sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
cf76d367d46cf5852389a884b43d733134d01ea0f13cf6fbe41c1fca9a54deeb | MATLAB | 906 | 31 | function plotMouseROIsCCF(dorsalMaps, allFOVs)
% Plots the ROI centroids colored by areas
% Figure
allenMapSMc(dorsalMaps) % Creates figure by itself
% Paper ready figure/axis formatting% Paper ready figure/axis formatting
panelwidth = 2.25;
panelheight = 3;
leftoffset = 0.5;
bottomoffset = 0.5;
formatFigure(gcf, pan... |
20dab410e69f4426272a81ba62a044bd1f1cc365d77704e440eb8262b50cbec7 | MATLAB | 907 | 38 | function [thetahat kappa] = circ_vmpar(alpha,w,d)
% r = circ_vmpar(alpha, w, d)
% Estimate the parameters of a von Mises distribution.
%
% Input:
% alpha sample of angles in radians
% [w number of incidences in case of binned angle data]
% [d spacing of bin centers for binned data, if suppl... |
c5e28c2c7c6c4e5983cd9e2f52b778c05d148fb4b63ca06fa081c5f572eac770 | MATLAB | 907 | 35 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% cor2mni
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function mni = cor2mni(cor, T)
% function mni = cor2mni(cor, T)
% convert matrix coordinate to mni coordinate
%
% cor: an Nx3 matrix... |
cc96a778e6660133bfeae98b4ae337cd214972bf7eff7505b34578cc05c8fd67 | MATLAB | 908 | 22 | function lead_sm = LeG_alignElecs(lead,d)
%"lead" is xyz coordinates (patient space mm) of contacts of a lead with
%deepest first (ground truth). "d" is intercontact spacing of contacts in
%mm. Spacing is adjusted between contacts to match "d". Next contact is
%placed "d" away from last in direction of average vect... |
d77c9cf0e9be418a571c0effa32602cc9220412aac0cb1aba9804bd1d49996c9 | MATLAB | 908 | 27 | function data=createdatamatc(data,E,Fs,win)
% Helper function to create an event triggered matrix from univariate
% continuous data
% Usage: data=createdatamatc(data,E,Fs,win)
% Inputs:
% data (input time series as a column vector) - required
% E (events to use as triggers) - required
% Fs (sampling ... |
aa9b0e8eb78ff2c3f65e9fc98c93d63b54086a044918d0872c00464b5be35003 | MATLAB | 909 | 32 | function A_normalized = normalize_matrix(A, normalization_method, a_norm)
% This function normlizes the columns of A
% A: the matrix to be normalized
% normalization_method: 'L2 norm' or 'unit abs';
% a_norm: norm
% Set defaut value for 'normalizationMethod'
if ~exist('normalization_method', 'var')
normalization_... |
96ba95b1c32f79ab843b503b180b69a42bfb32e1be15f16defc17bd18f5199fc | MATLAB | 910 | 26 | function [P bins] = ProbDist2D(x, nbins);
%PROBDIST2D
% Usage: [P bins] = [P bins] = ProbDist2D(x, nbins);
%
% This function calculates the discrete probability distribution for a
% variable that is in a two dimensional phase space. Because the variable
% exists in a two dimensional phase space, we have to bin in x... |
a723e773b1662b4139b3cf2f8aed95aa060c50c76dd57c116402816d622d177a | MATLAB | 910 | 21 | % This make.m is for MATLAB and OCTAVE under Windows, Mac, and Unix
try
Type = ver;
% This part is for OCTAVE
if(strcmp(Type(1).Name, 'Octave') == 1)
mex libsvmread.c
mex libsvmwrite.c
mex train.c linear_model_matlab.c ../linear.cpp ../tron.cpp ../blas/*.c
mex predict.c linear_model_matlab.c ../lin... |
c4f448967b0c61795750ec9fbfd7475ff98bbe4e2b52b6660b224db9fc7cc78a | MATLAB | 910 | 24 | function estimate = estimateWMmask(signal,tensor)
thres1 = 9/27;
thres2 = 0.25;
t3 = 0.8;
% thres1 = 9/27;
% thres2 = 0.25;
% t3 = 1;
%
% thres1 = 16/27;
% thres2 = 0.5;
idxb0 = find(squeeze(squeeze(tensor(1,1,:)+tensor(2,2,:)+tensor(3,3,:))) < 101);
idxb1 = setdiff(1:size(tensor,3),idxb0);
me... |
0bddb08396735341c96347aa068c14f81d92f80e62729c4db7b59dabb49ee8fe | MATLAB | 911 | 52 | function [new_item,new_item2, order] = sort_cells(varargin)
% Sorts two matrices by ordering the maximums of the first and using that
% order to rearrange both
% #1 = max, #2 = min
if nargin == 3
item=varargin{1};
item2=varargin{2};
num=varargin{3};
elseif nargin == 1
item=varargin{1};
item2=varar... |
4278db573b3ed71af2727266e95c4d6cd88056f2f1aa5ca6acef2a86ad05fb8b | MATLAB | 911 | 24 | function [adfreq, n, ts, fn, ad] = plx_ad_v(filename, ch)
import CMBHOME.PLX2Mat.*
% plx_ad_v(filename, channel): Read a/d data from a .plx file
%
% [adfreq, n, ts, fn, ad] = plx_ad_v(filename, ch)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% channel - 0-based channel number
%
% a/... |
ee5287611084fc4c485d277d0ac4a5bb0cb2ca2407a8250ee9b4d470267dfdc6 | MATLAB | 911 | 30 | function CBIG_waitUntilFinished(progressFile, noJobs)
% CBIG_waitUntilFinished(progressFile, noJobs)
%
% This is a helper function that holds off the next jobs until submitted
% jobs are finished. This is useful when the next batch of jobs depend on
% this submitted batch.
%
% Input:
% - progressFile:
% Text... |
e71471829b0203c3cf0b870c4acbf86e2c5c12d3c0ea1cc94ebcfea1a6e15b3a | MATLAB | 912 | 19 | function [data]=Trinh_addTriggerChannelBack(data,channels_to_interpolate,data_trigger)
% extracted from Giac_EEGinterpolate
% adds trigger channel back into the data
% created for adding Trigger Channel for MUSICOM WP4.1
% 12/10/22 Trinh Nguyen (IIT)
for ch_to_add = 1: length(channels_to_interpolate)
tmp_ch... |
2fe3c297c445bcf0e90776683f9205a763ae3996ecec7e446cdaeaadb5cb172f | MATLAB | 913 | 25 | function [order] = vertices_to_cw_polygon(x, y)
% VERTICES_TO_CW_POLYGON Sort a set of 2D points by angle around their
% centroid, so that they form a simple (non-self-intersecting) polygon.
%
% order = VERTICES_TO_CW_POLYGON(x, y) returns the permutation "order"
% such that x(order), y(order) traces the points in... |
cbf25d0194b9a28457c44869bb88425122b094e462de985efe194a459b893486 | MATLAB | 913 | 34 | function ea_fsl_reslice(input, reference, output, interp, verbose)
% Reslice images which are in the same space but with different resolutions
% using flirt.
% Overwrite the input image if no output name specified.
if ~exist('output', 'var')
output = input;
end
% Set default interp method to trilinear
% Can choos... |
ef451fcad3547ce46726e46bc78385d6a20ee793562c566764d9eaec3856b005 | MATLAB | 913 | 23 | % length() - length of memory mapped underlying array
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Nov. 2008
% Copyright (C) 2008 Arnaud Delorme, SCCN, INC, UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free So... |
1ba677a4cc68708d5d79ab93770be7f735ecaf46cd00e35df810bb60599f5958 | MATLAB | 914 | 36 | function data = readNPY(filename)
% Function to read NPY files into matlab.
% *** Only reads a subset of all possible NPY files, specifically N-D arrays of certain data types.
% See https://github.com/kwikteam/npy-matlab/blob/master/tests/npy.ipynb for
% more.
%
[shape, dataType, fortranOrder, littleEndian, tot... |
4987b85a19063b47ef21abf53a29ef978b3c904a9ff763a07f09289ec7961fe2 | MATLAB | 914 | 34 | function s = cvx_where
%CVX_WHERE Returns the location of the CVX system.
% CVX_WHERE returns a string containing the base directory of the CVX
% modeling framework. Within that directory are some useful
% subdirectories and files:
% functions/ new functions
% examples/ sample cvx models
%... |
7ac0dbb18eddd88ac6711076877d98dc7d14604473cdae75e914d8e00127c0ba | MATLAB | 914 | 14 | function paramBC = qualityParamValuesForUnitMatch(ephysMetaDir, rawFile, ephysKilosortPath, gain_to_uV, kilosortVersion)
% defaults
paramBC = bc.qm.qualityParamValues(ephysMetaDir, rawFile, ephysKilosortPath, gain_to_uV, kilosortVersion);
% unit match specific
paramBC.detrendWaveform = 0; % If this is set to 1, each ... |
a1533c3387866b9249609aaf1c8ec6a1fbe2a50c69deff1c1b10a6a984b60d9f | MATLAB | 914 | 33 | function [edges,idx,edgemap]=uniqedges(elem)
%
% [edges,idx,edgemap]=uniqedges(elem)
%
% return the unique edge list from a surface or tetrahedral mesh
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% elem: a list of elements, each row is a list of nodes for an element.
% elem can have 2, 3 or ... |
a21f3126f250718556ced8b95001f900b7447146377d8ef35184a3a2473c16e9 | MATLAB | 914 | 35 | function nedge=savegts(v,f,fname,edges)
%
% nedge=savegts(v,f,fname,edges)
%
% save a surface mesh to GNU Triangulated Surface Format (GTS)
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2011/02/23
%
% input:
% v: input, surface node list, dimension (nn,3)
% f: input, surface face element list, dimens... |
037eb8aa2ba1ac17184a2e369d7d439b775312c97e38d8183d73056e833079dd | MATLAB | 915 | 37 | function self = ShiftTrain(self, delta)
% Circularly shifts ALL spike trains by a given amount
%
% input:
% self: The original object, with self.cel set the cell desired to be
% shuffled.
%
%
% parameters:
% delta: Amount to shift the spike trains by. Can be positive or
... |
37edc6696e8b1e6a34ce89d852d8ba65cb93ac29125efa3053d3fc2eed0b724c | MATLAB | 915 | 27 | %% Figure 8 analysis
YOURDATAPATH = '';
% Load ROIs and border classifier data
fileList = searchFilesRecursive(YOURDATAPATH, 'allROIs.mat');
load(fullfile(fileList.folder, fileList.name))
% Using only cue-modulated
allROIs = allROIs([allROIs.modCue] == 1);
% Using only cells within the 5 main areas
areas = {'M2', 'M1'... |
5491b0f4e962aea9ecc7a5cb2f205ab3f1c4ec0e191c263877abf46c0eee6f41 | MATLAB | 915 | 43 | function lfband(fit,varargin)
% adds confidence bands around the plot of a locfit() fit.
%
% for 2-d fits, produces separate surface plots of upper and
% lower confidence limits.
%
% Bands are based on 95% pointwise coverage, using a single
% (i.e. global) estimate of sigma^2.
xfit = lfmarg(fit);
% placing 'band','g'... |
f2e2837bed2e029dfbf1a3100486004a4a1682cec451c28e559989dbcb3df21a | MATLAB | 915 | 31 | function settingFileFullPath = getSettingFileFullPath(functionName)
% settingFileFullPath
%
% Returns the full path of the settings file.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Version History
%
% 1.0.0.0:
% - Initial release.
%
% 1.1.0.0:
% - Updated to support... |
43e2ff875978b4b9064cc5aad65603b7fc6344c1a7f258e377025f98f1ab4869 | MATLAB | 916 | 26 | function d2=ea_options2tdhandles(tdhandles,d2)
try
allbackdrops=get(tdhandles.tdbackdrop,'String');
[~,bdix]=ismember(d2.backdrop,allbackdrops);
set(tdhandles.tdbackdrop,'Value',bdix);
if get(tdhandles.tdbackdrop,'Value')>length(allbackdrops) || get(tdhandles.tdbackdrop,'Value')<1
set(tdhan... |
5d35046026a0fcd06f05ada2be3d044de463868e7db5be9fc1555f8622103b7f | MATLAB | 916 | 27 | function Correct_all5D(headpath,fileexpnum)
%give this function the path of the folder you want to start in as headpath
%then give it the starter or the regex before the numbering starts
%iterates through all files and does the motion corretion using
%ADP_Motion_Correction5D
cd(headpath);
filelist=dir;
for k=1... |
7853e8833d7c41c226e4e68a5757b222dfa3f0388612e907407fe1c9d268a2d3 | MATLAB | 916 | 30 | %GetNextField - Get next field from a Batch object (iterator mode).
%
% This is a helper class to easily read and parse batch files.
%
% USAGE
%
% [b,field] = GetNextField(b);
%
% b batch object
% Copyright (C) 2007 by Michaël Zugaro
%
% This program is free software; you can redistribute it and/or... |
279fdd78fef116f55dbe8713a6b6eab9c0a9888c93da19a559bca9c781783eb5 | MATLAB | 917 | 29 | function allROIs = getLogProbsAllROIsGMM(allROIs, model, metricField)
% Computes log probabilities for all neurons under area-agnostic GMM
% components
% Get metrics z-scored for all neurons
switch metricField
case 'PCs'
metrics = cat(1, allROIs.PCs);
metrics = metrics ./ std(metrics); % z-score
... |
3c90926bf4de24ad52d890f4928945fa6d184272d5902e67d9f232088e462c71 | MATLAB | 918 | 46 | function pval = circ_medtest(alpha,md)
%
% [pval, z] = circ_medtest(alpha,w)
% Tests for significance of the median.
% H0: the population has median angle md
% HA: the population has not median angle md
%
% Input:
% alpha sample of angles in radians
% md median to test for
%
% Output:
%... |
554399b14106f1d76e5d4ae9dab7425662e4ec459d79fc98dedf1c0d4e333333 | MATLAB | 919 | 23 | function x = sym( x )
% SYM Symmetrize.
% SYM(X), where X is a matrix, returns the symmetric or Hermitian part
% of X; that is, SYM(X) = 0.5 * ( X + X' ). If X is an array, SYM(X)
% symmetrizes each of the submatrices X(:,:,k). X must satisfy
% size(X,1) = size(X,2).
%
% SYM(X) is useful in CVX when... |
4229f5e1678af2fb13b1bf315df7e8d67c71c67bd675db7c386bfd1078c04c3a | MATLAB | 920 | 42 | function load_scope(files,refresh_rate,sample_frequency)
close all
shot_size=round(sample_frequency/refresh_rate);
ring=zeros(shot_size*20,1)';
fig = figure('Position',[500,500,800,600],...
'NumberTitle','off',...
'Name','Scope',...
'doublebuffer','on',...
'HandleVisibility','on',...
'... |
65e3e5ae3fb67a4a11c1e3c00d407aa6b09f9d5ce001db7fcc13c500a7627f9a | MATLAB | 920 | 24 | function binnedGrid = binVals2D(values, positions, xEdges, yEdges)
% Computes a cell array of binned values based on their 2D locations and
% the geometry of a grid
nX = length(xEdges) - 1;
nY = length(yEdges) - 1;
binnedGrid = cell(nY, nX); % grid is formatted like an image
% Iterate all points and assign them to a ... |
b2cdeca3c74c2d840628327f29d86514bd5db1ca3c16253723db255931b46932 | MATLAB | 920 | 35 | function fwrite3(fid, val)
%
% fwrite3.m
%
% Original Author: Bruce Fischl
% CVS Revision Info:
% $Author: nicks $
% $Date: 2007/01/10 22:55:09 $
% $Revision: 1.2 $
%
% Copyright (C) 2002-2007,
% The General Hospital Corporation (Boston, MA).
% All rights reserved.
%
% Distribution, usage and copying of thi... |
e2427173b798a8af8118d9c0e6a970271245b3ffd66f187940482efc2974e1df | MATLAB | 920 | 45 | function x = cvx_r2c( x, dim )
%
% Quick exit for complex quantities
%
if ~isreal( x ),
error( 'Matrix must be real.' );
end
%
% Determine expansion dimension
%
sx = size( x );
if nargin < 2,
dim = [ find( sx > 1 ), 1 ];
dim = dim( 1 );
elseif ~isnumeric( dim ) || dim <= 0 || dim ~= floor( dim ),
er... |
1c23ed49dd964f44220731d88d7c027cd9bfefddb29d11461fc5110c53af0264 | MATLAB | 921 | 27 | % Functions enabling use of multiple colormaps per figure.
%
% version 2.3, 3/2007
%
% freezeColors - Lock colors of plot, enabling multiple colormaps per figure.
% unfreezeColors - Restore colors of a plot to original indexed color.
%
% demo/html
% freezeColors_pub.html - Published demonstration.
%
% te... |
1c7c7365cbec2fdbe0c2ee52949756040bb36c68b784f05fc6f67505afa27eec | MATLAB | 921 | 43 | function vol=volzAdj1(vol,adjv,env)
% Usage ... y=volzAdj1(vol,adjvec,env)
vdim=size(vol);
if nargin<3, env=ones(vdim(end),1); end;
if length(env)==1,
env=(1-[1:vdim(end)]/(vdim(end)/env));
plot(env)
elseif length(env)==2,
tmpenv=(1-[1:vdim(end)]/(vdim(end)/env(1)));
tmpenv=exp(tmpenv*env(2));
env=tmpenv;
... |
60d3ce08a9cd629aad0110c115c6fbe1ea2161e6c4ec910508c6c838f8c41155 | MATLAB | 921 | 39 | function frame = getnext(vr)
%FRAME=GETNEXT(VR)
% This method is a shortcut for
% if (next(vr))
% frame = getframe(vr);
% else
% frame = [];
% end
%
% Although this method can be more convenient than calling NEXT and GETFRAME
% separately, there is no way to distinguish between a zero-si... |
7625a8b31248fbb330b31358faa56ab71fcd25efbd98aab9c4a7e82a24389583 | MATLAB | 921 | 34 | function surf2parcel = surface_to_parcel(surf_data, parcellation)
%
% Usage:
% surf2parcel = surface_to_parcel(surf_data, parcellation)
%
% Description:
% Map surface data to a parcellation (authors : @MICA-MNI, @saratheriver)
%
% Inputs:
% surf_data (double array) - Surface vector, size = [v x 1].
% parcellati... |
1b24bcfb23dc5c050891368e98fb04893a2b95852e33beb27ab37f20cacc5b87 | MATLAB | 922 | 26 | function s = cvx_subsref_check( nin, nin_norm, S )
if nin < nin_norm,
s = 'Not enough input arguments';
elseif nin == nin_norm,
if ~isa( S, 'struct' ),
s = 'Subscript argument to SUBSREF and SUBSASGN must be a structure.';
else
Sf = fieldnames( S );
if length( Sf ) ~= 2,
... |
b99b96a7ab6814e83df20be37e7dc04b6b6b69e29ed1e804009a20fab38568ab | MATLAB | 922 | 31 | function uid = root(tree)
% XMLTREE/ROOT Root Method
% FORMAT uid = root(tree)
%
% tree - XMLTree object
% uid - UID of the root element of tree
%
% Return the uid of the root element of the tree.
%
% See also XMLTREE
% By construction, root is necessarily the element whos UID is 1.
% However, xml_parser should... |
feee994e54a8628475d15b40128eb8965d84d31a9875add0c4ecdd020a09a50c | MATLAB | 922 | 34 | function ops = align_iterative_modified(data, ops)
fracImgPreAlign = getOr(ops, 'fracImgPreAlign', 1/2);
maxImgPreAlign = round(size(data,3) * fracImgPreAlign);
ops.mimg = pick_reg_init(data);
dsold = zeros(size(data,3), 2);
err = zeros(ops.NiterPrealign, 1);
%%
tempSubPixel = ops.SubPixel;
ops.SubPixel = Inf;
for i... |
39ea7e71ced820a469b886ccb505ae073e50aa835c0b8b027b122e9c993039e3 | MATLAB | 923 | 30 | function data=createdatamatpb(data,E,Fs,win)
%
% Helper function to create an event triggered matrix from a single
% channel of data.
% Usage: data=createdatamatpb(data,E,Fs,win)
% Inputs:
% data (input time series as a single vector) - required
% E (events to use as triggers) - required
% Fs (samp... |
9b8cdbd442180de9b53f625cd931f5b7abfafeed26ca97c62b68b4a74a422537 | MATLAB | 923 | 30 | function s = semedian(x,varargin)
%semedian - Compute standard error of the median.
%
% USAGE
%
% s = semedian(x)
%
% x vector or matrix over which the error should be computed
% Copyright (C) 2013 by Michaël Zugaro
%
% This program is free software; you can redistribute it and/or modify
% it unde... |
58b9bad6430bb41d1681286f289dece87df4891c1352475b8cc5873de8653b83 | MATLAB | 924 | 29 | function outpoints = mni2tal_brett(inpoints)
% Converts coordinates from MNI brain to best guess
% for equivalent Talairach coordinates
% FORMAT outpoints = mni2tal(inpoints)
% Where inpoints is N by 3 or 3 by N matrix of coordinates
% (N being the number of points)
% outpoints is the coordinate matrix with Talairach ... |
b28d2a94f1e059612e4cc5d201eddb06c1459c7eea6d57edeb3eed9dac4f1a37 | MATLAB | 924 | 36 | function val=jsonopt(key,default,varargin)
%
% val=jsonopt(key,default,optstruct)
%
% setting options based on a struct. The struct can be produced
% by varargin2struct from a list of 'param','value' pairs
%
% authors:Qianqian Fang (q.fang <at> neu.edu)
%
% input:
% key: a string with which one look up a value fro... |
d75be38d6cd8afce52e7a14d2980c20a664605ae4b1590e3e8d9895c2b6755d9 | MATLAB | 924 | 33 | function pred=ea_predict_Bmap(bmap,connfile,sk,usemask)
if ~exist('sk','var')
sk='';
end
if ~exist('usemask','var');
usemask='';
end
[pth,fn,ext]=fileparts(bmap);
b1=ea_load_nii(bmap);
intercept=ea_load_nii(fullfile(pth,[fn,'_intercept',ext]));
if exist(fullfile(pth,[fn,'_deviation',ext]),'file')
dev=ea_l... |
afcb2f32d1f1be770398c9ce060f0f8a7572286bce59dd6676172c932e167295 | MATLAB | 925 | 14 | % Chapter 7: Statistical estimation
%
% counting_problem_poisson.m - Section 7.1.1: Counting problems with Poisson distribution
% ML_covariance_est.m - Section 7.1.1: Covariance estimation for Gaussian variables
% probbounds.m - Section 7.4.3: Probability bounds example with Voronoi diagram
% e... |
4ec5ffc685885ed95b5e0459ad04f611f3e33058ab73612f79dbc22ce57903d8 | MATLAB | 926 | 31 | function child = children(tree,uid)
% XMLTREE/CHILDREN Return children's UIDs of node uid
% FORMAT child = children(tree,uid)
%
% tree - a tree
% uid - uid of the element
% child - array of the UIDs of children of node uid
%__________________________________________________________________________
%
% Re... |
bae8fbf8880c16a104541aae0f2bace3603e1d4a9ab3a80080853421424da51c | MATLAB | 926 | 35 | function cleanimg=deislands3d(img,sizelim)
%
% cleanimg=deislands3d(img,sizelim)
%
% remove isolated islands for 3D image (for each slice)
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% img: a 3D volumetric image
% sizelim: maximum island size (in pixels) for each x/y/z slice
%
% output:
% c... |
768df46abcf9d3d04b872082724670370f45be3dbf4c9b6481eab2c72c67e326 | MATLAB | 928 | 26 | function handles = refreshspine(handles)
roi_cent = handles.roi_seed;
spId = [];
if ~isempty(handles.dendrite)
for k = 1:length(handles.dendrite)
dend_outline = handles.dendrite(k).dend_outline;
if ~isempty(dend_outline)
in_dendr = inpolygon(roi_cent(:,1), roi_cent(:,2), dend_outline(:,1... |
7e0f86c490eae8776b7820d193720f5069481086cd853f86e68ae6d3b7a55d57 | MATLAB | 928 | 24 | function [event] = PL2EventTs(filename, channel)
% PL2EventTs(filename, channel): read event timestamps from a .pl2 file
%
% [event] = PL2EventTs(filename, channel)
% [event] = PL2EventTs(filename, 1)
% [event] = PL2EventTs(filename, 'KBD2')
%
% INPUT:
% filename - if empty string, will... |
d9d80dff2cce09893cd019f7593c6efbae4b58d9535b60dd6af7afe634e4fa28 | MATLAB | 928 | 40 | function slicebw=ea_centralcomponent(slicebw,mask,options)
%% determine mask center:
[yy,xx]=find(mask);
maskcenter=[mean(xx),mean(yy)];
stats=ea_conncomp(slicebw);
if stats.NumObjects>1
maxdist=10000;
for i=1:stats.NumObjects
if length(stats.PixelIdxList{i})>10
sliceobj=slicebw;
... |
5eb1f9a2e04cd6a1bedb31ca7418cd5ce80275721f0c2d54c5c796e686e5a6df | MATLAB | 929 | 30 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% demo script for mesh generation from binary volumetric image
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% preparation
% user must add the path of iso2mesh to matlab path list
% addpath('../');
% user need t... |
b51b1a143ca0e5ae683b5eba583d1bd177df8785531769982c7cbf0fc9f95775 | MATLAB | 929 | 34 | function disp(obj)
% Display a file_array object
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: disp.m 4136 2010-12-09 22:22:28Z guillaume $
if numel(struct(obj))>1,
fprintf(' %s object: ', class(obj));
sz =... |
593465b83f6ed39d83aed959ae3dc1c9df8abfb1621813b0bd51f8499fc3faf4 | MATLAB | 930 | 40 | function [hF, tl] = fig(layout, position, color)
% Set tick dir out for all figures, sets for system for consistency
set(groot,'defaultAxesTickDir', 'out');
set(groot,'defaultAxesTickDirMode', 'manual');
set(groot,'defaultAxesYColor', [0,0,0]);
set(groot,'defaultAxesXColor', [0,0,0]);
% Figure out how to turn "Box" o... |
a0ed59e91b8eb1ffe20c94bb7d4a1bbfe09f9eace67628d49046bf579656b0d7 | MATLAB | 930 | 41 | function [r mu] = circ_axialmean(alphas, m, dim)
%
% mu = circ_axialmean(alpha, w)
% Computes the mean direction for circular data with axial
% correction.
%
% Input:
% alpha sample of angles in radians
% [m axial correction (2,3,4,...)]
% [dim statistic computed along this dimension, 1]
%
% ... |
2f1161e764df3c2acfaacb05660ce646ff9f0f75ebb03becf410dbd0b983841c | MATLAB | 931 | 29 |
% img = image on which to overlay heatmap
% heatmap = the heatmap
% (optional) colorfunc .. this can be 'jet' , or 'hot' , or 'flag'
function omap = heatmap_overlay( img , heatmap, colorfun )
if ( strcmp(class(img),'char') == 1 ) img = imread(img); end
if ( strcmp(class(img),'uint8') == 1 ) img = double(img)/255; en... |
8eb129ad0b8575d31483c120c9ac7a64a3d5285afa4384138ce83c77d11752e9 | MATLAB | 931 | 34 | function [ y, symm ] = cvx_s_hermitian( m, n, symm ) %#ok
%CVX_S_HERMITIAN Complex Hermitian matrices. This is no longer used by
%cvx_create_structure, but it is used by cvx_sdpt3.
if m ~= n,
error( 'Hermitian structure requires square matrices.' );
end
nsq = n * n;
c = 0 : n - 1;
c = c( ones( 1, 2 * n ), : );... |
b13b223785339ea42579f97c5333a90d68860b8cfa36af18f165cc66942e739f | MATLAB | 931 | 35 | %% Demo of the KDRANGEQUERY function.
%%
%% Guy Shechter
%% guy at jhu dot edu
%% June 2004
%% Generate a set of 1000 reference datapoints in R^2
ReferencePts = rand(1000,2);
%%% Build the k-d Tree once from the reference datapoints.
[tmp, tmp, TreeRoot] = kdtree( ReferencePts, []);
%%% and find all the poi... |
3e3e54070066271c77fd9abcd5d2858cf170e4f1861bf60699d6b294405abb9e | MATLAB | 932 | 38 | function [ real_matrix , perm_matrix ] = subfun_GenerateNetworkCalcMatrix_PermMatrix( Par_parcels , Net_parcels )
%
%% merge and delete 0 value
parcels = [Par_parcels Net_parcels];
parcels(parcels(:,1)==0,:) = [];
parcels(parcels(:,2)==0,:) = [];
Max_label = [max(Par_parcels),max(Net_parcels)];
%% calc real matrix
rea... |
4700d62e02c13f3737ad6dadbb4f3530ad4451a65c41af6cc104b85a8c548f86 | MATLAB | 932 | 36 | function savetetgenele(elem,fname)
%
% savetetgenele(elem,fname)
%
% save a mesh tetrahedral element list to tetgen .ele format
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% elem: tetrahedral element list, dimension (ne,4)
% columns beyound the 4rd column are treated as
% marke... |
7bff5cf3c1a141194c4e294e0d9416dc30450e686cf5ba9a4dd566e049a60a43 | MATLAB | 932 | 22 | function z = ldivide( x, y )
%Disciplined convex programming information for LDIVIDE:
% For DCP purposes, the LDIVIDE division operator X.\Y is equivalent to
% (1./X).*Y. The left-hand term must be constant and non-zero; and if the
% right-hand term is nonlinear, t constant must also be real.
%
%Disciplined geom... |
89cb356a61383a83a85ec85988565b2ba4704ead9a94619371d3cfd0201f0c76 | MATLAB | 932 | 31 | function [N,C]=check_consistency(data1,data2,sp)
% Helper routine to check consistency of data dimensions
% Usage: [N,C]=check_consistency(data1,data2,sp)
% Inputs:
% data1 - first dataset
% data2 - second dataset
% sp - optional argument to be input as 1 when one of the two data sets is
% spikes times stored as... |
f18a1572cdb73d203742338cc11f79589da956bf6506f2453f43efabfb467de3 | MATLAB | 932 | 15 | function [] = NETCDFdisplay(filename)
%NETCDFDISPLAY
% [] = NETCDFdisplay(filename) displays information about specified SOFA file
% SOFA API - function netcdf/NETCDFdisplay
% Copyright (C) 2012 Acoustics Research Institute - Austrian Academy of Sciences
% Licensed under the EUPL, Version 1.1 or – as soon the... |
2c06b278cabd1cf39f96279f5adb3b0ada326d44f0cfbcbf3cbef1a130c688ea | MATLAB | 933 | 41 | %%********************************************************
%% Arrow:
%%
%% Fx = Arrow(pblk,f,x,options);
%%
%% if options == 0;
%% Fx = Arr(F)*x
%% if options == 1;
%% Fx = Arr(F)^{-1}*x
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%********... |
ee7e7650ffb5a1fb158c149e223feca0b61d693ace85d86243fcf1896a1dded4 | MATLAB | 933 | 27 | function sz = cvx_size_check( varargin )
%CVX_SIZE_CHECK Verifies size compatability.
% SZ = CVX_SIZE_CHECK( ARG1, ..., ARGN ) verifies that the arguments are
% compatible in size in the same sense as required by the + operator.
% That is, any arguments that are not scalars must be of the same size.
% No typ... |
650c1fdb38abfbe6967f3a3df87d17264f3a2153cb45321269b5d6beabdd9a3b | MATLAB | 934 | 33 | %% Figure 1 main
YOURDATAPATH = '';
%% Load ROI data and Allen CFF
fileList = searchFilesRecursive(YOURDATAPATH, 'infoFOVs.mat');
load(fullfile(fileList.folder, fileList.name))
fileList = searchFilesRecursive(YOURDATAPATH, 'allROIs.mat');
load(fullfile(fileList.folder, fileList.name))
load('allenDorsalMap.mat');
%% P... |
6938ff154a66e13b2f3f5f75a188855e47f584c2b083b447fefc42e18ad3966b | MATLAB | 934 | 30 | function res = PFNpc_integ2(params,inputs,inits)
% This one doesn't have any effect of MS on tau. Compare to PFNpc_integ.m
% params = array where first row is AF, second row is OF
% inputs = array where:
% [ AF directions;
% AF speeds;
% OF directions;
% OF speeds;
% time ]
% Calculate single... |
1a6d79b7275d9bb7e7b453ede18fa19cbdfd76799247a6f75ef6552b7471791b | MATLAB | 935 | 26 | function [P bins] = ProbDist2D(x, nbins);
%PROBDIST2D
% Usage: [P bins] = [P bins] = ProbDist2D(x, nbins);
%
% This function calculates the discrete probability distribution for a
% variable that is in a two dimensional phase space. Because the variable
% exists in a two dimensional phase space, we have to b... |
4da08bf8232ffc0be7ba8a323939ef77c6f3c1a21a24c546c26fa4f61994e36e | MATLAB | 935 | 23 | function ea_exportfiducials(options, filename)
% Save fiducials as comma separated value file in patient folder
% Last Revision: 10/04/2018
% Thushara Perera (c) 2018 Bionics Institute
% Input:
% - lead dbs options struct
% - filename with extension *.fcsv for Slicer or *.csv for Excel
% Output:
% - fiducial ... |
8ad0fa72374f144453ba03ae75bd63a8294ecdfdefab401cfdb3d62da200cced | MATLAB | 935 | 38 | % Local Regression and Likelihood, Figure 8.3.
%
% Discrimination/Classification, iris data for different
% smooting paramters.
%
% Note that the iris.mat file contains the full iris dataset;
% only Versicolor and Virginica are used in this example.
%
% The `Species' variable contains species names. `Specn' has
% them ... |
e62b908bf6f3d881e368abdecd9da01409339cbf0a06c7c14c6701b341686bb3 | MATLAB | 935 | 23 | function binnedmatrix = toy_simulation(Network_opts,Assembly_opts)
% creating matrix
binnedmatrix=poissrnd(Network_opts.meanspikebin,[Network_opts.nneurons Network_opts.nbins]);
allassemblyneurons = unique([Assembly_opts.assembly_neurons{:}]);
nonassemblyneurons = setdiff(1:Network_opts.nneurons,allassemblyneu... |
5cfe00b39f94a677ff51a92a68ab62241134440544a45787caa65aceb94180cb | MATLAB | 937 | 32 | function data=change_row_to_column(data)
% Helper routine to transform 1d arrays into column vectors that are needed
% by other routines in Chronux
%
% Usage: data=change_row_to_column(data)
%
% Inputs:
% data -- required. If data is a matrix, it is assumed that it is of the
% form samples x channels/trials and it is ... |
b9748e85f398c02bbb8dec9a7ab252b15dba38df17b075834788f4d66c6c96be | MATLAB | 937 | 31 | function DownsampleRecordingTo1000Hz(animal, srate, numchans)
%Inputs/Requirements: animal ID, sampling rate (25000kHz here), total number of channels
%LFP\Full folder in animal's analysis directory (exp_dir) must contain full
%LFP files for each channel.
%Output: LFP\LFP1000 folder containing downsampled LFP f... |
c93a0b98ab916e7c504dc7d2d9be98cb88bd25428113789a5d4e35ead03f913a | MATLAB | 937 | 30 | function outmap = cifti_diminfo_make_series(nummaps, start, step, unit)
%function outmap = cifti_diminfo_make_series(nummaps, start, step, unit)
% Create a new series diminfo struct.
%
% Only the nummaps argument is required.
if nargin < 2 || isempty(start)
start = 0;
end
if narg... |
d547d3239c731882569566c488ca763461df68a1014ea797b6f499021f7f1845 | MATLAB | 937 | 31 | %% Entropy Demo 2
% This demo goes through calculating the entropy using a single discrete
% time series.
% Data Type: Discrete
% Number of Variables: 1
% Information Analysis: Entropy
% Trial Based or Single Trial: Single Trial
% Significance Testing: N/A
% Delays: N/A
% Generate the data
nData = 100;
data = randi(... |
2267e00cb3f27c9a0ac7a4848256f1b356bb8801601dba42cfdd05a45bedb2a8 | MATLAB | 939 | 28 | function bn = bacon_numbers(A,u)
% BACON_NUMBERS Compute the Bacon numbers for a graph.
%
% bn = bacon_numbers(A,u) computes the Bacon numbers for all nodes in the
% graph assuming that Kevin Bacon is node u.
% allocate storage for the bacon numbers
% the ipdouble call allocates storage that can be modified in... |
9a48c388a810f5266bfad0db162f0a1f00156434a3328f36a546d2f9cd8d676a | MATLAB | 939 | 32 | function vals=ea_corrsignan(vals,ps,obj)
allvals=cat(1,vals{:});
allps=cat(1,ps{:});
nnanidx=~isnan(allvals);
numtests=sum(nnanidx);
switch lower(obj.multcompstrategy)
case 'fdr'
pnnan=allps(nnanidx); % pvalues from non-nan value entries
[psort,idx]=sort(pnnan);
pranks=zeros(length(psort),... |
d3d8b22e75146bf5c0286c9a3ba8b275f9b3720530196d87a9b3a00faafd94b3 | MATLAB | 939 | 30 | function y = base64(action,x)
% Base64 binary-to-text encoding/decoding scheme
% FORMAT y = zstream('encode',x)
% x - data stream to encode (uint8)
% y - Base64-encoded data stream (uint8)
% FORMAT y = zstream('decode',x)
% x - data stream to decode (uint8)
% y - Base-64 decoded data stream ... |
0f294d9b846df4b140b1880279b82b344efbcc6f87aa6ac1bb415be12ee32643 | MATLAB | 941 | 33 | function [eig_vec, eig_val] = calc_network_eigenmode(network, num_modes)
% calc_network_eigenmode.m
%
% Calculate the eigenvectors (eigenmodes) and eigenvalues of the input
% network
%
% Inputs: network : symmetric connectivity matrix [N x N]
% N = number of row/columns
% num_modes : numb... |
994b569252032184521c43a75fe9a78ab283ab7f48fcb027371d085dd2c85271 | MATLAB | 941 | 29 | function out=ea_query_sim_connectomematrix(seedmap,connectomename,outputfname)
% Function to create invert map as used in Li & Hollunder 2021 Biol. Psychiatry
s=ea_load_nii(seedmap);
seed=s.img(:);
out=s;
out.fname=outputfname;
C=matfile([ea_space([],'connectomes'),'fMRI',filesep,connectomename,filesep,'AllX.mat'],'W... |
b5790bd6b6352315d01e34924c517495c6b144f208b7ad10d6a49dfec66d90d5 | MATLAB | 941 | 25 | function embedded = embed(timeseries, lag, D)
%EMBED Time-series lag embedding.
% EMBEDDED = EMBED(TIMESERIES, LAG_SAMPLES, DIMENSION) takes a scalar
% (M x 1) time series and returns a vector time series of dimension
% ((M - lag_samples*(dimension-1)) x dimension) time series by lag
% embedding the... |
6b3f1d784e3df5a1228f2879862570a9d24f3c107e235efd1da1a13ada20830b | MATLAB | 942 | 36 | %%***************************************************
%% min sum_k bk*yk
%% s.t. sum yk*Hk <= 0
%% y1 = 1
%% Hk = -hankel(ek) if 1 <= k <= n
%% = -hankel(0,e(k-n+1)) if n+1 <= k <=2*n-1
%%
%% [blk,At,C,b] = sdphankel(n);
%%***************************************************
function [blk,At,C,b] = sdp... |
7af8fd166c051085d244b635df775baff94df3d723fcc44e98f2708f2cba4a2d | MATLAB | 942 | 51 |
%
% for each delta in deltas , adds map
% delta binary orders smaller to A
% stacks dimensions of maps in A
%
function [ Apyr , dims ] = formMapPyramid( A , deltas )
my_eps = 1e-12;
num_deltas = length(deltas);
max_delta = max(deltas);
num_pyr = 1 + num_deltas;
dim = [ size(A) num_pyr ];
Apyr = zeros( dim ... |
a9ed0753b8ab57aca2d9e1059761c0cc1d5e8425d2828599b7df60c5c71d3fb7 | MATLAB | 942 | 22 | function ClincFreq_Norm2MNI_T1_clinc(indat,inroi,outdir,outname,voxelsize,pth)
[patdat,namdat,extdat] = fileparts(indat);
% [patroi,namroi,extroi] = fileparts(inroi);
% load([pth,filesep,'Norm2T1_segment.mat']);
load([pth,filesep,'Norm2T1_clincal.mat']);
pathspm = which('spm.m');
[patspm,namspm,extspm] = fileparts(pat... |
290a150b383a7ba204c1f4f98e6a0d53693a6ddde9f31f4cf08e88edb7e0ab7e | MATLAB | 943 | 38 | function setXYLim(ax, setX, setY, spacers)
% Makes the axis limits for X and Y fit the data plotted
if nargin < 4
spacers = [0, 0, 0, 0]; % No space between axis and data
end
% Allocate for XY data
locs = [];
for ob = ax.Children'
% Switch on what kinds of objects we could get
if isprop(ob, 'Position')
... |
6fd08dfcdf286d8bf156267b1842ceeeb6e7407e24820ff115e5ac2f2efa37c0 | MATLAB | 943 | 33 | function vr = close(vr)
%VR=CLOSE(VR)
% Closes video VR and releases any system resources necessary to access it
% (e.g. threads, file handles, etc.). Do NOT just clear a videoReader
% object without first closing its handle:
%
% % BAD code--typically will leak system resources
% vr = videoReader(...);
% .... |
03ef9eff603b9c53243e51f47e6d59fd3db2fed30d3b6d959d081b41193e212a | MATLAB | 944 | 37 | function value = get(tree,uid,parameter)
% XMLTREE/GET Get Method (get object properties)
% FORMAT value = get(tree,uid,parameter)
%
% tree - XMLTree object
% uid - array of uid's
% parameter - property name
% value - property value
%
% Get object properties of a tree given their UIDs.
%
% See also XML... |
10ac7190f6022ad98427589fc709cd68403cf87858ac510634cdd08ca5f4da33 | MATLAB | 944 | 35 | function a = autocorr(x,Q,dim)
%AUTOCORR Perform autocorrelation via FFT
%
% IOSR.DSP.AUTOCORR(X) performs autocorrelation via FFT on vector X. For
% matrices, the autocorrelation is performed on each column. For N-D
% arrays, the autocorrelation is performed on the first non-singleton
% dimension.
%
% IOSR... |
299b9b109af1710c29d596337b2649325a1274cfa3a103f259162a07e2e91a23 | MATLAB | 944 | 42 | function [signals, PC, V, data] = pca1(data)
% PCA1: Perform PCA using covariance.
%
% Usage:
% [signals, PC, V] = pca1(data)
%
% data (in) - MxN matrix of input data
% (M dimensions, N trials)
% signals - MxN matrix of projected data
% PC - each column is a principal component
% V ... |
3fd2f5877eaf2acc215f225b6b9b4aeca80bc47f40be5dd551fe774cb0f69a13 | MATLAB | 944 | 38 | function [ catabledim ] = bz_FindCatableDims( tryarrays )
%UNTITLED Summary of this function goes here
% Detailed explanation goes here
%
%INPUT
% tryarrays cell array of arrays you'd like to try to concatenate
%
%OUTPUT
% catabledims dimensions along which you can concatenate
%
%DLevenstein 2018
%%
%Remove any... |
5af7369c68353b429bc1d86354262ce5e696acb39ea225daffee6522a0ad5005 | MATLAB | 944 | 40 | function [diffData2] = circDiff(data,dim,type)
% function [diffData] = circDiff(data,dim,type)
%
% computes the difference between each point accounting for the
% fact that the values are circular.
% INPUTS:
% data - circular data type vector or matrix
% dim - dimension to operate on, default=1
% type - 'deg' or '... |
91b0df804eb481b489499cb39364f26a5456698c07f8492da7fec66d8be36c29 | MATLAB | 944 | 20 | %% invPolyArcLength3 - Numerically calculate the parameter (t) of parameterized [0,1] -> R^3 polynomial
% *given* an arc length (measured from 0) i.e. find the corresponding t to an arc length
% (e.g. given in [mm] from the origin) or in other words numerically invert polyArcLength3
%
% Andreas Husch
% Centre Hospitali... |
c24a2beb3dd7da6feeb54fad4720bbe14d5cfe9ddd6e0bc73c982a811b76b8fd | MATLAB | 944 | 26 | function ea_Amap(varargin)
% creates a simple weighted average map ("weighted average" map in Horn
% 2017 AoN). Supply empty regressor var to create unweighted average
% map.
% ea_Amap(fis,regressor,outputname,mask,sk) % sk can be 'k','s','sk'
% for smoothing and normalization options. Mask onl... |
283ac7e957ee3b42512c7b82a7fc3add946d21b041d5ffede8d2fdff82c92f77 | MATLAB | 945 | 38 | function lx = makeLocationMap( dims , nam , N )
Nmaps = size(dims,1);
lx = zeros(N , 2^13 + 3 );
px = {};
for i = 1 : Nmaps
px{i}.r = partitionindex( dims(1,1) , dims(i,1) );
px{i}.c = partitionindex( dims(1,2) , dims(i,2) );
end
for i = 1 : Nmaps
for j = 1 : dims(i,1)
for k = 1 : di... |
31decf7a15c97d4fe24a383f7d99495f90b7dd818d71fe9673bf22b63e6e364b | MATLAB | 946 | 26 | function itd = azimuth2itd(azimuth,f)
%AZIMUTH2ITD Convert azimuth in degrees to ITD
%
% ITD = IOSR.AUDITORY.AZIMUTH2ITD(AZIMUTH,F) converts the azimuth AZIMUTH
% in degrees at frequency F to interaural time difference according to
% Kuhn's model [1].
%
% References
%
% [1] Kuhn, G.F. (1977), Model for the... |
49b8c7a67a5c84882e1d19cabeb9af5062eb0efb5f792e26eec3e80f52bc78d2 | MATLAB | 946 | 30 | function flag=deletemeshfile(fname)
%
% flag=deletemeshfile(fname)
%
% delete a given work mesh file under the working directory
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% fname: specified file name (without path)
%
% output:
% flag: not used
%
% -- this function is part of iso2mesh toolbox (h... |
016f9701e8dfedb935bf5ae4ea1520f68e4b4b348a03705c398483abf062c5c9 | MATLAB | 947 | 34 | % Section 4.6.3: Find the fastest mixing Markov chain on a graph
% Boyd & Vandenberghe "Convex Optimization"
% Joëlle Skaf - 09/26/05
%
% The 'fastest mixing Markov chain problem' is to find a transition
% probability matrix P on a graph E that minimizes the mixing rate r, where
% r = max{ lambda_2, -lambda_n } with la... |
2cae875e5ec2ff66ad62a25b163715e668874d4f4d1bffbec2e992ec20101e2e | MATLAB | 948 | 29 | %%***************************************************************
%% convertRcone: convert rotated cone to socp cone
%%
%% [blk,At,C,b,T] = convertRcone(blk,At,C,b);
%%
%%***************************************************************
function [blk,At,C,b,T] = convertRcone(blk,At,C,b)
T = cell(size(blk,1),1);
for p =... |
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