSHBM_Epilepsy_check_example_results(out_dir)
% ====================================
%% Help
% ====================================
%
% CBIG_MSHBM_Epilepsy_check_example_results
%
% Checks that the individual-specific parcellation and language laterality
% index (LI) produced by CBIG_MSHBM_Epilepsy_wrapp... |
3d8629a61c615827daac3986e5b499a3ddee4087ab20190f8b483cc92b1d2523 | MATLAB | 2,166 | 47 | function CBIG_ArealMSHBM_generate_radius_mask_Schaefer(resolution, mesh, out_dir)
% CBIG_ArealMSHBM_generate_radius_mask_Schaefer(resolution, mesh, out_dir)
%
% This script will generate radius mask for Schaefer2018 parcellations in a given
% surface space <mesh>.
%
% Input:
% - resolution: (string)
% The resolu... |
6abe82e189519d4716b2fdb01febe576dccad7fc9f2a4c41ca043ebae5362256 | MATLAB | 2,167 | 57 | % this script runs through an analysis testing whether patterns of brain
% activity generalize across different psychological domains
%load data, this contains an fmri data object called 'obj', a 'design' matrix
%specifying group membership of each image in the data object (columns 1-18
%indicate study, columns 19:27 ... |
89b8f66ca6b0a518d27b6c4c5735dae9afe65624f461f2c91dd343ba6a622918 | MATLAB | 2,168 | 71 | function z = triumtriu(x,y,K)
% z = triumtriu(x,y,K)
%
% TRIUMTRIU Computes y = x * y
% Both r and u should be upper triangular.
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, ... |
b5dbf0bfcc9fd2ba77a35c23cf8458502470b59032f10896e287d99b8a514349 | MATLAB | 2,168 | 54 | function stimParams = extractStimParams(triggerParams,pulse)
%write in DRC logic
%organizes 'TriggerParams' and 'Stim' into relevant params
%relevant params:
stimParams.trigDelay = triggerParams.stimDelay;
pre = regexp(pulse.pulsename,'_\d$','split');
stimParams.rawPulse = pulse.pulsename; %PulseID
stimParams.... |
24b50f85334866a03be6c84dfa7a6aa50c08d5c3472e5c7e799b3a24a20d8fa5 | MATLAB | 2,169 | 43 | % 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... |
98dc7bb7f68de8f3faec72ea765d1aa0d86a91645759102b39c3f64ee9563964 | MATLAB | 2,170 | 49 | % 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... |
e2def4fff893446d6f058fcfb48d96e863beb05ee024977fa34b7810ecbdca2d | MATLAB | 2,172 | 56 | function [ cfg ] = formatconfig( fname )
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically relevant behaviors of the ecosystems.
% Copyright (C) 2015 Vanni Bucci, Georg... |
0365d62c41c9ab686a56ff2e59e119f17463cc8fe1cd3bce9c753bec9f447bed | MATLAB | 2,173 | 66 | function element_node = mesh_base_one ( node_num, element_order, ...
element_num, element_node )
%*****************************************************************************80
%
%% MESH_BASE_ONE ensures that the element definition is one-based.
%
% Discussion:
%
% The ELEMENT_NODE array contains nodes indices ... |
301aab34034f8feb0db78fbf508ad21e829a95cd1b6f73e5ae43ac0cb581a964 | MATLAB | 2,173 | 47 | function [pkResp,sigPkResp,sig,pkIDX,pkIDXsig] = ...
pkF_alt(Ftrace,frameStart,nFrameWindow,sigRespSDthresh)
% pkF_alt output peak response of input Ftrace within nFrameWindow from frameStart.
%
% [pkResp,sigPkResp,sig,pkIDX,pkIDXsig] = pkF_alt(
% Ftrace, --> fluorescence traces (cell,vector or ... |
62f7042bcda3505efd0f4a81c78f446fd18903fe91627e100be3989e5f051ef6 | MATLAB | 2,173 | 61 | %% Examples on the "General Heuristic" of 0.2V/mm as proposed in the literature
%
% Andreas Husch, University of Luxembourg, 2019
% andreas.husch(at)uni.lu
%
function pointHandle = plotModelAndGeneralHeuristic(ax)
load('astrom_table3_3v.mat'); %#ok<LOAD> % loads PW, D, T for 3V
%[activation_model_3v, gof] = fitMode... |
d29cea2995a3ed531a83b5f52ec2727df8ebc080cb3c20289c1e0efc0980d682 | MATLAB | 2,173 | 71 | function [cmdout, tempf] = ea_dcm2nii(inputimage, outputimage)
% Wrapper for dcm2nii, only used for reorientation and cropping
%
% dcm2ii is not stable enough in some cases (will write out corrupted file
% with 1KB size). Use 'ea_rocrop' instead to do reorientation and cropping.
% Save to a new file, when 'outputimage... |
070ea955b18c67ab99657dd674e6712ad67ce47f32424e2193744952d62fbf49 | MATLAB | 2,174 | 62 | function [blocks,k,dag] = graphComponents(A)
% GRAPHCOMPONENTS : Connected or strongly connected components of a graph.
%
% blocks = graphComponents(A);
% [blocks,dag] = graphComponents(A);
%
% Input: A is the n by n adjacency matrix for an n-vertex graph.
%
% Output: blocks is an n-vector of intege... |
ee4a1c1b3577c3d2ac8e579d781799f43148c74ee536b451e4a5b48e012ae7f3 | MATLAB | 2,176 | 65 | function ea_unifiedmapping_save_settings(explorer,save_as)
% Saves the relevant settings of the tractset object to a mat file
% Properties can't be saved as variables :(
% Or with the struct flag because tractset is
% a class and not a struct :(
% Convert to variables first and then save
c... |
20af533a4042fd0035b658b891769ff0183a22cc7bde926ccb7bd8a3024792a6 | MATLAB | 2,177 | 41 | %% applyANTSTransformToPolyCoeffs - transform polynomial coefficient matrix in world coordinats of sourceRefImage to
% world coordinates in targetRefImage applying a ANTS affine transformation
%
% Parameters: coeffs - Nx3 matrix, coeffs(end,:) is the bias term (x^0)
% antsTransformFileStrings - '[antsTra... |
ac0c5a4a36788a724dd4641dafe6b1c5b3ad0adb236ac3118a8913affd1ddeb8 | MATLAB | 2,177 | 63 | function extractObjectFeatures(params)
% extractObjectFeatures(params)
%
% ----------------------------------------------------------------------
% Matlab tools for "Predicting human gaze beyond pixels," Journal of Vision, 2014
% Juan Xu, Ming Jiang, Shuo Wang, Mohan Kankanhalli, Qi Zhao
%
% Copyright (c) 2014 N... |
b49a214fbff97a69a1f437efce567eed814b5a7aa5e730453eec3531f5143ffa | MATLAB | 2,177 | 45 | % 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... |
4fb8a364833cecfeea7fe15c5b2729346eaae8e94942bad5ed192c6300d201cf | MATLAB | 2,178 | 60 | function fileNames = splitTifChans(mergedChanTif,varargin)
% splitTifChans Split ScanImage .tif with multiple channels into .tif files with single channels.
% fileNames = splitTifChans(mergedChanTif,varargin)
%
% Additional input arguments:
% '1' --> saves only tif with specified channel, replace with ... |
539a74d4fb92671de191ca2cadb60d1bbdcb6234544e4ef1a207494fbcc853cd | MATLAB | 2,178 | 72 | function [peakTheta, peakLowGamma, peakHighGamma] = peakFrequencies(lfp)
%Determines the peak frequencies in theta, low gammma, and high gamma bands
%of significant theta epochs in an lfp.
%check to see if valid LFP channel
if ~all(lfp.signal == 0)
%determine theta epochs
[thetaEpochs, ~, ~] = ThetaEpochs(lfp)... |
f503381ed4ae5c7d40e0b32145b45665042ad9177d17d574d39a377cb63803ed | MATLAB | 2,178 | 66 | function res = PC_response_de(params,inputs,initcond)
% This function generates a vector of intensity values over time for one
% half of the PB innervated by PFNp_c, to a sequence of single-modality
% experience (either AF or OF).
% Setup with arguments.
% inputs are sensory info
thetavec = inputs(1,:); % ra... |
5dc9c27ac4b15a52dc685f144a4544cfbb22ca380bc7b12ecdf1fa094c24735d | MATLAB | 2,179 | 52 | % SOFA API - demo script
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences
% Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the European Commission - subsequent versions of the EUPL (the "License")
% You may not use this work except in compliance with t... |
b784b11962c631a30e26f2810fd6c6dcc610cee6a252ca4c9e35aaa8901ec386 | MATLAB | 2,180 | 69 | function com = pop_expevents(EEG, filename, unit)
% pop_expevents() - export events to CSV file
%
% Usage:
% >> pop_expevents(EEG);
% >> pop_expevents(EEG, filename);
% >> pop_expevents(EEG, filename, unit);
%
% Inputs:
% EEG - EEGLAB dataset
% filename - text file name
% unit - display latency and... |
5f8c9a860196e6c78a990af78f1398953bc35b4bc77de1eb154c6a2f29cc5c3d | MATLAB | 2,181 | 60 | function CBIG_ASDf_plotFactorsThresholded_wrapper(output_dir)
% CBIG_ASDf_plotFactorsThresholded_wrapper(output_dir)
%
% Wrapper function to plot bootstrap thresholded factors
%
% Input:
% - output_dir:
% Absolute path to directory where output results will be saved
%
% Example:
% CBIG_ASDf_plotFact... |
6c852e6902fa75f0387c21516bddab8321305286fc73b6f578bd3875a0494dcb | MATLAB | 2,181 | 47 | % 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... |
cee38c525f693fad5c60376785a8da19e185f25a2d0468552abab4bc468cc03e | MATLAB | 2,181 | 49 | function stress_tensor = calc_stress(V, C, topo, tensions, cell_pressures, strain)
% CALC_STRESS Compute the tissue-level (Batchelor/virial) stress tensor
% from edge tensions and cell pressures, under Lees-Edwards (sheared)
% periodic boundary conditions.
%
% stress_tensor = CALC_STRESS(V, C, topo, tensions, cell_p... |
564784c6faa4013c8697ef91b518193825c49e0bd64b71fab01a241ab41d5859 | MATLAB | 2,182 | 60 | function dice = ComputeDiceBetweenLabels(surface, orig_surface, label1, label2)
% e.g. ComputeDiceBetweenLabels('<SUBJECTS_DIR>/<SUBJECT>/surf/lh.sphere', '<SUBJECTS_DIR>/<SUBJECT>/surf/lh.white', 'lateraloccipital_gt', 'lateraloccipital')
% e.g. ComputeDiceBetweenLabels('<SUBJECTS_DIR>/<SUBJECT>/surf/lh.sphere', '<SU... |
dfa420ae81281b4f2b0dedcdc5a6051fa67c43719737191cc3210c5b0ffd1c41 | MATLAB | 2,182 | 63 | function BFoutput = monotonicityCalc(BFoutput,PkResponseVar,varargin)
%could write this up as a cell function, but meh
tempMap = reshape(BFoutput.(PkResponseVar)',numel(BFoutput.dBlist),...
numel(BFoutput.freqList),size(BFoutput.(PkResponseVar),1));
[~,maxLvlIDX] = max(BFoutput.dBlist);
if ~isempty(varargin)... |
0202a9227568a9a620d2e7b09b2c33f64947706a14ca2745b9ef7278417e74a2 | MATLAB | 2,183 | 56 | function smooth_image = LCN12_smooth(image,smooth_kernel,mask)
% LCN12_smooth.m
%
% This function will smooth an image with a 3D Gaussian kernel optionally
% within a mask
% INPUT:
% image = 3D matrix
% smooth_kernel = array of Gaussian kernel size (in voxels)
% Optional input: mask = 3D binary mask
% OUTPUT:
%... |
4935f8f99757fde2d5fd3effa9c2dcd39aef80ea9234dd11caa72be7a1f9a4e6 | MATLAB | 2,183 | 43 | function data_out = importvelocity(filename, dataLines)
%IMPORTFILE Import data from a text file
% M001HBASELINE1VELOCITY = IMPORTFILE(FILENAME) reads data from text
% file FILENAME for the default selection. Returns the data as a table.
%
% M001HBASELINE1VELOCITY = IMPORTFILE(FILE, DATALINES) reads data for
... |
7e887b8ff997bfcebafa289d2f77d82a013f223467d44f20638a24371677d6fc | MATLAB | 2,183 | 82 | function [] = fig2pdf3d(ax, filename, options, media9_or_movie15, pdforxelatex)
%FIG2PDF3D Convert axes to PDF with embedded interactive 3D image.
%
% usage
% FIG2PDF3D(ax, filename, media9_or_movie15, pdforxelatex)
%
% input
% ax = axes object handle
% filename = file name string (default = 'surface')
% media... |
8d255c802954c0098b6e59a42807ba4be92773329e74cf8c48032fc976cfe37f | MATLAB | 2,183 | 69 | function data = AFOFdata_struct_CL_2(inputdata, filenames)
% USE THIS FOR EXP8 (CEM)
% how it works:
% fly = AFOFdata_struct_CL_2(data,filenames) where data and filenames are
% outputs from AF_OF_importer()
for e = 1:length(inputdata)
for t = 1:size(inputdata{e}{1},1)
trial.filename = filenames{e};... |
0efc6f93348bf967e38a38888688751b6efb50ea9328436f552f7d682f823c31 | MATLAB | 2,185 | 79 | function ea_deletePL(varargin)
if nargin == 1 % Used in ea_stimparams.m
PL = varargin{1};
else % Used in convis
resultfig = varargin{1};
varname = varargin{2};
mode = varargin{3};
PL = getappdata(resultfig, [mode,varname]);
setappdata(resultfig, [mode,'fibersfile'], 'nan');
setappdata(resul... |
659c18ae755c7679c55b468e61ed910712f7bd8017107cd6283214e7607dc0cb | MATLAB | 2,185 | 71 | function [] = idtf2u3d(fn)
%IDTF2U3D Convert IDTF to U3D file.
%
% usage
% IDTF2U3D
% IDTF2U3D(IDTF_filename)
% IDTF2U3D(IDTF_filename, U3D_filename)
%
% optional input
% idtffile = filename string for IDTF file (default = 'matfig.idtf')
% u3dfile = filename string for U3D file (default = 'matfig.... |
e39bfd0fc71aae80de2213227418cd1a7386b1afde1987f8618038ed663e93d9 | MATLAB | 2,186 | 55 | function [ci, sizes]=CBIG_ArealMSHBM_find_components(avg_mesh, ini_labels)
% [ci, sizes]=CBIG_ArealMSHBM_find_components(avg_mesh, ini_labels)
%
% This script will find all distributed components for parcels of a given parcellation
% label <ini_labels> and reorder the parcellation labels of each components. For exampl... |
73299ed58ff5085676210d825855ccfe5349a540526e944dc2eb617a6dd1550c | MATLAB | 2,188 | 83 | function A = fast_ica(x,pcomponents,nit)
% Originally written by the Finish (Aapo) team;
% Modified by the PIB team in Aug. 21, 2007
% PIB - Biological Information Processing Lab - UFMA - Brazil
% Modified by V�tor Lopes dos Santos Aug. 2011.
if nargin < 3, nit=100; end
% fprintf ('Removing mean...\n');
... |
1c1b630ec9469f97a04ff1accbec639d6720b9797b950fb2e38de7a63089ba34 | MATLAB | 2,189 | 85 | %XMLDEMO2 Demonstrate how to read an XML file, modify it and save it
%
% Description
% This script demonstrates the use of the xmltree class to
% open an XML file, access data stored in it, modify a value
% and save the new XML file.
%
% This demonstration script need the file 'example.xml' created
% ... |
478574624ea2145db4e11a4e8f5e92a352bd4c9cbd77864257d9224ee9d9c564 | MATLAB | 2,189 | 74 | function interVal=ea_diode_interpimage(img,yx,zpad)
% BiLinear interpolation using 4 pixels around the target location with ceil convention
% RGB = 1 for gray scale images.
% img can be a single layer matrix or a RGB layer colored image
% yx =[y_value, x_value]; It can be either horizontal or vertical vector
%
% zpad i... |
a01ceb6a95063974cf48ed40e492d5cf3eae23acbf0c03e8bcccd73e1dc58d85 | MATLAB | 2,189 | 57 | function self = FixDir(self, max_allowed_flips)
% Corrects errors in headdirection tracking
%
% Assumed root.b_headdir is in degrees
%
% Max allowed flips is the maximum number of consecutive lost samples
% (default = 5)
%
% Neuralynx head direction recordings often have missed samples, registered
% as either 0 or NaN.... |
08fd96f0f74a4443be5aa79b90bbd6fe54f9323afb0dd1bde0a48e806920d297 | MATLAB | 2,190 | 68 | % Script for testing the string array feature of SOFA
%% Test Strings as application-specific variable
% Load some arbritrary HRTFs
hrtf = SOFAload(fullfile(SOFAdbPath, 'database','ari','dtf_nh2.sofa'));
% Add a string array
str={};
for ii=1:hrtf.API.M
str{ii,1}=['String' num2str(round(rand(1,1)*10000))];
... |
0ccbef444d9e9f6a5044837515233744f986c2c9740fea3de50b835d4691a6f3 | MATLAB | 2,190 | 62 | function ea_export_ls_index(serverdir,options)
% very simple static dir2html export function.
fid = fopen([options.prefs.ls.dir,'index.html'], 'w+');
fwrite(fid,'<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">');
fwrite(fid,'<html xmlns="http:... |
795a8f25509aefc31853c17cb2d896e12dcceaece4a784a30658191620b4d746 | MATLAB | 2,190 | 70 | % pop_expica() - export ICA weights or inverse matrix
%
% Usage:
% >> pop_expica( EEG, whichica); % a window pops up
% >> pop_expica( EEG, whichica, filename );
%
% Inputs:
% EEG - EEGLAB dataset
% whichica - ['weights'|'inv'] export ica 'weights' or ica inverse
% matrix (... |
0d1fbbad653a88cf15ddd0d529a3b2499618275b6408a25c6b7553021dd32392 | MATLAB | 2,191 | 73 | function task_contrasts = get_HCP_task_contrasts
tasks = {'SOCIAL', 'MOTOR', 'GAMBLING', 'WM', 'LANGUAGE', 'EMOTION', 'RELATIONAL'};
%% SOCIAL
task_contrasts.SOCIAL = {'social_random';
'social_tom';
'social_tom_random'};
%% MOTOR
task_contrasts.MOTOR = {'motor_cue... |
9f9c18750336e7f915660020a9bc25f3eaf4231afb6bbfc4ec8b9ae4d4fa693f | MATLAB | 2,191 | 65 | function parcel2surf = parcel_to_surface(parcel_data, parcellation, fill)
%
% Usage:
% parcel2surf = parcel_to_surface(parcel_data, parcellation, fill)
%
% Description:
% Map parcellated data to the surface (authors : @MICA-MNI, @saratheriver)
%
% Inputs:
% parcel_data (double array) - Parcel vector, size = [p x ... |
ad83c86c67f34a26cd65f2351412a022928f601b9ad94c392070dd6e60b3d005 | MATLAB | 2,191 | 67 | function [betas, stats] = CBIG_fitGLM_4t(subInfoFile, GMICVFile, q)
% [betas, stats] = CBIG_fitGLM_4t(subInfoFile, GMICVFile, q)
% What is the subtype order?
% Offset by 1, the RID column
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
SUB_COL = 1+2;
FRO_COL = 1+3;
P... |
c5e6514ea3b1f266a22808a6e721cda9a55d855c33032a9d1e55c33ca9d5f839 | MATLAB | 2,193 | 81 | %% Precompute distributions for special word retrieval model (SWR)
%
%%
% Choose the dataset
dataset = 1; % 1 = psych review abstracts 2 = NIPS papers
if (dataset == 1)
% Set the hyperparameters
BETA1 = 0.000001;
BETA2 = 0.000001;
% load the psych review data in bag of words form... |
87bddf88f31e46415291eb37a3f06458b504c9524dac75e6e30b7a0afd123fb9 | MATLAB | 2,194 | 94 | %MRSTRUCT_WRITE save mrStrut to file.
% outFileStr = mrstruct_write(mrStruct,fileStr)
%
% Save mrStruct of file. If nargin==1 or fileStr is not valid
% a dialog box will prompt the user for input.
%
% Examples:
% fileNameStr = mrstruct_write(myExperimentStruct);
% mrstruct_write(myExperimentStruct,'c:\my_... |
347f9d11b69787d28b13de7474d636b5d304c873c1f12f27dd30c161b8e18289 | MATLAB | 2,195 | 49 | %% Mutual Information Demo 1
% This demo goes through calculating the mutual information for time locked
% trials from two discrete time series.
% Data Type: Discrete
% Number of Variables: 2
% Information Analysis: Mutual Information
% Trial Based or Single Trial: Trial Based
% Significance Testing: Off
% Delays: Off... |
0fa0baf2afe3fc5343a1840e150bf3be2e819962b4cb6e5c487e31561c71e456 | MATLAB | 2,196 | 59 | function keydata = readSvnKeyword(filename,keyword,crop)
%READSVNKEYWORD Read data from a file tagged with an SVN keyword
%
% The function takes an input filename and searches that file for a
% Subversion keyword. The data associated with the keyword are returned
% in a character array. Keyword data are placed... |
9b2a387713ff2ba8657d34922254a57682b070c9b8fdd8eaef14bfbe209df9cc | MATLAB | 2,196 | 49 | function [blockInfo] = PL2ReadFirstDataBlock(filename)
% PL2ReadFirstDataBlock(filename): read first data block, return block info
%
% example:
%
% blockInfo = PL2ReadFirstDataBlock(filename)
% while blockInfo.Type > 0
% % process data from the block
% % ...
% % read the next data block
% blockInf... |
9e0636308885f60c28c26857212441d75f67bf84ecdf73ca7c3786d3440b9f9f | MATLAB | 2,197 | 60 | % adjustcylinder() - Adjust 3d object coordinates to match a pair of points
%
% Usage:
% >> [x y z] = adjustcylinder( x, y, z, pos1, pos2);
%
% Inputs:
% x,y,z - 3-D point coordinates
% pos1 - position of first point [x y z]
% pos2 - position of second point [x y z]
%
% Outputs:
% x,y,z - up... |
bf0764537ccbeb16798a03326e30e0dba8c36f92b32aac6f0cc359079447ddda | MATLAB | 2,198 | 73 | function [a,C] = biconnected_components(A,varargin)
% BICONNECTED_COMPONENTS Compute the biconnected components and
% articulation points for a symmetric graph A.
%
% [a C] = biconnected_components(A) returns a list of articulation points
% a and the component graph C where each non-zero indicates the connected
% comp... |
ed6bd0c2b0dbc723880c534c4291f19a8024a74088b90a059bc0787fc2ba3d39 | MATLAB | 2,199 | 73 | function varargout = GetBatch(batch)
%GetBatch - Get batch job output.
%
% USAGE
%
% [output1,output2,...] = GetBatch(batch)
%
% batch batch parameter returned by <a href="matlab:help StartBatch">StartBatch</a>
%
% OUTPUT
%
% output1... one matrix or cell array for each output parameter of the
... |
4c1c80aa7c25f6dfa6b1ffdd203965aa0b92e0826438785f3ce0dde140d1478d | MATLAB | 2,200 | 56 | function [keep_species_merge,species_names_filtered_merge] = mergeData(experimentBlocks,keep_species,data_counts,species_names,intervene_matrix_filtered)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series ... |
567689c27d66f0fc0036ca4851efd42c16ded8e602f6c01bd4f418cbd3a98c01 | MATLAB | 2,202 | 99 | %% Preprocess
% Perform ICA on raw data
Step1_Preprocess_Export_Active;
Step1_Preprocess_Export_Passive;
Step1_Preprocess_Export_ActiveExt; % ISI=400,700, include Step2
% Re-reference: for raw wave analysis
Step2_Preprocess_Rereference;
% Subtract by ERP: for GC analysis
Step2_Preprocess_Granger;
% Exclude bad chann... |
6a619332ddb4505272b8d6c6d26a4e8c432eec243a6160ded4422e1e36d38751 | MATLAB | 2,202 | 49 | function ADA = getada1(ADA, A,Ajc2,perm, d, blkstart) %#ok
% ADA = getada1(ADA, A,Ajc2,perm, d, blkstart)
%
% GETADA1 Compute ADA(i,j) = (D(d^2; LP,Lorentz)*A.t(:,i))' *A.t(:,j),
% and exploit sparsity as much as possible.
% Ajc2 points just beyond LP/Lorentz nonzeros for each column
% blkstart = K.qblkstart par... |
4ff6981fe72b606ece8dcc53533723ff9e2b49eb6238ef30ed3fbe87e34396dd | MATLAB | 2,203 | 74 | clc; close all; clear;
Start = tic;
%% Inputs
numSig = 5;
t = linspace(0,1,1000); % Time vector
nbins = 5;
methods = {'Euclidean', "CityBlock", "Minkowski", "Chebyshev", "Sorensen", "Gower", ...
"Soergel", "Kulczynski", "Canberra", "Lorentzian", 'Intersection', 'WaveHedges', ...
'Czekanowski', '... |
17adb22cef4ae6c38958b828ec75da2d898e26b323c0d32a528cd8128b922196 | MATLAB | 2,204 | 119 | function a= rotation_xyz(dim,forty)
% Takes the dimensions of a cube as argument and returns the array a which contains the indices to rotate a cube of that dimension.
%% Rotate over the X axis
X90=[];
for i=dim:-1:1
for t=0:(dim-1)
X90=[X90, i+t*dim^2];
end
% Use i as starting value for next loop
y=i;
for j=1... |
175ee0d4417ed0cb24612b464327f6db6cb00633d00b05e7923dbe38cf2b18ee | MATLAB | 2,205 | 79 | function o = nifti2struc
% Create a data structure describing NIFTI-2 headers
%__________________________________________________________________________
% Copyright (C) 2005-2012 Wellcome Trust Centre for Neuroimaging
%
% $Id: nifti2struc.m 6314 2015-01-23 17:00:51Z guillaume $
persistent org;
if ~isempty(org)
... |
739cba1660f2a1691e10883e9e459deb72816795d55f7d2d6c0b4e645b5abcea | MATLAB | 2,205 | 49 | function [rec, diag_hist, vertical_hist, rad_final,A] = set_radius(data,a,radius_start,radius_end,threshold,type,iter)
% Find the radius to provide target percent recurrence
% If radius_start is too small
[rec, ~, ~, ~] = line_hist(data,a,radius_start,type);
while rec == 0 || rec > thres... |
d758c1237d8104b51889ba3da19a521f2dacdaf0aa770fdcd5ca0311286f7a0c | MATLAB | 2,205 | 119 | function a= rotation_xyz(dim,forty)
% Takes the dimensions of a cube as argument and returns the array a which contains the indices to rotate a cube of that dimension.
%% Rotate over the X axis
X90=[];
for i=dim:-1:1
for t=0:(dim-1)
X90=[X90, i+t*dim^2];
end
% Use i as starting value for next loop
y=i;
for j=1... |
159f1e7f2b0bdb675cbf6b004f933ad11c11a21e9473f2ca22c6b6b42b459dc9 | MATLAB | 2,207 | 54 | function [node,elem]=vol2restrictedtri(vol,thres,cent,brad,ang,radbound,distbound,maxnode)
%
% [node,elem]=vol2restrictedtri(vol,thres,cent,brad,ang,radbound,distbound,maxnode)
%
% surface mesh extraction using CGAL mesher
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2009/01/06
%
% input:
% vol: a 3D vo... |
3105c1e37db7acc9e48dd5351757a7651baac210936a13cca7907337d81b3650 | MATLAB | 2,208 | 92 | % rri_xhair: create a pair of full_cross_hair at point [x y] in
% axes h_ax, and return xhair struct
%
% Usage: xhair = rri_xhair([x y], xhair, h_ax);
%
% If omit xhair, rri_xhair will create a pair of xhair; otherwise,
% rri_xhair will update the xhair. If omit h_ax, current axes will
% be used.... |
6f8f197ac6082d19472c754e315bc508813b33a0844953be209aa7865b1376ed | MATLAB | 2,208 | 77 | function hm=plottetra(node,elem,varargin)
%
% hm=plottetra(node,elem,opt)
%
% plot 3D surface meshes
%
% author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
%
% input:
% node: a node coordinate list, 3 columns for x/y/z; if node has a
% 4th column, it will be used to set the color at each node.
% ... |
5ab1bf7ff7869754cc06272011fcb92550b48210a5f98698b11080bc01a4be8e | MATLAB | 2,209 | 62 | % pcexpand() - expand data using Principal Component Analysis (PCA)
% returns data expanded from a principal component subspace
% [compare pcsquash()]
% Usage:
% After >> [eigenvectors,eigenvalues,projections] = pcsquash(data,ncomps);
% then >> [expanded_data... |
eb110b8b2f84c7b661d98b8bf3a22d3d93a180abe0cfbf510fc57636792647f2 | MATLAB | 2,209 | 77 | function [col_shift,M] = correct_bidirectional_offset(Y,nFrames,us)
% look and correct for phase artifacts due to bi-directional scanning
% with thanks to Fabian Sinz for useful discussions.
if ~exist('us','var'); us = 10; end
if ~exist('nFrames','var'); nFrames = 50; end
if isa(Y,'char')
Y = read_file(Y,1,nFram... |
1c5ee37f6f0191e9735014bef007c8231c4b5c72eebd98f0aed7c37411707d9c | MATLAB | 2,211 | 91 | function [n, npw, ts, wave] = plx_waves(filename, ch, u)
% plx_waves(filename, channel, unit): Read waveform data from a .plx file
%
% [n, npw, ts, wave] = plx_waves(filename, channel, unit)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% channel - 1-based channel number
% unit - unit number... |
20fd0a699521395a9663c6fcb343678908b9c5e816a84bc1b17209e6257ce388 | MATLAB | 2,213 | 71 | function ans = isinside(smallRect,rect,clip)
%ISINSIDE checks whether one rectangular area is completely inside another
%
% SYNOPSIS ans = isinside(smallRect,rect,clip)
%
% INPUT smallRect : defintion of rectangular area which should be inside of
% rect :
% both rectangular areas are define... |
03c0c330ec925f0fc9501886cb4030010a78ee52b8bffdae6574b311f0cb7689 | MATLAB | 2,214 | 66 | % moveaxes() - move, resize, or copy Matlab axes using the mouse
%
% Usage: >> moveaxes
% >> moveaxes(fig)
% >> moveaxes off
%
% Note: clicking the left mouse button selects an axis
% dragging the left mouse button resizes a selected axis
% dragging the right mouse button copies a selected ax... |
9814ebcb1c429b50e74deaeafa26acfe6d12354529916688eff5dba7d4090a88 | MATLAB | 2,215 | 52 | %% Conditional Entropy 1
% This demo goes through calculating the conditional entropy for time
% locked trials from two continuous time series.
% Data Type: Continuous
% Number of Variables: 2
% Information Analysis: Conditional Entropy
% Trial Based or Single Trial: Trial Based
% Significance Testing: N/A
% Delays: ... |
f1f40ca7ca4986392077899898e1a595681a5594fbc783c000816437d2a5d9d6 | MATLAB | 2,215 | 48 | % 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... |
f9a96d51e2f9734a89b81bf228750d164c0a8d6720f6c5921138439e890b9d51 | MATLAB | 2,217 | 64 | function [Serrp,Serrj]=uispecerr(S,J,err,trialave,numsp)
% Function to compute lower and upper confidence intervals on the spectrum
% Usage: [Serrp,Serrj]=uispecerr(S,J,err,trialave,numsp)
% Outputs: Serrp (Serrp(1,...) - lower confidence level, Serrp(2,...) upper
% confidence level), similarly for Serrj
%
% Inp... |
8ee69ad876b01e21acc4f4d094f70e0eb64fee4bdbcf590b53180fd0fca8c4eb | MATLAB | 2,219 | 83 | function ps = CBIG_pairwiseCmpMeans(subInfoFile, GMICVFile, Q)
% ps = CBIG_pairwiseCmpMeans(subInfoFile, GMICVFile, Q)
% All these info is baseline info
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
[RID_dx, ~, ~, ~, ~, ~] = get_data(subInfoFile, GMICVFile, 3);
% ... |
31a8f0193d3fd829b9f0a48e72fd2290d1848ed0801f52fe56d09d18e2d5e50d | MATLAB | 2,221 | 66 | function add_ndt_paths_and_init_rand_generator
% This function adds all the appropriate directories for the NDT toolbox to work
% and initializes the random number generator based on the clock (by default
% Matlab uses the same seed everything it is started which can lead to unwanted behavior).
%=================... |
afdc9d51ecaa477b665a492765790db3e48348d2b4c9e8d10f19143e792a5f2e | MATLAB | 2,221 | 49 | function [lh_full_label, rh_full_label] = CBIG_hMRF_get_left_right_overlapping_labels(lh_mask, rh_mask,...
label, num_cluster_per_hemi)
% [lh_full_label, rh_full_label] = CBIG_hMRF_get_left_right_overlapping_labels(lh_mask, rh_mask,...
% label, num_cluster_per_hemi)
%
% This function reformats the input label vect... |
2e1ead670775442d0d568beb83b0fff48858a7883fa8759b713311c1fe7d373b | MATLAB | 2,222 | 53 | % 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... |
8fb6ef53bb741c0fa72b558c32afeabb7b03a4948fe291f4247f0e155b0e6f9f | MATLAB | 2,222 | 50 | function [blockInfo] = PL2ReadNextDataBlock(blockInfo)
% PL2ReadNextDataBlock(blockInfo): read next data block, return block info
%
% example:
%
% blockInfo = PL2ReadFirstDataBlock(filename)
% while blockInfo.Type > 0
% % process data from the block
% % ...
% % read the next data block
% blockInfo... |
36a96d6b7a1143490420d5a3d36fd3f67ae0275939cd89b6ac80f626d29f8fa2 | MATLAB | 2,223 | 63 | % CYLINDER: A function to draw a N-sided cylinder based on the
% generator curve in the vector R.
%
% Usage: [X, Y, Z] = cylinder(R, N)
%
% Arguments: R - The vector of radii used to define the radius of
% the different segments of the cylinder.
% N - The number of po... |
615a601df5967ca70f5df35b8a3c3417518aa90c4ede41a697616f9bd36a1db7 | MATLAB | 2,223 | 73 | function [thresholdvalue, targetID] = prep_TurnOverAna(handles)
% thresholdvalue = 3;
thresholdvalue = handles.defaultPara.spineRetain;
targetID = 1;
N = length(handles.datafilename);
mainfig_pos = get(handles.mainfigure, 'Position');
scrsz = handles.scrsz;
pos = mainfig_pos;
... |
ad5944fcce85f882d25d88385b604741fa8fda35d1812bf918f8d70b82874a44 | MATLAB | 2,223 | 60 | % Periodic Boundary Conditions version
function [perimeters, areas, a1, a2, orientation] = cell_shape_info(V, newC)
% CELL_SHAPE_INFO Compute shape descriptors (area, perimeter, principal
% axes, orientation) for every cell polygon under periodic boundary
% conditions (PBC).
%
% [perimeters, areas, a1, a2, orientati... |
7c3970b1d3dd29efba927862025831b092f9ca009b96c7c0efe915541c54d4e6 | MATLAB | 2,226 | 68 | function ssEvents = fun_spindle_coordination(ssEvents, srate, samples)
% Calculates sleep spindle coordination metrics. Takes each spindle event
% on each channel and finds how many other channels the same spindle
% occurred.
%
% Required inputs:
%
% ssEvents: A struct containing all sleep spindle events (output from
... |
1ca039039b24b97d90b7dc418b18461593655de040f3f133a1a2ec0e968c0e42 | MATLAB | 2,228 | 59 | function clusterInfo = getClusterInfo(filename)
% GETCLUSTERINFO reads the phy generated file 'cluster_info.tsv' and
% returns a table with the variables assigned into an output table
% 'clusterInfo'. It will have size NxM, with N clusters and M variables.
% clusterInfo = getClusterInfo(filename)
% INPU... |
3c6811648c47a805b8208ceb9f613881f491215fa783594791096aa34a4ded98 | MATLAB | 2,228 | 75 | function hh=plotedges(node,edges,varargin)
%
% hm=plotedges(node,edges,opt)
% or
% hm=plotedges(node,loops,opt)
%
% plot a 3D polyline or close loop (1d manifold)
%
% author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
%
% input:
% node: node coordinates, dimension (nn,3); if node has a
% 4th colu... |
592aa32854ce3b131dde99b290e8f81ae79a1c5c756f7f95cbd8c8d13c8d4413 | MATLAB | 2,228 | 59 | function obj=geom_raster(obj,varargin)
% geom_raster Plot X data as a raster plot
%
% Option 'geom': 'line' or 'point'
p=inputParser;
my_addParameter(p,'geom','line');
parse(p,varargin{:});
obj.geom=vertcat(obj.geom,{@(dobj,dd)my_raster(dobj,dd,p.Results)});
obj.results.geom_raster_handle={};
end
function hndl=my_r... |
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