sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
560b1ae472aa6977de9e76156f3aaf51267b3a63ec6f5f7e6417950fc18a5642 | MATLAB | 25,661 | 696 | function [ subject ] = nmri_processing(subject, data, params)
%[ subject ] = nmri_processing(subject, data, params)
%
% This function will do the source space processing including
% power @sensor level (for QC)
% source recon
% power @source
% connectivity @source
%
% subject = subject structure, see nmri_read_s... |
7844488624a353508b798c1b5be811d6e4cc35850f16a9f88373a8aa3af1469d | MATLAB | 25,672 | 824 | function PlotEphysStats(ExpName, Params, HomeDir, oneFigureHandle)
% plot ephys statistics for MEA data
% Parameters
% -----------
% ExpName : str
% Params : structure
% The following fields are used
% groupColors : (nGroup x 3 matrix)
% the RGB colors to use for each group during plotting
%
% Hom... |
3f481dc5dbe452a8c67cbb09567e7de6dfbdf8d73852b98d323e057c0b106665 | MATLAB | 25,736 | 565 | classdef SingleCapillaryReporter < handle
% SingleCapillaryReporter - Class for detecting and analyzing capillary segments in ultrasound tracks
%
% This class uses Hidden Markov Models (HMM) to identify capillary segments
% based on velocity and spectral features extracted from particle tracks.
... |
28483a1724e83cbf41947cba44c7934a9017d561b7ef8deb1dab942ac02d65eb | MATLAB | 25,742 | 658 | function Figure5(datapath,codepath, savedir)
% datapath = 'C:\Users\mld9131\Documents\GitHub\Papers\MLD\Figure5\Data';
% codepath = 'C:\Users\mld9131\Documents\GitHub\Papers\MLD\Figure5\Code'
% savepath = Z:\david\maggie\data\
%% A. Schematic of the simplex
% add path and load DS projection data
%location of analysi... |
cbd51f4dca66d6c31df9f28c8fe53205c7e0ae3eda73c313aa463d91d3f8d8b4 | MATLAB | 25,831 | 770 | function varargout = legendflex(varargin)
%LEGENDFLEX Creates a more flexible legend
%
% legendflex(M, param1, val1, ...)
% legendflex(h, M, param1, val1, ...)
% [legend_h,object_h,plot_h,text_str] = legendflex(...)
%
% This offers a more flexible version of the legend command. It offers a
% different method of posit... |
f9369e0243b03286a53a2b60a9655649ec14af80b05839afba4d9877705f5976 | MATLAB | 25,840 | 598 | % POP_SELECTEVENT - Find events in an EEG dataset. If the dataset
% is the only input, a window pops up to
% ask for the relevant parameter values.
%
% Usage: >> [EEGOUT,event_indices] = pop_selectevent( EEG, 'key1', value1, ...
% ... |
506cc525b4f3210b94e62a3c02c318869681a0ed7ef9558ca09d89397285c7e9 | MATLAB | 25,888 | 672 | function [NetMet] = ExtractNetMet(adjMs, activityMatrix, lagval, Info, Params, originalCoords, channels, oneFigureHandle)
% EXTRACTNETMET Extract network metrics from adjacency matrices
%
% Parameters
% ----------
% adjMs : N x N matrix
% lagval : int
% lag for use in STTC calculation (in ms)
% Info : structure ... |
d671044dde8b8fe022c1b5413124f9736f8e5d6622e33f4290eff9da31d2cbc1 | MATLAB | 25,896 | 492 | function plot_trial_by_trial_correlation
close all
clear all
clc
% Plot trial-by-trial pairwise activity correlation.
% Select a folder containing data.
folder_name = uigetdir;
cd(folder_name)
% Control.
load('behavior_control.mat')
load('activity_control.mat')
load('activity_iti_control.mat')
behavior = behavior_co... |
a86077f2f74d53e6ee648005cc4352a0cc5e4a0debce26a087918889e5482377 | MATLAB | 26,018 | 499 | % STD_PRECLUST - select measures to be included in computation of a preclustering array.
% This array is used by POP_CLUST to find component clusters from a
% specified parent cluster.
% Selected measures (dipole location, ERPs, spectra, scalp maps, ERSPs,
% ... |
d8d923df105ae10a6b03e0d651396e63573e46c3e9d3ad26d7756a77bc58709e | MATLAB | 26,032 | 669 | % POP_EDITEVENTVALS - Edit events contained in an EEG dataset structure.
% If the dataset is the only input, a window pops up
% allowing the user to insert the relevant parameter values.
%
% Usage: >> EEGOUT = pop_editeventvals( EEG, 'key1', value1, ...
% ... |
f24638fd45939dd4b5cc56150eb590b18ea581c9f412c90732416531cd5b25e8 | MATLAB | 26,158 | 544 | classdef McsAverageSegment < McsHDF5.McsSegmentStream
% Holds the contents of a SegmentStream with spike data
%
% Important fields:
% AverageDataMean - (1xn) cell array, each cell holding arrays of
% (samples x averages) values, where 'samples' is
% the ... |
7a22e1af13007d279a419ee8e99255155cceef01bee1747023ca11c3512ae8ef | MATLAB | 26,231 | 697 | function [FourModelsigthre]=arrange_nodal_Slope2(Nodal_metrics,indminNodalStrmdall,indminNodalindre,notenoughNodalStr,Pathnew,opt,scale,Pathnewplot,pthretype,result_name)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
354bf60880658d89cf04687f4deb8433ecdc5a7d120d36246b8270cbd59a0a5a | MATLAB | 26,243 | 777 | function [sS, ok, msgs] = som_set(sS, varargin)
%SOM_SET Create and check SOM Toolbox structs, give values to their fields.
%
% [sS, ok, msgs] = som_set(sS, [field, contents, ...])
%
% sM = som_set(sM,'name','SOM#1.1');
% [dummy,ok,msgs] = som_set(sData);
% sT = som_set('som_topol','... |
3e2a7d255c5ffaf6bd4f7acf6c04547a167fb56ee3aeccc513ca3734eb4d2379 | MATLAB | 26,243 | 550 | % POP_HEADPLOT - plot one or more spherically-splined EEG field maps
% using a semi-realistic 3-D head model. Requires a
% spline file, which is created first if not found.
% This may take some time, but does not need to be
% done again for this chan... |
386a38acac572c5fa7ded45f9d1de5f1f40f260e5126fa4e96b3e1110f336b82 | MATLAB | 26,287 | 634 | clear;
cd(fileparts(matlab.desktop.editor.getActiveFilename));
%% Requirements
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% IMPORTANT: This script is designed for Windows system + WSL %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 1: have a GPU
parallel.gpu.enableCUDAF... |
77f2bfad9b6a7e4757a7723be4a6025b539c96a9f0ce79a61a71580702c6a779 | MATLAB | 26,319 | 660 | classdef ImageEditor < handle
% ImageEditor - Simple tool for editing grayscale segmentation masks
% Sets values to any specified value while preserving other grayscale values
% Supports three orthogonal views (View 1, 2, 3)
% Usage:
% editor = ImageEditor(segmentation) % From matrix
% edi... |
4b1a1a7ff96caf0a9b401ff3109197d0dc6037fde4bf2aca306c08c2a1a08ffe | MATLAB | 26,434 | 533 | function [header] = read_4d_hdr(datafile, configfile)
% hdr=READ_4D_HDR(datafile, configfile)
% Collects the required Fieldtrip header data from the data file 'filename'
% and the associated 'config' file for that data.
%
% Adapted from the MSI>>Matlab code written by Eugene Kronberg
% Copyright (C) 2008-2009, Centre... |
2e1343bb556dc769848ac68863a4bcc3e79ae93f468ed693a6a320178546e004 | MATLAB | 26,446 | 588 | function plot_communication_subspace_similarity_across_time
close all
clear all
clc
% Plot communication subspace similarity across time during delay.
% Select a folder containing data.
folder_name = uigetdir;
cd(folder_name)
q = 3;
% Control.
load('behavior_control.mat')
behavior = behavior_control;
load('populat... |
8033c1f41c9446f3fc9b89a644d7378c68d83aa30153bafe968c1bc6579c0375 | MATLAB | 26,454 | 896 | function coactPaper_figureS07()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=6;
fontsize=6;
close all
fh=initFig('width',18.6,'height',11+2,'font','Arial','fontsize',fontsize);
x=15;y=5;
panel_01(x,y,fontsize);
panelLetter2(x-letGapX-4,y-letGapY+3,alphabet(1,labelCase),'fontSize',labelSize,'isBo... |
02171f6254769b8429861567afacc3e1d4c27ca44e08d7029ad03fb4e3376321 | MATLAB | 26,488 | 666 | % validate_pSFT
%
% This script validates the pSFT estimation pipeline by simulating stimulus and BOLD time series from pre-defined pSFT parameters.
% It then estimates the pSFT parameters and compares the estimates to the ground truth.
% Results are saved under `validate-pSFT/estimates/validation_pSFT_n<num_subjs>_yyy... |
c40bec4a2531c6751295962fde6a4966caaac572a6d5e1d3c074a7b97c881359 | MATLAB | 26,694 | 571 | % This script is used to analyze the in vivo data for the manuscript.
% USAGE:
% InVivo_Script_BiExp_Relax_Manuscript
%
% OUTPUTS:
% IVIM parameter maps for different models
%
%
% AUTHOR:
% Dr. Helge Zoellner (Johns Hopkins University, 2025-06-12)
% hzoelln2@jhmi.edu
% Dr. Julia Stab... |
156ee395b060f9da8e9edb822d5f471944cfda4f430beb288bda077021710445 | MATLAB | 26,800 | 610 | % STD_PRECOMP - Precompute measures (ERP, spectrum, ERSP, ITC) for channels or
% components in a study. If channels are interpolated before
% computing the measures, the updated EEG datasets are also saved
% to disk. Called by POP_PRECOMP. Follow with POP_PLOTSTUDY.
% ... |
907ce4910b3498315f9f68ec64dd7fb75da76d0b9df9d3abc9bcb7c637d9dff7 | MATLAB | 26,845 | 680 | % TFTOPO - Generate a figure showing a selected or representative image (e.g.,
% an ERSP, ITC or ERP-image) from a supplied set of images, one for each
% scalp channel. Then, plot TOPOPLOT scalp maps of value distributions
% at specified (time, frequency) image points. Else, imag... |
b381a80cd893dcfe4782234c635526e26042d85a0e79302db1ed1ef8b3619829 | MATLAB | 27,085 | 647 | classdef Reservoir
% Recurrent neural network reservoir class
properties (Constant)
ResultNames = {'psi', 'vmi', 'xmi', ... % emergence measures
'loss', 'tstar', ... % performance measures
'ps', 'pe', 'pse'}; % probability measures
... |
1e1398fbd8c68375d5e401867bd6f4bd9f27f05cb18dafc11a501eb19395a779 | MATLAB | 27,113 | 846 | function varargout = mri_view(varargin)
% MRI_VIEW MATLAB code for mri_view.fig
% MRI_VIEW, by itself, creates a new MRI_VIEW or raises the existing
% singleton*.
%
% H = MRI_VIEW returns the handle to a new MRI_VIEW or the handle to
% the existing singleton*.
%
% MRI_VIEW('CALLBACK',hObject,ev... |
6f3daedf080bfbefeeda21721a4b9d545a34852b47daf9201f1ad6cc4011eaf2 | MATLAB | 27,113 | 640 | %% Script to run pipeline app and propagate settings back to Params
clear app
app = MEANAPApp;
app.MEANAPStatusTextArea.Value = {'Welcome! The MEA-NAP GUI is launched.'};
% GUI resizing
% app.UIFigure.SizeChangedFcn = createCallbackFcn(app, @updateAppLayout, true);
% Default home directory
app.MEANAPFolderEditField... |
4dc3696c237d9e82287333f0361ec18b59d18a12dc8a288e16cada645e5b31e5 | MATLAB | 27,199 | 813 | function varargout = meta_SOMclusters(meth,SOMResults,varargin)
% varargout = meta_SOMclusters(meth,SOMResults,varargin)
%
% Multi-function toolbox for working with sets of clusters,
% particularly those extracted from SOM parcellation
%
% [cl,anyStudy,studyByCluster] = meta_SOMclusters(SOMResul... |
0747855b328f012f9901df6b674ebe63944c148c8aac8c66334c957e57eda502 | MATLAB | 27,680 | 585 | % POP_NEWSET - Edit/save EEG dataset structure information.
%
% Usage:
% >> [ALLEEG EEG CURRENTSET] = pop_newset( ALLEEG, EEG, CURRENTSET,...
% 'key', val,...);
% Inputs and outputs:
% ALLEEG - array of EEG dataset structures
% EEG - current dataset structure ... |
7fb5bf61127e9315bf4436b6e13bfdebc6bc8cb33fcae2ba199505b23708e5f5 | MATLAB | 27,723 | 730 | function fieldtrip2fiff(filename, data, varargin)
% FIELDTRIP2FIFF saves a FieldTrip raw data structure as a fiff-file, allowing it
% to be further analyzed by the Neuromag/Elekta/Megin software, or in MNE-python.
%
% Use as
% fieldtrip2fiff(filename, data)
% where filename is the name of the output file, and data i... |
bb69e06db65cbb67a16a32e7852633875297c56a175c3367d0aa447e11470066 | MATLAB | 27,745 | 807 | % spots2pos - Extract position samples from spots files.
%
% Extract position samples from one or more spots files, separate or merge
% multiple LEDs, interpolate missing samples, synchronize, resample, save to
% .pos file(s) and concatenate.
%
% Spots files can be generated by DeepLabCut (in csv format) or by
% p... |
433688a4f01116f3c4337c5bcdf7a12ab2a480e5b99d8f6a6f8e5d8d0ca62c0f | MATLAB | 27,904 | 588 | % pop_dipfit_settings() - select global settings for dipole fitting through a pop up window
%
% Usage:
% >> OUTEEG = pop_dipfit_settings ( INEEG ); % pop up window
% >> OUTEEG = pop_dipfit_settings ( INEEG, 'key1', 'val1', 'key2', 'val2' ... )
%
% Inputs:
% INEEG input dataset
%
% Optional inputs:
% 'hdmfile' ... |
c140244e7a905be53d271ff021aeb27b06624b1cac74d7e38b1def40dc33ba47 | MATLAB | 27,905 | 686 | %Axon analysis and quantification code associated with Gutman-Wei et al.,
%2025 - main script
%Originally written in MATLAB 2019a
%Updated version of tracing analysis, which can be used for all tracing
%comparisons of axons and dendrites. This main script reads tracing files
%formatted in SWC file format and saved as ... |
6b5eb40f9b4aedf6a71d471aa48f4cb09f1ec5c1d08585beace47616518cfb72 | MATLAB | 27,915 | 704 | %% [totalField,fieldmapSD,mask]=UnwrapPhaseMacroIOWrapper(input,output,maskFullName,algorParam)
%
% Input
% --------------
% input : input directory contains NIfTI (*mag* and *ph*) files or structure containing filenames
% output : output directory that stores the output (Unwrapped total field and field... |
ce30f81e889d6e800c521487dfee49350ae0102bcf0894e728ff0c92f2719525 | MATLAB | 27,951 | 901 | function coactPaper_figureS17()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=5;
fontsize=6;
close all
fh=initFig('width',18.6,'height',22,'font','Arial','fontsize',fontsize);
x=11;y=5;
panel_01(x,y,fontsize)
panelLetter2(x-letGapX-2,y-letGapY,alphabet(1,labelCase),'fontSize',labelSize,'isBold',... |
bf361eb781e8a196effe97003fab7319627339802e46184cbce8049a6e8b8ed0 | MATLAB | 28,024 | 728 | %% sepia
%
% Description: This is a GUI of sepia, which is a pipeline control tool
% for standard QSM processing. It supports the following processing steps:
% (1) phase unwrapping
% (2) background field removal
% (3) QSM
% All these processing steps can be performed in one go or worked as
% standalones.
%
% After perf... |
614bf2ec691ba7fa0ed9df11d709d66d3fa5aaae8aacede320e3a9e9624df48b | MATLAB | 28,123 | 492 | % parameters file for iEEG experiments
% previous: paramsEcog.m
% (c) Jiri, Dec10 - now! :o)
params = struct;
%% set paths
localComputerSettings;
addpath(genpath(params.storage.dir_neuroHammer));
dbstop if error;
%% paradigm information
params.paradigm = struct(...
'usedParadigm', 'carDriving', ... % optio... |
b480b13b6a641541779f251b1df1dfde1ab0c01c13c13a78d1a8920f01431814 | MATLAB | 28,198 | 715 | function tests = tapas_physio_examples_test()
% Tests all PhysIO examples both as matlab scripts and via batch editor and
% compares relevant parts of physio-output structure and
% multiple_regressors file to reference results, saved by
% physio_update_examples when deploying
%
% tests = tapas_physio_examples_test()... |
da1867288f6f79d43026426ed88a517154c6589e35810957cbe583e7e69d0ff8 | MATLAB | 28,214 | 601 | function res = woe_corrV76(res,i)
% =========================================================================
% woe_corr V7 : V5 cascade with a probabilistic tie resolver at the bottom.
%
% Identical to V5 (woe_corr_full) for:
% §1-§6 matrix construction (votes, weights, AD, ADi, Cfi)
% §7-overrides (extreme, cat2... |
15f18e68c62a208522c8161bc3b502d65153c3a26aa5f69629c2853b17ec8da9 | MATLAB | 28,221 | 115 | function [omega_1, crush_counter_init, crush_counter_max, step_size] = get_RF_pulse(B1, numStep)
% B1 = input.paramStruct.B1;
% gyr = input.paramStruct.gyr;
% isGaussWave = input.paramStruct.isGaussWave;
gyr = 42.576;
isGaussWave = 1;
numPulse = 10; % number of ... |
e463207757348a49fdfed1405c67658f7d377e35e086c08406b5a99caa60e86e | MATLAB | 28,225 | 836 | function dimord = getdimord(data, field, varargin)
% GETDIMORD determine the dimensions and order of a data field in a FieldTrip
% structure.
%
% Use as
% dimord = getdimord(data, field)
%
% See also GETDIMSIZ, GETDATFIELD, FIXDIMORD
% Copyright (C) 2014-2022, Robert Oostenveld
%
% This file is part of FieldTrip, s... |
98eb6160cc72a9375c1d3b7a9f4cae72248f9ec0c150e994a3138fd1b923afe5 | MATLAB | 28,253 | 620 | function TS_Combine(HCTSA_1,HCTSA_2,compare_tsids,merge_features,outputFileName,forceWrite)
% TS_Combine Combine hctsa .mat datasets
%
% Writes the new combined dataset to a new .mat file
% Any data matrices are combined, and the TimeSeries and Operations tables are
% updated to reflect the concatenation.
%
% Note th... |
1b3ac1a8b63bdc80c21792728e3c37cc5caa835e22feea197a28b237dfcf698e | MATLAB | 28,276 | 719 | function varargout = view_NBSPredict(varargin)
% VIEW_NBSPREDICT MATLAB code for view_NBSPredict.fig
% VIEW_NBSPREDICT, by itself, creates a new VIEW_NBSPREDICT or raises the existing
% singleton*.
%
% H = VIEW_NBSPREDICT returns the handle to a new VIEW_NBSPREDICT or the handle to
% the existing si... |
f675ae1f10fc59e9c5a7d662f4d75eddfb9d8ef57844753273c93ee8666f3f53 | MATLAB | 28,348 | 834 | function coactPaper_figureS22()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=6;
fontsize=6;
close all
fh=initFig('width',18.6,'height',21.5,'font','Arial','fontsize',fontsize);
x=9;y=7;
panel_01(x,y,fontsize);
panelLetter2(x-letGapX-1,y-letGapY,alphabet(1,labelCase),'fontSize',labelSize,'isBold'... |
4a07496057f811247acc85e8b4b3730ce43217dc0480260dcabe0adae9113e31 | MATLAB | 28,453 | 756 | function coactAnalysesPipeline(rootDir, sessionName,chName,detectionintervals,varargin)
if mod(length(varargin),2)~=0
warning('options should be given as pair(s) of name and value')
return
end
verbose=false;
ttlCh=[];
accelerometerCh=[];
videofile={};
reAnalyses=false;
detectionCh={};
for idx=1:length(vararg... |
aa49ad59eb6cd0e667d7a275c5fb0a1455980760986bab8e883cf86c78ec6a7b | MATLAB | 28,515 | 614 | function varargout = eBridge(varargin)
%eBridge.m
%Identify channels within an EEG montage forming a low-impedance
%electrical bridge.
%
% Website : https://psychophysiology.cpmc.columbia.edu/software/eBridge/index.html
%
%Please cite as: Alschuler DM, Tenke CE, Bruder GE, Kayser J. (2014). Identifying electrode bridgi... |
108aa45266824297fb21404a566da974b11b8b2d87183f10a54b9a1612bb159a | MATLAB | 28,517 | 663 | classdef BioformatsImage
% BIOFORMATSIMAGE MATLAB implementation of the BioformatsImage package
%
% OBJ = BIOFORMATSIMAGE(FILENAME) creates a new BioformatsImage
% object to read an image file. This class uses the Bioformats
% toolbox, a standalone Java library for reading and writing life
... |
b69063b8567bf8d530d423d2d359f4b68628378b5bb3cd06ece2c1d7469af9d0 | MATLAB | 28,595 | 908 | function coactPaper_figure02()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=6;
fontsize=6;
close all
fh=initFig('width',18.6,'height',21,'font','Arial','fontsize',fontsize);
x=13;y=3;
panel_01(x,y,fontsize);
panelLetter2(x-letGapX-5,y-letGapY+5,alphabet(1,labelCase),'fontSize',labelSize,'isBold'... |
d06668a6236f1ba7bfff75482390d5af1a7d9a3a6d2797701c8d64e74724d961 | MATLAB | 28,601 | 623 | % STD_READDATA - load measures for data channels or
% for all components of a specified cluster.
% Called by plotting functions
% STD_ENVTOPO, STD_ERPPLOT, STD_ERSPPLOT, ...
% Usage:
% >> [STUDY, datavals, xvals, yvals, events, params] = ...
% ... |
8813e07833b763bfa423fc24b0a3e698f8c2c1f604556d1d68a5a8ed0b71101e | MATLAB | 28,656 | 687 | %% Reference script: Intrinsic Properties
% This script reproduces the analysis pipeline used in the associated
% manuscript but requires raw data that are not provided. Users should adapt
% as needed for their own data.
%% Description of analysis:
% Date: 2024.10.03
% Title of analysis: Kcng4 Active Properties... |
5c067f99a02af334e67bebfae677fdbeb1240820355ef3af4c48080ebae326f8 | MATLAB | 28,689 | 726 | function [CBF_nocalib, ATT_map, ABV_map, Tex_map, ITT_map, resultExternal] = xASL_quant_External(path_PWI4D, x)
%xASL_quant_External Perform quantification using FSL BASIL/FABBER/VABY
%
% FORMAT: [CBF_nocalib, ATT_map, ABV_map, Tex_map, ITT_map, resultExternal] = xASL_quant_External(path_PWI4D, x)
%
% INPUT:
% path_... |
20c92a4cb906542dc7503c1572a24a47e5242f4b2178dbec681300e97d0fa55d | MATLAB | 28,723 | 623 | function [sens] = ft_datatype_sens(sens, varargin)
% FT_DATATYPE_SENS describes the FieldTrip structure that represents an MEG, EEG,
% sEEG, ECoG, or NIRS sensor array. This structure is commonly called "grad" for MEG,
% "elec" for EEG and intranial EEG, "opto" for NIRS, or in general "sens" if it could
% be any one.
... |
a3407e540eb7ee1493c5a74571ce22c9ce42910fb7dcf147736ca0cbbc70b1f6 | MATLAB | 28,736 | 690 | function [ avw, machine ] = avw_img_read(fileprefix,IMGorient,machine,verbose)
% avw_img_read - read Analyze format data image (*.img)
%
% [ avw, machine ] = avw_img_read(fileprefix,[orient],[machine],[verbose])
%
% fileprefix - a string, the filename without the .img extension
%
% orient - read a specified orientatio... |
3dd3dd5708a2a0fe3d7cdc516515b848571b3e6a1e2ff3c4f5057e7a8d2631a8 | MATLAB | 28,750 | 558 | % STD_ERSPPLOT - plot STUDY cluster ERSPs. Displays either mean cluster ERSPs,
% or else all cluster component ERSPs plus the mean cluster
% ERSP in one figure per condition. The ERSPs can be plotted
% only if component ERSPs were computed and saved in the
% ... |
15348d2258a5d939ffc59d822b25080a608e40a7655eb557a179539cefc2f1a8 | MATLAB | 28,782 | 772 | function out = NL_d2(y, tau, maxm, theilerWin)
% NL_d2 d2 routine from the TISEAN package.
%
% The function estimates the correlation sum, the correlation dimension and
% the correlation entropy of a given time series, y. Our code uses the outputs
% from this algorithm to return a set of informative features about the... |
98f2fb3ccfa084e20b51bccdccbccc45a680a059bdc6f139ea65a3e0b8c0c5ca | MATLAB | 28,814 | 635 | %% SPM12 FFX batch code for Responsibility project. Can run "main" (conventional) and "comp" (computational) models.
%
% J Schultz 2019-2024
clear, %close all
warning('off','MATLAB:dispatcher:nameConflict')
spm12
%% ----------- Main settings ----------------------------------------------
% ----- Determine task(s)
% ... |
b0a8a859e402db83f0ae03939358458908cc34891672d95287b3078fc5300167 | MATLAB | 28,828 | 615 | function outstruct = cifti_parse_xml(bytes, filename)
outstruct = struct();
%truncate at null terminator to remove extension padding
nulls = bytes == 0;
if any(nulls)
bytes = bytes(1:(find(nulls, 1) - 1));
end
tree = xmltreemod(bytes);
setfilename(tree, filename);%probably helps with... |
075d32ffbd37498ca9b6565c77feda5dae91dee1b1a168ad9f6d874b7eda1d95 | MATLAB | 28,830 | 576 | %% Script to plot brain maps of cortical hierarchy and SCZ epicenters, and their
%% correlation with MIND associations.
% Copyright (C) 2026 University of Seville
% Written by Natalia García San Martín (ngarcia1@us.es)
% This file is part of Hierarchy Longitudinal MIND Gradients Psychosis toolkit.
%
% Hiera... |
b4540fa2e66dbbdeddb2d163c32249251bb458a6dadb2c2cf22a9b6d27d6317c | MATLAB | 28,847 | 67 | %% 400 EXAMPLES OF ASSEMBLY CONFIGURATIONS WITH 10 ASSEMBLIES IN A HONEYCOMB STRUCTURED TECTUM
% THERE ARE 40 CONFIGURATIONS WHICH ARE EMBEDDED IN TECTA OF INCREASING
% DEGREE v = 8 , ... 17
%
% THE ASSEMBLIES WERE CREATED IN HONEYCOMB STRUCTURED TECTUM OF DEGREE 8
% FROM n = 26 POINTS DRAWN FROM A 2D-NORMAL DISTRIBUTI... |
0e025280e4d3581ce654d901f27262b825406673154c20bc75dad56fb12a516e | MATLAB | 28,888 | 624 | function res = arg_define(vals,varargin)
% Declare function arguments with optional defaults and built-in GUI support.
% Struct = arg_define(Values, Specification...)
% Struct = arg_define(Format, Values, Specification...)
%
% This is essentially an improved replacement for the parameter declaration line of a function.... |
2384e0ba76f1a1d3567f2f05775fdceb38ce21ae07a5270d75008cc73e986f05 | MATLAB | 28,932 | 970 | function mwizard(file)
%MWIZARD - M2HTML Graphical User Interface
% MWIZARD launches a Matlab GUI front-end to edit parameters
% that are then used by M2HTML to generate HTML documentation.
% MWIZARD(FILE) allows to specify a mat-file FILE from which
% default parameters are extracted and can be updated.
%
% For... |
97961e0dfef40b8882418c571d3f3cd89d7c9d096ee07ee3bc00317af5804e11 | MATLAB | 29,084 | 533 | % POP_CHANPLOT - graphic user interface (GUI)-based function with plotting
% options for visualizing. Only channel measures (e.g., spectra,
% ERPs, ERSPs, ITCs) that have been computed and saved in the study EEG
% datasets can be visualized. These can be computed using th... |
a8b91e8a9f55d82ce90937bef69c7817160883630558b66f4e801849e1ca063f | MATLAB | 29,107 | 678 | % EEG_CONTEXT - returns (in output 'delays') a matrix giving, for each event of specified
% ("target") type(s), the latency (in ms) to the Nth preceding and/or following
% urevents (if any) of specified ("neighbor") type(s). Return the target event
% and urevent numbers... |
1317b78700a75bbc2ce83845afe82be3bb2ebcf32bab33ee81e0f0bea46fb8d1 | MATLAB | 29,131 | 641 | % STATCOND - compare two or more data conditions statistically using
% standard parametric or nonparametric permutation-based ANOVA
% (1-way or 2-way) or t-test methods. Parametric testing uses
% FCDF from the Matlab Statistical Toolbox.
% Usage:
% >> [stats, df, p... |
590cf30c4698d24dc29917a37adc7b3c20ff3cb582048b42b98257faaaf5a509 | MATLAB | 29,213 | 574 | %% simple sessions summary
% run 'manual_timestamps_analysis' to process TDT matfilese first;
% this script will load the sta traces and make plots for individual
% sessions and animal average
excel_file = 'C:\Users\zzhang21\Dropbox\Matlab\Aggression\2023_NAcGRAB_Aggression.xlsx'; % sessions to process
sheet_name ... |
3da2a193c72229b7933348d8a077bfe9ab863c3fa6ae58379072eef59e3082e3 | MATLAB | 29,362 | 505 | function [EEG, Sorig, Sclean, f, amps, freqs, g] = cleanline(EEG, varargin)
% Mandatory Information
% --------------------------------------------------------------------------------------------------
% EEG EEGLAB data structure
% ----------------------------------------------------------... |
1330d7b9dd5cbf44f1ab4dbce8f078924e59f6d49241b975b2beeaa7bbef684a | MATLAB | 29,466 | 708 | function [xCurrent,Resnorm,fval,exitflag,extra_arguments,output,lambda,Jx] =LevenbergMarquardt(obj,xGuess,lb,ub,opt)
%% LEVENBERG-MARQUARD ALGORITHM WITH BROYDEN UPDATES FOR THE JACOBIAN
%
% LevenbergMarquardt is similar to lsqnonlin with the levenberg-marquardt
% algorithm with the three main advantages:
%
... |
508281f2f72c0a9919389d243ff2c07ee111d6a9eab42c2082e364a0699d8053 | MATLAB | 29,527 | 838 | function avw_img_write(avw, fileprefix, IMGorient, machine, verbose)
% avw_img_write - write Analyze image files (*.img)
%
% avw_img_write(avw,fileprefix,[IMGorient],[machine],[verbose])
%
% avw.img - a 3D matrix of image data (double precision).
% avw.hdr - a struct with image data parameters. If
% ... |
f599fc4d61de5dd52aef7d229f141c27effc97057169d77456b5f965e4863ec1 | MATLAB | 29,662 | 593 | % POP_PRECOMP - precompute measures (spectrum, ERP, ERSP) for a collection of data
% channels. Calls STD_PRECOMP.
% Usage:
% >> [STUDY, ALLEEG] = pop_precomp(STUDY, ALLEEG); % pop up interactive window
% Inputs:
% STUDY - STUDY set structure containing (loaded) EEG dataset s... |
7d3a3249b02a7d02fccbdab06adf8195cf604c9bd7a1585db0a62b564e06d349 | MATLAB | 29,811 | 542 | function plot_pairs(groups, group_1, group_2, group_1_n, group_2_n, total_n, stats, saveLocation)
% Colors
color_black = [0 0 0];
color_dark_blue = [0 0.3373 0.5608];
color_light_blue = [0.3804 0.7529 1.0000];
color_light_gray = [.7 .7 .7];
color_dark_gray = [0.4196 0.4196 0.4196];
plotColor... |
d51f9591bae36d23abe0cd8515f8c6731fc526b799b0a2e1e3185d9d5e3749f6 | MATLAB | 30,050 | 743 | function vl_compilenn(varargin)
%VL_COMPILENN Compile the MatConvNet toolbox.
% The `vl_compilenn()` function compiles the MEX files in the
% MatConvNet toolbox. See below for the requirements for compiling
% CPU and GPU code, respectively.
%
% `vl_compilenn('OPTION', ARG, ...)` accepts the following options:
%... |
71cd3c7c23004b9b7d47e1b294cdc191b6ae2c94299a84d26759b6652cf6c02d | MATLAB | 30,101 | 946 | function varargout = eigenb(varargin)
%EIGS Find a few eigenvalues and eigenvectors of a matrix using ARPACK.
% D = EIGS(A) returns a vector of A's 6 largest magnitude eigenvalues.
% A must be square and should be large and sparse.
%
% [V,D] = EIGS(A) returns a diagonal matrix D of A's 6 largest magnitude
% e... |
de3627433401e90177c804f0c836762ab038b278c2777c291885905f5fc8dc93 | MATLAB | 30,160 | 747 | function [figureHandle, cb] = StandardisedNetworkPlotNodeColourMap(adjM, coords, edge_thresh, z, zname, z2, z2name, plotType, ...
FN, pNum, Params, lagval, e, figFolder, figureHandle, saveFigure, cellTypeMatrix, cellTypeNames)
% Plots graph network with node size pro... |
374553cc6c6119d8688b05117f72152efd92209e6259c88316ab3d03f97d004e | MATLAB | 30,512 | 605 | function print2eps(name, fig, export_options, varargin)
%PRINT2EPS Prints figures to eps with improved line styles
%
% Examples:
% print2eps filename
% print2eps(filename, fig_handle)
% print2eps(filename, fig_handle, export_options)
% print2eps(filename, fig_handle, export_options, print_options)
%
% This fun... |
462b17dd2cba61a890649130f7abaede732a9cecd722fbb01a39191a4bd85439 | MATLAB | 30,661 | 751 | function [fh, EEG, com] = pop_prop_extended(EEG, typecomp, chanorcomp, winhandle, spec_opt, erp_opt, scroll_event, classifier_name, varargin)
% POP_PROP_EXTENDED See various common properties of an EEG channel or component
% Creates a figure containing a scalp topography or channel location,
% erpimage of the data,... |
90bd0b2dfd678770960ebd26b5360260b91e30ad60cd3587a5a1836bfaaf2243 | MATLAB | 30,754 | 832 |
%EXPORT_FIG Exports figures suitable for publication
%
% Examples:
% im = export_fig
% [im alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... -transparent
% export_fig ... -native
% export_fig ... -m<val>
% export_fig ... -r<va... |
3200f462d86d8419a163aabb3f294a7a3da216cd6d385200307e3c3cdee45fb0 | MATLAB | 30,867 | 522 | % POP_EDITSET - Edit EEG dataset structure fields.
%
% Usage:
% >> EEGOUT = pop_editset( EEG ); % pops-up a data entry window
% >> EEGOUT = pop_editset( EEG, 'key', val,...); % no pop-up window
%
% Graphic interface:
% "Dataset name" - [Edit box] Name for the new dataset.
% In the right column o... |
f73140ca1d4554beafb5f0870686359bf8ec04d37fe2f9449cc87481e0beb85f | MATLAB | 31,020 | 1,043 | function mwizard(file)
%MWIZARD - M2HTML Graphical User Interface
% MWIZARD launches a Matlab GUI front-end to edit parameters
% that are then used by M2HTML to generate HTML documentation.
% MWIZARD(FILE) allows to specify a mat-file FILE from which
% default parameters are extracted and can be updated.
%
% For... |
7a5170323cfeb335af6b1810932ae55528d1933cd870a0d52c3f09c861714a90 | MATLAB | 31,077 | 838 | function [err, V, Info, ErrMessage] = BrikLoad (BrikName, param1, param2)
%
% OLD USAGE for backward compatibility, see New Usage
%
% [err, V, Info, ErrMessage] = BrikLoad (BrikName, [form], [MachineFormat])
% or
% [V,Info] = BrikLoad (BrikName, [form], [MachineFormat])
% or
% [V] = BrikLoad (BrikName, [form], [Ma... |
c77ee51ce6890e0861038336933100d2e881d5e75ed72ee0c4b7eb838b602bf7 | MATLAB | 31,109 | 768 | function [fitParamsStep3] = fit_OspreyPrelimStep3(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep2,GAP)
%% [fitParamsStep2] = fit_OspreyPrelimStep3(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM)
% Performs the second step of the LCModel preliminary analysis
% ... |
50251af13c6c17cc410871ea828be049b725f0f2570a5f40ad1f1a0f81db9d23 | MATLAB | 31,151 | 715 | function varargout = TMSfunseg(varargin)
% TMSFUNSEG M-file for TMSfunseg.fig
% TMSFUNSEG, by itself, creates a new TMSFUNSEG or raises the existing
% singleton*.
%
% H = TMSFUNSEG returns the handle to a new TMSFUNSEG or the handle to
% the existing singleton*.
%
% TMSFUNSEG('CALLBACK',hObject... |
546cf7638492e2b90aae4c382ba4062b75646a02f42c1ee9d8eb6558f390365e | MATLAB | 31,165 | 767 | function SPM = spm_spm_lqc(SPM)
% [Re]ML Estimation of a General Linear Model
% FORMAT SPM = spm_spm(SPM)
%
% Required fields of SPM:
%
% xY.VY - nScan x 1 struct array of image handles (see spm_vol)
% Images must have the same orientation, voxel size and data type
% - Any scaling should have already been... |
54b6b8542a663b02024654cd6cd14d492cda978618ce4fc266dd01fb6cfd092c | MATLAB | 31,215 | 707 | classdef Violin < handle
% Violin creates violin plots for some data
% A violin plot is an easy to read substitute for a box plot
% that replaces the box shape with a kernel density estimate of
% the data, and optionally overlays the data points itself.
% It is also possible to provide two s... |
a77f913133ec8ff705c4622d791c98e1377c12ec466e25316251054383171348 | MATLAB | 31,266 | 1,030 | function atlas = ft_read_atlas(filename, varargin)
% FT_READ_ATLAS reads an template/individual segmentation or parcellation from disk.
%
% The volumetric segmentation or the surface-based parcellation can either represent
% a template atlas (for example AAL or the Talairach Daemon), it can represent an
% individualiz... |
7ff684d6fb0bf8c12f09d0a8a4e7d0b59c33d87bb008b94eb7f61c16f817df16 | MATLAB | 31,291 | 871 | %% Figure 1
%% 1.1 IRI subscales & PCL-R factors
clc; clear; close all
load data
figure('units', 'normalized', 'outerposition', [0 0 1 1])
T = tiledlayout(2, 4);
% 1. IRI-PT
nexttile
H_IRI_PT = histogram(data.IRI_PT, 'BinWidth', 1, 'FaceColor', [0.5 0.5 0.5], 'EdgeColor', 'white');
H_IRI_PT.LineWidth = 1.5;
hold ... |
64716aa690c2343efe1dbdc83ca3bfc16ba047a788828a387799b889c04d960a | MATLAB | 31,300 | 785 | function [fitParamsStep2] = fit_OspreyPrelimStep2(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM,GAP)
%% [fitParamsStep2] = fit_OspreyPrelimStep2(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM)
% Performs the second step of the LCModel preliminary anal... |
e05b8348477e3317b54f6d13deddb43083743a5aa2df20daa947f979f94d1600 | MATLAB | 31,317 | 891 | %% example streamlined analysis
% go to analysis dir
cd('/home/uni10/nmri/projects/GoeEpiLongterm/nfocke/AllGGE_redux') % this needs to me modified for your needs
if ~exist('nmri_all_subjects','file')
% add scripts paths, if not yet present
addpath(genpath('scripts'))
end
% call the params include
nmri_include_re... |
8051b484ccf64b7c6a18717b4ce4783b0930461b7d3be746ae17c6a3b20cef96 | MATLAB | 31,345 | 381 | function osp_iniQuantifyWindow(gui)
%% osp_iniQuantifyWindow
% This function creates the initial quantify window in the gui.
%
%
% USAGE:
% osp_iniQuantifyWindow(gui);
%
% INPUT: gui = gui class containing all handles and the MRSCont
%
% OUTPUT: Changes in gui parameters and MRSCont are wri... |
fc1913cd83ba49a7e3555d8feef0154aee9a51097c8b5891d93071a31a1efe7c | MATLAB | 31,396 | 752 | %% ========================================================================
% NEURAL REJUVENATION HYPOTHESIS - COMPLETE MANUSCRIPT CODE (REVISED R4)
% ========================================================================
% Population-Level Neural Rejuvenation Dynamics in Addiction:
% A Computational Framework for Un... |
413e3c2763f26cf97615bc24b9083f693f462afd31a9449ae18a34736a9aecd4 | MATLAB | 31,462 | 778 | % PLOTTOPO - plot concatenated multichannel data epochs in a topographic
% or
% rectangular array. Uses a channel location file with the same
% format as TOPOPLOT, or else plots data on a rectangular grid.
% If data are all positive, they are assumed to be spectra.
% Usage:
% ... |
6d11df941c360fce66366174e1f5365acaf6e32da58647782d5982ca48721f88 | MATLAB | 31,659 | 795 | function [fitParamsStep2] = fit_OspreyPrelimStep2coMM3(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM, soft,constTarget)
%% [fitParamsStep2] = fit_OspreyPrelimStep2(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM)
% Performs the second step of the LCMod... |
6137eb4aabf41a48c3206b9421f1cff7c67c8e50d8217829d09e440322d5dbb1 | MATLAB | 31,698 | 537 | % Downloaded from https://www.mathworks.com/matlabcentral/fileexchange/20846-weighted-correlation-matrix
%
% =============== start of license.txt =======================
%
% Copyright (c) 2008, Liber Eleutherios
% All rights reserved.
%
% Redistribution and use in source and binary forms, with or without
% m... |
ef756f5b88249dffe2862003e640afa9edb96831532366da3bd8bb96699a7f3d | MATLAB | 31,698 | 777 | %%read cpx
function data = read_cpx(file, border, flip_img, kspace, read_params, compression_parameter)
%--------------------------------------------------------------------------
% data = read_cpx(file, border, flip_img)
%
% read_cpx: Function for reading the whole cpx-file and writes the data in
% a predef... |
7cbdade6bd45e486ad7729ccb4b14a050e36a1ea3e3706c7ee6176b653fd5eae | MATLAB | 31,826 | 862 | function ft_write_cifti(filename, source, varargin)
% FT_WRITE_CIFTI writes functional data or functional connectivity to a cifti-2
% file. The geometrical description of the brainordinates can consist of
% triangulated surfaces or voxels in a regular 3-D volumetric grid. The functional
% data can consist of a dense o... |
50b139f20b1b470620e1a3c3cec128886e37a3a069ef428fac2689d146dbf2bd | MATLAB | 32,142 | 864 | %% In Vivo Imaging Analysis Pipeline for James, Oswell, McCall, Hsu et al., 2024
%
% Code here will produce the data for Fig. 2E-Q and all associated
% supplemental figures
%
% For aesthetic purposes, most data was exported from these sections in csv
% and txt files and imported in Prism, where most statistical tests w... |
7f6ac48e9f8adb59232f5a7575ee7ccdab363300e856615554ea101c3034f6fe | MATLAB | 32,172 | 799 | function [fitParamsStep2] = fit_OspreyPrelimStep2MMExp(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM,GAP)
%% [fitParamsStep2] = fit_OspreyPrelimStep2(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM)
% Performs the second step of the LCModel preliminary... |
bbb01d712f4bba3e111916b69cffc55522f54b59c9ca7847147b601bdde300d7 | MATLAB | 32,254 | 802 | function [fitParamsStep2] = fit_OspreyPrelimStep2freeGauss(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM)
%% [fitParamsStep2] = fit_OspreyPrelimStep2freeGauss(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM)
% Performs the second step of the LCModel pr... |
58a40c16db1aee50ced856a7283050c9d59ec80763c43e0f877f8c8b63d3bb5e | MATLAB | 32,329 | 712 | classdef Violin < handle
% Violin creates violin plots for some data
% A violin plot is an easy to read substitute for a box plot
% that replaces the box shape with a kernel density estimate of
% the data, and optionally overlays the data points itself.
% It is also possible to provide ... |
0f9de73e4bf14c7493b4d109a10081736e91019d193c95b0404fd1758a13268e | MATLAB | 32,450 | 785 | function varargout = run_NBSPredictGUI(varargin)
%RUN_NBSPREDICTGUI MATLAB code file for run_NBSPredictGUI.fig
% RUN_NBSPREDICTGUI, by itself, creates a new RUN_NBSPREDICTGUI or raises the existing
% singleton*.
%
% H = RUN_NBSPREDICTGUI returns the handle to a new RUN_NBSPREDICTGUI or the handle to
% ... |
b5368aa478cf80c360193c4b1588db16039433a2af7ac66fad35c900b850e86e | MATLAB | 32,472 | 810 | function vl_compilenn(varargin)
%VL_COMPILENN Compile the MatConvNet toolbox.
% The `vl_compilenn()` function compiles the MEX files in the
% MatConvNet toolbox. See below for the requirements for compiling
% CPU and GPU code, respectively.
%
% `vl_compilenn('OPTION', ARG, ...)` accepts the following options:
%... |
0bd8d4655660ba61d0bad43cba1dfd5ffb5f9e2b8284f0fe4d582185914c6551 | MATLAB | 32,593 | 1,051 | % figure3_tf_itemdistance_plot.m - Plot beta power scaling with item distance
%
% This script loads pre-calculated TF power data organized by item distance
% (angular distance between memory items) and creates Figure 3 from the paper.
%
% KEY FINDING:
% Beta power (15-25Hz) at central channels scales with item distan... |
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