sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2a2e502cfc18a21aaf7bd7f596234f9e3b4c5bc39a9ffd0da9d20fc729df0fb1 | MATLAB | 6,065 | 228 | function [vertices, edges, colors, points, point_colors] = u3d_pre_line(ax)
%U3D_PRE_LINE Preprocess line output to u3d.
%
% usage
% points = U3D_PRE_LINE
% points = U3D_PRE_LINE(ax)
%
% optional input
% ax = axes object handle
%
% output
% points = position vectors as columns of matrix, as row cel... |
e6be506e646ef3c61f9b194c53bb5d3fa69d15773094ca25fbb03fb73874b2f2 | MATLAB | 6,065 | 172 | function [x, y, orientation] = FlyTracker(filename, FrameRange,...
NBackFrames, opt1, sqrsize,...
alpha, ellipse)
%FLYTRACKER
% Usage:
% [x, y, orientation] = FlyTracker(filename, FrameRange, ...
% NBackFrames, opt1, sqrsize,...
% ... |
58bf50092fce9eff55c03fa355ea8ca4b3c2e5698c67b82c0e55eb655c528195 | MATLAB | 6,068 | 210 | function fig_handles = plot_channel_level_hb( ...
layout, data2use, clim, date_value, task_type, montage_type, ...
hbr, interp_limit, output_dir)
%FNIRSPOWER.HELPERS.PLOT_CHANNEL_LEVEL_HB
% Plot channel-level HbO and optional HbR topographies using FieldTrip.
%
% Usage:
% fig_handles = fnirspower.helpe... |
abe02190c6d4b1edd2ade6964222d7a484d7b91dcf4029a0f8142b1ce385d8a0 | MATLAB | 6,068 | 135 | function perm_id = rotate_parcellation(coord_l, coord_r, nrot)
%
% Usage:
% perm_id = rotate_parcellation(coord_l, coord_r, nrot)
%
% Description:
% Rotate parcellation (authors: @frantisekvasa, @saratheriver)
%
% Inputs:
% coord_l (double array) - Coordinates of left hemisphere regions on the sphere, size = [m x... |
36019a1d0df6984d4303b805d62246ae8732fe33554c262cb8a619c595cdb1c6 | MATLAB | 6,075 | 174 | function list = find(varargin)
% XMLTREE/FIND Find elements in a tree with specified characteristics
% FORMAT list = find(varargin)
%
% tree - XMLTree object
% xpath - string path with specific grammar (XPath)
% uid - lists of root uid's
% parameter/value - pair of pattern
% list - list of uid's of matched ... |
2998028d690118d0448fdf031466e618c3f312c0ade276fa43686057fc76783e | MATLAB | 6,077 | 173 | function imData=bigread2(path_to_file,sframe,num2read)
%reads tiff files in Matlab bigger than 4GB, allows reading from sframe to sframe+num2read-1 frames of the tiff - in other words, you can read page 200-300 without rading in from page 1.
%based on a partial solution posted on Matlab Central (http://www.mathworks.... |
0a6f64cf285198bcc48c39f0001d0773d0469764b5e4346e8ea5af4cf43576b8 | MATLAB | 6,079 | 152 | function ea_exportvatmapping(M,options,handles)
selectedregressor=M.clinical.vars{M.ui.clinicallist};
selectedregressor=selectedregressor(M.ui.listselect,:);
if size(selectedregressor,2)==1
bh='global';
elseif size(selectedregressor,2)==2
bh='lateralized';
else
ea_error('Please select a regressor with entr... |
ae0ced97f754705ab1587a963aab88685a0dd419ed98d41b8bca75a3ad55ab93 | MATLAB | 6,082 | 168 | function affinefile = ea_flirt(varargin)
% Wrapper for FSL linear registration
fixedimage = varargin{1};
movingimage = varargin{2};
outputimage = varargin{3};
if nargin >= 4
writeoutmat = varargin{4};
else
writeoutmat = 1;
end
if nargin >= 5
if isempty(varargin{5}) % [] or {} or ''
otherfiles = {... |
ec8c8ff1124fc135d8b3330c8a73fdfe6440738ea2f72648b7980e4c40ea4052 | MATLAB | 6,083 | 154 | % mmo() - create a memory-mapped data class
%
% Usage:
% >> data_class = mmo(data);
%
% Inputs:
% data - input data or data file
%
% Outputs:
% data_class - output dataset class
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Nov. 2012-
% Copyright (C) 2008 Arnaud Delorme, SCCN, INC, UCSD
%
% This progra... |
775f7eba09a7714b6c6b0371024ac2cec524f79b17b62ce03eb75ffeb792fcbc | MATLAB | 6,087 | 170 | function [y,k, DAy] = loopPcg(L,Lden,At,dense,d, DAt,K, b,p,ssqrNew,cgpars, restol)
% [y,k, DAy] = loopPcg(L,Lden,At,dense,d, DAt,K, b,p,ssqrNew,cgpars, restol)
%
% LOOPPCG Solve y from AP(d)A' * y = b
% using PCG-method and Cholesky L as conditioner.
% If L is sufficiently accurate, then only 1 CG-step is needed.
% It... |
bedf52c2436c0704ce31bb5a3a5fec24e42f947518491c3cb1d0ff0b0f0dbe91 | MATLAB | 6,094 | 147 | % pop_importegimat() - import EGI Matlab segmented file
%
% Usage:
% >> EEG = pop_importegimat(filename, srate, latpoint0);
%
% Inputs:
% filename - Matlab file name
% srate - sampling rate
% latpoint0 - latency in sample ms of stimulus presentation.
% When data files are exporte... |
b5f05a87d15803efeb5029c648b8b6f532b47f7d85721ddc24f7df46ae5ff23b | MATLAB | 6,096 | 216 | function hdr = load_nifti_hdr(niftifile)
% hdr = load_nifti_hdr(niftifile)
%
% Changes units to mm and msec.
% Creates hdr.sform and hdr.qform with the matrices in them.
% Creates hdr.vox2ras based on sform if valid, then qform.
% Does not and will not handle compressed. Compression is handled
% in load_nifti.m, which ... |
f4abd2e9c25543b3deeceb830b99a5a6404fa094ecb696b5f41938fec3ad7b3c | MATLAB | 6,097 | 166 | %% d_signature_responses_generic.m
%
%
% *USAGE*
%
% This script plots selected signature responses calculated by
% prep_4_apply_signatures_and_save.m, and tests their significance, for
% conditions and contrasts defined in DAT. It
%
% # calls a_set_up_paths_always_run_first, then loads DAT/DATA_OBJ*/DATA_OBJ_CON*
% ... |
1712f3a5b8a09c6c98577b2f86d182508ff30c78bec5d2b37ba4ef35b7d983e1 | MATLAB | 6,098 | 178 | function compiledData = compileResultsCSV(inputFolder, outputFolder, options)
% COMPILERESULTSCSV Compile manual tracking results from multiple trackers
% into a single table with physical unit conversions applied.
%
% Scans an input folder for subdirectories (one per tracker). Within
% each tracker subdirectory it loo... |
f2cd46f058f29f08f37853accf2054326af682bcfc7f2a987350fb455233032f | MATLAB | 6,105 | 182 | % Minimize beamwidth of an array with arbitrary 2-D geometry
% "Convex optimization examples" lecture notes (EE364) by S. Boyd
% "Antenna array pattern synthesis via convex optimization"
% by H. Lebret and S. Boyd
% (figures are generated)
%
% Designs an antenna array such that:
% - it has unit sensitivity at some targ... |
261e9e67a639d4b8970bd808337b161d68c532784a59e71a83503b9b1c0d28c1 | MATLAB | 6,111 | 183 | function [tracking] = bz_processConvertOptitrack2Behav(fbasename,varargin)
% USAGE
%
% bz_processConvertOptitrack2behavior(fbasename,varargin)
%
%
% INPUTS
% fbasename -basename of the recording (this is only used in generating
% the .mat output file)
% <options> optional list of pro... |
143bec3defa54350c3613fe501e634eeb7b6cbae83f8e66c61f471e3ac58e574 | MATLAB | 6,112 | 151 | function rename_dicm(files, fmt)
% Rename dicom files so the names are meaningful to human.
%
% RENAME_DICM(files, outputNameFormat)
%
% The first input is the dicom file(s) or a folder containing dicom files.
% The second input is the format for the result file names. Support format
% include:
%
% 1: run1_... |
c64ade66bc88bf6b2d6ee37fa991ad152cc311db0276f6541b2e134c1bac840c | MATLAB | 6,116 | 163 | function [placeFieldTemplate] = bz_findPlaceFieldsTemplate(varargin)
% [placeFieldTemplate] = bz_findPlaceFields1D(firingMaps)
% Creates a template with all cells acording to the arragement of their
% place fields in a 1D maze.
%
% INPUTS
%
% placeFieldStats cellinfo structure from bz_findPlaceFields1D with ... |
e697405b563285eb761388c8cd0bcd477a6e2bb1048f4ce91098f1f2e156c670 | MATLAB | 6,117 | 139 | function [results]=CBIG_gwMRF_graph_cut_clustering_iter_split(prams)
% This function loads the data, normalizes it and calls the clustering function
%
% Input
% - prams = a struct containing various input parameters
%
% Ouput
% - results = a struct containing the labels and various addi... |
b80961ec8ad90cf6b0d585f2aa942f5b17e224243f5ac107f654586db77ade4e | MATLAB | 6,119 | 164 | function plotfluordirections_tile(avgfluor,redtemps,ROIs,Xpix,Ypix,framerate)
%plot the data averaged for each ROI
%show the ROI?
fn=fieldnames(avgfluor);
[numROIs,triallength]=size(avgfluor.(fn{1}));
%make the layout as 3 separate figures
fig1=figure('units','normalized','outerposition',[0 0 0.2 1]);%make each figure... |
82587fe09bcf13d4636b6959d27ddc72933100db3016239d60c66a9bc5a6eb99 | MATLAB | 6,122 | 115 | function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr,t)
% Multi-taper coherency - point process times
%
% Usage:
%
% [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr,t)
% Input:
% data1 (structure array of spike times with dimension... |
f9ec12cece677f157e9be852f8e7229da52c8495649b0abad76aac29b3829e81 | MATLAB | 6,127 | 190 | %%
% FIRST,
% process the metadata as usual:
[out filenames] = AF_OF_importer('230511','f3e1');
fly = AFOFdata_struct_CL(out,filenames); % for exp7
%%
% SECOND, set up for & run concatCEM
% here's the setup
date = '251021';
fpt = 148; % frames per trial
driver = 'SS02255';
datename = 'oct2125_f3';
%... |
464be9fdb15e20fdc6eb86473740b06a39f0e2c19048b50caf0875d8f6af7057 | MATLAB | 6,130 | 192 | function [Theta_sol]=...
constrained_solution_MetaInfer(rp,X,F_prime,o_use_initial_guess,algorithm,nCores)
% 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 relevan... |
22878615a5f0d96428c71e00478239c6940f51384fa505e18e28411472894bad | MATLAB | 6,133 | 177 | function [res, errStr]= dtdstruct_init(varargin)
% function [res, errStr]= dtdstruct_init(typeStr, mrStruct, [mrData1, nameStr1, [mrData2, nameStr2, ...]])
%
% Creates a valid dtdStruct of the type DTD
%
%typeStr 'DTD':
% [res, errStr]= dtdstruct_init(typeStr, eigenVec, eigenVal, [mrData1, nameStr1, [mrData2, nameSt... |
c1182c466fb36b19f766a18d3899832cace87892d24c9e8e143379b3e0e19af1 | MATLAB | 6,133 | 154 | function myPLS_plot_loadings_1D(var_type,var_PLS_type,vars_PLS,vars_b_vect,vars_mean,vars_std,...
vars_lB,vars_uB,var_names,signif_LC,nGroups,fig_pos,save_opts)
% This function plots one-dimensional loadings (e.g. behavior, 1D imaging
% metrics) of all significant latent components (LCs) as barcharts.
%
% Inputs:
... |
54bb50e598334ff7675375e8b44656445c16b753b7b8e45e186e0bca5490f7cf | MATLAB | 6,136 | 181 | function [Spike, spikeWaves, allSpikeWaves, startSpike] = dacq_tetrode(basePath, cutFiles, dotnums, startSpike)
%[root.spike root.wmfs] = dacq_tetrode(dataPath,prefix,varargin)
%
%For a given directory and file prefix, checks for any *.cut files. For all
%if any are found, cross references with .# file to create a CMBH... |
c1c8f7e94dfb2d239273716042303e9ba0c3ee1f781bb4a30355da0f07a34674 | MATLAB | 6,138 | 113 | function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpt(data1,data2,params,fscorr,t)
% Multi-taper coherency,cross-spectrum and individual spectra -continuous data and point process as times
%
% Usage:
%
% [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpt(data1,data2,params,fscorr,t)
% Input:
% ... |
53d73f420628a542d6e75675d827e6e347469b4b04de0e4d4dcc1ebd349fdadc | MATLAB | 6,139 | 139 | function this = subsasgn(this, subs, A)
% Subscript assignment for GIfTI objects
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: subsasgn.m 6513 2015-08-05 17:52:13Z guillaume $
switch subs(1).ty... |
36e372872ae4b8a57a152bd666c6db677e7b4a6be5564f045f0ac33b16691a3f | MATLAB | 6,148 | 164 | function [keep_species,intervene_matrix_filtered,data_counts_filtered,species_names_filtered,total_count_norm,biomass_norm,scaleFactor,med_counts,med_biomass] = preProcessData(intervene_matrix,data_counts,species_names,biomass,experimentBlocks,uniqueExperiments,blockIdx,paramFileName)
% This file is a part of the MDSI... |
86551d68f4c623f40fb2c45791d78ad310464024ba974a31372f6eb25fea1945 | MATLAB | 6,148 | 162 | function Obj = SOFAupdateDimensions(Obj,varargin)
%SOFAupdateDimensions
% Obj = SOFAupdateDimensions(Obj) updates the dimensions in the SOFA
% structure
%
% Obj is a struct containing the data and meta.
% The dimension sizes are created as .API.X and updated corresponding to the
% conventions
% flag i... |
2d60f741015a7c7b37487aa2c016d699d1bb149d2e7111ba41daa84ff7d37c3f | MATLAB | 6,149 | 168 | function Spikes = findSpikes(NSx, varargin)
% findSpikes
%
% Searches NSx data structure for spikes by thresholding. The output is
% compatible with NEV.Data.Spikes data structure.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Use OUTPUT = findSpikes(NSx, 'threshold', 'preThres... |
bc001e05f619ebde688e4201c2428d14e744247f8b49a56db31ebd704b9176ab | MATLAB | 6,149 | 233 | % cbar() - Display full or partial color bar
%
% Usage:
% >> cbar % create a vertical cbar on the right side of a figure
% >> cbar(type) % specify direction as 'vert' or 'horiz'
% >> cbar(type,colors) % specify which colormap colors to plot
% else
% >> cbar(axhandle) % specify the axes to draw cbar in
%
% ... |
9dc4d11d6d477f83d1b98792ff7016b81ebf22134a9992a9e95f4fbe12d4675e | MATLAB | 6,152 | 147 | function lh_rh_Neighborhood = CBIG_hMRF_generate_fs6_lhrh_nborhood(outdir)
% CBIG_hMRF_generate_fs6_lhrh_nborhood(outdir)
%
% The left and right fsaverage6 hemispheres were first registered using the Freesurfer's 'mris_left_right_register'
% function. After registration, the closest right hemisphere vertex was found f... |
1363d05d875b5d5e32047ccc61db1db796a37340b296f2928c467bce544c9c1d | MATLAB | 6,160 | 209 | % compheads() - plot multiple topoplot() maps of ICA component topographies
%
% Usage:
% >> compheads(winv,'spline_file',compnos,'title',rowscols,labels,view)
%
% Inputs:
% winv - Inverse weight matrix = EEG scalp maps. Each column is a
% map; the rows correspond to the electrode positions
... |
288b0461077c9382f638016594f95342349610a45613146a14029061e9a40ff9 | MATLAB | 6,162 | 171 | function obj = stat_violin(obj,varargin)
% stat_violin display violin plots of y data for unique x
%
% Options can be given as 'name',value pairs:
% - all options from see stat_density() are present:
% 'bandwidth', 'kernel', 'npoints', 'extra_y'
% - 'normalization': 'area' (default) all violins have the same
% areas. W... |
abddde077696ac7e115c5768ba70a72d8fe30c4299e566aa547f2200d75e65fd | MATLAB | 6,164 | 218 | 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 ... |
9a1253965b30056451d7065a63beb879867405a13988b6a4d968277a48d2af33 | MATLAB | 6,170 | 167 | function ea_apply_coregistration(varargin)
% Wrapper to apply linear transformation
%
% The 4th parameter (transformation) can be:
% 1. Not specified, the transformation will be automatically detected
% if there is only one transformation file in the folder.
% 2. String ('SPM', 'ANTs', 'FSL' and 'BRAINSF... |
ee3faf55cffc2c987dd8bd70b6cf77049786a3f81a8add667df5335fdd4ca738 | MATLAB | 6,175 | 181 | %% Evaluate the Reliability of Functional Connectivity Analysis
% Generate simulated data for 2 neurons
% Control the spike firing rate
% Control the level of synchronous firing
clc
clear
% close all
%% Parameter settings
% *************************
para_Len = 1000; % Length of the sequence (number of time... |
963855600b9da05ec01282d502609e4eaa6bf7d06a258f00db1840233599dbd6 | MATLAB | 6,176 | 113 | function chronux
% This library performs time-frequency analysis (mostly using the
% multi-taper spectral estimation method) of univariate and multivariate
% data, both for continuous processes such as LFP/EEG and for point
% processes such as spike times. Point process can either be stored as
% times or as a binned pr... |
00e426d320c1548e0ccd2fbdae62d5b007d4a2fef3e1c9deab003720e1a0f566 | MATLAB | 6,177 | 121 | % Several examples for using StructDlg
%%
% Note: The values the user enters to the dialog box for numeric fields are being 'eval'-uated,
% so inputs such as (sin(0.34)+2)^my_func(34.2) are possible.
% The field's numeric limits can be displayed by placing the mouse over the field.
%
%
% Free Strings: Limited ... |
5a7848a923f9a4b8d971f974822bcf278772049704e823be8b8e2e26d75b5b62 | MATLAB | 6,178 | 160 | function varargout=ea_ft_mesotracking_reisert(options)
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn
if ischar(options) % return name of method.
varargout{1}='Mesoscopic Fibertrack... |
b55f17b8bf7dc8536312984011a9b3104724d99299edc2435bdfd6bb023d294a | MATLAB | 6,180 | 144 | % 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... |
b27b966526ded4ed4c54a9006a54fe5bbc57bd59f65b1d5d61a536745e5d48ff | MATLAB | 6,182 | 191 | % Load NIFTI or ANALYZE dataset, but not applying any appropriate affine
% geometric transform or voxel intensity scaling.
%
% Although according to NIFTI website, all those header information are
% supposed to be applied to the loaded NIFTI image, there are some
% situations that people do want to leave the origi... |
ade22a1eccad3810d8dc7802f994b24a2f02cb3da2851cfbed3454e2f71ec32b | MATLAB | 6,183 | 170 | function [ cluass,cluNRG ] = bz_GradDescCluster( simMat, varargin )
%[cluass] = bz_GradDescCluster(simMat) clusters recording sites given a pairwise
%similarity matrix using gradient descent to find minimize within-cluster
%interaction energy. (i.e. maximize within-cluster coherence, see Berenyi
%et al 2014 for deta... |
bc0b7b84455a8764653b45f31287d56ddeac2600642cca54fcca53d067929e19 | MATLAB | 6,183 | 219 | function A = convnfft(A, B, shape, dims, options)
% CONVNFFT FFT-BASED N-dimensional convolution.
% C = CONVNFFT(A, B) performs the N-dimensional convolution of
% matrices A and B. If nak = size(A,k) and nbk = size(B,k), then
% size(C,k) = max([nak+nbk-1,nak,nbk]);
%
% C = CONVNFFT(A, B, SHAPE) controls the s... |
f6edca7fe0e1a6a1a3c3c75f915df046497c68f1632825793b8b5b293cd7435a | MATLAB | 6,184 | 192 | % This functions computes the FFT of the data and aftewards the PLV and
% power
%
% INPUTS:
% EEG EEGLAB structure
% OPTIONAL INPUTS:
% condition indexes for different conditions (size Nepochs x 1 )
% If not proveded or empty it is computed for all trials
% Default []
% ... |
152e981583c93db433f8927adf5bea4a053d7a50a6574c11f0a13034dc5a9669 | MATLAB | 6,191 | 209 |
%% 1. Create strings listing where the toolbox and the tutoral data directories are
toolbox_directory_name = '../../ndt.1.0.4/' % put name of path to the Neural Decoding Toolbox
raster_data_directory_name = 'Zhang_Desimone_7objects_raster_data/'; % put name of path to the raster data
%% 2. Plot a rasters a... |
f2223b92074d62fc1c8294e4e3c0463625099f1da0f80690ea88bb0e303b6e61 | MATLAB | 6,200 | 124 | function [all_XTr_pseudo all_XTe_pseudo] = turn_all_simultaneous_data_into_pseudo_populations(all_XTr_simul, all_YTr, all_XTe_simul, all_YTe, feature_to_siteID_mapping)
% A helper function that takes simultaneously recorded data and turns it into pseudo-populations.
% This function should return results that are v... |
e3dfab305af59d1d432c59d2ecc68916a000cacf3e9a9822c7d771a6ea36e2da | MATLAB | 6,201 | 204 | function [out1,out2,out3] = ginput(arg1)
%GINPUT Graphical input from mouse.
% [X,Y] = GINPUT(N) gets N points from the current axes and returns
% the X- and Y-coordinates in length N vectors X and Y. The cursor
% can be positioned using a mouse (or by using the Arrow Keys on some
% systems). Data poin... |
f748dce2ccc12c30911272824fad9c2d5f5843f42b51929966a0a078d94e71f1 | MATLAB | 6,211 | 177 | function CBIG_factorHierachy(k_bestRun)
% CBIG_factorHierachy(k_bestRun)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
noSplits = size(k_bestRun, 1)-1;
K_0 = k_bestRun{1, 1};
K = k_bestRun{end, 1}-1;
which2_order_avgCorr_beta = cell(noSplits, 3);
which2_order_avg... |
b8a869bd8e053c9916a9b281c1ec145c3a2a5c56b822bd44dda8767bd5f7d85d | MATLAB | 6,212 | 192 | % This functions computes the FFT of the data and aftewards the PLV and
% power
%
% INPUTS:
% EEG EEGLAB structure
% OPTIONAL INPUTS:
% condition indexes for different conditions (size Nepochs x 1 )
% If not proveded or empty it is computed for all trials
% Default []
% ... |
25d2423ed73afd2cd53f4efd76724d7c2b6b6a1c0fbedcbaa2b8e2f625243dea | MATLAB | 6,213 | 160 | function positions = GetPositions(varargin)
%GetPositions - Get position samples.
%
% USAGE
%
% positions = GetPositions(<options>)
%
% <options> optional list of property-value pairs (see table below)
%
% =========================================================================
% Properties Valu... |
b33bd892639cc4a11ca55db1bac3303ba2c14a7d2449deefe785a6f6ddd0574b | MATLAB | 6,216 | 150 | classdef max_correlation_coefficient_CL
% max_correlation_coefficient_CL is a classifier object (CL)
% that learns a mean population vector (template) for each class from the
% training data. When the classifier is tested, the correlation coefficient
% is calculated between a test point and each of the class tem... |
1a2f43b8411000f8ba4833895ea2bac4f3f0175c1471f3a269339ab9ecba314a | MATLAB | 6,219 | 142 | function [id_sites, id_dx, id_age, id_sex, id_motion, id_fiq, id_scores, id_factorLoading] = CBIG_ASDf_getSubData(...
sub_info_file,id_sub, behav_score_file, idx_scores, factorLoading_file)
% [id_sites, id_dx, id_age, id_sex, id_motion, id_fiq, id_scores,
% id_factorLoading] = CBIG_ASDf_getSubData(sub_info_file, id... |
43a256e0614d4ca1e6274a220f11dadd1f7a7c27459d2b85bd0c792086df74a4 | MATLAB | 6,222 | 181 | function [PowerPhaseRatemap,spikebinIDs] = bz_PowerPhaseRatemap(spikes,filteredLFP,varargin)
%[PowerPhaseRatemap,spikebinIDs] = bz_PowerPhaseRatemap(spikes,filteredLFP,varargin)
%
%INPUTS
% spikes structure containing spikes.times from bz_getSpikes
% filteredLFP structure containing filteredLFP.timesta... |
cc33c58ece2ccc1d2dda819416b4211d17bd8aa54406607d2d4629450966074e | MATLAB | 6,222 | 184 | function varargout=wt(d,varargin)
%% Continous Wavelet Transform
% Creates a figure of wavelet power in units of
% normalized variance.
%
% USAGE: [wave,period,scale,coi,sig95]=wt(d[,params])
%
% d: a time series
% wave: the wavelet transform of d
% period: a vector of "Fourier" periods associated with wave
... |
1be774ca45fcb2a8cdb58fc331236433f926197aeb34c732a8253d6c8a182681 | MATLAB | 6,230 | 151 | function tests = testLyapunov
%TESTLYAPUNOV Contract tests for the lyapunov wrapper.
tests = functiontests(localfunctions);
end
function setupOnce(tc)
tc.TestData.lorenz = nonantest.signals('lorenz', 3000);
tc.TestData.fs = 1/0.03;
end
function teardown(~)
dbclear all
end
% ------------------------------------------... |
c3fb552753ffb1a82b838619570e25a8d720728e814167957eeee8f7d7bd80ee | MATLAB | 6,234 | 216 | %%
% MSE script
% first, run per-fly getPFNdata.m, e.g.
[leftmeans rightmeans] = getPFNdata(allflies,[1:19],[1:10],5,[1,2]);
% then run this
for f = 1:10
ivc{f} = makeIVC(leftmeans{f},rightmeans{f},3,2);
end
%%
for f = 1:10
for i = 1:19
means(f,i) = mean(ivc{f}{i});
sems(f,i) = st... |
6d61f09ca9fd0a4648f2b58a7a2e4e2dd2a7113fbe70239a695a0df52be00a69 | MATLAB | 6,235 | 175 | % THIS SCRIPT RUNS BETWEEN-PERSON CONTRASTS
% Assuming that different conditions are tested on different groups of
% participants. For within-person contrasts, where each individual has an
% image for each condition being compared, use DAT.contrasts, not this.
% If conditions being compared include images for differen... |
88f193973969e4d683364560378eea58cd8c61408103e0a7392ad115f3ebecb1 | MATLAB | 6,236 | 172 | function [x, y, orientation] = FlyTracker(filename, FrameRange,...
NBackFrames, opt1, sqrsize,...
alpha, ellipse)
%FLYTRACKER
% Usage:
% [x, y, orientation] = FlyTracker(filename, FrameRange, ...
% NBackFrames, opt1, sqrsize,...
% ... |
c9c25cd0dc442994c184d2a089927725b213e056ac9e05f99b46594eaa96b478 | MATLAB | 6,240 | 230 | function AlignTsp2Whl(fbasename,colorvec,varargin)
% USAGE:
% AlignTsp2Whl(fbasename,colorvec)
%
% convert .tsp file to .whl file. Requires the .meta file
%
% INPUT:
% 'fbasename': the file base names ('fbasename.tsp', etc.)
% 'colorvec': a 2 value vector [colFront colRear] which defines which
% color from [R G ... |
2e667bac3a2dc7e610cf9e12228b3d4c46adb0ef79a8d6edb3114f95d3a8f400 | MATLAB | 6,242 | 137 | %% control_mvpa_reg_cov_permutation.m
%
% POSITIVE CONTROL for the permutation test added to prep_3a's
% domvpa_reg_cov block (prep_3a v_next, 2026/09/23).
%
% WHY THIS EXISTS
% predict() returns pred_outcome_r, mse, rmse, meanabserr and cverr, and
% nothing inferential - there is no p-value anywhere in its output stru... |
9ba64d0a412e7d7da4c6ab517b9430295762d8dd756ab693d858835e3dad7edc | MATLAB | 6,242 | 164 | function vol2surf_fc = CBIG_IndCBM_compute_vol2surf_fc(lh_surf_file, rh_surf_file, vol_file, template_file, output_file)
% vol2surf_fc = CBIG_IndCBM_compute_vol2surf_fc(lh_surf_file, rh_surf_file, vol_file, template_file, output_file)
%
% This function computes the functional connectivity between the cerebellum
% in t... |
cbf5b1e2daa92523bc9c7c21426dcc4b4c08d8f3619a23ced1b418e543cb2f10 | MATLAB | 6,242 | 181 | function [nPeaks, nTroughs, mainPeak_before_size, mainPeak_after_size, mainTrough_size, ...
width_before, width_after, widthTrough, peakLocs, troughLocs, PKS, TRS, troughLoc] = getWaveformPeakProperties(thisWaveform, param)
% Flexible handling of different spike widths
waveformWidth = size(thisWaveform, 2);
if wave... |
963f5db6f67d7c0349f0b573db0880aee2b1cd81b6b802f949660aab548f57ec | MATLAB | 6,244 | 168 | %% Check whether contrasts are defined
% ------------------------------------------------------------------------
if ~isfield(DAT, 'contrasts') || isempty(DAT.contrasts)
% skip
disp('No contrasts specified. Skipping contrast estimation');
return
end
%% Specify which montage to add title to. This is ... |
5e3484b3119f55c4f01a48b5123168f29076f831aa9f44227583a6e83391f7e0 | MATLAB | 6,245 | 180 | function cc = ea_conncomp(A)
% conncomp Find connected components in 2D grayscale or label image
% Four-connected neighborhood is used.
%
% CC = CONNCOMP(A) returns the connected components CC found in A.
% A is a two dimensional array (image) of sixe I-by-J. Elements in A should
% be positive, if A... |
94085befd7d7fc686ecdd3b59e2147cb5a7e22b46f92f905e8f5ad22de727061 | MATLAB | 6,249 | 174 | %%*****************************************************************************
%% HSDsqlpcheckconvg: check convergence.
%%
%% ZpATynorm, AX, normX, normZ are with respect to 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 ... |
1883c094bfcef923830881c746f19e941ac331d67a680ed94949e1d15a2b58dc | MATLAB | 6,251 | 113 | function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpt(data1,data2,params,fscorr,t)
% Multi-taper coherency,cross-spectrum and individual spectra -continuous data and point process as times
%
% Usage:
%
% [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpt(data1,data2,params,fscorr,t)
% Input:
... |
693d5aa141f4541dcf22e6042601d32be7647fd58b4bf9bbf820f880dc396f05 | MATLAB | 6,255 | 162 | function aggtree(spikes)
% AGGTREE Generates a graphical summary of an aggregation procedure.
% AGGTREE(spikes)
% Takes a spike-sorting data structure that has undergone hierarchical
% aggregation and visualizes the hierarchy.
% The function draws its output over the current axis. The labels of the
% initi... |
6a3624af76065bc6c4a58527c3bdbe1bbdb8487742df3eccdd8b7f9c191140cc | MATLAB | 6,255 | 204 | classdef report_generator < handle
%REPORT Summary of this class goes here
% Detailed explanation goes here
%% Public Properites
properties
name;
fid;
output_dir;
report_dir;
css_dir;
img_dir;
end
%% Private Properties
prop... |
87756c0f0543d0ed03bcd10789bfe4fd3c6091ee5154658e9ddff1b5a1d4bb45 | MATLAB | 6,257 | 173 | function [weightedMean,weightedStdOfMean,weightedStdOfSample] = weightedStats(data, weightsOrSigma,sw)
%wStats calculates weighted statistics (mean, stdev of mean) for a list of inputs with corresponding weights or {std}
%
%SYNOPSIS [weightedMean,weightedStd] = weightedStats(data, weightsOrSigma,sw)
%
%INPUT data:... |
51cd994c87a4757681dc3b670de4715e4bf0697a83528300761c7809b507307b | MATLAB | 6,259 | 173 | function M2T = mni2tal_matrix()
% MNI2TAL_MATRIX - Talairach to MNI coordinates (best guess)
%
% MNI2TALAIRACH = mni2tal_matrix
%
% MNI2TALAIRACH is a struct containing rotation matrices
% used by mni2tal and tal2mni
%
% See also, MNI2TAL, TAL2MNI &
% http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html
%
% $Revis... |
64fa005983a07afff6377d37dec3a955de89fe96b4110bdf55b09d1669b402ad | MATLAB | 6,263 | 165 | function dir_angles = ea_diode_darkstar(roll,pitch,yaw,dirlevel,radius)
vizz = 0;
%% create vectors symbolizing the gaps between directional contacts at 60, 180 and 300 degrees
% and transform them to match lead trajectory and directional level
dirlevel = dirlevel(1:3);
ven = [0 0.65 -0.75 ]';
dor = [0 0.65 0.75 ]';
[... |
9314154d3835f84d08d30c20ed3df865bdc0bf79b5046163250a4781f206550b | MATLAB | 6,267 | 193 | % Combined sizing of drivers, repeaters, and wire
% Section 5.2, L. Vandenberghe, S. Boyd, and A. El Gamal
% "Optimizing dominant time constant in RC circuits"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 11/25/05
% Modified by Michael Grant - 3/8/06
%
% The first driver drives an interconnect ... |
06aeb980650e749486fabd6b2c6c91cc1c6b531a9f222b421f94b8de5b726e0d | MATLAB | 6,272 | 137 | %% LaBGAScore_pet_dcm2bids.m
%
%
% *USAGE*
%
% This script completes partial BIDS conversion of (TSPO) PET data by a previous
% run of KUL_dcm2bids.sh
%
%
% *OPTIONS*
%
% * tracer_string default 'DPA714', tracer identifier for name of pet dir and filenames
% * filename_search_string default 'TSPO', string ... |
b5d9444628f9394d4bdb06e45abfa09418311f0cbf6ed11fcf8b17b9f18cc8fe | MATLAB | 6,276 | 149 | function varargout = impexp_run_nifti2dtdStruct(cmd, varargin)
% Template function to implement callbacks for an cfg_exbranch. The calling
% syntax is
% varargout = impexp_run_nifti2dtdStruct(cmd, varargin)
% where cmd is one of
% 'run' - out = impexp_run_nifti2dtdStruct('run', job)
% Run a job, and r... |
4da523a8bedb9d3096dead24e5371cb7ef1f2a29031c8a1c0fd861e20adef55a | MATLAB | 6,279 | 203 | function [p,F] = CircularANOVA(angles,factors,method)
%CircularANOVA - One or two-way ANOVA on circular data.
%
% Circular ANOVA can be performed using one of three methods with different
% assumptions and limitations:
%
% 1) Watson & Williams (1956)
% The data are drawn from von Mises distributions with ... |
f94b1de71d08196d28c48d454af1388203b6e83248c5e2820eb573aa584acbdd | MATLAB | 6,280 | 138 | function [x,y] = optstep(A,b,c, y0,y,d,v,dxmdz, K,L,symLden,...
dense,Ablkjc,Aord,ADA,DAt, feasratio, R,pars)
% [x,y] = optstep(A,b,c, y0,y,d,v,dxmdz, K,L,symLden,dense,Ablkjc,Aord,...
% ADA,DAt, feasratio, R,pars)
%
% OPTSTEP Implements Mehrotra-Ye type optimality projection for
% IPM-LP solver.
%... |
07e4445427cbb0c654582e55ca74b1e349bd9bc72514452c35041d3d6b09fc90 | MATLAB | 6,285 | 197 | % Load NIFTI or ANALYZE dataset, but not applying any appropriate affine
% geometric transform or voxel intensity scaling.
%
% Although according to NIFTI website, all those header information are
% supposed to be applied to the loaded NIFTI image, there are some
% situations that people do want to leave the origi... |
b793f0cd8ab8425cd499380e2b577aef51aa55998873bda0bcc8c255db65da9b | MATLAB | 6,287 | 151 | function [C, log] = SOFAmerge(A,B)
%SOFAmerge
% [C, log] = SOFAmerge(A,B) merges the SOFA objects A and B to a single one, C.
%
% A and B are structs containing the data and meta. A and B
% must be of the same SOFA conventions.
%
% C is a struct containing merged data
% log contains log data
% SOF... |
341be72a173ec172d78464ae399b3135ed6bc0da8896c1b33b708b3586792306 | MATLAB | 6,289 | 113 | function chronux
% This library performs time-frequency analysis (mostly using the
% multi-taper spectral estimation method) of univariate and multivariate
% data, both for continuous processes such as LFP/EEG and for point
% processes such as spike times. Point process can either be stored as
% times or as a binn... |
b590bc0e0708dcce88aed6c8d82c79e8a9d3ad9ea964c115eeb9816e9a415401 | MATLAB | 6,290 | 120 | function ea_gentrackingmask(options,threshold)
directory=[options.root,options.patientname,filesep];
ea_newseg(fullfile(directory,options.prefs.prenii_unnormalized),0);
b0_anat = [ea_stripext(options.prefs.b0),'_',ea_stripext(options.prefs.prenii_unnormalized)];
if exist([directory,'ea_coreg_approved.mat'], 'file')
... |
5ef7a7a6ce490fce401fa7d7e2713a2f1f88ac91e0dd6552482cebee86cecba5 | MATLAB | 6,291 | 186 | function OutWin = createWindow(varargin)
% Create a Hann or exp. window with specified onsets/offsets
%
% OutWin = iosr.auditory.createWindow(WinLen, Type, Duration)
%
% Other (non-symmetric) uses include:
%
% OutWin = iosr.auditory.createWindow(WinLen, ...
% Hann, ...
% OnDuration, ...
% Hann, ...
% ... |
09653e7ab6afe6e701536afe622ace1e4d8abd2cca170b6ddd6c0bfbc7c03ecd | MATLAB | 6,295 | 154 | function [min_bound_per_contact, max_bound_per_contact, S] = ea_get_currents_per_contact(min_conc,max_conc,min_segm,max_segm, reconst, side, check_S)
% create bounds (limits) for current optimization
% and adjust the amplitude in S
% min_conc,max_conc,min_segm,max_segm - thresholds for contacts
% reco... |
2a299e5984c43be3ae32406ca81ae0c452a57e59221baf12c10f81510b53e157 | MATLAB | 6,298 | 231 | function [chg]=KummerComplex(a,b,z)
%
%KUMMERCOMPLEX Confluent hypergeometric function 1F1
% (Kummer function).
%
% KUMMERCOMPLEX(a,b,z) is the confluent hypergeometric
% function 1F1 (Kummer function) for complex
% parameters a, b and complex variable z.
%
% Example:
% KUMMERCOMPLEX(1+0.5i,2-3.1i,... |
6b697a3b3d93eddb697821d95531780d869984f7d55db57ef85447b3902b749f | MATLAB | 6,300 | 164 | function [coherence,f,s] = MTCoherence (lfp1,lfp2,varargin)
%MTCoherence - Compute Coherence by multi-taper estimation.
%
% The spectrum is computed as the average spectrogram, using the <a href="http://www.chronux.org">chronux</a> toolbox.
%
% USAGE
%
% [coherence,f,s] = MTSpectrum(lfp1,lfp2,<options>)
%
% lf... |
d842611561c78410d2ea3a3a80b34f665d7c8dbc4676878f5d479c63335fb96f | MATLAB | 6,300 | 197 | %% Example: Mapping images to an atlas and visualizing them with a river plot
% Often, we would like to map a results image (e.g., t-map or functional connectivity map)
% to an atlas to help localize where the activity is. The table() method is one way to do this,
% as it auto-labels regions using an atlas. Here, we w... |
984767ffe45a49a870791650d73a183c79a0582e8b2b2f3d74d5d25ccb913f11 | MATLAB | 6,305 | 168 | function ea_ants_run(cfg)
% Proxy to run ANTs registration based on provided configurations
% Make sure the transformation folder and output folder exist.
ea_mkdir(fileparts(cfg.outputbase));
ea_mkdir(fileparts(cfg.outputimage));
ants_transforms = dir(fullfile(fileparts(cfg.outputbase), '*_desc-ants.*'));
refinewarp... |
1adeaf3ab17aa2be57ae7890c26839c72b6a60d50c063d8bc9e382c5cd093cf2 | MATLAB | 6,307 | 136 | function [Obj, log] = SOFAexpand(Obj,VarName)
%SOFAexpand
% Obj = SOFAexpand(Obj) expands the singleton dimensions of all variables.
% Only variables will be expanded. Data and attributes won't. Note that
% also Obj.API.Dimensions will be updated to the new dimensions.
%
% Obj = SOFAexpand(Obj,VarName) ex... |
e42b6726d78a88b56d5ec1ba82d248dcdfd85b73050daa8d1c7b9f385be2edee | MATLAB | 6,308 | 183 | function [cont,dirflag] = getContents(directory,varargin)
%GETCONTENTS Get the contents of a specified directory
%
% This function returns the contents of a specified directory.
%
% CONT = IOSR.GENERAL.GETCONTENTS(DIRECTORY) returns the files and
% folders in a directory and returns them to the cell array cont. I... |
9866bb0c56a8db4b39226ae9be2c79b21e1d5fe883ece48fe7278fb54e591fb7 | MATLAB | 6,313 | 180 | %% Use spike data
clc
close all;
addpath(genpath('functions'))
load([save_folder_name '\' file_name_spike '.mat'],'root')
num_cells = length(root);
num_points = length(root(1).ts);
dt = root(1).ts(2)-root(1).ts(1); % unit: s
%% Spatial rate map of the whole population
positions_data = [root(1).x root(1).y] / 100; % ... |
a97d7f46cf5dbfe0463d32032074f462d21a417fd671ec81c455dfff602f1ef2 | MATLAB | 6,318 | 251 | function [pval table] = circ_hktest(alpha, idp, idq, inter, fn)
%
% [pval, stats] = circ_hktest(alpha, idp, idq, inter, fn)
% Parametric two-way ANOVA for circular data with interations.
%
% Input:
% alpha angles in radians
% idp indicates the level of factor 1 (1:p)
% idq indicates the level... |
fa09045d6c4ee3e0d0b3c52bba8c1b87678ac0400f5ff21363631d8820381061 | MATLAB | 6,324 | 158 | function p_10foldCV = CBIG_MMLDA_10foldCV_wrapper(out_dir)
% p_10foldCV = CBIG_MMLDA_10foldCV_wrapper(out_dir)
%
% Wrapper function to do 10 fold cross validation.
%
% Input:
% - out_dir : absolute path to the output directory
%
% Output:
% - p_10foldCV: correlation p values used for FDR correction later
%
% Exam... |
16ab0c87792dc831a4405d5e8f80f6998aa6c65d409755c13d71d68959ca20a1 | MATLAB | 6,325 | 146 | function this = subsasgn(this, subs, A)
% Subscript assignment for GIfTI objects
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: subsasgn.m 6513 2015-08-05 17:52:13Z guillaume $
switch subs(1).type
c... |
e5023022508bdd4a501598d842e57b6ff4fb6776e8228802f1b5abf4c2ca52ef | MATLAB | 6,329 | 166 | function varargout = ea_waveletfusion(varargin)
% EA_WAVELETFUSION MATLAB code for ea_waveletfusion.fig
% EA_WAVELETFUSION, by itself, creates a new EA_WAVELETFUSION or raises the existing
% singleton*.
%
% H = EA_WAVELETFUSION returns the handle to a new EA_WAVELETFUSION or the handle to
% the exis... |
5190e4c2d9afa86c58be2e61900fc83ad440e393ec944d6732630459d3b130d6 | MATLAB | 6,334 | 167 | %To combine vessel diameter along pericytes across animals
stimAllTrials=[];
allnames={
'Tser4954b_res_cfr.mat'
'Tser4954_res_cfr4.mat' %original _cfr was returning the same vessel measures as in 4954b;
'Tser5199_res_cfr.mat'
'Tser5072_res_cfr.mat'
'Tser5215_res_cfr.mat'
};
groupname='stimAllTrials';
all_rr1a_micro... |
9279fce3ff129c4203ed60d06c736e403c98d746408f980a9c58aa0e0d3a1ee0 | MATLAB | 6,336 | 238 | function [arclen,seglen] = arclength(px,py,varargin)
% arclength: compute arc length of a space curve, or any curve represented as a sequence of points
% usage: [arclen,seglen] = arclength(px,py) % a 2-d curve
% usage: [arclen,seglen] = arclength(px,py,pz) % a 3-d space curve
% usage: [arclen,seglen] = arc... |
a8a71241297804ea8dbe35d71e023482505ae0310282e34a86de2435bd38e173 | MATLAB | 6,337 | 184 | function plugin = plugin_getweb(type, pluginOri, mode)
if nargin < 1, help plugin_getweb; return; end;
if nargin < 2, pluginOri = []; end;
if nargin < 3, mode = 'merge'; end; % 'merge' or 'newlist'
% convert plugin list format if necessary
if isfield(pluginOri, 'plugin'), pluginOri = plugin_convert(pluginOri); end;
... |
e4d7614f36d663000f6d4d7b9d89df84d4e0a1644d7ef05713880099223c032c | MATLAB | 6,339 | 161 | function DataSimulationFunction(ModelParams,SeqParams,SimParams)
Sufix(1).name='BrainExtracted';
Sufix(2).name='';
savedata = 1;
B0_dir=[0 0 1];
gyro = 42.57747892;
modelname = SimParams.Output_dir ;
for BackGroundFieldRemoval = [1 2]
M0=load_nii(ModelParams.M0map_file);
R1=load_nii(ModelParams.R... |
07c3d92b51687e07e8f846ff4d407b24cf335296124089c99570b5787bbbd2fa | MATLAB | 6,340 | 155 | function [S_all, S_same, S_other, W_same, B_all, B_same, B_other] = segregation_by_type_eqcont(M, Ci, Ti, varargin)
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% segregation_by_type_eqcont.m
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% DESCRIPTION:
% ... |
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