sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3530c091d7f756ac5d0ff4ce21c143e3e50861066d3c7b8f66d2e9ecc948db75 | MATLAB | 2,087 | 45 | function Neighborhood = CBIG_hMRF_update_whole_brain_neighborhood(Neighborhood_lh, Neighborhood_rh,...
Neighborhood_lh_rh, c, d)
% Neighborhood = CBIG_hMRF_update_whole_brain_neighborhood(Neighborhood_lh, Neighborhood_rh,...
% Neighborhood_lh_rh, c, d)
%
% This function constructs a sparse matrix with parameters c... |
48f44cd1bbe415545a1fb965e5ac3d5b1c9ae0806342fb58dc3f4fb9fac03ccf | MATLAB | 2,087 | 76 | function [newnode,newelem]=mergemesh(node,elem,varargin)
%
% [newnode,newelem]=mergemesh(node,elem,varargin)
%
% concatenate two or more tetrahedral meshes or triangular surfaces
%
% author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
%
% input:
% node: node coordinates, dimension (nn,3)
% elem: tetrahedra... |
6f6a551f984f64c9f60cd4adb85869f800a1d35fc63c00cdb5bb665cfb2fce13 | MATLAB | 2,087 | 59 | function [PSTH, trig, sweeps, timeAxis] =...
getPSTH(discreteStack, timeLapse, kIdx, binSz, fs)
%GETPSTH returns a peri-stimulus triggered histogram given a triggered
% aligned stack in the form MxNxT, where M is the number of channels to
% align, N is the number of samples (time) and T is the number of aligning
% ... |
25264e2f49f93cdf2d8a9a408d0e0c1d94913e99218652a863d8be7234b7bbdd | MATLAB | 2,088 | 57 | function [] = ADP_Motion_Correction5D(inFolder, outFolder, rigid)
if(nargin<3)
rigid = true;
end
fprintf('\nFolder %s\n',inFolder);
% outFolder = strrep(inFolder,'RawData','MotionCorrected');
fprintf('\nLoading...');
[Y, Yred] = makeStacks5D(inFolder, 10);
fprintf('... |
7b9c6c8bceebf8fb1cf6f9191bf80c36ed5f359ea785ebbad0ffeeff5d846b6f | MATLAB | 2,088 | 65 | function shifted = CircularShift(m,s)
%CircularShift - Shift matrix rows or columns circularly.
%
% Shift each matrix row (or column) circularly by a different amount.
%
% USAGE
%
% shifted = CircularShift(m,s)
%
% m matrix to rotate
% s shift amount for each row (horizontal vector... |
185a4d8d4a1ba53420fd5a40aba0ffd278413702838da89625b4d370aef85682 | MATLAB | 2,089 | 69 |
function [arrayShape, dataType, fortranOrder, littleEndian, totalHeaderLength, npyVersion] = readNPYheader(filename)
% function [arrayShape, dataType, fortranOrder, littleEndian, ...
% totalHeaderLength, npyVersion] = readNPYheader(filename)
%
% parse the header of a .npy file and return all the info contained
... |
e3fd02c0ddb762056433942e88c37e221d15c4ba99db4fa30a2f6efaf9991cb6 | MATLAB | 2,089 | 95 | function h = plot_phases(data, color)
% Produces a polar plot of phase angles. Input data must be in radians.
% Requires circStats package
%
%%
% Authors: Dan Denis
% Date: 2021-07-14
%%
if iscell(data)
for i = 1:length(data)
% Remove any NaN
data{i}(isnan(data{i})) = [];
... |
ff5091271c636cc5f584f9e6f799f031eb93cdd6a24e68ee34cd2737d98c259a | MATLAB | 2,089 | 79 | function t = circ_confmean(alpha, xi, w, d, dim)
%
% t = circ_mean(alpha, xi, w, d, dim)
% Computes the confidence limits on the mean for circular data.
%
% Input:
% alpha sample of angles in radians
% [xi (1-xi)-confidence limits are computed, default 0.05]
% [w number of incidences in case ... |
360e6f93d923e93c8af3dd29085c30686f1f5779a30e64507a6b5f27dbb8697b | MATLAB | 2,091 | 46 | % 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... |
d8e2ba580717cd90cdf671c0fb3ac60000a722de7d4e34758f507a97b5b330dc | MATLAB | 2,091 | 72 | %isdvector - Test if parameter is a vector of doubles satisfying an optional list of tests.
%
% USAGE
%
% test = isdvector(x,test1,test2,...)
%
% x parameter to test
% test1... optional list of additional tests (see examples below)
%
% EXAMPLES
%
% % Test if x is a vector of doubles
% ... |
b1e9fb75b5cb49818b470ed92c36f7cce1cf89c79a7063a41014ebaf89b73f20 | MATLAB | 2,092 | 59 | %% A TabPanel Example
% This example shows how to use tabs within a layout. It also shows how to
% use the TabPanel Callback property to update other GUI elements when the
% visible tab is changed.
%
% Copyright 2009-2013 The MathWorks, Inc.
%% Open the window
% Open a new figure window and remove the toolbar and menu... |
9ddb2afe28058ddce4daa42277604a6774717268ebe4efed0baffe0a8c230607 | MATLAB | 2,093 | 75 | function res = runOptimization(proc, scenario_fun, k, opts)
% Run multi-start parameter estimation
%
% res fields:
% res.est_params - best scaled parameters, in interval [0,1]
% res.p - best unscaled parameter vector, in interval [lb,ub]
% res.par - parameter struct
% res.fval ... |
a48acdd4c26230dc20f533bcc71892dc29f2df858bee5e40532ca1caafebcf00 | MATLAB | 2,093 | 76 | function palm_dpxwrite(varargin)
% Write a curvature file (DPV or DPF), in ASCII format.
%
% palm_dpxwrite(filename,dpx)
% palm_dpxwrite(filename,dpx,crd,idx)
%
% - fname is the file name to be created
% - dpx contains the values for each vertex or face
% - crd contains the vertex coordinates or face indices
% - idx co... |
55648a10b612ff04968911e664828d8151c4ae3e04d5382e599b06be863c6450 | MATLAB | 2,094 | 40 | fprintf(1,'Executing %s at %s:\n',mfilename(),datestr(now));
ver,
try,
if isempty(which('spm')),
throw(MException('SPMCheck:NotFound', 'SPM not in matlab path'));
end
[name, version] = spm('ver');
fprintf('SPM version: %s Release: %s\n',name, version);
fprintf('SPM p... |
f8699d0d80d71da4cd54798fe8ab6c494df75a9ce56f69c6a31d99561b6d861c | MATLAB | 2,094 | 70 | % Detecting a small subset of infeasible linear inequalities
% Section 5.8, Boyd & Vandenberghe "Convex Optimization"
% Written for CVX by Almir Mutapcic - 02/18/06
%
% We consider a set of linear inequalities A*x <= b which are
% infeasible. Here A is a matrix in R^(m-by-n) and b belongs
% to R^m. We apply a l1-norm h... |
74814f0eb90a1f0843321b2978ce03604baf22708b8019a568d47b748db92a6a | MATLAB | 2,095 | 63 | classdef Panel < matlab.ui.container.Panel & uix.mixin.Panel
%uix.Panel Standard panel
%
% b = uix.Panel(p1,v1,p2,v2,...) constructs a standard panel and sets
% parameter p1 to value v1, etc.
%
% A card panel is a standard panel (uipanel) that shows one its
% contents and hides the othe... |
ea3332b4f2cf0384cca6d0c70add1a8bab8c8167d3f93e445887aef99bd71eea | MATLAB | 2,095 | 53 | fn = fieldnames(rightall{1});
reverse = {'five','four','three','two','one','ten','nine','eight'...
,'seven','six','eleven'};%'fifteen','fourteen','thirteen','twelve','eleven'};
reverse=reverse';
flippedR = orderfields(rightmeans,reverse);
figure; %set(gcf,'Position',[10 100 1350 600]);
set(gcf,'Position',[400... |
1c87da6542100cf3a8a6c28b1f19dc14a27af2e02f1729153c883c57d9177df3 | MATLAB | 2,096 | 67 | function palm_msetwrite(varargin)
% Write a .mset file, i.e. an ASCII file
% containing multiple matrices (2D arrays).
%
% palm_msetwrite(filename,Mset)
% palm_msetwrite(filename,M1,M2,M3,...)
%
% filename : File name to be created.
% Mset : Cell array with the arrays.
% M1, ... : Contrasts as individual arrays.
%... |
7f1ed4d8c8b1469a49835ee781a1ceea82803e26ce60e50470eab836f0354d03 | MATLAB | 2,096 | 59 | function varargout = window(wname,N,varargin)
%WINDOW Window function gateway.
% WINDOW(@WNAME,N) returns an N-point window of type specified
% by the function handle @WNAME in a column vector. @WNAME can
% be any valid window function name, for example:
%
% @bartlett - Bartlett window.
% @barthannwin ... |
9f6ced22fb619068c12383ab405fda6fb35812b0ae21cbb0f6dca1946cf68fc6 | MATLAB | 2,096 | 65 | function ea_save_settings(tractset,save_as)
% Saves the relevant settings of the tractset object to a mat file
% Properties can't be saved as variables :(
% Or with the struct flag because tractset is
% a class and not a struct :(
% Convert to variables first and then save
calcthreshold = ... |
1ba4b0c43788bc51ca004a1fc62e474cd0f57e17b95c3887f21d7e4c5daaa5d2 | MATLAB | 2,097 | 44 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
25252158ce603e32fd0f8a5276463ebc0352f62d4ef6f65ad6339e340968d785 | MATLAB | 2,097 | 63 | function [lambda_opt, lambda_vals, err_fit_vals, err_pen_vals, x_grid] = lcurve_lambda( ...
obj_builder, lambda_vals, x0, lb, ub, fmin_opts)
%LCURVE_LAMBDA Pick λ via L-curve corner using perpendicular distance.
%
% [lambda_opt, lambda_vals, err_fit, err_pen, x_grid] = lcurve_lambda(obj_builder, lambda_vals, ... |
7ca332a491efcdfa430ae4ef1b9c1c89dcf822e900cf317a07c17f2fe1402de6 | MATLAB | 2,097 | 65 | function [p_left,p_right,c] = ExampleSurfacePlotFunction(surface,vertex_id,data,cmap,data_label)
% This is just a example for how to plot the medial and lateral sides of a
% surface in the same plot
% Inputs:
%
% surface = a structure with two fields: vertices (the vertices making up
% the surface) and faces (the fa... |
5442a90b798655aa9cda27d40c0438dde2fb23a140614dc8aa4d6f8b5bbdbc5e | MATLAB | 2,098 | 60 | %
% KDTREE Find closest points using a k-D tree.
%
% CP = KDTREE( REFERENCE, MODEL ) finds the closest points in
% REFERENCE for each point in MODEL. The search is performed in an
% efficient manner by building a k-D tree from the datapoints in
% REFERENCE, and querying the tree for each datapoint in
% MODEL.
%
... |
29ae369e04c7dc3cc38850ee5a859e19b3ca80ee80221832a7910e1dd28a4c7d | MATLAB | 2,100 | 66 | function r = urn(varargin)
%URN Generate random number sequence without duplicates
%
% IOSR.GENERAL.URN(N) returns an N-by-N matrix containing a random
% sequence of integers in the interval 1:N without duplicates. The
% integers are unique down each column.
%
% IOSR.GENERAL.URN(M,N) and IOSR.GENERAL.URN([M,N... |
191cc26d6745b7940a3ba43605e0d557f0df3bdd36b6633b44315e2882c5811b | MATLAB | 2,101 | 90 | function result = cvmrelnet(object, lambda, x, y, weights, offset, foldid, ...
type, grouped, keep)
if nargin < 10 || isempty(keep)
keep = false;
end
typenames = struct('deviance','Mean-Squared Error','mse','Mean-Squared Error',...
'mae','Mean Absolute Error');
if strcmp(type,'default')
type = 'mse';... |
4cfbcaa31cfb025bdf6c2dfe9e8e8b22f94c613e6f95bfa69548ed3aa9fa6048 | MATLAB | 2,101 | 86 | function [n, ts_left, ts_right] = nex_int(filename, varname)
% nex_int(filename, varname): Read interval variable from a .nex file
%
% [n, ts_left, ts_right] = nex_int(filename, varname)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% varname - variable name
% OUTPUT:
% n - number of... |
eb0562a1a7e05c525efc1763b29cbc889b3b863b62bbf178924bcad74ad3d7de | MATLAB | 2,102 | 49 | function ftr = ea_warp_fibers_MNI2native(pt_folder, MNI_connectome, transform, anchor_img)
% Warp normative connectome to the native space
% By Butenko, konstantinmgtu@gmail.com
arguments
pt_folder % full path to the patient in Lead-DBS dataset
MNI_connectome % full pat... |
148b228645e65182b559e270768f7129e5abab893e4f230007c90a584a5369b7 | MATLAB | 2,103 | 67 | function ea_write(options)
% check if sides is specified correctly for visualization
if isfield(options, 'subj')
options=ea_detsides(options);
end
if options.d2.write || options.d3.write
if strcmp(options.atlasset,'Segment patient anatomy')
ea_subcorticalsegmentation(options);
if ~options.native %... |
6c1be378f1959aa7524a22f86e8ddbc941e301304f5f99712975010153a246cb | MATLAB | 2,103 | 64 | function codeKeeper = syncPatternDetectNEV(NEVStruct)
% syncPatternDetectNEV
%
% Finds the code for the SYNC pattern on the SYNC output of Blackrock
% Microsystems Neural Signal Processor (NSP) recorded by analog input
% channel 16 and thresholded as extracted spikes and saved in the NEV file.
%
% INPUT
%
% NEVSt... |
0dd3549deb6a037bfda0e571db81f091ebe2ef70dad9a6706a035bd84e95ef60 | MATLAB | 2,105 | 57 | % Floor planning
% Section 8.8.1/2, Example 8.7, Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 11/13/05
% (a figure is generated)
%
% Rectangles aligned with the axies need to be place in the smallest
% possible bounding box. No overlap is allowed. Each r... |
25542c8940dc6999c23d979e01f7a883fa4ec3c15373da7868f4d4edae034ab9 | MATLAB | 2,105 | 67 | % std_comppol() - inverse component polarity in a component cluster
%
% Usage: [compout pol] = std_comppol(compin);
%
% Inputs:
% compin - component scalp maps, one per column.
%
% Outputs:
% compout - component scalp maps some of them with inverted
% polarities, one per column.
% pol - logic... |
bcfeb31b7a74939f4889f5dbf394d4872143d30792c10760ed43be22e5077749 | MATLAB | 2,105 | 54 | function [handles] = callgaussfilt_master(handles, dataID, fps, w1, w2)
if nargin<2
dataID = 1;
end
handles = loadtrace(handles, dataID);
if ~isempty(handles.spineROI)
spID = handles.spine_title;
spineROI = handles.spineROI;
trace_stamp = handles.spine_dff;
[tc2, finalBaseline_out] = F_Preprocess_v... |
9975acd5b33d62e45d36836c9c32e27ca09bd79ed7797217e5a55bb8305f5aaf | MATLAB | 2,106 | 62 | function num_pVals = CBIG_ASDf_fitGLM_hypoTest(k, X, y, numReg, output_name)
% num_pVals = CBIG_ASDf_fitGLM_hypoTest(k, X, y, numReg, output_name)
%
% This function fits GLM and performs hypothesis test for the GLM, and
% plots the results. If output_name is specified, the plot will be saved.
%
% Input:
% - k:
% ... |
431f9e26185168fdf02856f69aa0d05a7ba3eb402f33a38e5b115bdd4ad7a5c3 | MATLAB | 2,108 | 63 | function [sROI, matROIs] = ReadJImageROI(cstrFilename, shape)
% ReadJImageROI - FUNCTION Read an ImageJ ROI into a matlab structure
%
% Usage: [sROI, matROIs] = ReadJImageROI(strFilename, shape)
%
% if(numel(cstrFilename)>1)
% sROI = [];
% matROIs = [];
% fprintf(2,... |
4d6b2535cdbe8f6cec2c31403d9f8a160ed9bf469157b6c5e6d8c2096a1451d1 | MATLAB | 2,108 | 55 | function clustergroup = readTSV(filename)
%IMPORTFILE Import numeric data from a text file as a matrix.
% CLUSTERGROUP = IMPORTFILE(FILENAME) Reads data from text file FILENAME
% for the default selection.
%
% CLUSTERGROUP = IMPORTFILE(FILENAME, STARTROW, ENDROW) Reads data from
% rows STARTROW through ENDROW o... |
a744b9e0d693413c5d789e8105d119c9f3dba483410d51e19fb947ffbf6c3875 | MATLAB | 2,108 | 42 | function Obj=SOFAconvertLISTEN2SOFA(LISTEN, subjectID)
% Obj=SOFAconvertLISTEN2SOFA(LISTEN, subjectID) converts the HRTFs described in LISTEN
% (see LISTEN HRTF format) to a SOFA object.
%
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences;
% Licensed under the EUPL, Version 1... |
b7a5669d2ca1a9092fd009d73da200ee7b69edc64ed8cb2fb87f02db1cc6925f | MATLAB | 2,108 | 63 | function fig = draw_volume_bluewhitered_gallery(volume_to_plot, data_to_plot, camera_view, markersize)
% draw_volume_bluewhitered_gallery.m
%
% Draw multiple data on 3D volume using blue-white-red colormap for
% negative-zero-positive values
%
% Inputs: volume_to_plot : volume of mask in nifti format (3D array)
% ... |
5ce20547fb8738340249dbbab48bae732902b3984cd4494c12e7197386faa690 | MATLAB | 2,109 | 72 | function [n, ts, sv] = plx_event_ts(filename, channel)
% plx_event_ts(filename, channel): read event timestamps from a .plx or .pl2 file
%
% [n, ts, sv] = plx_event_ts(filename, channel)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% channel - 1-based external channel number or channel ... |
cc171f95ab4e4924099e8c9ffb2f0d2f6e69eb67e5cb284bcb0a410d73a9c8f2 | MATLAB | 2,109 | 70 | function stats = CBIG_fitLME_4t(subInfoFile, GMICVFile, q)
% stats = CBIG_fitLME_4t(subInfoFile, GMICVFile, q)
% What is the subtype order?
% Offset by 1, the RID column
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
SUB_COL = 1+2;
FRO_COL = 1+3;
PAR_COL = 1+1;
fpri... |
8d34d7a938128b74fd160e0e91ff9f575bb6fbd41962bb0ec0e687f00fe05c66 | MATLAB | 2,112 | 63 | function [in_order, avg_corr] = CBIG_MMLDA_hungarian_match_factors(ref_dir, in_dir, ref_order)
% [in_order, avg_corr] = CBIG_MMLDA_hungarian_match_factors(ref_dir, in_dir, ref_order)
%
% Do a hungarian matching between reference betas and input betas and return the order and correlation of input betas.
%
% Input:
% -... |
a468e4072ff2e581030476e9e37fea43c7010bed5da4b47a68d6d4f1ff1f380c | MATLAB | 2,112 | 65 | function [eigvals,fss,alpha_1,Beta_1]=...
linstability_get_steadystates_and_eigenvalues(profile, Beta, alpha)
% 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 rele... |
2589113cfd664aab2c5699ebc17fea0377a4ec7ef03ac8ff8281ebb118a82b82 | MATLAB | 2,114 | 82 | function z = newdual( prob, name, reps )
narginchk(2,3);
%
% Check problem
%
if ~isa( prob, 'cvxprob' ),
error( 'First argument must be a cvxprob object.' );
end
global cvx___
p = prob.index_;
vars = cvx___.problems( p ).duals;
%
% Check name
%
if isempty( name ),
error( 'Anonymous dual variables are not al... |
0d7aa508f1ebab1d3099ba0168af2c722f8c90a9d5b307ac09b770b0216f209e | MATLAB | 2,115 | 67 | function p = PlotSpikeWaveforms(W,varargin)
%PlotSpikeWaveforms - Plot spike waveforms.
%
% USAGE
%
% p = PlotSpikeWaveforms(W,<options>,<options2>)
%
% W waveforms obtained using <a href="matlab:help GetSpikeWaveforms">GetSpikeWaveforms</a>
% <options> optional list of property-value pairs... |
8d0cd4426ef506cea0c231fb38e90d47f6d14638b4ea6ce5376d4934a580cac3 | MATLAB | 2,115 | 67 | function [ params ] = readconfig( fname )
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically relevant behaviors of the ecosystems.
% Copyright (C) 2015 Vanni Bucci, Geor... |
4f4a2b7180fa82463c756715d790b17b3c7d8969723fce1cc3a71f6fc12da53f | MATLAB | 2,117 | 69 | % SET_NESTED_FIELD set a value somewhere in a struct
%
% SET_NESTED_FIELD(obj, indx, val) sets the location denoted by `indx`
% (a pointer sequence into `obj`) in `obj` equal to `val`, and returns
% a modified copy of `obj`.
%
% See also GET_NESTED_FIELD
function obj = set_nested_field(obj, indx, val)
if len... |
a5f54c540d0e77cf85f0ee05ea65d1f035f83f2625006b1fa0c63c1bd7441a45 | MATLAB | 2,117 | 73 | function [ratemap, ang_hd, mr, peak] = plot_polar_rate_map(self, cel, params, MaxRho)
% root.plot_polar_rate_map(cel);
% root.plot_polar_rate_map(cel, params, MaxRho);
%
% params is optional - [title, u2 score] (default [1 1])
% MaxRho is optional - positive number, upper bound of Rho
%
% andrew 3 april 2010
if ~exist... |
399ca7d3944e1795c0a541499ceac77e4c31c9b7ce6e743c71bf94bbdb2e9f49 | MATLAB | 2,120 | 55 | % ====================================
%% Help
% ====================================
%
% CBIG_train_MSHBM_Epilepsy_submit
%
% Submits CBIG_train_MSHBM_Epilepsy.m as a single PBS job to the headnode.
% Run this script from the compiler node. It resolves all environment
% variables on the compiler node (where they are s... |
54c3fdd5c57540d753181d70fb454882bd2dcce69edb407731eaac52c6bc05b0 | MATLAB | 2,120 | 63 | % rsc = linmap(val,valMin,valMax,mapMin,mapMax)
% ---------------------------------------
%
% Performs a linear mapping of val from the range [valMin,valMax] to the range [mapMin,mapMax]
%
% Inputs:
% val Input value
% valMin Minimum value of the range of val
% valMax Maximum value of the range of val
% m... |
ca325c20887613d1aa63b40dacdbf99a57a0de3211a9448f41a3dd2121159cd8 | MATLAB | 2,120 | 57 | function [f_fd,f_fd_deriv,intervene_matrix_fd,perturbations_fd] = estForwardDiffDeriv(T,data,keep_species,intervene_matrix,perturbations)
% 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
%... |
d0479550969307db7e9ba219c5a1c92566d6e51c9472b7904d656ef1b63c4dd4 | MATLAB | 2,120 | 74 | function [] = u3d_in_latex(fname, media9_or_movie15)
%U3D_IN_LATEX LaTeX code which includes a U3D file.
%
% usage
% U3D_IN_LATEX(fname, media9_or_movie15)
%
% input
% fname = LaTeX file name (a '_small.tex' will be appended)
% media9_or_movie15 = LaTeX package to use for including the 3D file
%
% out... |
dcc09179d9ee352a1880c4fc1d36c6f33febc5ccea5e6a7e5c65694ca622d110 | MATLAB | 2,120 | 59 | function [loadmovieflag, Mem_max, w, handles] = loadbin_init(handles)
if isempty(handles.RegPara)
RegPara = [];
variableinfo = who('-file', fullfile(handles.filepath, handles.filename));
if ismember('RegPara', variableinfo)
load(fullfile(handles.filepath, handles.filename), 'RegPara')
... |
3f45778c823a309200851b09d331ec8bed430904ee2f2c7c8aab10c5e73c0587 | MATLAB | 2,121 | 78 | function [vertex_coords, faces] = read_surf(fname)
%
% [vertex_coords, faces] = read_surf(fname)
% reads a the vertex coordinates and face lists from a surface file
% note that reading the faces from a quad file can take a very long
% time due to the goofy format that they are stored in. If the faces
% output variable ... |
cd018055b42f2acb3abe02896d5f71c17f3cfc80239be45728dc2b372f8abc65 | MATLAB | 2,122 | 59 | function [A_global_L2] = benchmarkCdiffDataL2Opt(cfg, T,BMD,keep_species,data_counts)
% 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 e... |
43b38cbe804d54a5ed366abe029fedfb939fe7aed77bb8d546777e0f4ed5d32d | MATLAB | 2,123 | 64 | function z = conv(x,y)
%Disciplined convex programming information for CONV:
% Convolutions are a combination of both multiplications and additions.
% Therefore, to insure that the no-product rule is satisfied, CONV(X,Y)
% requires that either X or Y be constant. Further conditions may also
% apply depending o... |
5a0427577e3c1b27fc2cb96dd7856ff527defc7621e5f1f45117aeb132bff154 | MATLAB | 2,124 | 57 | function tf = CBIG_Yeo2011_check_example_results(output_dir)
% result = CBIG_Yeo2011_check_example_results(output_dir)
%
% This function compares the example results saved in <output_dir> with the
% reference results.
%
% Input:
% - output_dir:
% The output directory where example results are saved.
%
% Outp... |
7c18421a11fbeb91c08cc368e9e224c3128baca1c286735ab36de6a9f5290d40 | MATLAB | 2,124 | 65 | function [betas, stats] = CBIG_fitGLM_3t(subInfoFile, GMICVFile, q)
% [betas, stats] = CBIG_fitGLM_3t(subInfoFile, GMICVFile, q)
% What is the subtype order?
% Offset by 1, the RID column
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
SUB_COL = 1+3;
COR_COL = 1+1;
f... |
b82c9708147a96ea34e04a854cb567e8441379b1e7577da58589eac6069f0a60 | MATLAB | 2,124 | 69 | function plot_four_tapers(w1,w2,w3,w4)
% Plots four different taper desings on a single graph.
% Inputs:
% [w1 w2 w3 w4]: an array of taper widths
%
% Original code written by Lieven Vandenberghe.
% Updated by Almir Mutapcic 12/2005
n = size(w1,1);
colormap(gray);
width = zeros(2*n,4);
width([1:2:2*n-1],:) = [w1... |
075ecc8523f2fb50a281105b1f920868cb3999c6e9a3031bc8ce7bd980921bee | MATLAB | 2,127 | 90 | function [pval med P] = circ_cmtest(varargin)
%
% [pval, med, P] = circ_cmtest(alpha, idx)
% [pval, med, P] = circ_cmtest(alpha1, alpha2)
% Non parametric multi-sample test for equal medians. Similar to a
% Kruskal-Wallis test for linear data.
%
% H0: the s populations have equal medians
% HA: the s pop... |
51caec223cc21af240c27bbbeddcc051e78a9926518fb1c57c709ef4d0edf117 | MATLAB | 2,127 | 78 | function [vertex_coords, faces] = read_surf(fname)
%
% [vertex_coords, faces] = read_surf(fname)
% reads a the vertex coordinates and face lists from a surface file
% note that reading the faces from a quad file can take a very long
% time due to the goofy format that they are stored in. If the faces
% output variable ... |
85a094ff104f40ec06eff8985a7b5bdde3c93e4b35e175785a72a41761403930 | MATLAB | 2,127 | 61 | function plotOneBorderOnMapCCF(dorsalMaps, allROIs, metricField, randomBorder, smoothSD, cmapInfo)
% Plots one random border over a metric map, with the cell positions
% associated to that border
% Figure
allenMapSMc(dorsalMaps, [-3.6, 0, -2, 3]) % Creates figure by itself
% Plot params
msz = 8;
xLimits = [-4 0];
yLi... |
923b5c381d62d5c68f3879f0c1336c37db7b92a5e7fb6f3a159c0649295cd894 | MATLAB | 2,127 | 73 | function z = psdjmul(x,y, K)
% z = psdmul(x,y, K)
%
% PSDMUL for full x,y. Computes (XY+YX)/2
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.3 by Imre Polik
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F.... |
3ad78e4825ad736a356376836ce16365b4dc4078c49c93968e0c79d18d7eb90a | MATLAB | 2,128 | 73 | % Demonstration of estimating covariance between paired measures of meta-d'
% (e.g. two tasks from the same individuals)
%
% SF 2019
clear all
Ntrials = 400;
Nsub = 100;
c = 0;
c1 = [-1.5 -1 -0.5];
c2 = [0.5 1 1.5];
group_d = 2;
group_mratio = 0.8;
type1_sigma = 0.2;
rho = 0.6;
type2_sigma = 0.5;
for i = 1:Nsub
... |
2ebc6a1e05b92a9708692d1ce4c26b5cc49163b7a992ce7d5b5e05f58bcff475 | MATLAB | 2,129 | 83 | % Optimal doping profile optimization with current gain constraint.
% Boyd, Kim, Vandenberghe, and Hassibi, "A tutorial on geometric programming"
% Joshi, Boyd, and Dutton, "Optimal doping profiles via geometric programming"
% Written for CVX by Almir Mutapcic 02/08/06
% (a figure is generated)
%
% Determines the optim... |
f3390df1d3c9b90075bcd8fc6e68ebed0c1dddc065b8fe9d4a77ae13bdce6397 | MATLAB | 2,129 | 54 | function ea_plan_revision(directory,sourceels,revs)
options = ea_getptopts(directory);
backupRecon = strrep(options.subj.recon.recon, '.mat', '_backup.mat');
if isfile(backupRecon)
copyfile(backupRecon, options.subj.recon.recon);
end
load(options.subj.recon.recon);
save(backupRecon, 'reco');
for rev=1:length(revs... |
fe77b261bc4e64d228afe34f17063d3bd6c78941a5acb7485a7297eab83bd586 | MATLAB | 2,129 | 60 | function Serr=specerr(S,J,err,trialave,numsp)
% Function to compute lower and upper confidence intervals on the spectrum
% Usage: Serr=specerr(S,J,err,trialave,numsp)
% Outputs: Serr (Serr(1,...) - lower confidence level, Serr(2,...) upper confidence level)
%
% Inputs:
% S - spectrum
% J - tapered fourier trans... |
2ebae0f310df216b2ed7f93f42fced5bd004ff181ea7ef26c97de1b252be5e50 | MATLAB | 2,130 | 43 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
8f3f15d8e89134d9bcba837d0057363feccbb9d34c817b5f37c8e6713dac0300 | MATLAB | 2,130 | 69 | % Section 4.5.4: Design of a cantilever beam: recursive formulation (GP)
% Boyd & Vandenberghe "Convex Optimization"
% (a figure is generated)
% Almir Mutapcic 02/08/06
%
% We have a segmented cantilever beam with N segments. Each segment
% has a unit length and variable width and height (rectangular profile).
% The go... |
77b9052b78ed7a7739ee7311db14fee3928882f584409543ff59c58e724377e3 | MATLAB | 2,132 | 71 | % This function is only used to save Analyze or NIfTI header that is
% ended with .hdr and loaded by load_untouch_header_only.m. If you
% have NIfTI file that is ended with .nii and you want to change its
% header only, you can use load_untouch_nii / save_untouch_nii pair.
%
% Usage: save_untouch_header_only(hd... |
9734ea622204ff6cb81e0f5bb0270873dfdcbe97df3dceb6a4231af6e2256831 | MATLAB | 2,133 | 68 | % MEANS: Means, standard errors and variances. For column vectors, means(x)
% returns the mean value. For matrices or row vectors, means(x) is a
% row vector containing the mean value of each column. The basic
% difference from the Matlab functions mean() and var() is for a row vector,
%... |
c71b35cc67bb62b938c17f0e876f1f4df3bc65881d7b4810c9e88059db353086 | MATLAB | 2,134 | 75 | %isivector - Test if parameter is a vector of integers satisfying an optional list of tests.
%
% USAGE
%
% test = isivector(x,test1,test2,...)
%
% x parameter to test
% test1... optional list of additional tests (see examples below)
%
% EXAMPLES
%
% % Test if x is a vector of doubles
% ... |
d6c407d545fa5e75b8218403f4fcee8f767a65ccc7de101ac4e1d5e4cb22b858 | MATLAB | 2,136 | 58 | function [corr, avg_corr_sorted, I] = CBIG_ASDf_computeCorrBetweenRuns(inputDir, k)
% [corr, avg_corr_sorted, I] = CBIG_ASDf_computeCorrBetweenRuns(inputDir, k)
%
% This function computes pair-wise correlation between each run (random
% initialization). In addition, for reach run, it computes the average correlation
% ... |
648b1869c376efaebd564d8f7395d36d516bd6aa5bba05776a203da795f937e4 | MATLAB | 2,137 | 74 | function dx = distanceMatrix( dims , lx , cyclic_type )
%% some useful numbers to access nodes at each resolution level
d = prod(dims,2);
N = sum(d);
dx = zeros(N,N);
Nmaps = size(dims,1);
offsets = zeros(Nmaps,1);
for i=2:Nmaps
offsets(i) = d(i-1) + offsets(i-1);
end
sd = {};
for i=1:Nmaps
... |
c0c28ba36478310596d615538e99ed96965435988bd3cc81867cff552d281afc | MATLAB | 2,137 | 75 | % firfiltdcpadded() - Pad data with DC constant and filter
%
% Usage:
% >> data = firfiltdcpadded(data, b, causal);
%
% Inputs:
% data - raw data
% b - vector of filter coefficients
% causal - boolean perform causal filtering {default 0}
%
% Outputs:
% data - smoothed data
%
% Note:
% f... |
8fd52dab422e2f6c13cb31ea17505e6ec538084542fcd8f5e284631218883803 | MATLAB | 2,138 | 75 | %isivector - Test if parameter is a vector of integers satisfying an optional list of tests.
%
% USAGE
%
% test = isivector(x,test1,test2,...)
%
% x parameter to test
% test1... optional list of additional tests (see examples below)
%
% EXAMPLES
%
% % Test if x is a vector of doubles
% ... |
a3378b5fec7115057e3aa29bf34a84be605dbbb8b955f2b04ceb898c647b30e1 | MATLAB | 2,138 | 70 | % get holdout set for lasso contrasts, 2nd-level batch scripts
% hard-coded options
% 'fivefold_leave_whole_subject_out' : 5-fold cross-validation, leaving
% whole subject out (all images from subject across all conditions)
% 'leave_one_subject_out' : leave one whole subject out
holdout_set_type = 'fivefold_leave_who... |
439d01aae367e1e4444c17b51d75364399611171352c39d2fb35788d072b834c | MATLAB | 2,139 | 73 | % Minimum volume ellipsoid covering union of ellipsoids
% Section 8.4.1, Boyd & Vandenberghe "Convex Optimization"
% Original version by Lieven Vandenberghe
% Updated for CVX by Almir Mutapcic - Jan 2006
% (a figure is generated)
%
% We find a smallest ellipsoid containing m ellipsoids
% { x'*A_i*x + 2*b_i'*x + c < 0 }... |
abb42010661c6eada6fd8c0ebbf54fbe196bdb28dee5dcaff5cfcb9e6e7c0665 | MATLAB | 2,139 | 94 | function [adfreq, n, ts, nf, w] = nex_wf(filename, varname)
% nex_wf(filename, varname): Read waveform variable from a .nex file
%
% [adfreq, n, ts, nf, w] = nex_wf(filename, varname)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% varname - variable name
%
%
% OUTPUT:
% n - number... |
cd5452f81e7f611a6aca9e112da662c9f890f1a849d71cdee115252c2a095f31 | MATLAB | 2,140 | 48 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
f6f5985508c3920dcbc92b120b60c605ab95cb70e77036e503c42b95cfad8fea | MATLAB | 2,140 | 79 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
% compare laminar profile of perfusion signals and cell body density
%% set parameters
% basic parameters
NumROIs = 360;
Numlayers = 15;
AnalysisDir = ['/Users/guofanhua/Desktop/gfh/work/StandardBrainTemplateAndAtlas/BigBrain_Lam... |
2cbadcecf53ae176a111cc9cf19b6012b882edd0c590f423444fc3a00793cf9b | MATLAB | 2,141 | 73 | % Exercise 4.27: Matrix fractional minimization using second-order cone programming
% From Boyd & Vandenberghe, "Convex Optimization"
% Joëlle Skaf - 09/26/05
%
% Shows the equivalence of the following formulations:
% 1) minimize (Ax + b)'*inv(I + B*diag(x)*B')*(Ax + b)
% s.t. x >= 0
% 2) ... |
39e9c4952cd8ed699568c0ee8418c73313381b51fbd47475a2cee73bc0da4941 | MATLAB | 2,141 | 51 | function installRes = plugin_askinstall(pluginName, pluginFunc, forceInstall)
if nargin < 3, forceInstall = false; end;
if nargin < 2 || ~exist(pluginFunc)
if ~forceInstall
db = dbstack;
if length(db) > 2 && ~strcmpi(db(end).name, 'checkouteeglab.m');
error([ 'Cannot find ' plugin... |
bd66f896d1f210b57bf2587ddfe9ed553ec2a9423fc6c3f3e5eb92d303b456c2 | MATLAB | 2,141 | 71 | function [coords,goodz]=ea_reconstruct_coords(trajectory,trajvector,options)
[cimat,reldist]=ea_sample_cuboid(trajectory,options);
vizz=0;
switch options.subj.postopModality
case 'MRI'
headtemp=ea_load_nii(fullfile(ea_getearoot,'templates',filesep,'electrode_contacts','mr','template.nii'));
case 'CT'... |
776bd61b36c45fa9fc6df8d4d9509821ec20d32f17f8ba673379954f53b387fa | MATLAB | 2,142 | 70 | function y = berhu( x, M, t )
%BERHU Reverse Huber penalty function.
% BERHU(X) computes the reverse Huber penalty function
%
% BERHU(X) = ABS(X) if ABS(X)<=1,
% (ABS(X).^2+1)./2 if ABS(X)>=1.
%
% BERHU(X,M) computes the reverse Huber penalty function with halfwidth M,
% M.*B... |
3e3b321768494065113a044b6689c1e7954c97be3c0dab7879af1240fe5cfff4 | MATLAB | 2,143 | 94 | function [res, errStr]= ftrstruct_init(typeStr)
% function [res, errStr]= ftrstruct_init(typeStr)
%
% Creates a valid and empty ftrStruct or fiberStruct
%
% typeStr: {'ftrStruct' | 'fiberStruct'}
% default is 'ftrStruct'
%
% return values
% res: the empty ftrStruct or fiberStruct
% errStr: If ... |
92b083cafc2eb91fa27128a8c18eed4626eda648c6020f623dcabf686f108bab | MATLAB | 2,143 | 57 | function [tf,reason,where] = SOFAcompare(Obj1, Obj2, varargin)
%SOFASOFAcompare
% TF = SOFAcompare(A, B) compares A and B and
% returns logical 1 (true) if they are identical.
%
% [TF,REASON,WHERE] = SOFAcompare(A, B) provides the REASON
% and shows WHERE the difference arose.
%
% ... = SOFAcompare(... |
ae7ed5e1bc22a0540595352791567495057e8fe21bf5e131c90019727ac17a67 | MATLAB | 2,143 | 78 | %%***********************************************************
%% etp: Education testing problem.
%%
%% (dual problem) maximize e'*d
%% subject to B - diag(d) >= 0
%% d >= 0
%%
%% (primal problem) minimize Tr B*X
%% subject to X >= 0
%% ... |
04981f2878f8a421da3b014535dc409ab26dc3dc231ec86aa2fc408902c4c462 | MATLAB | 2,145 | 64 | classdef CardPanel < uix.Container & uix.mixin.Panel
%uix.CardPanel Card panel
%
% b = uix.CardPanel(p1,v1,p2,v2,...) constructs a card panel and sets
% parameter p1 to value v1, etc.
%
% A card panel is a standard container (uicontainer) that shows one
% its contents and hides the othe... |
78380d9075b01f57ff33dc1afced2aa959efbbe5ddd0a4957b9374ccd3ef7624 | MATLAB | 2,145 | 94 | %BIPOLAR returns an M-by-3 matrix containing a blue-red colormap, in
% in which red stands for positive, blue stands for negative,
% and white stands for 0.
%
% Usage: cmap = bipolar(M, lo, hi, contrast); or cmap = bipolar;
%
% cmap: output M-by-3 matrix for BIPOLAR colormap.
% M: number of shades in the color... |
a6e7c12ddf1b284b7463cf94791e8b04d15cb5509511d3512de4af8d4182c325 | MATLAB | 2,145 | 91 | % Examples 5.6,5.8: An l_p norm approximation problem
% Boyd & Vandenberghe "Convex Optimization"
% Joëlle Skaf - 08/23/05
%
% The goal is to show the following problem formulations give all the same
% optimal residual norm ||Ax - b||:
% 1) minimize ||Ax - b||
% 2) minimize ||y||
% s.t... |
389d18427adc59e3a512dff5875d4df2a5205b57fef78bea6f224d0a74555d9c | MATLAB | 2,147 | 58 | function [dat] = bz_scrubTracking(dat)
% USAGE
% [dat] = bz_scrubTracking(dat)
%
% INPUTS
% dat - struct created by calling dat = importdata(file.csv) on a csv
% file exported from a .tak file
%
% OUTPUTS
% dat - the same struct 1) outliers removed
% 2) median filtering
% ... |
3f33ccb059f4f3d36442cf7669693a16933af8958e2b750a1886728b6e857d04 | MATLAB | 2,147 | 75 | function obj = geom_label(obj,varargin)
% geom_label Display data as labels
%
% Example syntax: gramm_object.geom_label('Color','auto','dodge',0.6)
% Geom label displays text (provided as 'label' in the constructor call
% gramm()). At the X and Y locations provided in the constructor call.
% Appearance of the text can ... |
421ff82facc06b3095eafcd53b34a36fdb98512ccd8f0507b95fa9fb0ad3a552 | MATLAB | 2,147 | 51 | function M_t = BMP_solution_ihMT(t, M, R1a, R2a, dw, w1, w2, kab, kba, M0a, M0b, T2b, R1b, T1d, rfmt)
% BMP_SOLUTION_IHMT Solves the Bloch-McConnell-Provotorov equations for ihMT.
%
% dM/dt = A * M + C
%
% Inputs:
% t - Evolution time duration (s)
% M - Initial magnetization state vector [Mxa; Mya; M... |
968a8f52bd49c71d572749547db22a03c0da1efef312278c06eb913a5cdff2f2 | MATLAB | 2,147 | 68 | function CBIG_MMLDA_forest_plot(A, xlimCmd, out_name)
% CBIG_MMLDA_forest_plot(A, xlimCmd, out_name)
%
% This function gives a forest plot based on GLM results (estimated difference
% between factors and standard error).
%
% Input:
% - A:
% N x 3 matrix. Outputs from hypothesis test. N is number of comparisons... |
92335492262fd0035d53534803e976a44754063fad469ce852a8ebba6a63ceaa | MATLAB | 2,148 | 52 | function ea_normsubcorticalsegm(options)
directory=[options.root,options.patientname,filesep];
if exist([directory,'mmnormalized.mat'],'file')
return
end
mkdir([directory,'atlases',filesep,'mni',filesep]);
mniatldir=[directory,'atlases',filesep,'mni',filesep,options.patientname,filesep];
natatldir=[directory,'at... |
2981b90ca4a5c7881873049601254bfedb1906593641c2d0115d66a0fd8d9397 | MATLAB | 2,149 | 59 | function dpvl = palm_dpxlabel(dpx,adj)
% Label a DPV file (vertexwise data).
%
% Usage:
% dpxl = palm_dpxlabel(dpx,adj)
%
% - dpx : Data per vertex or per face to be labelled. It should be
% a logical vector, and the values marked as "true" are
% the ones labelled.
% - adj : Sparse adjacency matri... |
5f835c4cd2cd8f73bbc23e52b0e30d340dcb38355818bc1fcfde2d7002f4bf75 | MATLAB | 2,150 | 60 | function [H] = globalrescale(f);
% GLOBALRESCALE creates the homogenous spatial transformation matrix
% for a 7 parameter rigid-body transformation with global rescaling
%
% Use as
% [H] = globalrescale(f)
%
% The transformation vector f should contain the
% x-shift
% y-shift
% z-shift
% followed by the
% p... |
8ad0b613b8b2a029f7cda5e813bea073ba6628c0333a5f178ac8e0ad816788c9 | MATLAB | 2,150 | 88 | %% figure S3
load('figureS3_data')
load('figure4_data.mat', 'motif_time');
%% A
Z = linkage(squareform(distance_matrix), 'ward');
n_clus = 7;
T = cluster(Z, 'maxclust', n_clus);
% Cluster number (1-7) to motif number (0-6) mapping
cluster_to_motif = zeros(n_clus, 1);
for k = 1:n_clus
cluster... |
4d808454ab4482de771725584c96968b2adfe6f7b088b92944c1a2177564a197 | MATLAB | 2,151 | 87 | function [track_info,pos_info_val] = bz_olypherInfo(data,round_to,smoothing)
% USAGE
% [track_info,pos_info_val] = bz_olypherInfo(data,round_to,smoothing)
%
% INPUTS
% data - matrix (M x N x D) where M is the number of cells to analyze,
% N is the number of trials for each cell, and D is t... |
f9d7cafd9563f2a41401782c4b4659c8bad142e264028e20eed1978d9617d235 | MATLAB | 2,151 | 81 | % NIFTI Object
%
% create - Create a NIFTI-1 file
% disp - Disp a NIFTI-1 object
% display - Display a NIFTI-1 object
% fieldnames - Fieldnames of a NIFTI-1 object
% nifti - Create a NIFTI-1 object
% subsasgn - Subscript assignment
% subsref - Subscript referencing
%
% other opera... |
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