sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
39d8f321491770d19022b82a8677f0fe836b3731c1a9f2a730bf3d59a1f2b136 | MATLAB | 4,066 | 105 | function affinefile = ea_coregimages(options,moving,fixed,ofile,otherfiles,writeoutmat,masks,interp)
% Generic function for image coregistration
%
% 1. Moving image will keep untouched unless the output points to the same
% image.
% 2. 'otherfiles' will always be overwritten. If you don't want them to be
% overwr... |
52ba7dbd4c82db8c3874cdccf643c709bcadd46f8a885c09b54504ab6dccdaa8 | MATLAB | 4,066 | 113 | function [hObject, handles] = dan_plot_psg(hObject, handles)
%%
% Authors: Dan Denis
% Date: 2021-07-14
%%
% This function actually takes care of the plotting of the psg data
plotParam = handles.plotParam;
% Get the sample at the beginning of plot
startTime = (plotParam.currSample - 1) / handles.psg.hdr.srate; ... |
acbb143f597d6b96aac061f1ca04986141e3b7edd15b27684eb75109e7c458ba | MATLAB | 4,066 | 135 | function hm=plotsurf(node,face,varargin)
%
% hm=plotsurf(node,face,opt)
%
% plot 3D surface meshes (2d manifold) or polylines (1d manifold)
%
% author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
%
% input:
% node: node coordinates, dimension (nn,3); if node has a
% 4th column, it will be used to se... |
d8fd14fc23a51daf6998375bb840bdc14c3a45aa5f5f66ff5c8ccb90130f19c3 | MATLAB | 4,068 | 96 | function [bad_channels] = RFT_detect_FlatCorrNoise_electrodes(ft_struct,eeglab_template_file,steps_to_do,criteria)
%%% From a fieldtrip structure (with N trials), concatenates all trials,
%%% create an eeglab structure with this 'single concatenated trial',
%%% Detects channels that are either 'flat-lined', 'line-no... |
73cb4d0f7f49af437bd6b06cfeca0b3bf271459f63dcebcce8950f61915e8007 | MATLAB | 4,069 | 128 | function handles = ea_lc2handles(lc, handles)
% Apply Lead-Connectome options struct (lc) to GUI handles.
% Shared by lead_connectome and lead_dbs Connectome tab (ea_init_connectome_tab).
% General settings: parcellation
parcellations = ea_lc_getitems(handles.parcellation);
if ~isempty(parcellations)
if ~isfield(l... |
13a65b235494dfcf429ae0dad6fdd0b906c4e3aa7a81d5ad1e4bd5e25f043a2f | MATLAB | 4,071 | 157 | function hh = CBIG_herrorbar(x, y, l, u, symbol)
% hh = CBIG_herrorbar(x, y, l, u, symbol)
%HERRORBAR Horizontal Error bar plot.
% HERRORBAR(X,Y,L,R) plots the graph of vector X vs. vector Y with
% horizontal error bars specified by the vectors L and R. L and R contain the
% left and right error ranges for ... |
5eb1f29bad416ca9b0322f0d80380137076a49306f8fd4c88e7e5783310f3456 | MATLAB | 4,071 | 124 | function [ redred, localred ] = DoubleRedundancyMMI(varargin)
%%DOUBLEREDUNDANCYMMI Compute the PhiID double-redundancy of input data,
% assuming it follows a Gaussian distribution and using the MMI PID.
%
% NOTE: assumes JIDT has been already added to the javaclasspath.
%
% R = DOUBLEREDUNDANCYMMI(X, TAU), where X i... |
90b935568bb34cdaf8d00d875276d74d6f69b1ca040e257207765737921c9d22 | MATLAB | 4,071 | 100 | function varargout = save_string(tree, formatting)
% XMLTREE/SAVE Save an XML tree in an XML file
% FORMAT varargout = save(tree,formatting)
%
% tree - XMLTree
% formatting - 1 for indenting of tags, 0 for no formatting
% varargout - XML string
%_______________________________________... |
6fb763040b42882045d1b9e7df7fc85b30024c8cf6e36a7e102f9b489678e9cc | MATLAB | 4,073 | 136 | % eegh() - history function.
%
% Usage:
% >> eegh( arg );
% >> eegh( arg1, arg2 );
%
% Inputs:
% - With no argument, it return the command history.
% - arg is a string: with a string argument it pulls the command
% onto the stack.
% - arg is a number>0: execute the element... |
e0669626d726338cde0e093125fa66b5c5a7c23fe47fd7015f4b2c9b23d96289 | MATLAB | 4,073 | 106 | function varargout = guideApp(varargin)
% GUIDEAPP MATLAB code for guideApp.fig
% GUIDEAPP, by itself, creates a new GUIDEAPP or raises the existing
% singleton*.
%
% H = GUIDEAPP returns the handle to a new GUIDEAPP or the handle to
% the existing singleton*.
%
% GUIDEAPP('CALLBACK',hObject,ev... |
7be02c7f1efd6a5e4b89b718c36fa8028ce86a82cd07dd98dd6ec32201032d31 | MATLAB | 4,076 | 109 |
% mediation_example_script1 and 2 do the same analysis.
% ...script1 is very terse, and includes the essential commands only.
% ...script2 is longer and includes more checking that files are available, etc.
% Go to the directory this script is stored in and run the script from
% there.
disp('Mediation example script... |
aae5544e95fa3aacbad9609af05f36bd22ede01bc9b512bb4a7781deaafeaad6 | MATLAB | 4,076 | 111 | % concatdata - concatenate data stored into a cell array into a single
% array. only concatenate along the last dimension
% Usage:
% [dataarray len dims] = concatata(cellarraydata);
%
% Input:
% cellarraydata - cell array containing data
%
% Output:
% dataarray - single array containing all data
%... |
658f81463d47bc4edbde354a927a95226591dc8cae3def2cdb01e5a9b00f57ad | MATLAB | 4,078 | 129 | %%*****************************************************************************
%% sqlpmisc:
%% unscale and produce infeasibility certificates if appropriate
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004.
%%******************************************... |
1a10a398352197f84306ac79cd4400bc35c8c76b2da1113ec9fda43af6b53471 | MATLAB | 4,079 | 113 | %WAVETEST Example Matlab script for WAVELET, using NINO3 SST dataset
%
% See "http://paos.colorado.edu/research/wavelets/"
% Written January 1998 by C. Torrence
%
% Modified Oct 1999, changed Global Wavelet Spectrum (GWS) to be sideways,
% changed all "log" to "log2", changed logarithmic axis on GWS to
% a n... |
50f89eab33db4a684731a02b98259c3159ce285f5ac1c2acea0dc417ddc4f8c6 | MATLAB | 4,083 | 109 | function [rpos, rneg, results_table] = LaBGAScore_region_table_safe(fcn, r, varargin)
% LaBGAScore_region_table_safe Call a region-table function and always get 3 outputs.
%
% [rpos, rneg, results_table] = LaBGAScore_region_table_safe(fcn, r, ...)
%
% Thin wrapper around CanlabCore's @region/table (or the vendored... |
633bb3ba5fb7f28bd35052a2d583cda409698405def9983fc8a76aa9c08f86b7 | MATLAB | 4,084 | 96 | function [relativeSpikeTimes, tx] =...
getRasterFromStack(...
discreteStack,... Discrete stack containing the alignment points
kIdx,... Boolean array indicating which trials should be ignored
koIdx,... Boolean array indicating which events should be kept.
timeLapse,... 2 element array contaning the ... |
c20bb26f6964a5e5f93ada3b0a96b5bfab9733ac99a5a651566a8a315115b308 | MATLAB | 4,085 | 178 | function [physdata] = phys_merge(physfile, trigfile, mergedfile, secs2disp, sigfigs)
%phystrigs Adds "faked" triggers to physiology file
% Outputs
% physdata: Input physiology data with an additional column
% containing the "fake" scanner triggers.
% The scanner triggers column is mostly zeros, but... |
95cc77015bdce37801e63d9e5ca9fb0c3fa0c99017b91c1db08efe4de0b217b2 | MATLAB | 4,087 | 107 | function [tassmOut, indxConverted] = smactinClean(tassmIn, varName, colIndxArr, thresholdArr)
%SMACTINCLEAN: search for observations in either speckle or single-molecule properties in tassm that are LOWER OR EQUAL TO input threshold and replace them with NaN.
%
% SYNOPSIS: [tassmOut, indxConverted] = smactinClean(tassm... |
cbf0173704386d80651d323f72b8e7488d7a87aa4dbcf86a821fc89a01722172 | MATLAB | 4,087 | 107 | function [Y,YD,intervene_matrix_sim] = numInitGVL(tspan,C,Y0,interveneTimes,perturbation_begin_end,assumeStiff)
% 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 rel... |
c875f65f047cc7bcfbb73b497cd823cd684e33a16eb173cff69decad272ec3ee | MATLAB | 4,089 | 135 | function [HbO_subj_full, HbR_subj_full, muA760_full, muA850_full, amplitude_scale] = ROImua_to_HbOchan( ...
p, e, brain_nodes_idx, d_mu_a_est, hb_ratio, varargin)
%FNIRSPOWER.MEASPRED.ROIMUA_TO_HBOCHAN
% Convert a subject-specific ROI map to relative Hb and absorption fields.
%
% roi_amp_std specifies the ... |
ecd2ccd76f49e4c492cbe0ee37986d10af544c5555106e2da1f2a10431fe8091 | MATLAB | 4,089 | 113 | % written by Yiyuan Han, Essex BCI-NE Lab, 13/12/2019
% binary classification between two specific conditions
function [fISPC,sFeatures,fWeights,perfMat] = binaryClass(class1,class2,blockTagsAC,blockDatasetAC,mode,folderpath,featureNum)
%% Extract the data in specific conditions
% These two classes should be modifi... |
3c7a86ab3f35e73caa4fc9e8076de17e65c40042d0331b7412afa32ada0941ac | MATLAB | 4,093 | 113 | % eegfiltfft() - (high|low|band)-pass filter data using inverse fft
% (without using the Matlab signal processing toolbox)
% Usage:
% >> [smoothdata] = eegfiltfft(data,srate,locutoff,hicutoff);
% >> [smoothdata] = eegfiltfft(data,srate,locutoff,hicutoff,epochframes,filtorder,revfilt);
%
% Inputs:
% ... |
c4860f0000c0d26ad5cf2694a28a84e95a2bc9fa8d6ae8e26a91f664268892c9 | MATLAB | 4,094 | 82 | function write_nifti2_hdr(filename, hdr)
% WRITE_NIFTI2_HDR
%
% Use as
% write_nifti2_hdr(filename, hdr)
% where
% filename = string
% hdr = structure with nifti-2 header information
%
% See also READ_NIFTI_HDR, READ_CIFTI, WRITE_CIFTI
% Copyright (C) 2013, Robert Oostenveld
%
% This file is part of Fi... |
f90520e41d31e2c6beae0015d82f2121cee8877b42b2162e7a5df3db85ce0525 | MATLAB | 4,097 | 118 | function dicm_val_rep(dcmFile, tag, val, newFile)
% Replace tag value with val in dicmFile, and save as newFile.
%
% dicm_val_rep('myFile.dcm', 'PatientName', 'sub-002', 'newFile.dcm');
% dicm_val_rep('myFile.dcm', '0177,0011', 'sub-002'); % use hex for tag
%
% The first three input argument are manditory. The forth ... |
967cdf49fbb79ddca4fe66f78a25498744dfa1eb6c9fd1b68ece667edd4af6a2 | MATLAB | 4,100 | 128 | % jointprob() - rejection of odd columns of a data array using
% joint probability of the values in that column (and
% using the probability distribution of all columns).
%
% Usage:
% >> [jp rej] = jointprob( signal );
% >> [jp rej] = jointprob( signal, threshold, jp, normalize, discre... |
9e0479de435ee75faf1c875c8c987cbe3c79b1d11f5a1208981e33410c01692e | MATLAB | 4,100 | 148 | function savemsh(node,elem,fname,rname)
%
% savemsh(node,elem,fname,rname)
%
% save a tetrahedral mesh to GMSH mesh format
%
% author: Riccardo Scorretti (riccardo.scorretti<at> univ-lyon1.fr)
% date: 2013/07/22
%
% input:
% node: input, node list, dimension (nn,3)
% elem: input, tetrahedral mesh element list... |
afa7b3a94590db96e17080521582e5f35a978d242db010940206d7c99c5081f8 | MATLAB | 4,100 | 112 | function data = AFOFdata_struct2(inputdata, filenames)
% USE THIS FOR EXP2 SLIPS
% how it works:
% fly = AFOFdata_struct(data,filenames) where data and filenames are
% outputs from rotoball_importer()
for e = 1:length(inputdata)
for t = 1:length(inputdata{e}{1})
trial.filename = filenames{e};
... |
a0c5f67dbf3780a628d1fe2b7c7ff2a11cf6bd3b1567d2db2d80da9a07aa9917 | MATLAB | 4,102 | 101 | % makeelec() - subroutine to make electrode file in eegplot()
%
% Usage: >> makeelec(chans)
% >> [channames] = makeelec(chans)
%
% Inputs:
% chans - number of channels
%
% Author: Colin Humprhies, CNL / Salk Institute, 1996
%
% See also: eegplot()
% Copyright (C) Colin Humphries, CNL / Salk Institute, A... |
931b4d1e9d2bb772034b25c2840d87f69b7ed815526b48c76881dd308b6d5087 | MATLAB | 4,106 | 103 | function [offsets, aligned] = ...
alignwaveforms(template, waveforms, mx)
%ALIGNWAVEFORMS Finds best alignment of waveforms to a reference.
% OFFSETS = ALIGNWAVEFORMS(TEMPLATE,WAVEFORMS,MAXSHIFT), where TEMPLATE
% is an 1 x T vector and WAVEFORMS is an N x T matrix, returns an N x 1
% vector ... |
c4de95b4cf71cc1cf2c0770e1293a23f1a4888f2b3468c9aad95433a422c5e7d | MATLAB | 4,110 | 100 | function [m,max_card_matching]=matching(A,varargin)
% MATCHING Compute a maximum cardinality matching
%
% m=matching(A) returns a matching between the vertices of an undirected
% graph. A matching is a subset of edges where each vertex in incident on
% only one edge. A maximum cardinality matching is the largest poss... |
f26be53d10a73c9ab84df168b8896a687ca0ba4f3c28e4d96b20b182ed960dd1 | MATLAB | 4,111 | 116 | % biosig2eeglabevent() - convert biosig events to EEGLAB event structure
%
% Usage:
% >> eeglabevent = biosig2eeglabevent( biosigevent, interval, mode)
%
% Inputs:
% biosigevent - BioSig event structure
% interval - Period to extract events for, in frames.
% Default [] is all.
% mode... |
2ea7b4cf1c81f021251bc080ccacdf34b2e2e7bea87ffd25e7c5b7eca1d602e0 | MATLAB | 4,114 | 103 | function varargout = pickerGUI(varargin)
% PICKERGUI MATLAB code for pickerGUI.fig
% PICKERGUI, by itself, creates a new PICKERGUI or raises the existing
% singleton*.
%
% H = PICKERGUI returns the handle to a new PICKERGUI or the handle to
% the existing singleton*.
%
% PICKERGUI('CALLBACK',hO... |
164b8a2072a95da9395f2a8b8d80288245d6a7604e29ad0084aa78e3ec666194 | MATLAB | 4,118 | 107 | function [XtrR, XteR, nuis] = residualizeFold(Xtr, Xte, Ctr, Cte)
% residualizeFold Train-only nuisance regression for one cross-validation fold.
%
% [XtrR, XteR, nuis] = residualizeFold(Xtr, Xte, Ctr, Cte)
%
% Regresses the nuisance covariates out of the feature matrix, estimating the
% nuisance coefficients on... |
76e55a716b09759699c21b9672b89348640715c1e6ccb500fa11fac16d6dba48 | MATLAB | 4,118 | 122 | function OUT = run_variance_subject(snirf_path, nirs_model, baseline_sec, block_sec, iter_blocks, n_iter, concat_baseline_sec)
%RUN_VARIANCE_SUBJECT Run subject-level block-resampling analysis for GLM beta variability.
%
% OUT = fnirspower.pipeline.run_variance_subject( ...
% snirf_path, nirs_model, baseline_... |
82348a00898d2fdf2c9cc7d52c576a30243d3f8055375de7d04cf7ec8c3079bf | MATLAB | 4,118 | 137 | function Z = palm_inormal(varargin)
% Applies a rank-based inverse normal transformation.
%
% Usage: Z = inormal(X)
% inormal(X,c)
% inormal(X,method)
% inormal(X,...,quanti)
%
% Inputs:
% X : Original data. Can be a vector or an array.
% c : Constant to be used in the transf... |
db8aae7796089c10ca2c5b6365c4f9648e28acad9c158e1679c89cc7aa0d9447 | MATLAB | 4,122 | 122 | %% RUN_ABSORPTION_ESTIMATION_STEP
% Driver script: ensure μa exists, then run absorption estimation.
% - Finds latest GLM outputs (Hb and ΔOD) under project paths.
% - If μa recon is missing, reconstructs it from ΔOD betas.
% - Calls fnirspower.pipeline.run_absorption_estimation with resolved files.
%% Resolve p... |
aac80721fe349ec075fdd82a847e16ccd5f89eea3d698552df25ca5a8e47289e | MATLAB | 4,124 | 112 |
function [sessionArmChoice] = getSessionArmChoice(varargin)
% Compute and get session arm choice over all session subfolders
%
% USAGE
%
% [tracking] = getSessionTracking(varargin)
%
% INPUTS
% basePath (default: pwd) basePath for the recording file,
% in buzc... |
bcd83abc792df9a8fbc6b5d2d753e34b87ea10f94d85443015de4affac0b8581 | MATLAB | 4,124 | 143 | function myOISscr1_wrap(flist,saveid,opt1,opt2,vars2load,skip1load,checkflag)
% Usage ... myOISscr1_wrap(filelist,saveids,option1str,optionAllstr,loadVars,skip1load,checkflag)
%
% Ex.
% opt1=sprintf('''do_load'',[1:6200],''do_crop'',''do_bin'',[2 2 2],''do_binfirst'',''do_motc'',''do_maskreg'',''do_intc''');
% opt2... |
2034d2683cee9b4b67d4086d816ba4c05f7e00878525038747a936235e8872a9 | MATLAB | 4,127 | 122 | function logAnalysisFile(AnalysisFileName, writePath)
% The purpose of this utility is to provide a record of analyses run by
% writing out to a log file the state of the code that was used to analyze
% the data. It writes the log file into the current directory if only a
% filename is provided. An absolute path is req... |
64cef535b0bf939dd66a5e6b1d73c95689d0c28ec0070da253199670af7ed453 | MATLAB | 4,127 | 126 | % rejkurt() - calculation of kutosis of a 1D, 2D or 3D array and
% rejection of outliers values of the input data array
% using the discrete kutosis of the values in that dimension.
%
% Usage:
% >> [kurtosis rej] = rejkurt( signal, threshold, kurtosis, normalize);
%
% Inputs:
% signal... |
93f325d814e19b3988ec4db4cc5f65bfda6efbb622c0599a7c925ca1b03b13de | MATLAB | 4,132 | 130 | function [p U UC] = circ_raotest(alpha)
% [p U UC] = circ_raotest(alpha)
% Calculates Rao's spacing test by comparing distances between points on
% a circle to those expected from a uniform distribution.
%
% H0: Data is distributed uniformly around the circle.
% H1: Data is not uniformly distributed around th... |
65f83c05cd1a1edd39b415d9469775022ffe4b8445f2d6f55a9969e48731dcef | MATLAB | 4,135 | 114 | function varargout = ea_textdisp(varargin)
% EA_TEXTDISP MATLAB code for ea_textdisp.fig
% EA_TEXTDISP, by itself, creates a new EA_TEXTDISP or raises the existing
% singleton*.
%
% H = EA_TEXTDISP returns the handle to a new EA_TEXTDISP or the handle to
% the existing singleton*.
%
% EA_TEXTDI... |
aec19aedd821ea80de5f378c36788f9f727afacd204b5ef36f26f0109b16af99 | MATLAB | 4,136 | 88 | function CBIG_MMLDA_view_vol_slice_with_underlay(in_vol, underlay_vol, mni_space, color_map_name, plane, min_thresh, max_thresh, out_dir, out_name)
% CBIG_MMLDA_view_vol_slice_with_underlay(in_vol, underlay_vol, ...
% mni_space, color_map_name, plane, min_thresh, max_thresh, out_dir, out_name)
%
% Overlay input volum... |
ac246d51ce462b9a9a7b8c75725e576500ad3435679658296a66f2982aabb0dd | MATLAB | 4,139 | 108 | function postprocess_write_file_for_cytoscape(filename_prefix,Theta,...
bayes_factors,names)
% 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... |
8f917e52bcf8596126ec8d517a651b6811133ce73de3db5d90c5a1ef15c0216d | MATLAB | 4,142 | 132 | function cvglmnetPlot(cvobject,sign_lambda,varargin)
%--------------------------------------------------------------------------
% cvglmnetPlot.m: plot the cross-validation curve produced by cvglmnet
%--------------------------------------------------------------------------
%
% DESCRIPTION:
% Plots the cross-valida... |
b7e6aff0d3a6cfb14a0ccbb700f5247042c5d2bcda59537665850a53c7a78d78 | MATLAB | 4,143 | 99 | %% Read Medtronic Framelink XML Configuration File
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% mail@andreashusch.de, husch.andreas@chl.lu
function config = readMedtronicXMLTrajectory(filepath)
xml = x... |
41734020059ac00a009e21c8564027b30e92c80c774fb046f7ecd0d1f013d63a | MATLAB | 4,144 | 125 | % FEASREAL Generates a random sparse optimization problem with
% linear, quadratic and semi-definite constraints. Output
% can be used by SEDUMI. All data will be real-valued.
%
% The following two lines are typical:
% > [AT,B,C,K] = FEASREAL;
% > [X,Y,INFO] = SEDUMI(AT,B,C,K);
%
% An extended version is:
% > [... |
2114135837f649972ea9d774dd5b16bc69cf206d1f496d6254e69f833a4aa04b | MATLAB | 4,145 | 119 | function [ARIs, RIs] = computeRANDIdxAllROIsGMMs(allROIs, options, areas, nSplits)
% Split the dataset into nSplit 50/50 splits balanced within area, for each
% split, get all ROI GMM classifications from each split, compute adjusted
% RAND index between the classifications across the two splits, repeat
% Get train t... |
c8dbe8b4b6386bb69ada055d236354381569717ede386094149099db6a3b88df | MATLAB | 4,145 | 185 | function y = newvar( prob, name, siz, str, geo )
narginchk(2,5);
%
% Check problem
%
if ~isa( prob, 'cvxprob' ),
error( 'First argument must be a cvxprob object.' );
end
p = prob.index_;
global cvx___
%
% Check name
%
if isempty( name ),
nstr = [];
elseif ischar( name ),
nstr = struct( 'type', '.', 'sub... |
173373cc5042f79117167e3d4d51aa67477310fd6eeccf7dd91359b098ed20e8 | MATLAB | 4,148 | 137 | % lapplot() - Compute the discrete laplacian of EEG scalp distribution(s)
%
% Usage:
% >> laplace = lapplot(map,eloc_file,draw)
%
% Inputs:
% map - Activity levels, size (nelectrodes,nmaps)
% eloc_file - Electrode location filename (.loc file)
% For format, see >> topo... |
292163df128aec8f29bed36d2f7d90dc43ab487ad6c315f11baded8597003d87 | MATLAB | 4,148 | 119 | classdef zscore_normalize_FP
% zscore_normalize_FP is a feature preprocessing (FP) object that z-score
% normalizes each feature by calculating the mean and standard
% deviation using the training set data and then subtracting this mean and
% dividing by this standard deviation for both the training and tes... |
b57639ca82b3e1367416f988a9c4932ef261369933943a1288b117a21f369074 | MATLAB | 4,148 | 119 | function ea_options2handles(options,handles)
if isempty(handles.patientlist.Data.subjId) || isempty(handles.patientlist.Selection) || ~isfield(options, 'modality')
arrayfun(@(x) set(x, 'Enable', 'off'), handles.registrationtab.Children);
arrayfun(@(x) set(x, 'Enable', 'off'), handles.localizationtab.Children)... |
861f9041ccd91035d0ea4b297217d6e933303074a1c1d2022818fa96222d3c99 | MATLAB | 4,149 | 143 | function z = cvxprob( varargin )
global cvx___
cvx_global
tstart = tic;
if ~iscellstr( varargin ),
error( 'Arguments must be strings.' );
end
%
% Clear out any old problems left at this depth. These will be here due to
% an error while constructing a CVX model, or due to the user deciding to
% start over when con... |
dbcc5d186b33be3b2fc90bd8bfe2fdd57017fa785e414f7ffe197507f072528b | MATLAB | 4,150 | 121 | % =========================================================================
% Script: Simulation_study2_1_B1_B0.m
% Authors: Zijian Gao,Qianxue Shan,Weitian Chen
% Email: zijian.gao@link.cuhk.edu.hk
% Date: 2025-12-19
% Version: 1.0
%
% Copyright (c) 2025 Zijian Gao, Qianxue Shan,... |
9b1c53e8990ec06cec529677f47c049cd8e4950cd273d5deb47a7313bc0fea0b | MATLAB | 4,153 | 130 | function [normdata,intmean,intstd] = NormToInt(data,normtype,int,sf,varargin)
%NormToInt(data,normtype, int,sf) normalizes the data to a subset of time
%(int). Has options for multiple normalization types.
%
%INPUTS
% data [Nt x Ndim]
% normtype 'mean','median' 'Z', 'max', 'percentile', 'modZ' for modified Z-s... |
e2ece3c92e9348cde97de999eb21e52bd394e4ed84600df7ced38e9238fe44d8 | MATLAB | 4,154 | 106 | function V = vm_minimize(V, C, KP, P0, KA, A0, max_relaxation_steps, force_tol)
% VM_MINIMIZE Relax vertex positions to (local) mechanical equilibrium
% using the FIRE (Fast Inertial Relaxation Engine) algorithm.
%
% V = VM_MINIMIZE(V, C, KP, P0, KA, A0, max_relaxation_steps, force_tol)
% iteratively moves vertice... |
5f5f9d73d20f0ae85a4357b5e94b5bc3f8da3f6c2ce4da357f58dd39ebe6ea91 | MATLAB | 4,155 | 122 | % eeg_countepochs() Count how many epochs there are of each type
%
% Usage:
% >> eeg_countepochs(EEG);
%
% Inputs:
% EEG - input dataset
% epochmarker - ['type'|'eventtype'] indicates which part of the
% EEG.epoch structure the different trial types are stored in. Depending
% on what sy... |
60ce0ffcf3c65c9543611a069874868a4033547e80d288a9938af39aea38ff2e | MATLAB | 4,155 | 114 | function ConvertTwoLFPFilessToOne(datasetfolder,recordingname,varargin)
% Converts previous _SWLFP.mat and ThetaLFP.mat files to a single
% StateScoreLFP.mat file.
%INPUT (optional) If no inputs included, select folder containing .lfp
% and .xml file in prompt.
%
% datasetfold... |
37bf0134274bf902fa2725d85eb37bd05ab1ede43908e523fe6a4e96bc2ae42e | MATLAB | 4,157 | 106 | function [diffRadOut, detectPairOfMpd, mpdOriginal] = getTrackMpd(tracksIn)
%GETTRACKMPD: calculate maximum pairwise distance of each detections in single-molecule tracks
%
%SYNOPSIS: [diffRadOut, detectPairOfMpd, mpdOriginal] = getTrackMpd(tracksIn)
%
%INPUT: tracksIn : (struct) input tracks, has at least follow... |
1b17cfe65274584edffda7dda9fae1c8bfb2fb9d514132ecf586a3947995620e | MATLAB | 4,159 | 130 | function [p U UC] = circ_raotest(alpha)
% [p U UC] = circ_raotest(alpha)
% Calculates Rao's spacing test by comparing distances between points on
% a circle to those expected from a uniform distribution.
%
% H0: Data is distributed uniformly around the circle.
% H1: Data is not uniformly distributed around th... |
682109be0e17f5b0821f270b0a1f7fccea7f1bf9dc622b44199ec2874e20da09 | MATLAB | 4,159 | 112 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Assign Shirer Network to Brainnetome ROI
% Author: Yuan Zhang
% Date: 2025-07-25
%
% Description:
% This script maps each Brainnetome atlas ROI (BN_ROI) to a Shirer
% 14-network parcellation based on the overlap of voxel locations.
% For... |
c584dff2a58bf8f20dafbbece3cd94b2965893dabdb187bf9d7bbf421e5c85de | MATLAB | 4,160 | 115 | function [R,Rperm,Rnaned,Rpermnaned,h]=ea_Rmap(varargin)
% creates a correlation nifti file given a set of images and a
% regressor ("R map" in Horn 2017 AoN)
% ea_Rmap(fis,regressor,outputname,mask,sk,corrtype) % sk can be 'k','s','sk'
% for smoothing and normalization options. Mask only necessary if
% choosing 'k' o... |
caac326f69ca664954a95e00aed984e32722bdc19e2b38c9b65593899c559f60 | MATLAB | 4,162 | 78 | function [S,t,f,R,Serr]=mtspecgramtrigpt(data,E,win,movingwin,params,fscorr)
% Multi-taper event triggered time-frequency spectrum - point process times
%
% Usage:
%
% [S,t,f,R,Serr]=mtspecgramtrigpt(data,E,win,movingwin,params,fscorr)
% Input:
% data (univariate spike data -1d structure array of spike ti... |
0c765d03d1c2cec89944258dc5fb6a72459cf106003760f1fd6ae45d260d24ef | MATLAB | 4,163 | 126 | % eeg_rejsuperpose() - superpose rejections of a EEG dataset.
%
% Usage:
% >> EEGOUT = eeg_rejsuperpose( EEGIN, typerej, Rmanual, Rthres, ...
% Rconst, Rent, Rkurt, Rfreq, Rothertype);
%
% Inputs:
% EEGIN - input dataset
% typerej - type of rejection (1=raw data; 0=ica).
% Rmanual ... |
3015d45758db678a97174d6b38922ba0852bf87325e1a69a3e2a3d69aeaa94f7 | MATLAB | 4,164 | 108 | function [out, azi, ele, idx] = SOFAspat(in,Obj,azi,ele,flag)
% SOFAspat
% [out, azi, ele, idx] = SOFAspat(in,Obj,azi,ele) spatializes the sound IN using
% the HRTFs from OBJ according to the trajectory given in AZI and ELE.
% Input:
% in: vector with the sound
% Obj: SOFA object containing the HRTFs
% azi, ... |
f9f2dec2ab14c1199594a06d259571648bac1c3d8e724c54ae6765a4db715a7c | MATLAB | 4,167 | 120 | clc; clear;
addpath("E:\Data Analysis\2P Imaging\Programs\Fiji.app\scripts");
addpath('D:\Git\FindUSN\CalciumDataProcessing\Preprocessing\MotionCorrection');
% Select the root folder to process
rootFolder = uigetdir(pwd, 'Select Root Folder to Process');
if rootFolder == 0
error('Folder selection canceled.');
end... |
986de0fac00e3d159dce845095edf94f6b8123ef1988af27d5deed17a23b5659 | MATLAB | 4,169 | 86 | function [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpb(data,params,fscorr)
% Multi-taper coherency matrix - binned point process
%
% Usage:
%
% [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpb(data,params,fscorr)
% Input:
% data (in form samples x channels) -- required
% params: structure with field... |
85a728a56babc9cbce051a75b3593dd158dffaa56ed2275272a88fcfcdb510da | MATLAB | 4,171 | 109 | %function [xml, rxml] = LoadXml(FileBase)
%loads the xml file using xmltools (have to have it in the path)
% rxml returns it's original layout - very messy structure but contains all
% the xml file contents.
% xml - is the ouput structure which is backwards compatible to LoadPar
% output, so you can use it instead ..al... |
e525567c554f8ae66d4d8466fa0c81f2d60883d84e36a782b9175f01b751a515 | MATLAB | 4,171 | 84 | function [correct_class_decision_values normalized_rank_results rank_confusion_matrix] = get_rank_and_decision_value_results(cv, YTe, classifier_labels, decision_values, create_rank_confusion_matrix)
% This helper method calculates the normalized rank results, the decision values for the correct class, and the rank con... |
799010cdfb9be3914b33b9b34ddb0b8deef52a8c5110c7cd34de5667ea97c638 | MATLAB | 4,172 | 107 | function ea_gencheckregfigs(options, type)
if ~exist('type', 'var')
type = {'coreg', 'norm'};
elseif ischar(type)
type = {type};
end
if ismember('coreg', type)
fprintf('\nExporting coregistration check images to %scheckreg...\n', [options.subj.coregDir,filesep]);
% Make dir
ea_mkdir(fullfile(optio... |
c7d621e09c101e772160538d8ea5cb3676b6b42e7228bf9b0c1895d7c677b2f6 | MATLAB | 4,172 | 147 | % Iterations over different delamination durations
% To speed up comment line 71 in
% SOP_multicell_LI_adapted_weighted_with_trigger_PerimSave.mat before
% running this script to avoid saving simulations movies for each
% iteration
clear all; close all; clc;
model.ratio = 'rho';
model.zone = 'Gaussian-like prone... |
02050fff7d97f43045949f33bae630fef37718a52cc024c0303c4df2ab9dd420 | MATLAB | 4,173 | 111 | function [ viewinfo ] = EventVewPlot
%UNTITLED Summary of this function goes here
% Detailed explanation goes here
obj = findobj('tag','EventExplorerMaster'); FO = guidata(obj);
%Two options of current timepoint: Event Number, arbitraty timepoint
%FA/misses for DetectionReview
switch FO.viewmode
case 'timepoin... |
dfffca02f3731572c14d147cc672c7614babf7dff8bb377e7900864fc387ec98 | MATLAB | 4,173 | 128 | function lab = eigK(x,K)
% [lab,q,f] = eigK(x,K)
%
% EIGK Computes the spectral values ("eigenvalues") or even the complete
% spectral decomposition of a vector x with respect to a self-dual
% homogeneous cone K.
%
% > LAB = EIGK(x,K) This yield the spectral values of x with respect to
% the self-d... |
90a966c1e7ccb3decf8f8935a4ad2b98af5b38f768f9787c53c367b138ec3a52 | MATLAB | 4,174 | 103 | function [tau, curve, info] = ami(x, L, opts)
%AMI Average mutual information versus lag.
% TAU = AMI(X,L) returns the lag of the first local minimum of the average
% mutual information of X with itself, computed over lags 0:L. TAU is the
% embedding delay for phase space reconstruction.
%
% [TAU,CURVE] = AMI(X... |
8ce7250a5d62bc96cd5013169b8be0609be818e8fec4ffc33feeb7436533e0dc | MATLAB | 4,175 | 162 | function x = sparsify( x, mode )
global cvx___
narginchk(2,2);
persistent remap
%
% Check mode argument
%
if ~ischar( mode ) || size( mode, 1 ) ~= 1,
error( 'Second arugment must be a string.' );
end
isobj = strcmp( mode, 'objective' );
pr = cvx___.problems( end );
touch( pr.self, x );
bz = x.b... |
ca7d00b51bdd5b339e5aca716304f0711a2fb8e073439fab6275c9cfecaa6a79 | MATLAB | 4,176 | 88 | function CFA_ReOrientDataForAna
answ = inputdlg('1:T1,2:T2,3:EPI,4:withT1,5:CT','which conditions?',1,{'1'});
modality = str2num(answ{1});
if modality==4
answ2 = inputdlg('1:T2,2:EPI,3:CT','which modality for OtherMode image',1,{'1'});
modother = str2num(answ2{1});
end
PG = uigetdir(pwd,'Need Reorient directory... |
1a8e0be6dc937c43e8279f9c4fa52197daf6837c4be33d1f25143d5a124c0e67 | MATLAB | 4,177 | 170 | function fit = lognet(x,is_sparse,irs,pcs,y,weights,offset,parm,nobs,nvars,...
jd,vp,cl,ne,nx,nlam,flmin,ulam,thresh,isd,intr,maxit,kopt,family)
[noo,nc] = size(y);
if noo ~= nobs
error('x and y have different number of rows in call to glmnet');
end
if nc == 1
[classes,~,sy] = unique(y);
nc = length(cl... |
6da2cdde400a4c62463d4acd7632c13e3fd626e305cd3d796e4e49397b7571cf | MATLAB | 4,178 | 127 | datafolder = '/Users/dlevenstein/Dropbox/Research/Datasets/BWData/';
%Make List of all Recordings in data folder
recordings = dir(datafolder);
recordings(strncmpi('.',{recordings.name},1)) = []; %Remove entries starting with .,~
recordings(strncmpi('~',{recordings.name},1)) = [];
numrecs = length(recordings);
%%
au... |
9fa4cccbadce61f7cbc2abed7b47315e0a7ee6396ec42c975feea30db98b4e51 | MATLAB | 4,178 | 113 | classdef ea_slicer_for_lead
properties
install_path
executable_path
installed_version
upstream_version
download_url
end
properties (Access = private)
release_tag = 'v231122-beta'
release_version = struct('linux', '0.1.0-2023-11-22', 'mac', '0.1.0-202... |
daeee4192a18c8e196d47dea14a80ed4929879ead8c3d0733c493200f17bd376 | MATLAB | 4,180 | 103 | % pop_chancenter() - recenter cartesian X,Y,Z channel coordinates
%
% Usage:
% >> chanlocs = pop_chancenter(chanlocs); % pop up interactive window
% >> [chanlocs centerloc] = pop_chancenter(chanlocs, center, omitchan);
%
% Inputs:
% chanlocs = eeglab channel location structure (see readlocs())
% center ... |
08962877ca49cdc63c04f8525679f90d8a3b616fa0a88bc10e9dd149f2fa34cd | MATLAB | 4,183 | 117 | function [string, file_name] = user_string(string_name, string)
%USER_STRING Get/set a user specific string
%
% Examples:
% string = user_string(string_name)
% isSaved = user_string(string_name, new_string)
% [value, file_name] = user_string(...)
%
% Function to get and set a string in a system or user specific... |
b911f51967aaf1cb0e7a993ce458f6f9d1bf6effdaa1bd4fcd176c002aeab239 | MATLAB | 4,184 | 148 | function result = cvlognet(object, lambda, x, y, weights, offset, foldid, ...
type, grouped, keep)
if nargin < 10 || isempty(keep)
keep = false;
end
typenames = struct('mse','Mean-Squared Error','mae','Mean Absolute Error',...
'deviance','Binomial Deviance','auc','AUC','class','Misclassification Error');
... |
50f994512db190de4179d297619111776e8884461eb8bde99e4a79ac3e6e1207 | MATLAB | 4,186 | 132 | function plot_spectogram(psd, freqs, lims, stages, plotType, varargin)
% Plot a spectogram. Will either plot a heatmap depicting power in all
% frequeny bands, or as lines depicting band-averaged power
%
% Required input:
%
% psd = freqs x epoch array
% freqs = vector indicating frequency at each row
% lims = [lo hi] f... |
740f4e048d3662d76044ee49eb6aef29ece0560a94e1da403366ca2d74aeb946 | MATLAB | 4,186 | 90 | % 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... |
f05f387c3ab69c022c7d783cc4a7f108afcc634f99cdf74dd7155d51c1b673b2 | MATLAB | 4,188 | 114 | function ref = ea_create_threshold_union_ref_nii(outPath, inFiles, thr, voxSize)
% CREATE_THRESHOLD_UNION_REF_NII
% Make a zero-filled reference NIfTI whose FOV is the union bounding box
% of all *thresholded* regions (V > thr) across input images.
%
% outPath : '.nii' or '.nii.gz'
% inFiles : char or cellstr of NIfTI ... |
422e31d7175ba227b35456bbf7fcc3bf40fa6ec8b9e678cc840656593ea9e6f5 | MATLAB | 4,190 | 122 | function displayGUIplots(handles, ifspine, ifdendrite)
if nargin == 1
if ~isempty(handles.roi)
ifspine = 1;
else
ifspine = 0;
end
if ~isempty(handles.dendrite)
ifdendrite = 2;
else
ifdendrite = 0;
end
end
if ifspine == 0 && ifdendrite == 0
roimap = ze... |
9580d73a98516c6cba5586168cf7fff6073d6d52d1a6ef7cb9957b40093386e4 | MATLAB | 4,191 | 106 | function [rotcorr, rrcorr] = fast_cross_correlation(rois, rrois, dim,forty)
angles=rotation_xyz(dim,forty);
corr=zeros(size(rois,2),'single');
%rot_angle=zeros(size(rois,2),'single');
rcorr=zeros(size(rrois,2),'single');
%rot_rangle=zeros(size(rrois,2),'single');
% Construct numerator and denumerator tables, that c... |
5c548d79338cc84403be4fe3b3a2aeb28bdbff9bdb7e9a28adca33924dee08a1 | MATLAB | 4,192 | 106 | function [rotcorr, rrcorr] = fast_cross_correlation(rois, rrois, dim,forty)
angles=rotation_xyz(dim,forty);
corr=zeros(size(rois,2),'single');
%rot_angle=zeros(size(rois,2),'single');
rcorr=zeros(size(rrois,2),'single');
%rot_rangle=zeros(size(rrois,2),'single');
% Construct numerator and denumerator tables, that c... |
3c4368710bb4e80faaf21308e02019fbcc48bbf695c71e003c920a7f269c4003 | MATLAB | 4,193 | 114 | % 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... |
0505ed20c59ad99ecc26bfe13ce3c823545e654b4c862a3a3a29ac4215e64b2d | MATLAB | 4,196 | 121 | function g = loudWeight(f,phon)
%LOUDWEIGHT Calculate loudness weighting coefficients
%
% G = IOSR.AUDITORY.LOUDWEIGHT(F) returns loudness-weighting linear-
% magnitude coefficients for frequencies F (Hz). The function is based on
% the loudness at 65 phons defined in ISO 226:2003. The coefficients are
% scale... |
491f7eb47ca2c5f6b88aafbe90e006c751356bf012eaaca1976a405945c9f564 | MATLAB | 4,197 | 114 | function [delta,h,alpha] = iswnbr(w,thetaSQR)
% [delta,h,alpha] = iswnbr(vSQR,thetaSQR)
%
% ISWNBR Checks feasibility w.r.t. wide region/neighborhood of Sturm-Zhang.
% vTAR:= (1-alpha)*max(h,v) projection v onto theta-central region
% delta = (sqrt(n)/theta) * norm(vTAR - v) / norm(v)
%
% ********** INTERNAL FUNC... |
86227b6c31b935b1f7c2bc0ad58d0e21af74d028301c425c63784630b1d119bf | MATLAB | 4,198 | 147 | function obj=geom_bar(obj,varargin)
% geom_point Display data as bars
%
% Example syntax (default arguments): gramm_object.geom_bar(0.8)
% This will add a layer that will display data as bars. When
% data in several colors has to be displayed, the bars of
% different colors are dodged. The function can receive an
% opt... |
a673007ac67ba0f700bee4fbbd2fb76416c69d42e3ed9921b498f3238b301948 | MATLAB | 4,199 | 110 | function [SleepState] = bz_ThetaStates(basePath,makePlot)
% [SleepState] = bz_ThetaStates(basePath)
% Takes the output of SleepScoreMaster and separtes WAKEstate into
% WAKEtheta and WAKEnontheta by applying the same threshold calculated form
% REM sleep. This is not an ideal way and needs to be improved.
% F.Sha... |
a9fc0ee7e4d8f8d2387ceb01639ffc42422bc36db5ce294c5c496cb60eb3bca7 | MATLAB | 4,199 | 109 | %function [xml, rxml] = LoadXml_SleepScore(FileBase)
%loads the xml file using xmltools_ss (have to have it in the path)
% rxml returns it's original layout - very messy structure but contains all
% the xml file contents.
% xml - is the ouput structure which is backwards compatible to LoadPar
% output, so you can use i... |
1b7f3aeb8c46bf4ebf8e7529453835da263f064d86bbef91d2dfc850b174de9c | MATLAB | 4,200 | 153 | function p = PlotTicks(xy,varargin)
%PlotTicks - Plot ticks.
%
% USAGE
%
% p = PlotTicks(x,y,<options>,<options2>)
%
% x list of tick abscissae
% y list of tick ordinates
% <options> optional list of property-value pairs (see table below)
% <options2> options for func... |
0b7f98de1a1741456999b5d1cc9b04a8b17467b8ae74ce02245e352300870921 | MATLAB | 4,202 | 85 | %Baseline
%load 'StimSM', stimAllTrials';
tstart_i=-2;
tstop_i=0;
% (StimCombined.m, stimAllTrials.mat)
rr1a_percentmeansBase=nanmean(all_rr1a_percent(tt>=tstart_i&tt<tstop_i,:));
rr1a_percentsemBase=nanstd(rr1a_percentmeansBase)/sqrt(size(rr1a_percentmeansBase,2));
yproj2max_percentmeansBase=nanmean(all_yproj2... |
2426c44fd591a43dd6abeee4626c12c8e60912a24f111bf74274ed868057f25d | MATLAB | 4,203 | 120 | function CBIG_ASDf_computeBootstrapZScores_wrapper(in_dir, out_dir)
% CBIG_ASDf_computeBootstrapZScores_wrapper(in_dir, out_dir)
%
% Wrapper function to compute bootstrapped z-scores and p-values
%
% Input:
% - in_dir:
% Absolute path to directory where bootstrapped factor estimates
% are saved... |
1eb4a276015e6541ffead4ebb838b15b67a8f9ab4a6a5177aca97c67960bff9e | MATLAB | 4,206 | 170 | function [ftr lens] = saveFTR(finame,datastruct,I,vox,info,saveit)
if nargin == 5,
saveit = true;
end;
cc = {};
csc = {};
cD = {};
lens = [];
if isempty(vox),
warning('Empty field vox: guessing');
vox = [2 2 2];
end;
reparam_step = 0.9*min(vox); %mm
P = datastruct.state;
labels = zeros(length(I),1);... |
45a8c21f8dddad288d4463c37fd8c4a25603ac7811baf034af569296ae61c6fa | MATLAB | 4,207 | 135 | % Elmore delay sizing for an interconnect network.
% Boyd, Kim, Vandenberghe, and Hassibi, "A Tutorial on Geometric Programming"
% Boyd, Kim, Patil, and Horowitz, "Digital circuit optimization via geometric programming"
% Written for CVX by Almir Mutapcic 02/08/06
% (a figure is generated)
%
% We consider the problem o... |
5912afdac2a8c809136de6b0e135eda96b8272dba7df5c8028ee2e679f2f05fd | MATLAB | 4,210 | 109 | function [svn_profile,svn_str] = buildSvnProfile(folders,keywords,strs,rec)
%BUILDSVNPROFILE Read data from files tagged with SVN keywords
%
% This function extracts SVN keyword data from specified files, and
% returns the filename, path and keyword data to a cell array (and
% optional char array).
%
% Keyw... |
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