sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
8d88533d921b96418ffc8dcc79840f1ea96aa265acaad80bb8b747d4bf661b9e | MATLAB | 1,455 | 38 | function [strucMatrix_ctx, strucLabels_ctx, strucMatrix_sctx, strucLabels_sctx] = load_sc(parcellation)
%
% Usage:
% [strucMatrix_ctx, strucLabels_ctx, strucMatrix_sctx, strucLabels_sctx] = load_fc(parcellation)
%
% Description:
% Load structural connectivity data (author: @saratheriver)
%
% Inputs:
% parcellati... |
e4a2e366e983df4118fe586e33629979a5460fdebf6854af6e826a6027f418f0 | MATLAB | 1,455 | 40 | function [ params ] = data_analyze( e,s,b,TYPE )
%DATA_ANALYZE Summary of this function goes here
% Detailed explanation goes here
globalsConditions;
close all;
optionsMinsearch = optimset('MaxFunEvals',50000, 'MaxIter',50000, 'TolFun',1e-12, 'TolX',1e-12);
pInit = [0 0.5]; pLow = [-360 -1]; pHigh = [360 2]; angle = ... |
fd885b4977cc600fba4c906f2ef6f0398738b09135c8846b507f76309c89351c | MATLAB | 1,455 | 42 | function plotAllTraces(data,typerange,figtitle,Ylimits,colorset)
% This takes the dF/F calculated data from calc_dFF() and plots the mean
% (bold) and the individual traces (thin dashed lines) for each trial type
% in the dataset. figtitle should reflect the dataset you're plotting.
% typerange is the range of tr... |
672fa65e0a650e5b16a632eaf92319ba3157332754adcb46329bb32e867b2753 | MATLAB | 1,456 | 43 | function tree = flush(tree,uid)
% XMLTREE/FLUSH Flush (Clear a subtree given its UID)
%
% tree - XMLTree object
% uid - array of UID's of subtrees to be cleared
% Default is root
%__________________________________________________________________________
%
% Clear a subtree given its UID... |
718ca3f5a2e1526c1779edd716da8c8cf308c9bc109bde67aa8f920f67c22105 | MATLAB | 1,456 | 55 | function [infoEPI,infoMag1,infoMag2,infoPh] = Read_JsonHeader(p,subnr,sessnr,scannr)
%% Retrieve file names from sessions folder
% FieldMaps
fname = cell(0,0);
d = dir(char(fullfile(p.sessionDIR,p.sessNames{sessnr,subnr})));
listname = {d(~startsWith({d.name}, '.')).name};
[~,idx] = find(contains(listname,'gre_field')... |
7be008a9743dabd4838d655069f69f5a3bbf07fa226e089f4610980456d27195 | MATLAB | 1,457 | 46 | function [ElecType,ElecIdxLin] = LeG_calcGrayWhite(app,ElecFullIdx)
%Calculates gray/white class for an electrode given the index location
%"ElecFullIdx". ElecFullIdx is a matrix of index values specifying the
%volume of the electrode.
%
%Tyler Davis
%20190629
Thresh = app.graywhite.threshold; %0.1
DefaultT... |
c0965fd52f74581e23ae4cc078fa79dcdffa5b2f1ecd1ab3341816d617075979 | MATLAB | 1,457 | 51 | function Rdosl_exact = cal_RATIO_dosl_exact(R1a, R2a, R1b, MPF, R, T2b, T1d, dw, w1)
M0b = MPF;
M0a = 1-M0b;
fb = M0b/M0a;
kba = R*M0a;
kab = kba*fb;
D = 1/sqrt(15)/T2b;
N_scale = 5;
R1rho = zeros(2,2);
for i = 1:2
if i == 1
curr_dw = dw;
... |
ed8eee185e1f9c6beb9ca1c4c84bab18a84fc60b8c367e7ecd9fdbb9c52f75d3 | MATLAB | 1,458 | 46 | function S = LeG_removeSubSurf(S)
%method to remove small surfaces enclosed within a main surrounding
%surface
%
%20210206
%TD
sv = S.vertices;
sf = S.faces;
minpts = size(sv,2)+1;
pd = pdist2(sv,sv,'euclidean','smallest',minpts+1);
epsln = ceil(prctile(pd(end,:),99));
idx = dbscan(sv,epsln,minpts); ... |
0dbe464b20a47ed303d33c457a5a1d230ecbd8322758d87a6cc5a905263b937a | MATLAB | 1,459 | 59 | function [ s,b ] = anglereg( x, theta, tolerance, maxiter )
% ANGLEREG - Linear-circular regression
% Performes a linear-circular regression (Kempter et al, 2012)
%
% [ S,B ] = ANGLEREG(X,THETA)
% [ S,B ] = ANGLEREG(X,THETA,TOLERANCE)
% [ S,B ] = ANGLEREG(X,THETA,TOLERANCE,MAXITER)
%
% ARGUMENTS
% * X: A ve... |
458a58031161337aa8686464086ea3fbcd0764be45f23bb33c344e398b619a92 | MATLAB | 1,459 | 44 | %%*******************************************************************
%% HSDNTdirfun: compute (dX,dZ), given dy, for the NT direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%******************************************************************... |
7199a5efcea1375e42a3b3bae754f78694bfa85c90c52b05e7ff295f5d60eb76 | MATLAB | 1,459 | 51 | function p = PlotHVLines(positions,direction,varargin)
%PlotHVLines - Plot vertical (resp. horizontal) lines at listed x (resp. y).
%
% USAGE
%
% p = PlotHVLines(positions,direction,options)
%
% positions list of abscissae/ordinates
% direction optional direction: 'h' or 'v' (default = 'v')
% <o... |
736e49af8b36a3d7c487325b65b52206fa9175bfbd5d73e5c83de23eac021abf | MATLAB | 1,459 | 61 | function [res, errStr]= dtdstruct_write(dtdStruct, fileName)
%
% function [res, errStr]= dtdstruct_write(dtdStruct, fileName)
%
% writes a dtdStruct to the harddisk
%
% dtdStruct: should contain a valid dtdStruct
% fileName: should contain the path and file name. if it is empty or undefined, a file selection di... |
89821766bdd54d2c46ee9cf3a32b665e1c602455ae046f36d3137c97f56290b5 | MATLAB | 1,459 | 55 | % Example 6.2: Robust regression using the Huber penalty
% Section 6.1.2, Figure 6.5
% Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 09/07/05
%
% Compares the solution of regular Least-squares:
% minimize sum(y_i - alpha - beta*t_i)^2
% to th... |
b159bc078259607836a43281d2ab7378e6c425b2109e52311e69456b9d44beaf | MATLAB | 1,459 | 34 | % SOFA API - demo script
% load headphone IRs from a SOFA file from the ARI headphones database
% 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 EUP... |
e3af7a9001a1de26d39c676c899c08d4709bc3142fda2193367c37c18cfe9767 | MATLAB | 1,459 | 18 | % Chapter 4: Convex optimization problems
%
% chebyshev_center_2D.m - Section 4.3.1: Compute and display the Chebyshev center of a 2D polyhedron
% chebyshev_center.m - Section 4.3.1: Compute the Chebyshev center of a polyhedron
% cantilever_beam_rec.m - Section 4.5.4: Design of a cantilever beam... |
59f55de53dbba89d95ad86d5b88a62f538da83577fab1d1fc366012ff16b68dd | MATLAB | 1,460 | 53 | %glinspace - Gamma-corrected linearly spaced vector.
%
% USAGE
%
% x = glinspace(d1,d2,gamma,n)
%
% d1 start value
% d2 stop value
% gamma gamma value
% n number of values
%
% SEE ALSO
%
% See also glinspace.
%
% Copyright (C) 2013 by Michaël Zugaro
%
%... |
70daa954d1eae1cce5480336cb8a09fb6f21c28e34c198367c27a011bccf3b4a | MATLAB | 1,460 | 40 | function [n,dspchans] = plx_chanmap(filename)
% plx_chanmap(filename): return map of raw DSP channel numbers for each channel
%
% [n,dspchans] = plx_chanmap(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
%
% OUTPUT:
% n - number of spike channels
% dspchans - 1 x n array o... |
e78f35eee34b7b6510fb49d0adb81ccd1927b98397cbfe7f0561a5383594082c | MATLAB | 1,460 | 53 | % Section 5.2.5: Mixed strategies for matrix games (LP formulation)
% Boyd & Vandenberghe, "Convex Optimization"
% Joëlle Skaf - 08/24/05
%
% Player 1 wishes to choose u to minimize his expected payoff u'Pv, while
% player 2 wishes to choose v to maximize u'Pv, where P is the payoff
% matrix, u and v are the probabilit... |
0f928122ea062d7247dcd5707a0349c86021b2a5af76767f9ac2e24f597186a4 | MATLAB | 1,461 | 44 | function map_to_gii(node_gii_file_L, node_gii_file_R, V, outfile_L, outfile_R)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DESCRIPTION:
% Map vector of values to gifti
%
% USAGE:
% map_to_gii(pl_file, pr_file, outdir, subid)
%
% Inputs: node_gii_file_L, left nodes gifti file (... |
df6d9a33ac0d0ac1ce8dfb9f8facb725de5283bd665bf72b80f8c8a9a903dcac | MATLAB | 1,461 | 21 |
%% Cleartune Parameters
obj.cleartune.results = abj.cleartuneresults;% copy of results for auto tuning functions
obj.cleartune.efields = abj.cleartuneefields;% efields used to calc results
obj.cleartune.injected = abj.cleartuneinjected;% status to report file has injected values
obj.cleartune.optim = abj.CleartuneOpti... |
67966d0450c33b64eece5e12287093eb765513d2d3b7b8eb2fa088a960493e25 | MATLAB | 1,462 | 45 | %The goal of this function is to the time windows that have been manually selected as good/usable for
%a given animal and that match the tracks of interest.
%Also will collect info about which channel sets are best to use for each
%of those time windows (Value of 1, 2, 3 will indicate which of the
%three spreadshee... |
6a17b71db5fe7107c7ac0bfe757292aa76fcce32b2b594bc05a722ae02bb7934 | MATLAB | 1,462 | 50 | % File Array Object
%
% file_array - create a file_array
% horzcat - horizontal concatenation
% vertcat - vertical concatenation
% size - size of array
% length - length of longest dimension
% subsref - subscripted reference
% end - last index in an indexing express... |
9d1e5914d54bc6f5ccfc835d9b96a9006f293e0b463b1c7fde33743b22874b03 | MATLAB | 1,462 | 44 | function [xcm_u, ycm_u] = get_unwrap_xy(xcm, ycm)
% GET_UNWRAP_XY Unwrap center-of-mass trajectories across periodic
% boundary crossings, so trajectories are continuous instead of jumping
% by a box length whenever a particle crosses the periodic boundary.
%
% [xcm_u, ycm_u] = GET_UNWRAP_XY(xcm, ycm) takes trajecto... |
eb8caae6a8464a03d59aa6ad6e139a930ea7bc96a4efdf0b402c28723ba7c542 | MATLAB | 1,462 | 38 | function [nCoords, nDim, nVTMode, c] = plx_vt_interpret(ts, sv);
import CMBHOME.PLX2Mat.*
% plx_vt_interpret - interpret CinePlex video tracking data
%
% [nCoords, nDim, nVTMode, c] = plx_vt_interpret(ts, sv);
%
% Input:
% ts - array of timestamps (in seconds) (see plx_event_ts.m)
% sv - array of strobed event valu... |
fcac8600983a827648b9f0f3a8eeb50ff1f77bd7b965d7c08584b49ee829b27d | MATLAB | 1,462 | 70 | function genFDfromFTR(dtdname,ftrname,oversampling,selection,outname)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% genFDfromFTR(dtdname,ftrname,oversampling,selection,outname)
%
% generates fiber densities (colored and uncolred) and endpoint densities
%
% dtdname - na... |
77fb9106393e1d5a34b50dbf29b0c652a9dcddff04b02d25ace6f04f96789c8c | MATLAB | 1,463 | 41 | function params = parseArgs(params, input)
% This function takes in a structure, params, that defines a set of default
% parameter values, named according to its fieldnames. Input is either a
% structure with corresponding field name and user defined values or a set
% of property/value pairs, as formatted by varargin.
... |
204110264dbeba268f37793e3a2753cfd312aca83ccb850113bc27760a138848 | MATLAB | 1,464 | 49 | function subtree = branch(tree,uid)
% XMLTREE/BRANCH Branch Method
% FORMAT uid = parent(tree,uid)
%
% tree - XMLTree object
% uid - UID of the root element of the subtree
% subtree - XMLTree object (a subtree from tree)
%
% Return a subtree from a tree.
%
% See also XMLTREE
if uid > length(tree) || ...
n... |
48d232293bd525a21cac74d48bbf6d820ff2d86b4f7aad8b3466f7f20c94163b | MATLAB | 1,464 | 58 | % Nonnegative matrix factorization
% Argyris Zymnis, Joelle Skaf, Stephen Boyd
%
% We are given a matrix A in R^{m*n}
% and are interested in solving the problem:
%
% minimize ||A - Y*X||_F
% subject to Y >= 0, X >= 0
%
% where Y in R{m*k} and X in R{k*n}.
% This script generates a random matrix A and obt... |
8e2cd56a75d842eee2721df424078ce8f21ddc9ab2ea95c1336d0156019776e1 | MATLAB | 1,465 | 50 | function deletId = call_deletefeature(handles, rois)
assignin('base', 'handles', handles);
assignin('base', 'rois', rois);
im_norm = handles.im_norm;
roimap = max(bsxfun(@times, rois, reshape(1:size(rois,3),1,1,size(rois,3))),[],3);
roimap2 = roimap;
roimap2(roimap2>1) = 1;
% roimap2 = roimap2+im_norm;
scrsz = handle... |
8ef621714dcd94b375bcb50f5147ddf1466300e31b28bd361c1b171438d39826 | MATLAB | 1,465 | 45 | function plotBestBordersMapCCF(dorsalMaps, allROIs, metricFields, randomBorders, smoothSDPts, smoothSDImg, cmapInfo)
% Creates a binned and smooth map of cell metric values from the fields in
% metricField, then computes the spatial gradient of each map, combines
% them via the quadratic mean, and plots as an RGB image... |
23b522f9d926bbeea9db3eb983d20500760a4264ec7010e5b330aae2abdf269a | MATLAB | 1,467 | 33 | function [xmn,xmx,mni,mxi] = CORE_minmax(x)
%CORE_MINMAX Core computational routine for MINMAX.
% [XMN,XMX,MNI,MXI] = CORE_MINMAX(X) returns scalars such that
% XMN = X(MNI) = min(X) and XMX = X(MXI) = max(X). Ties in indices are
% broken in favor of the lowest magnitude index.
%
% NaN values are igno... |
3453afd548ae6e72545e6c24c3cddfcdf40794da2ef11efac066a27d6685d369 | MATLAB | 1,467 | 49 | function subtree = branch(tree,uid)
% XMLTREE/BRANCH Branch Method
% FORMAT uid = parent(tree,uid)
%
% tree - XMLTree object
% uid - UID of the root element of the subtree
% subtree - XMLTree object (a subtree from tree)
%
% Return a subtree from a tree.
%
% See also XMLTREE
if uid > length(tree) || ...
n... |
44218effb23739bfdc2e22b5c377a69649a955ffedb0f78b21eb906aa91683b3 | MATLAB | 1,467 | 45 | % errordlg2() - Makes a popup dialog box with the specified message and (optional)
% title.
%
% Usage:
% errordlg2(Prompt, Title);
%
% Example:
% errordlg2('Explanation of error','title of error');
%
% Input:
% Prompt - A text string explaning why the user is seeing this error message.
% Title ... |
84d8ef568cd3eed44e02abddddefacaf6bae8f88c1716764905c56772b700974 | MATLAB | 1,468 | 45 | function ea_load_group(handles, groupdir)
ea_busyaction('on', handles.leadfigure, 'group');
groupdir = erase(groupdir, filesep + textBoundary("end"));
set(handles.groupdir_choosebox, 'String', groupdir);
set(handles.groupdir_choosebox, 'TooltipString', groupdir);
analysisFile = ea_getGroupAnalysisFile(groupdir);
if ... |
b055d38bb82dae4cd0972769eec5c01fd3ef3a8f0314709f7ab2fbea2154f6b2 | MATLAB | 1,468 | 42 | % rspfunc() - sub-function used by rsget()
%
% Usage: res = rspfunc(pval, l, rval)
%
% Input:
% pval - p-value to optimize
% l - [l1 l2 l3 l4] l-values for Ramberg-Schmeiser distribution
% rval - expected r-value
%
% Output:
% res - residual
%
% Author: Arnaud Delorme, SCCN, 2003
%
% See also: rsget()
%
% R... |
bf8bd31d09870f5062df83b9ca888cfdb6fd5f602c312bb099211358de086ae1 | MATLAB | 1,468 | 17 | % CVX: Definitions of common convex sets.
% complex_lorentz - Complex second-order cone. {(x,y): norm(x)<=y}
% convex_poly_coeffs - Coefficients of convex degree-n polynomials. {p: p(x) convex}
% exp_cone - The exponential cone. {... |
994438a46a929564b050c4534b7ef72e4dd22c6cdbc5aa34b54d6d1a037798ad | MATLAB | 1,469 | 36 | function saveash5(data, path_to_file, options)
% save the variable stored in data in a h5 file named path_to_file (includes the
% path to the directory). The file is saved with the same class as data.
% options.groupname: the name of the group (default: /mov)
% options.append: append to existing file if it exists... |
c3062b6df941bef0f5d7810aee0c4c5f773e56a4f0e6952a26795a634a4e0458 | MATLAB | 1,469 | 39 | function [framestamp, stampinfo, handles]= loadfilesub(variableinfo, framestampvariable,...
stampinfovariable,k, filename, filepath, dirtemp, datafilename, handles)
framestamp = [];
stampinfo = [];
if ismember(framestampvariable, variableinfo)
a = load(dirtemp, framestampvariable);
fram... |
f9586c2cdd4eab050ea00abddad1b6720cc7dfe5d33e8936f30a665215a841b1 | MATLAB | 1,469 | 17 | % CVX: Definitions of common convex sets.
% complex_lorentz - Complex second-order cone. {(x,y): norm(x)<=y}
% convex_poly_coeffs - Coefficients of convex degree-n polynomials. {p: p(x) convex}
% exp_cone - The exponential cone. {... |
0f51f7a1dbae2c2436adf7febbb0442d0e9aeb191783d161a2b474931c5cfe08 | MATLAB | 1,470 | 47 | % gettempfolder() - return the temporary folder
%
% Usage: >> folder = gettempfolder;
%
% Output: a string containing the folder if a temporary folder can be found.
% Empty if the folder cannot be found.
%
% Author: Arnaud Delorme, SCCN, UCSD, 2012
%
% Copyright (C) Arnaud Delorme
% This program is free softw... |
15ee4aaec5488b93f3f20863f02fbe0959f422068bef863b2f2f7df03d84cd19 | MATLAB | 1,470 | 37 | function raster = rasterize(events, Fs, T)
%RASTERIZE Converts a list of events into a binary time series.
% RASTER = RASTERIZE(EVENTS) takes a vector EVENTS containing a list of
% indices and returns a binary vector RASTER with ones in locations
% given by EVENTS. E.g., RASTERIZE([1 5]) => [1 0 0 0 1].
... |
7ede0b37d4d43793c8a842e7f31dd1fe203b994db4c034443655e85b249c767f | MATLAB | 1,470 | 52 | function [varsel] = SelVar(handles, mainfig_pos)
varsel = [];
scrsz = handles.scrsz;
pos = mainfig_pos;
pos(1) = pos(1)+100;
pos(3) = pos(3)-300;
stampinfo = handles.stampinfo{1};
varNames = stampinfo.Properties.VariableNames;
hplot = figure(25); clf('reset')
set(hplot, 'NumberTitl... |
a60acfb3cf9a846812d0f949456501aa9bb1fe24c1574d6b15b75e118d242957 | MATLAB | 1,471 | 50 | %%*********************************************************
%% Atyfun: compute sum_{k=1}^m yk*Ak.
%%
%% Q = Atyfun(blk,At,permA,isspAy,y);
%%
%% Note: permA and isspAy may be set to [].
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%**************... |
3b51f695b5d7cac8a5952aa360e217960be0042f91f475232cfa54971492f263 | MATLAB | 1,472 | 33 | function eventInt = bz_eventIntervals(events,intervals)
%EVENTINT Separate given buzcode event struct by given time intervals
% events - buzcode event structure containing pulses and
% intervals - set of time intervals
% Requires: first field of events struct must be timestamps
% Jacob Kerr, 2020
loadStru... |
90a13816aa74cc1684039bd7412129d1fc826896deb304c6ae29e3e73cfea6d5 | MATLAB | 1,472 | 57 | function [s s0] = circ_std(alpha, w, d, dim)
% s = circ_std(alpha, w, d, dim)
% Computes circular standard deviation for circular data
% (equ. 26.20, Zar).
%
% Input:
% alpha sample of angles in radians
% [w weightings in case of binned angle data]
% [d spacing of bin centers for binne... |
941d2479c2296d3fdda3937b7c446a03ed3c91e5666f999986c355cf4cee09a4 | MATLAB | 1,473 | 46 | % readtxtfile() - Read text file into a Matlab variable
%
% Usage: >> str = readtxtfile( filename );
%
% Input:
% filename - [string] name of the file.
%
% Output:
% str - [string] content of the file.
%
% Author: Arnaud Delorme, SCCN / INC / UCSD, August 2009
% Copyright (C) Arnaud Delorme, August 2009
%
% This p... |
e79301469bf44169b0b6dc886021d2c8ae9279cedcb0ecdf5aefb5c055c8ab79 | MATLAB | 1,473 | 32 | function ssg_databrowse3d(spikes, assigns, show)
% SSG_DATABROWSE3D Feature projection GUI in 3D (work in progress).
% SSG_DATABROWSE(SPIKES) creates a 3-D databrowse figure. Call with a
% spike sorting object SPIKES and an optional assignments vector whose length
% corresponds to the number of waveforms ... |
94f776cbfe17a1675909bf5330340649981f5eb02787ffc3ac07048dad3c8d52 | MATLAB | 1,474 | 29 | plugin_find_master_script_directory
%% Summary of dataset
% Load and print summary of study from study_info.json and contrast info
% -------------------------------------------------------------------------
scriptname = which(fullfile('Second_level_analysis_template_scripts', 'b_reload_saved_matfiles'));
run(scriptna... |
1accc084fef34d049e72b8e15d55355ac2c287569505153a1c791fd00a36990c | MATLAB | 1,475 | 61 | function x = reshape( x, varargin )
% Disciplined convex/geometric programming information for RESHAPE:
% RESHAPE imposes no convexity restrictions on its arguments.
%
% Check size arguments
%
switch nargin,
case {0,1},
error( 'Not enough input arguments.' );
case 2,
[ temp, sz ] = cv... |
a4fe8ddc522d940e97757e955e8db2a31fce713baed0ce78fafd22347f58d6e3 | MATLAB | 1,475 | 50 | % Figure 8.9: Robust linear discrimination problem
% Section 8.6.1, Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 10/16/05
% (a figure is generated)
%
% The goal is to find a function f(x) = a'*x - b that classifies the points
% {x_1,...,x_N} and {y_1,...... |
aa374e4b5ed6732c454d5ac6be51e0f387a03ff4d20ac275e87f5189ea801843 | MATLAB | 1,475 | 31 | % std_readitc() - load ITC measures for data channels or
% for all components of a specified cluster.
% Usage:
% >> [STUDY, itcdata, times, freqs] = ...
% std_readitc(STUDY, ALLEEG, varargin);
%
% Note: this function is a helper function that contains a call to the
% std_re... |
fa7c3c5bc27abb81b647194cb3e26abe25935575de0a776e39d482ca778792d7 | MATLAB | 1,475 | 51 | function ea_spm_apply_coregistration(varargin)
% Wrapper to apply SPM coregistration transformation
fixedimage = varargin{1};
movingimage = varargin{2};
outputimage = varargin{3};
directory = fileparts(ea_niifileparts(movingimage));
if nargin >= 4
affine = varargin{4};
else
% determine the affine matrix to b... |
03dea9d78ad6b77e50398e69a8bc808d3d85574461114a2bfa828b7b0ebb6a3e | MATLAB | 1,476 | 75 | function r8mat_transpose_print_some ( m, n, a, ilo, jlo, ihi, jhi, title )
%*****************************************************************************80
%
%% R8MAT_TRANSPOSE_PRINT_SOME prints some of an R8MAT, transposed.
%
% Licensing:
%
% This code is distributed under the GNU LGPL license.
%
% Modified:
%
%... |
e9b6d3423b3f060a7d962c8fb8d87f94dc52b8a4bc9c4afd80b6198c5d578f3c | MATLAB | 1,476 | 54 | % inputs: b, Y, X1 in glmfit_multilevel format, varargin "plots"
b = stats.beta';
% remove random intercepts per person - not interested in this variance
Yc = cellfun(@(x) scale(x, 1), Y, 'UniformOutput', false);
Ycat = cat(1, Yc{:});
Xcat = cat(1, X1{:});
nobs = size(Xcat, 1);
Xcat = [ones(nobs, 1) Xcat];
mode... |
f486f639aabc06762dfe5088e60e8179f533f2ea14653da7ba51f30316be2410 | MATLAB | 1,476 | 66 | function [fibdensRGB fibdens epdens] = ftr2FDmaps(ftr,sz,sel,M)
if not(isempty(sel)),
idx = ftr.fiber{sel}.curveID;
else
idx = 1:length(ftr.curveSegCell);
end;
idx = idx(cellfun(@length,ftr.curveSegCell(idx))>1);
vox = ftr.vox;
nc = cellfun(@(x) ip(x,M*3),ftr.curveSegCell(idx),'UniformOutput',false);
nd ... |
9e77d861e1098ae9be691c841df13678de1a31374f73ef7ccd08e666c78aabb8 | MATLAB | 1,477 | 37 | function [ndcounts, inds] = histnd(data, bins)
%HISTND N-Dimensional histogram
% [NDCOUNTS, INDS] = HISTND(DATA, BINS);
% The DATA matrix is treated as a collection of D-dimensional row
% vectors and the entire range of the data is divided into BINS evenly
% spaced segments (default: 10) in and the d... |
27d73e2f1245e3e1cce18ef178878a154b2d59076d03281267cb1763c990740b | MATLAB | 1,478 | 68 | function varargout = plot(varargin)
% plot method for GIfTI objects
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: plot.m 7513 2019-01-15 15:17:29Z guillaume $
% if ishandle(varargin{1})
% h = figur... |
de26e6c5e6f5d0f62d4b3eefe6e638308f03cccc128b908248622aad7de4dc4b | MATLAB | 1,478 | 50 | function [whichnormmethod,template]=ea_whichnormmethod(directory,whatmethod)
if ~strcmp(directory(end),filesep)
directory=[directory,filesep];
end
whichnormmethod=''; % default exit empty.
if ~exist('whatmethod','var')
whatmethod='normmethod';
end
options = ea_getptopts(directory);
switch whatmethod
case... |
4d2c5dd88be58d71bffccca18dd94623ed910da0c23bc18345e017efb80df2fa | MATLAB | 1,480 | 41 | function sleepstagesOUT = dreem2danalyzer(sleepstagesIN)
% Convert a DREEM score file to a danalyzer score file.
%%
% Authors: Dan Denis
% Date: 2024-12-09
%%
sleepstagesOUT.stages = zeros(height(sleepstagesIN), 1);
for i = 1:height(sleepstagesIN)
if strcmpi(sleepstagesIN.SleepStage(i), 'SLEEP-S0')
... |
c531f3ada284194ab8044c94d55bcff513a818b6d9f669b9cc6b6ca8a19b42f4 | MATLAB | 1,482 | 39 | % covary() - For vectors, covary(X) returns the variance of X.
% For matrices, covary(X)is a row vector containing the
% variance of each column of X.
%
% Notes:
% covary(X) normalizes by N-1 where N is the sequence length.
% This makes covary(X) the best unbiased estimate of th... |
249915a800b4660b85ff5a08abd8ce39037698a2a4e86a0db299365f211e5bc7 | MATLAB | 1,483 | 52 | function outpoints = tal2icbm_fsl(inpoints)
%
% This function converts coordinates from Talairach space to MNI
% space (normalized using the FSL software package) using the
% tal2icbm transform developed and validated by Jack Lancaster
% at the Research Imaging Center in San Antonio, Texas.
%
% http://www3.interscien... |
3f9b14c7c9ee6e4722ce93fc9fdf18e4595533168d5e323bd42a5f8901f6c624 | MATLAB | 1,483 | 39 | function ea_thomas_menu(handles)
% Run THOMAS from Tools menu.
bids = getappdata(handles.leadfigure, 'bids');
subjId = getappdata(handles.leadfigure, 'subjId');
if isempty(bids) || isempty(subjId)
ea_cprintf('CmdWinWarnings', 'No patient selected!\n');
return;
else
subj = bids.getSubj(subjId{1});
% Ch... |
3aebba04fed204724eeced504e6ce2aa05f5c05db2c30005be9d5d15a58add67 | MATLAB | 1,484 | 40 | function [ i, j, v ] = find( x )
%Disciplined convex/geometric programming information for FIND:
% When used in CVX models, FIND cannot deduce the numeric value of a
% CVX variable. So it returns the indices of elements that are
% "structurally" nonzero; i.e., that are not *identically* zero.
% This is ... |
72e278409222bf368af7df0ee6eda9374146c16a73ef4cbdb7d3cbcb6bc684c5 | MATLAB | 1,484 | 55 | function [ ] = ColorbarWithAxis(cbounds,label,varargin)
%ColorbarWithAxis(cbounds,label) adds a colorbar to a imageplot and labels
%axis and bounds with > and <.
%
%TO DO
% change inputs to 'parms' with inputParser
% add 3std functionality
%
%DLevenstein 2016
%% inputParse for input options
parms = inputParser;
add... |
8aa82b76ae9dd49c0611af058825abcba3916daa9748a548b9c83fd75a5d1771 | MATLAB | 1,485 | 52 | function outpoints = tal2icbm_spm(inpoints)
%
% This function converts coordinates from Talairach space to MNI
% space (normalized using the SPM software package) using the
% tal2icbm transform developed and validated by Jack Lancaster
% at the Research Imaging Center in San Antonio, Texas.
%
% http://www3.interscien... |
fa2307e16fe926be29dc4a96a51ec070d03d342fc741dcf218313728b5860eb8 | MATLAB | 1,485 | 41 | function hdr = make_nifti2_hdr()
hdr = struct();
hdr.sizeof_hdr = int32(540);
hdr.magic = ['n+2' 0 13 10 26 10]; %should write reset this anyway?
hdr.datatype = int16(16); %default to float32
hdr.bitpix = int16(32);
hdr.dim = ones(1, 8, 'int64');
hdr.intent_p1 = 0.0;
hdr.intent_p2 = 0.0;... |
7ffd8e19c4aa007c4e252e0d57c6a505ef21c42768e0e76909449848a8ea7d98 | MATLAB | 1,486 | 55 | function splot_trajectory(self, cel, varargin)
% Plots scaled trajectory
%
% Plots animal trajectory for root.epochs (if multiple, they are all
% plotted on top of one another), along with spikes overlayed in red dots.
%
% andrew 3 april 2010
p = inputParser;
p.addRequired('self')
p.addRequired('cel', @isnumeric)
p.a... |
84c2a156532ae59d547bc85077b79789c0bf8cffa7d47d1c3a641b094dd3ff4b | MATLAB | 1,486 | 47 | function edu = CBIG_get_edu(rid_of_interest)
% edu = CBIG_get_edu(rid_of_interest)
% Fetch education years from .csv files
%
% Input:
% - rid_of_interest: the RID's of subjects of interest
%
% Output:
% - edu: 1st col is RID, 2nd col is (dummy) VISCODE, 3rd is (dummy) EXAMDATE, 4th is year
%
% Written by CBIG u... |
0c86a7f4c8a1c4d7fe6de1fa0e9cbb7c9de91bc2e41d7b93fa10386c761d0994 | MATLAB | 1,487 | 72 | function [imall,mycmap]=im_overlay4(im1,im2,ncolors,thesecolors)
% function [y,cmap]=im_overlay4(im1,im2,ncolors,thesecolors)
%
% im1: background gray-scale image (not-scaled)
% im2: foreground jet-scale image (indexed and min ignored)
verbose_flag=0;
if nargin<3,
%ncolors=ceil(max(im2(:)));
ncolors=256... |
3a59f9132c0499eb3ad6653e08764a75c41c8e8cf0a511195b912cc50fd28d17 | MATLAB | 1,487 | 41 | function hdr = make_nifti2_hdr()
hdr = struct();
hdr.sizeof_hdr = int32(540);
hdr.magic = ['n+2' char([0 13 10 26 10])]; %write resets this anyway
hdr.datatype = int16(16); %default to float32
hdr.bitpix = int16(32);
hdr.dim = ones(1, 8, 'int64');
hdr.intent_p1 = 0.0;
hdr.intent_p2 = 0.0... |
964cf9122b5b7a26a63b1d1c77d54b4da51fa0209c1763937b837c84014c8549 | MATLAB | 1,487 | 44 | mainfolderlist = {'1_1s';'2_2s5';'3_5s';'4_10s'};
mainfolder = '/Users/yiyuan/OneDrive - University of Essex/PG Research/0A_Journal/202004_unknown Journal_Probability Score/1_Results/0_Final Results/Results_Main/';
resultfolder = '/Users/yiyuan/OneDrive - University of Essex/PG Research/0A_Journal/202004_unknown Journa... |
f8028179462c4a8287693a6b12bc82ae929b11af9864945ccbe538a3471c2b91 | MATLAB | 1,487 | 53 | function NSxPowerSpectrum(NSx, channelNumber, colorCode)
% NSxPowerSpectrum
%
% Plots a power spectrum of a given channel.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Use NSxPowerSpectrum
%
% Use settingsManager(NSx, channelNumber, colorCode)
%
% NSx: The NSx file conta... |
30b30602fbe705e0813913c1a4538aa9151b9d7b67bd74da1d161e2db23eba1a | MATLAB | 1,488 | 17 | % Filter design
% <a href="http://stanford.edu/~boyd/papers/magdes.html">FIR Filter Design via Spectral Factorization and Convex Optimization</a>
% <a href="http://stanford.edu/class/ee364">EE364</a> lecture, <a href="http://stanford.edu/class/ee364/lectures/filters.pdf">Filter design and equalization</a>
%
% fir_cheb... |
4e92bce4f3367ea9c310ee86a2a51484e2f23aae94ddf7b2bcbc674f760fddb4 | MATLAB | 1,488 | 52 | % This example calls cgalmesher to mesh a segmented
% brain volume. The segmentation was done by FreeSurfer
% and there are 41 different types of tissues. Each tissue
% type is labeled by a unique integer.
fprintf(1,'loading segmented brain image...\n');
for i=1:256
brain(:,:,i)=imread('brain_seg.tif',i);
end
brain=... |
c2acc630c390ad2beb8d71dcd24293f1ba47bcd6ed28cab86d4e690908d69432 | MATLAB | 1,488 | 36 | %% control_set_after_use.m
%
% POSITIVE CONTROL for clean/set_after_use.py. Not a runnable analysis.
%
% This file reproduces the failure that motivated the checker: the option is
% guarded near the top, CONSUMED a few lines later, and only THEN set to the
% value the author intended. Nothing errors. The output directo... |
5b46391190ed97f20eb86b3768533b592e1e8efb265fe89315102257b336e230 | MATLAB | 1,490 | 42 |
function datToNPY(inFilename, outFilename, dataType, shape, varargin)
% function datToNPY(inFilename, outFilename, shape, dataType, [fortranOrder, littleEndian])
%
% make a NPY file from a flat binary file, given that you know the shape,
% dataType, ordering, and endianness of the flat binary file.
%
% The point he... |
e65ce2d418abf23abfca8d2a20171a809edf13ddd25a14c791d10114fb7ec99b | MATLAB | 1,490 | 37 | function CB_subzoom(handle, event)
%CB_MYFUNC Callback for UImyfunc.
hei_zoom = 0.85; % fractional height in zoomed state
wid_zoom = 0.85; % fractional width in zoomed state
%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Access Data %%%%%%%%%%%%%%%%%%%%%%%%%%%%
% First we get the target axes & its context menu -- these are ... |
f2a17d2e10e801ce66dcfc5685d07fb11f82cbc17130f1b47ef11c7e9d299eef | MATLAB | 1,490 | 67 | function varargout = plot(varargin)
% plot method for GIfTI objects
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: plot.m 5888 2014-02-19 19:54:12Z guillaume $
% if ishandle(varargin{1})
% ... |
425d914bdcd0c6daa13003cf6aa7426ef71a32a1b2b4aaaf36295b6d5c6df812 | MATLAB | 1,491 | 35 | function CBIG_ArealMSHBM_example_wrapper(out_dir)
% CBIG_ArealMSHBM_example_wrapper(out_dir)
%
% This script will run the test step in Example 4 to generate individual-level parcellation
% using gMSHBM. The other examples will be skipped since etimating group priors require
% multi-cpus which cannot be run without mul... |
6f076b3e9398be42fcdb4c781f2e1e5c662cba0f39051def1a91a90b03bd0800 | MATLAB | 1,491 | 53 | function [varargout] = quivermd(ax, x, v, varargin)
%QUIVERMD multi-dimensional quiver
% QUIVERMD(AX, X, V, VARARGIN) plots the column vectors in matrix V
% at the points with coordinates the column vectors in matrix X
% within axes object AX using plot formatting options in VARARGIN.
%
% usage:
% H ... |
8537fcea46bfb6829c1c66decb19dc33d5cc70667d2b6acf9e69dd054e6702fd | MATLAB | 1,491 | 35 | function [Params, lh_labels, rh_labels] = CBIG_MSHBM_example_wrapper(out_dir)
% [Params, lh_labels, rh_labels] = CBIG_MSHBM_example_wrapper(out_dir)
%
% This function will run examples sequentially
%
% Written by Ru(by) Kong and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
CBI... |
cc7f9415f773e1f073ed6b9502661f72e8dfdfbb149d8b8098c440b3f172e49c | MATLAB | 1,491 | 26 | % EEGLAB Toolbox to process EEG data
% Version 14.0.0
%
% eeglab() - Matlab graphic user interface environment for
% electrophysiological data analysis incorporating the ICA/EEG toolbox
% (Makeig et al.) developed at CNL / The Salk Institute, 1997-2001.
% Released 11/2002- as EEGLAB (Delorme, Makeig, et al.) a... |
02a030745c4258a6ecaa17725e048f2de564eae1c70d049526e5a5cbb0738646 | MATLAB | 1,493 | 27 | function a = lt( x, y )
% Disciplined convex programming information for LT (<):
% The left-hand side of a less-than constraint must be convex. The
% right-hand side must be concave. Of course, real constant and
% affine expressions are both convex and concave and can be used on
% either side as... |
310241ab59b80792632287c48904c5b60d4e45558fb1dff6e52f1736c9c662e8 | MATLAB | 1,493 | 55 | function [normal,normalf] = compute_normal(vertex,face)
% compute_normal - compute the normal of a triangulation
%
% [normal,normalf] = compute_normal(vertex,face);
%
% normal(i,:) is the normal at vertex i.
% normalf(j,:) is the normal at face j.
%
% Copyright (c) 2004 Gabriel Peyr�
[vertex,face] ... |
61900b332a6190a68e00860d0d14dbcf71bd2035bdce0dc36915679fac564d12 | MATLAB | 1,494 | 61 | if(ispc)
check_dir = 'dir';
else
check_dir = 'ls';
end
curr_path = pwd;
addpath(pwd);
[status, y] = system([check_dir ' AnalysisTools']);
if(status == 0)
addpath(fullfile(curr_path, 'AnalysisTools'));
end
[status, y] = system([check_dir ' AtlasSharpnessAndLabelMatch']);
if(status == 0)
addpath(fullfi... |
fbfdfc83130f8b4410e1055e59eb0ae3918dabef7b2942c1d9f3b56092f894ec | MATLAB | 1,494 | 48 | function [newDB] = bz_updateSQLFromFiles(nyuSharePath)
% USAGE
% [newDB] = bz_updateSQLFromFiles()
%
% INPUTS
%
%
%
%
%
% INPUTS
%
%
%
% DESCRIPTION
% This function takes a directory path as input (from /Datasets/ folder)
% and searches for recording session folders to add to the SQL database
%
% david tingley, 2018
... |
f196127f4fea198502d5646c372dc95571e89220092c038b12c2fbf6036dcb5e | MATLAB | 1,495 | 57 | function [res, errStr]= maskstruct_init(mrStruct)
% function [res, errStr]= maskstruct_init(mrStruct)
%
% Creates a valid and empty maskStruct
%
% return values
% res: the empty maskStruct
% errStr: If an error occured, errStr is identify the error
%
%
% Bjoern W. Kreher
% 12/07
%
% UNIX
res= []; errS... |
574da05c9961409d6fb96948d99e5b717350049ae22221c9b5d7031410fa0d8a | MATLAB | 1,496 | 55 | function features = LoadSpikeFeatures(filename,rate)
%LoadSpikeFeatures - Load spike features from file.
%
% USAGE
%
% features = LoadSpikeFeatures(filename,rate)
%
% filename spike file name (either .clu, .res or .fet)
% rate sampling rate
%
% OUTPUT
%
% The output is a list of... |
ba4b65233c3c5e75629381f9252a02f3b2cdc401792e31f1a7987c198d6c3353 | MATLAB | 1,496 | 47 | function R = myPLS_cov(X,Y,grouping,grouped_PLS)
% This function generates a cross-covariance matrix (stacked) for the PLS
% analysis
%
% Inputs:
% - X : N x M matrix, N is #subjects, M is #imaging variables
% - Y : N x B matrix, B is #behaviors
% - grouping : N x 1 vector, subject g... |
c4c1ad609da9ad234331204f212e1b8aa3fa31e3d220260a6191c87245db1e58 | MATLAB | 1,496 | 46 | % Section 11.8.4: Network rate optimization
% Boyd & Vandenberghe "Convex Optimization"
% Argyrios Zymnis - 05/03/08
%
% We consider a network with n flows and L links. Each flow i,
% moves along a fixed predetermined path (i.e. a subset of the links)
% and has an associated rate x_i. Each link j has an associated cap... |
b6d28a4597c91b37cc9f2e5f2c3c431bae416ca90cdf9d92037c3bfd4d7dff3c | MATLAB | 1,497 | 45 | function cleanx = CleanData(x, rnge, choice, epsilon);
%CLEANDATA
% Usage:
% cleanx = CleanData(x, rnge, choice, epsilon);
%
% This function will take in a data set x, a specific portion of that data,
% rnge, and look for any points below (choice = 'below') or above (
% (choice = 'above') the threshold e... |
0e84c3bf5212cf95f86d9a0051a29c648ff6a980d6bcecd7501bd59d5347ed87 | MATLAB | 1,498 | 36 | %% Figure 9 supp 1
% RUN fig9_analysis, then return here
fig9_analysis
% Load PETHs to plot
fileList = searchFilesRecursive(YOURDATAPATH, 'PETHs.mat');
load(fullfile(fileList.folder, fileList.name))
% Most-likely ROIs for each subpopulation, 2 from each area
areas = {'M2', 'M1', 'S1-fl', 'S1-hl', 'S1-tr'};
ROIinfo = ... |
16eec0e0e5352aa363545fc7e5e7a3023ef5acecf5a774657b9600d25743a54f | MATLAB | 1,498 | 45 | function all_boot_orders = myPLS_get_boot_orders(nBootstraps,grouping,grouped_boot)
% This function computes bootstrapping sampling orders for bootstrapping
% with resampling. Note that if groups are considered for resampling,
% groups can be not ordered.
%
% Inputs:
% - nBootstraps : #bootstrap samples
% - grou... |
1ae302d06f02432a835dfcc35bc54161a91c6d66145e9749f6c6fde5be93c909 | MATLAB | 1,498 | 62 | function scenario = scenario_sumr_constb_constp(par)
% r(Q+A,Q+A), b constant, p constant
scenario.name = "sumr_constb_constp";
% define parameter set (names)
scenario.parnames = {'r0','K','b0','p0'};
% organize parameters in structure form
scenario.make_par = @(p) struct( ...
'r0', p(1), ...
'K',... |
96aa4455999d334f067536ec9c8736000b2750537dee579d0b9e777793405820 | MATLAB | 1,498 | 76 | function i4mat_transpose_print_some ( m, n, a, ilo, jlo, ihi, jhi, title )
%*****************************************************************************80
%
%% I4MAT_TRANSPOSE_PRINT_SOME prints some of an I4MAT, transposed.
%
% Licensing:
%
% This code is distributed under the GNU LGPL license.
%
% Modified:
%
%... |
205971f5d7fc612b8e9689d66d508a7eda4ddedc55efafdc527092444cf944d1 | MATLAB | 1,499 | 42 | function a = file_array(varargin)
% Function for creating file_array objects.
% FORMAT a = file_array(fname,dim,dtype,offset,scl_slope,scl_inter,permission)
% a - file_array object
% fname - filename
% dim - dimensions (default = [0 0] )
% dtype - datatype (default = 'uint8-le')
% offset ... |
2b744109c8370c0022dde3f3fac953064a8ab23748e18834aaded707c0de904f | MATLAB | 1,499 | 43 | function [params] = readParameterFile(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 Bucc... |
6512b62f96a2e4c5cd70e90faf3b24ccfd277ca18ef58d5a8966fa0dcb5dbe81 | MATLAB | 1,499 | 56 | function baseline = CBIG_hypoTest_acrossStages(betas, stats)
% baseline = CBIG_hypoTest_acrossStages(betas, stats)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
fprintf('\n\n****************** Combine Factors, Across Stages ******************\n\n');
baseline = ze... |
26751d6b6a98f6d7126bc9545be4eade42fe540f16d22af8ecb2bb9d190cc3ce | MATLAB | 1,501 | 38 | function [time_projection] = assembly_activity(AssemblyTemplates,SpikeCount)
% Activities = assembly_activity(Patterns,Activitymatrix): computes the
% time course of the activity of assembly patterns defined in Patterns in
% the spike matrix Activitymatrix with single bin resolution.
%
% Description of inputs: ... |
4fc079144ce07f111f86f441902409f7e8bf43029c58f53df99acbb5872946ee | MATLAB | 1,501 | 30 | % std_readerpimage() - load ERPimage measures for data channels or
% for all components of a specified cluster.
% Usage:
% >> [STUDY, erpimagedata, times, trials, events] = std_readerpimage(STUDY, ALLEEG, varargin);
%
% Note: this function is a helper function that contains a call to the
% st... |
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