sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
da061e5755fb4519d0bd4d96b5c85fb3201d7249de66fd25ca43961b24812af7 | MATLAB | 15,020 | 308 | classdef NiftiFilepath
properties (Access = public)
patientId = [];
modality = [];
referenceSystem = [];
warningAttribute = [];
dataRootFolder = [];
end
properties (Access = protected)
directFilepath = [];
openDialogIfNotExists = [];
... |
5204c355c5e544967683b77a19af1e1959c8477e639e3d9d98d5d1be2a0702f0 | MATLAB | 15,025 | 301 | classdef libsvm_CL
% libsvm_CL is a Support Vector Machine (SVM) classifier object (CL)
% that uses the LIBSVM package (i.e., this function is Neural Decoding Toolbox
% wrapper for the LIBSVM package). A support vector machine is a classifier
% that learns a function f that minimize the hinge loss between the... |
0516a7cd72cb1cd11e3df1870c34c55f2b2ec063a662334df003ff8898eec07e | MATLAB | 15,076 | 427 | function [trackIndx,errFlag] = chooseTracks(trackedFeatureInfo,criteria,probDim)
%CHOOSETRACKS outputs the indices of tracks that satisfy the input criteria
%
%SYNOPSIS [trackIndx,errFlag] = chooseTracks(trackedFeatureInfo,criteria);
%
%INPUT trackedFeatureInfo: -- EITHER --
% Output of trac... |
37e04ba2b983521e2780b4263ebc4e7f6df56e8b0e2474e7fd720320e7aee562 | MATLAB | 15,078 | 344 | function [NEV] = F_openNEX(fileName)
% NEV = readNexFile(fileName) -- read .nex file and return file data in NEV File structure
% Sorted with Plexon Offline Sorter first !!!!!!!!
% V2.3
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% INPUT:
% fileName - if empty string, will use File Open dialog
%
% OUTPUT:
% NEV - a s... |
1a15b38d2a7c6c5515ac56938d073259d00b1544fa42847b61ccd413d75f7cc7 | MATLAB | 15,101 | 452 | function [success, commands] = ea_checkinstall(cmd,checkonly,robot,prefs)
success=1;
if ~exist('checkonly','var')
checkonly=0;
end
if ~exist('robot','var')
robot=0;
end
if ~exist('prefs','var')
prefs = [];
end
python_envs = ea_regexpdir(fullfile(ea_getearoot, 'classes', 'conda_utils', 'environments'), '.*\... |
12aa70fff151f06d7996bb0c473e0c49e0702f279f90e7621ee795e0813bd93b | MATLAB | 15,140 | 414 | % [ wave, f, t, coh, phases, raw, coi, scale, period, scalef ] = getWavelet( x, Fs, fMin, fMax, nbins, graphics )
%
% x:
% vector - wavelet analysis is applied
% multi-column matrix - wavelet analysis is applied to each column
% separately
%
% two-column matrix - treated as two time series and the csd, coherenc... |
06e7f676b969d07e60de14cb8d1198b5b35db77b99ab1e2475d89428cf0396a9 | MATLAB | 15,171 | 435 | function [Elements,varargout] = ea_plyread(Path,Str)
%PLYREAD Read a PLY 3D data file.
% [DATA,COMMENTS] = PLYREAD(FILENAME) reads a version 1.0 PLY file
% FILENAME and returns a structure DATA. The fields in this structure
% are defined by the PLY header; each element type is a field and each
% element prop... |
3f75461f0f12d13a58d8e4b48509abd39838fb71ab81809098b30c1f0eb52ea8 | MATLAB | 15,192 | 410 | function CBIG_ArealMSHBM_cMSHBM_estimate_group_priors_child(s, mesh, tmp_dir)
% CBIG_ArealMSHBM_cMSHBM_estimate_group_priors_child(s, mesh, tmp_dir)
%
% This is the child script to estimate group priors for the strictly contiguous individual
% areal-level parcellation generation. To speed things up, we parallize the s... |
7ca404a452e93f6e0e1df40b5dc36819722df2a04b2a7e1b075ea44573e7044d | MATLAB | 15,216 | 442 | function [ar, dataOUT] = fun_detect_artifacts(dataIN, sleepstages, varargin)
% Automated artifact rejection of sleep EEG data based on Hjorth
% parameters. This function is an attempt of a MATLAB implementation of the
% artifact rejection functions in the Luna toolbox. Artifact rejection
% works in two steps, first on ... |
680466acaef978dc6ffd626e5e4e07f045b3bdafca90c33e5741bc17796573d1 | MATLAB | 15,218 | 280 | % crossfreq() - compute cross-frequency coherences. Power of first input
% correlation with phase of second.
%
% Usage:
% >> crossfreq(x,y,srate);
% >> [coh,timesout,freqsout1,freqsout2,cohboot] ...
% = crossfreq(x,y,srate,'key1', 'val1', 'key2', val2' ...);
% Inputs:
% x ... |
432a3dd7cead3280ef451548d6dc10c1d9098e6d8395c02719c218488d1739c3 | MATLAB | 15,257 | 470 | function [gmtc,interpol_tc,voxelmask]=ea_extract_timecourses(options)
% Extract timecourses based on template
%% prepare voxelmask:
directory=[options.root,options.patientname,filesep];
% BIDS FIX: Add prefix to filename only
rest_r = ea_prependFilename(options.prefs.rest, 'r');
ea_warp_parcellation(rest_r, options);... |
608a2943cecb94f84d03ca55ea6891fcc2acce87cf9d8dec7484cfb582f5bdf0 | MATLAB | 15,258 | 479 | function cls = ea_spm_preproc_write8(res,tc,bf,df,mrf,resolution)
% Write out VBM preprocessed data
% FORMAT cls = spm_preproc_write8(res,tc,bf,df,mrf)
%____________________________________________________________________________
% Copyright (C) 2008 Wellcome Department of Imaging Neuroscience
% John Ashburner
% $Id: ... |
296aaa0855092f3f5422f0367616b7d97ccd3bbf91c43f48bedd5b48b3a7715e | MATLAB | 15,270 | 347 | % std_checkset() - check STUDY set consistency
%
% Usage: >> [STUDY, ALLEEG] = std_checkset(STUDY, ALLEEG);
%
% Input:
% STUDY - EEGLAB STUDY set
% ALLEEG - vector of EEG datasets included in the STUDY structure
%
% Output:
% STUDY - a new STUDY set containing some or all of the datasets in ALLEEG,
... |
e0f3378f40ed4edf51a34a9ea12a4fe44b43273fe2092858917b91233a61e209 | MATLAB | 15,320 | 388 | function [dist_from_hyperplane, Y, svm_dist_pos_neg, svm_dist_pos_neg_matrix] = plugin_svm_contrasts_get_results_per_subject(DAT, svm_stats_results, DATA_OBJ)
% [dist_from_hyperplane, Y, svm_dist_pos_neg, svm_dist_pos_neg_matrix] = plugin_svm_contrasts_get_results_per_subject(DAT, svm_stats_results, DATA_OBJ)
%
% The p... |
5f94facafbd5e9268938f9d28771c78580f986af04c743889991854883a5664d | MATLAB | 15,355 | 389 | % pop_topoplot() - Plot scalp map(s) in a figure window. If number of input
% arguments is less than 3, pop up an interactive query window.
% Makes (possibly repeated) calls to topoplot().
% Usage:
% >> pop_topoplot( EEG); % pops up a parameter query window
% >> pop_topoplot( EEG, ... |
12c38cbbb0aa4e8c50fc8168a3a80c266c0894cf9e3a058d4ddf731c00de73b5 | MATLAB | 15,358 | 417 | function CBIG_ArealMSHBM_gMSHBM_estimate_group_priors_child(s, mesh, tmp_dir)
% CBIG_ArealMSHBM_gMSHBM_estimate_group_priors_child(s, mesh, tmp_dir)
%
% This is the child script to estimate group priors for gradient-based individual
% areal-level parcellation generation. To speed things up, we parallize the script
% a... |
9f512fe4d9a443900a760fafef7fcf214f9d1203f571322934ab1b3921727668 | MATLAB | 15,392 | 488 | function SANDIinput = investigate_exchange_effectes_NEXI_SANDI_RicianNoise(SANDIinput)
%% Investigate the effect of exchange. Create sythetic signal using a modified NEXI model, made of NEXI + spherical compartment
% Read the input
delta = SANDIinput.delta ;
smalldel = SANDIinput.smalldel ;
sigma_SHresiduals = SANDIi... |
990bf3f736692c3889f8d2a0836491854b1e6a48ac3f35ab7b66be8c0acac4a6 | MATLAB | 15,404 | 397 | %% figure2
% --------------------------------------------------------------------------
% This script generates simulated data and calculates Transfer Entropy (TE)
% to the scenarios presented in Figure 2 of the paper.
%
% Two scenarios are simulated:
% 1. 'Connected' condition: Signal Y is generated direct... |
2927f241d631200855b07b2f06f4662e7fe1041109b1cc056fd51661393c8878 | MATLAB | 15,459 | 493 | % timtopo() - plot all channels of a data epoch on the same axis
% and map its scalp map(s) at selected latencies.
% Usage:
% >> timtopo(data, chan_locs);
% >> timtopo(data, chan_locs, 'key', 'val', ...);
% Inputs:
% data = (channels,frames) single-epoch data matrix
% chan_locs = channel loc... |
c4dc21bae9f6f559dba3bf221e3b86aa4331ff32faf8ba92225f5d5c4ae31178 | MATLAB | 15,466 | 509 | % Using 2D or 3D affine matrix to rotate, translate, scale, reflect and
% shear a 2D image or 3D volume. 2D image is represented by a 2D matrix,
% 3D volume is represented by a 3D matrix, and data type can be real
% integer or floating-point.
%
% You may notice that MATLAB has a function called 'imtransform.m' for... |
b7c7ff82b66e15ed0702d907adff605a3db4b98c7d99921b0063d6aa57663ced | MATLAB | 15,485 | 411 | function tree = xml_parser(xmlstr)
% XML (eXtensible Markup Language) Processor
% FORMAT tree = xml_parser(xmlstr)
%
% xmlstr - XML string to parse
% tree - tree structure corresponding to the XML file
%__________________________________________________________________________
%
% xm... |
8345c95f5e56031df9d06c5dbbb896ebbbe8db0ec9c2614e21f719042275f66d | MATLAB | 15,508 | 321 |
classdef biChordChart < handle
% Copyright (c) 2022-2023, Zhaoxu Liu / slandarer
% =========================================================================
% @author : slandarer
% 公众号 : slandarer随笔
% 知乎 : slandarer
% -------------------------------------------------------------------------
% Zhaoxu Liu / slandare... |
ce4474953564b42bbc209691d2c9d42a02014d0affaff3e05c6cf5ac4861e982 | MATLAB | 15,527 | 256 | function cm_data=TealRd(m)
cm = [6.30247194465418e+01 1.27292705808247e+02 1.47022775963106e+02
6.4390417891429e+01 1.28215535380952e+02 1.47809646181672e+02
6.57561163363162e+01 1.29138364953658e+02 1.48596516400239e+02
6.71218147812034e+01 1.30061194526363e+02 1.49383386618805e+02
6.84875132260906e+01 1.3098402409906... |
2b87eb711d06f6ee5da89a5447e4d8ca8a074340dcf382a853c703b8aecf2be9 | MATLAB | 15,535 | 485 | function varargout=LeG_msgbox(varargin)
%MSGBOX Message box.
% msgbox(Message) creates a message box that automatically wraps
% Message to fit an appropriately sized Figure. Message is a string
% vector, string matrix or cell array.
%
% msgbox(Message,Title) specifies the title of the message box.
%
% msgbox... |
14a96c43f1f2f6b8bf564fd082ac09df4cc06cca61ad5e9a01d3d4c0a86fefa3 | MATLAB | 15,538 | 412 | %% LaBGAScore_decoding_template_xclass_acc.m
%
%
% *USAGE*
%
% This script uses functions of the
% <https://sites.google.com/site/tdtdecodingtoolbox/ Decoding Toolbox
% (TDT)> to
%
%
% # run first-level (i.e. within-subject) (cross-)classification accuracy
% between conditions of your choice in a mask of your choice,... |
0a3f269a7a1e49d2baa73ef84598c20e0e59577d51899d5b8de297ef28e46c44 | MATLAB | 15,544 | 413 | function [vals,fibcell,usedidx] = ea_unified_discfibers_calcstats(obj,patsel,Iperm)
% NB: for PCA, we are going to reassign I later in the function
if ~exist('Iperm','var')
I=obj.responsevar;
else % used in permutation based statistics - in this case the real improvement can be substituted with permuted variables.... |
083a6cc1ce59459d9cfb7887d8091fc2185ee2d26d4bd5ad0eabc1264128d7ae | MATLAB | 15,573 | 423 | function obj = subsasgn(obj,subs,varargin)
% Subscript assignment
% See subsref for meaning of fields.
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: subsasgn.m 5985 2014-05-14 18:32:51Z john $
switch subs(1).type,
case {... |
5149d8e0ef99bcf9eff1efcb0e958aeb8b90f633b67dace9ef22814b8fa8bb6b | MATLAB | 15,609 | 333 | % std_readfile() - Read data file containing STUDY measures.
%
% Usage:
% >> [data param range1 range2] = std_readfile(filename, 'key', val);
%
% Inputs:
% filename - [string] read specific file, for instance 's1.daterp'
% containing ERP data for dataset "s1.set". It is also
% ... |
7ac8bb8d18b2fc4f2fc49ed0758278096174509bb1b1dfc11d6fa2921645f8c5 | MATLAB | 15,609 | 504 | function [GammaFit] = bz_FitISISharedGammaModes(logISIhist,logtimebins,varargin)
%UNTITLED Summary of this function goes here
% Detailed explanation goes here
%
% INPUTS
% logbins [numtimebins x 1] (or ISIs)
% logISIhist [numtimebins x numcells] probability density (N/(sum*dbin))
%
% Opt... |
c340d206c73f04f9a06bf48b07df10ef0d952015e5d5e4f918c524b368c2170d | MATLAB | 15,615 | 434 | %% LaBGAScore_atlas_rois_from_atlas.m
%
%
% *USAGE*
%
% This script creates rois by combining regions from one or more atlases,
% and automatically saves the rois as atlas objects and optionallly as .nii files
% in maskdir of secondlevel model
%
% There is an option to save a single file including all flat rois
% (i.e.... |
9e68dcb3ad365dff553a5107481effa8608f5cbf1c7922d7abe29c68ba599449 | MATLAB | 15,624 | 422 | function fit = fit_meta_d_mcmc_group(nR_S1, nR_S2, mcmc_params, fncdf, fninv, name)
% fit = fit_meta_d_mcmc_group(nR_S1, nR_S2, mcmc_params, fncdf, fninv)
%
% Given data from an experiment where observers discriminate between two
% stimulus alternatives on every trial and provides confidence ratings,
% fits equal-varia... |
06c1dd88e574175a780f9eb278959dfcc2a16913621086315e7006e84b956553 | MATLAB | 15,633 | 510 | % Name: Robert Kim
% Date: 03-29-2023
% Email: robert.f.kim@gmail.com
% fnc_generate_trials.m
% Description: Generate one trial (input matrix u + label struct lab) for
% one of the supported tasks:
% 'fg' : 2-channel figure-ground (signed-product target)
% 'instr' : 1-modality instruction-DMS (3 ch... |
7fed1af66d15e973cda9a5bc695015d62ed9349b5b54077ea85f6ab6d5ff73ae | MATLAB | 15,644 | 398 | function jdata=jdataencode(data, varargin)
%
% jdata=jdataencode(data)
% or
% jdata=jdataencode(data, options)
% jdata=jdataencode(data, 'Param1',value1, 'Param2',value2,...)
%
% Annotate a MATLAB struct or cell array into a JData-compliant data
% structure as defined in the JData spec: http://github.com/fangq/jdata... |
d2727fdeadf178dc63bbb3420a71922ddf4b77284e03a144443865baeed5bb1e | MATLAB | 15,645 | 283 | classdef time_interval_object < handle
% A helper object that creates time intervals based on bin widths, sampling intervals, etc.. These time intervals
% (vectors of times) can be used to plot decoding accuracies against or to get the latency when decoding results are above chance.
% The constructor of... |
cf5973b742e57b356bd8f2606516591b2bea040c88e2766526042a8270a2aa93 | MATLAB | 15,665 | 498 | function [Power, NPower] = PowerByChannel(animal, state, filtertype, probetype)
if strcmp(probetype,'ECHIP512')==1
load('F:\Ephys Analysis\VLSE neuro 4-4 - HPC2\probe_data\ECHIP512.mat')
numshanks=8;
numchans=512;
elseif strcmp(probetype,'ECHIP512_3xTg1-2')==1
numshanks=8;
numchans=512;
... |
ccd1c95a3efe3421be6b29537e1417adaca5b4bd8d775538ab58d8bb9a56ab26 | MATLAB | 15,676 | 420 | function [trajectory,trajvector]=ea_reconstruct_trajectory(priortrajectory,tra_nii,side,refine,options)
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn
if strcmp(options.subj.postopModal... |
0f0fc3f811c5d72758f73edbd800447b1b697b2356156bf8743d8b32981d342c | MATLAB | 15,682 | 383 | function [vals,fibcell,usedidx] = ea_unifiedmapping_calcstats(obj,patsel,Iperm)
%No fibcell and usedidx for sweetspotmapping or networkmapping
switch obj.drawTool
case {'sweetspotmapping','networkmapping'}
fibcell = {};
usedidx = {};
end
% NB: for PCA, we are going to reassign I later in the functi... |
d67dad10b3dca1cfe52bc05240c68811dcad9fa6d720d121a06f83af0b445a02 | MATLAB | 15,715 | 468 | function fit = glmnet(x, y, family, options)
%--------------------------------------------------------------------------
% glmnet.m: fit an GLM with lasso or elasticnet regularization
%--------------------------------------------------------------------------
%
% DESCRIPTION:
% Fit a generalized linear model via pe... |
38ce99a3ad4781a05acd313df651658c8328ad154987ac899a6672f2ded978f9 | MATLAB | 15,724 | 484 | function prepareFigure(fh,type)
% Special appdata settings:
% LegendLocation: see location values of legend
% PostProcessing: off, Psychometric Function, PsychometricData,
% FontTemplate
%% Settings
type = lower(type);
AX_FN = 'Helvetica';
LB_FN = 'Helvetica';
AX_FA = 'Normal';
LB_FA = 'Normal';
if strc... |
ecabf085668ba5ac8b3ae6384a1a3a331d65666c6e9056f72bfce49f0953c02a | MATLAB | 15,781 | 389 | % statcondfiledtrip() - same as statcond except that it uses the fieldtrip
% statistical functions. This is useful to perform
% a wider variety of corrections for multiple
% comparisons for instance.
% Usage:
% >> [stats, df, pvals, surrog]... |
9812b89c34f8ef0dc41d11742e1a5ec0f5ab2db1f6e3e9c6f3895289561d7cbe | MATLAB | 15,825 | 391 | function [colocalMeasure, numOfObjects] = condColocPt2Pt2Pt(refCoords,tarCoords, condCoords,...
mask,distThreshToColocWithCond, colocDistThresh, numRandomizations,alpha)
%CONDCOLOCPT2PT2PT runs conditional colocalization for 3 channel images with 3 punctate objects
%
%SYNOPSIS [colocalM... |
d693e82fc84224a88b85da1438c5e808ed961b5949fe6b5b8109c1efcbc0d499 | MATLAB | 15,844 | 387 | classdef (Abstract, CaseInsensitiveProperties = true) functionalPlot < ...
iosr.statistics.statsPlot
%FUNCTIONALPLOT Abstract superclass for functional plots
%
% As an abstract class, this class cannot be instantiated. It provides no
% public methods. The class is a super class for:
% - iosr.statisti... |
44f6354727e24bef7167a04c86657ac04004e5fddb74e435c809be4894e8ec0a | MATLAB | 15,939 | 468 | function results = PLSDA_paired_neuroimaging_pipeline(X, Y, subjectID, opts)
% PLSDA_paired_neuroimaging_pipeline Within-subject PLS-DA for paired designs.
%
% results = PLSDA_paired_neuroimaging_pipeline(X, Y, subjectID, opts)
%
% Discriminates two conditions measured in the same subjects (pre/post, on/off)
% f... |
a77d72485b09a5d488caf7ee2c83456ac4e51af980dd54388e50f51fc3e1e0ce | MATLAB | 15,939 | 271 | function [cm_data]=magma(m)
cm = [[ 1.46159096e-03, 4.66127766e-04, 1.38655200e-02],
[ 2.25764007e-03, 1.29495431e-03, 1.83311461e-02],
[ 3.27943222e-03, 2.30452991e-03, 2.37083291e-02],
[ 4.51230222e-03, 3.49037666e-03, 2.99647059e-02],
[ 5.94976987e-03, 4.84285000e-03, ... |
e6e5e81affea7e8c5425e5617a4bff8c74919a5a3ca8f2671d74beed2975bf0b | MATLAB | 15,941 | 427 | function varargout = spindle_visualiser(varargin)
% SPINDLE_VISUALISER MATLAB code for spindle_visualiser.fig
% SPINDLE_VISUALISER, by itself, creates a new SPINDLE_VISUALISER or raises the existing
% singleton*.
%
% H = SPINDLE_VISUALISER returns the handle to a new SPINDLE_VISUALISER or the handle to
%... |
18ef654deb73240873230e64ca0e0c0c0a5e562b56e8e6c31370fc56621b174e | MATLAB | 15,949 | 362 | %% v2struct
% v2struct Pack/Unpack Variables to/from a scalar structure.
function varargout = v2struct(varargin)
%% Description
% v2struct has dual functionality in packing & unpacking variables into structures and
% vice versa, according to the syntax and inputs.
%
% Function features:
% * Pack variable... |
f6f4ac34215364cbb750bd45e1dd343c8cb8726442f385522c319c52580730d9 | MATLAB | 15,974 | 419 | %% Modeling Drawer
% Read outputs from hBayesDM ".mat"
% only for prl_rp function currently
% subjID, trial, choice, outcome
% choice: (1=Left, 2=Right)
% outcome: (1=Reward, -1=No Reward)
% Liang-Yin Lu
clear all; close all;
%% Read Model data and reform data structure
datapath = fullfile(pwd,'Example_f... |
e1f6dc417f8c96e0f8c0162f7d66b314b52c1d7346f79036d2fb831031ffe2ff | MATLAB | 15,994 | 392 | %% modeltype4 - 4 neuron logic gate-like Izhikevich neuron system
% Generates data for a small Izhikevich neuron network designed to
% reproduce basic logic gate-like operations. A pulse stimulis is applied
% to two neurons. Those neurons send connections to a third and fourth
% neuron. The third neuron also sends a ... |
6022002e6b6f1b27f7eb174e51eab08914251b16d7a45357df0d26cc5274499d | MATLAB | 15,996 | 393 | function ps2pdf(varargin)
%PS2PDF Function to convert a PostScript file to PDF using Ghostscript
%
% Converts a postscript file into PDF. The resulting PDF file will contain
% one page for each page defined in the postscript files, so a multi-page
% postscript file, like those generated by using the '-append' option... |
6d07e646176df4befb95c170efa22d5766d3fae900e5b88458652dfe38527115 | MATLAB | 16,000 | 474 | function [mri] = ft_read_mri(filename, varargin)
% FT_READ_MRI reads anatomical and functional MRI data from different
% file formats. The output data is structured in such a way that it is
% comparable to a FieldTrip source reconstruction.
%
% Use as
% [mri] = ft_read_mri(filename)
%
% Additional options should be ... |
389bd7798e74a1db5d286b206e795c42a450fbb3a3c975d847b5414c6be1d28b | MATLAB | 16,043 | 394 | function DOMnode = xml_write(filename, tree, RootName, Pref)
%XML_WRITE Writes Matlab data structures to XML file
%
% DESCRIPTION
% xml_write( filename, tree) Converts Matlab data structure 'tree' containing
% cells, structs, numbers and strings to Document Object Model (DOM) node
% tree, then saves it to XML fi... |
81b07b847d855925c4d42444b7a2ee3e1c529d9ade7d39f0c32debac26736ac0 | MATLAB | 16,054 | 379 | function ea_importfs(varargin)
% This function imports freesurfer cortical reconstruction files into
% patient directory, and converts .pial files to cortex.mat
%
% External Dependencies:
% mri_convert (FreeSurfer)
%
% Function:
% 1) Locate freesurfer directory
% 2) Save cortex.mat to patientdirectory
% _________... |
debe13e2bc5b9ce4c7e49cad5354faa89663fecb478773853d4d520b14a85cd3 | MATLAB | 16,092 | 358 |
function [UDStates] = detectUD(varargin)
% Detect up and down states from LFP.
%
% USAGE
%
% [spikes] = bz_loadPhy(varargin)
%
% INPUTS
% (OPTIONAL)
% basePath -(default: pwd) basePath for the recording file, in buzcode format:
% whateverPath/baseName/
% folder mus... |
2d6704a5fe5261e16bfdb7fe8301fa93e13f5c7fb293d303e9c572be55528ede | MATLAB | 16,100 | 357 | function CBIG_MMLDA_brain_behavior_to_doc_wrapper(subinfo_dir, out_dir)
% This wrapper converts brain nifti files and behavior to documents used for MMLDA estimation.
% Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
if nargin < 1 || isempty(subinfo_dir)
... |
13b13dff13d34de45f651918b040b5acca4350ca4beef2e6684a38e83cb1a963 | MATLAB | 16,110 | 554 | % Using 2D or 3D affine matrix to rotate, translate, scale, reflect and
% shear a 2D image or 3D volume. 2D image is represented by a 2D matrix,
% 3D volume is represented by a 3D matrix, and data type can be real
% integer or floating-point.
%
% You may notice that MATLAB has a function called 'imtransform.m' fo... |
cb129c3c6342380f98b59dac6f5d918c3c71b8af070f73b41cfc858b3fcbdce7 | MATLAB | 16,117 | 446 | function CBIG_Yeo2011_GrowBoundaries(num_network, outdir, save_int_file)
% CBIG_Yeo2011_GrowBoundaries(num_network, outdir, save_int_file)
%
% This function takes the Yeo2011 Split Components and grow the boundaries.
% The Yeo2011 Split Components Label has its boundaries being eroded. This
% code aims to reverse the... |
e05fe4887b4e1020efc969853e3ebffd02bb4e6f3541b237e42752a71e4de351 | MATLAB | 16,124 | 457 | function [label, center, bCon, sumD, D] = litekmeans(X, k, varargin)
%LITEKMEANS K-means clustering, accelerated by matlab matrix operations.
%
% label = LITEKMEANS(X, K) partitions the points in the N-by-P data matrix
% X into K clusters. This partition minimizes the sum, over all
% clusters, of the within-clus... |
3bf31fab59e2d4123ff38e93f121a905653fcd5d2f9ecc27f688fa2be5336ee4 | MATLAB | 16,134 | 302 | function [smPropPerTimeBoxed, smTrackletIdPerBox] = gridSmPerTimeInt(smPropPerTimeInt, varargin)
%GRIDSMPROPPERTIMEINT: split movie frame into non-overlapping boxes and get SM information within each box
%
%SYNOPSIS: [smPropPerTimeBoxed, smTrackletIdPerBox] = gridSmPerTimeInt(smPropPerTimeInt, imageSize, varargin)
%
%E... |
4c617f785cb9d71f71a87f25d093ee879d50fb9d2307c8f77341a04ca2e657e9 | MATLAB | 16,149 | 403 | % pop_prop() - plot the properties of a channel or of an independent
% component.
% Usage:
% >> pop_prop( EEG); % pops up a query window
% >> pop_prop( EEG, typecomp); % pops up a query window
% >> pop_prop( EEG, typecomp, chanorcomp, winhandle,spectopo_options);
%
% Inputs:
% EEG ... |
6fdb0ab74b8f99427832e9d0ea69542577801d75562a82c1184ae5b22517e457 | MATLAB | 16,163 | 422 | function [vals,fibcell,usedidx] = ea_discfibers_calcstats(obj,patsel,Iperm)
% NB: for PCA, we are going to reassign I later in the function
if ~exist('Iperm','var')
I=obj.responsevar;
else % used in permutation based statistics - in this case the real improvement can be substituted with permuted variables.
I=I... |
44e31eb17c4337d3edf89bd0ffcdb6a7f5cbb0d8170a6a5a57086a2291a4f1ea | MATLAB | 16,166 | 371 | %% Correlating decoding accuracy with number of input units
% Script that runs multiple decoding analyses with increasing number of
% units. By bootstrapping each step, one can define the average decoding
% accuracy of each step.
close all; clearvars; clc
% Choose sessions to plot
scriptFullPath = matlab.desktop.edito... |
60724d9684721d2348c3d9414527816706d8ee2f4469da2800166f9a43861434 | MATLAB | 16,190 | 484 | function [ pupildilation ] = GetPupilDilation(basePath)
%This is a detector for extracting pupil diameter from an IR video of the
%eye.
%
%FILE REQUIREMENTS
% This detector assumes the presence of a few files:
% basePath/baseName.avi pupil video
% basePath/analogin.dat analog signal of frame pulses fr... |
05c4a01d3225f06266fd1b24ac6e11cba2abba57aa459ef774eecad9b4c6e948 | MATLAB | 16,191 | 504 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
if ~contains(path, '/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
addpath(genpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab'));
end
%% ======================= compare... |
558561dc5733a7dd1821fc76f9e1f959e80f41bfe7ffe0829495d3818f40d6eb | MATLAB | 16,192 | 484 | function [Y,W] = ndnanfilter(X,HWIN,F,DIM,WINOPT,PADOPT,WNAN)
% NDNANFILTER N-dimensional zero-phase digital filter, ignoring NaNs.
%
% Syntax:
% Y = ndnanfilter(X,HWIN,F);
% Y = ndnanfilter(X,HWIN,F,DIM);
% Y = ndnanfilter(X,HWIN,F,DIM,WINOPT);
% Y = ndnanfilter(X,HWIN,F,DIM,WINOPT,... |
6764850a75f5265cea4ab25fbc1ec705a93c666f928ccbf96960081aed92b77c | MATLAB | 16,192 | 421 | function tree = xml_parser(xmlstr)
% XML (eXtensible Markup Language) Processor
% FORMAT tree = xml_parser(xmlstr)
%
% xmlstr - XML string to parse
% tree - tree structure corresponding to the XML file
%__________________________________________________________________________
%
% xml_parser.m is an XML 1.0 (http:/... |
e4ec9a62428f0cd0e67c38223e3102700f777041fb3cd3efc7eed3c22bc5ab81 | MATLAB | 16,193 | 375 | % importevent() - Import experimental events from data file or Matlab
% array into a structure.
%
% Usage: >> eventstruct = importevent( event, oldevent, srate);
% >> eventstruct = importevent( event, oldevent, srate, 'key1', 'value1', ...);
%
% Input:
% event - [ 'filename'|array ] Filenam... |
86cdeea8102c98f443da57790ff3544618894a9b0244151106bd1d730fa4ccab | MATLAB | 16,208 | 467 | function [x y pos trials map mapping] = getBehavEvents(pos,bins)
% this function takes unlabeled position tracking data (LED or Optitrack) and,
% through a semi-automated process, scores individual trials where an animal
% traverses through the environment. Specifically, this code works well with the
% 2AFC T-maze, l... |
3e42d6ebacc665967dfecc1624d608c8413cc642b9e933c2720bbacce544c91f | MATLAB | 16,210 | 304 | % 设置基本目录
baseDir = 'E:\DAIRUI\REHO_study\fc_matrix\Data_450ROI_Music\';
groupDir = 'E:\DAIRUI\REHO_study\fc_matrix\Data_450ROI_Music\APFC_valueZero';
subjID = {'P01'; 'P02'; 'P03'; 'P05'; 'P06R'; 'P07'; 'P08'; 'P11'; 'P12'; 'P13'; 'P14'; 'P15'; 'P16'; 'P17'; 'P18'; 'P19'; 'P20'; 'P21'; 'P22'; 'P23'; 'P24'; 'P25'; 'P... |
761935782093771077ccb68e1f8db6a0bb7edad29bd6a0d2ac02b50c3851f8ee | MATLAB | 16,230 | 394 | function varargout = ea_vatsettings_horn(varargin)
% EA_VATSETTINGS_HORN MATLAB code for ea_vatsettings_horn.fig
% EA_VATSETTINGS_HORN, by itself, creates a new EA_VATSETTINGS_HORN or raises the existing
% singleton*.
%
% H = EA_VATSETTINGS_HORN returns the handle to a new EA_VATSETTINGS_HORN or the hand... |
fe82a86021f605aedb557f04d6a221ed941005ca3b27d2bea628e9ff1ad0b29f | MATLAB | 16,232 | 357 | function plotGlobalQualityMetric(varargin)
% Modified function that supports multiple input options
% ------
% Inputs
% ------
%
% Option 1: plotGlobalQualityMetric(ephys_path, save_path)
% ephys_path: Path to the ephys data directory containing Kilosort outputs
% save_path: Path where to save the output plot figur... |
b8011eabf381c50aeec4a9aa436267efbcc1f515f25b2567d46af1376f790f74 | MATLAB | 16,284 | 434 | function obj=stat_summary(obj,varargin)
% stat_summary Display summarized data for each value of X
%
% Example syntax (default arguments): gramm_object.stat_summary('type','ci','geom','lines','setylim',false)
% For each unique value of x, this can display various estimates of
% the location and variability of the corre... |
0f6fabcc0b3edcd70814c92d8a2557f07530dab746f7928719d25087ef23fba8 | MATLAB | 16,290 | 393 | % std_editset() - modify a STUDY set structure.
%
% Usage:
% >> [STUDY, ALLEEG] = std_editset(STUDY, ALLEEG, key1, val1, ...);
% Inputs:
% STUDY - EEGLAB STUDY set
% ALLEEG - vector of the EEG datasets included in the STUDY structure
%
% Optional inputs:
% 'commands' - {cell_array} change... |
4c73eb3544c643446e8bd5c5ce3ac904562aa3ccc23394f173ed909ec0d04833 | MATLAB | 16,294 | 576 | function [infoPackets, version] = openCCF(filename)
% openCCF
%
% This script reads a .ccf file and outputs it in a structure.
%
% filename: Name of the file to be opened. If the fname is omitted
% the user will be prompted to select a file.
% DEFAULT: Will open Open File UI.
%
% Channe... |
9e38deaec4ce1e2e31c1cea7ea7c6960ac3e09ad92357c24766e56b3f76ba9d4 | MATLAB | 16,311 | 362 | %% v2struct
% v2struct Pack/Unpack Variables to/from a scalar structure.
function varargout = v2struct(varargin)
%% Description
% v2struct has dual functionality in packing & unpacking variables into structures and
% vice versa, according to the syntax and inputs.
%
% Function features:
% * Pack... |
ffa3f67727da7467a7b5c5405bba781df0ed8c9856043b80d58a4f9fffebd4c9 | MATLAB | 16,313 | 509 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
if ~contains(path, '/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
addpath(genpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab'));
end
%% ======================= compare... |
c60c3c9d37983317edc76aea406cdf0e24073fa8af240cc512d77b198f5b0592 | MATLAB | 16,358 | 478 | function [dim, dE] = fnn(data,tau,MaxDim,Rtol,Atol,speed)
% [FN,dim] = fnn(data,tau,MaxDim,Rtol,Atol)
% data - column oriented time series
% tau - time delay
% MaxDim - maximum embedding dimension
% Rtol - threshold for the first criterion
% Atol - threshold for teh second criterion
% speed - a 0 for the co... |
34d67e5efbdec14ebd668c9d0f14b7265a2ea76c7942c402b0312cd78e071d65 | MATLAB | 16,394 | 531 | %% LaBGAScore_pet_run_plot_PLS_ENet_pipeline.m
%
%
% *USAGE*
%
% This script serves as a simple wrapper to run the PLS-DA and Elastic Net
% neuroimaging pipeline functions and their plotting functions on parcel-wise
% (whole-brain or ROI) PET data.
%
% The script takes excel outputs from the LaBGAScore_pet_model_TSPO_D... |
18da8a4d2073ffdedbc6395bde76ce3c1778a92c4d9467f903943fd0c12636b9 | MATLAB | 16,398 | 437 | function [Theta_select_probs,Theta_select,Theta_samples_select,Theta_bayes_factors] = MDSINESelectMCMC(X,F_hat_prime,growth_mean_p,growth_std_p,self_reg_mean_p,interact_std_p,perturb_std_p,numPerturb,nodeNum,Theta_init,Theta_indicator_init,params)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dyna... |
66c212bf85a3fd762b2c70b398123b92780fb2a68a4f3a14f9904a3cc7888d57 | MATLAB | 16,411 | 413 | %% LaBGAScore_secondlevel_roi_run_plot_PLS_ENet_pipeline.m
%
%
% *USAGE*
%
% This script serves as a simple wrapper to run the PLS-DA and Elastic Net
% neuroimaging pipeline functions and their plotting functions on fMRI ROI
% data saved by the prep_3a_run_second_level_regression_and_save script.
%
% To control for cov... |
412bdd9a83cafdba9ae20c1fd49b9bbfafa487f6451c79bbce10bbe284de15ff | MATLAB | 16,444 | 365 | classdef updater < handle
% Web-based software updater class with download and installation capabilities.
% Copyright (C) 2012 by Nima Bigdely-Shamlo, Swartz Center for Computational Neuroscience, INC,
% UCSD.
% Usage is only allowed under the same (non-commercial) license as Measure Projection toolbox.... |
0fa509fa994d29101d3add023902d7e37958420692f11868d63034e2857fd154 | MATLAB | 16,464 | 544 | %% neurDemo1
%
% neuroDemo1 reproduces the single neuron stimulation encoding figure.
% Note, the scratch directory in the simulations folder will be used to
% save data. These simulations will take up about 2 minutes to run and it
% will require about 2 GB of space.
%
% Other m-files required: modeltype1, in... |
9e4567af8a929f57945722f7fe81ee4603193c36350fc6631dec9ebde1157e59 | MATLAB | 16,486 | 429 | function tree = xml_parser(xmlstr)
% XML (eXtensible Markup Language) Processor
% FORMAT tree = xml_parser(xmlstr)
%
% xmlstr - XML string to parse
% tree - tree structure corresponding to the XML file
%__________________________________________________________________________
%
% xml_parser.m is an XML 1.0 (http:/... |
b5cada0c499c9afc25eacf29d0f2d33bc63eba58cbd094c33a14c7a4b22f882c | MATLAB | 16,486 | 472 | function result = glmnetPredict(object, newx, s, type, exact, offset)
%--------------------------------------------------------------------------
% glmnetPredict.m: make predictions from a "glmnet" object.
%--------------------------------------------------------------------------
%
% DESCRIPTION:
% Similar to othe... |
b14aecb914beb3df4132bd39ef6946d4e9d96e7449423f88f7b971076d6e29a8 | MATLAB | 16,511 | 368 | function [colocMeasure, numOfObjects] = simulatePt2Pt2BlobCondColoc(numRefDetect,...
numTarDetect,segmentation,cellMask,refColocWithCondFrac,tarColocWithCondFrac,...
tarColocWithRefAtCondFrac,tarColocWithRefNotAtCondFrac,varargin)
%SIMULATEPT2PT2BLOBCONDCOLOC simulate object positions t... |
e5c491177475673cc9ebbfe2c788bda9054e888f1c29b84c3903309c3e587ccc | MATLAB | 16,514 | 485 | function ea_svd_segmentation(images, anchorImage, segmenter, segmaskPath, alg4PVS,alg4WMH,alg4Lacunes,sub_ID,only_segmask,alg4MB)
% Add enlarged perivascular spaces, WMH and lacunes to segmask
% By Butenko, konstantinmgtu@gmail.com
arguments
images % struct of paths to images
anchorImag... |
dfca67bb2411fd743729a19cf41f8b4d14f45a9ca30f7721fa060f7f6203bd42 | MATLAB | 16,536 | 204 | % EEGLAB menus:
% File
% Import data
% Using EEGLAB functions and plugins
% From ASCII/float file or Matlab array - <a href="matlab:helpwin pop_importdata">pop_importdata</a>
% From Netstation binary simple file - <a href="matlab:helpwin pop_readegi">pop_readegi</a>... |
d2130e93d9602ca17f8cf9e4cd2deb8d54267baab8767fd30efb1e7e5cb28aef | MATLAB | 16,539 | 1 | function B=inpaint_nans(A,method)
% INPAINT_NANS: in-paints over nans in an array
% usage: B=INPAINT_NANS(A) % default method
% usage: B=INPAINT_NANS(A,method) % specify method used
%
% Solves approximation to one of several pdes to
% interpolate and extrapolate holes in an array
%
% arguments (input):
% A... |
6739954a011b1f8ada07a341b43d92ce4b6eedae129bdddd4b44195c063352c1 | MATLAB | 16,547 | 294 | function AnimalMetadata = bz_AnimalMetadataTextTemplate(basepath)
% This .m file is a generic template and will be copied to animal
% folders/session folders and will be called basename_AnimalMetadataText.m.
% It is represents code that will be used to
% create a basename.AnimalMetadata.mat file. Edits here will be re... |
8e061a11f92a8629c99f64300c254c16f629067ca050d74371946dbabeecc3fd | MATLAB | 16,549 | 385 | function [spine_evolve, num_turnover, Dendrite_CrossSess,...
filelist, targetdata, TranM, handles]...
= spineEvolveAna(handles)
% funcsel = prepCrossSessReg(handles);
% rb1 = 'Register to the last dataset';
% rb2 = 'Register to dataset 1';
% rb3 = 'Use existing transform matrix';
spine_evolve... |
9bccec39f86811dd9a298ba6570a017b009bceea8502a00f48aa12f13c6d783c | MATLAB | 16,570 | 439 | function htmlfile = LaBGAScore_prov_publish(scriptname, htmlsavedir, varargin)
%
%
% *USAGE*
%
% Drop-in replacement for the publish() call documented in the header of
% every LaBGAS second-level script. Where you would type
%
% publish('cfs_secondlevel_m14_s7_c2a_second_level_regression', ...
% 'outputDir'... |
33be04a8314ded4a6d508fce70bd415157b25abfffded0e99cd52ae96813c9c7 | MATLAB | 16,579 | 443 | function seed_tc=cs_fmri_conseed_nifti(restfile,seedfile,options)
directory=[fileparts(restfile),filesep];
options=ea_getptopts(directory,options);
options=ea_assignpretra(options);
[~,restfname]=fileparts(restfile);
[~,anatfname]=fileparts(options.prefs.prenii_unnormalized);
options.prefs.rest=[restfname,'.nii'];
... |
c8bd318314ac34e828480f127ddeea07d1bcc0d2abac54bbdfaece47ee96545e | MATLAB | 16,598 | 348 | function tests = testLyE
%TESTLYE Contract and known-answer tests for LyE_R and LyE_W.
%
% BENCHMARK DESIGN. Lyapunov estimators are tested here in three layers,
% weakest evidence last, because no single reference is sufficient.
%
% Layer 1 -- INVARIANCES. Properties that hold for every series with no
% refere... |
d85cb443b6070ca0763fab38d744b939f44031cdb41e2273837d92e622305d38 | MATLAB | 16,599 | 636 | function [selected_file, selected_path] = rri_select_file(varargin)
%
% USAGE: [selected_file, selected_path] = ...
% rri_select_file(dir_name, fig_title)
%
% Allow user to select a file from a list of Matlab competible
% file format
%
% Example:
%
% [selected_file, selected_path] = ...
% rri_select_... |
bff1123815a79e822bebcfeb2b4786f6ef5e7648eaf861c8baf560c8b245ed1f | MATLAB | 16,613 | 421 | function tree = xml_parser(xmlstr)
% XML (eXtensible Markup Language) Processor
% FORMAT tree = xml_parser(xmlstr)
%
% xmlstr - XML string to parse
% tree - tree structure corresponding to the XML file
%__________________________________________________________________________
%
% xml_parser.m is an XML 1.0... |
9cfac462cb20f3a246eb2e4921a7d642105450fcfc55af6632292e07bbc6f7cc | MATLAB | 16,616 | 446 | % help2html() - Convert a Matlab m-file help-message header into an .html help file
%
% Usage:
% >> linktext = help2html( filein, fileout, 'key1', val1, 'key2', val2 ...);
%
% Inputs:
% filein - input filename (with .m extension)
% fileout - output filename (if empty, generated automatically)
%
% Opti... |
623103fecf598b00f422822c4638385bc43cecb435fc4e9841713ea7aa584ec1 | MATLAB | 16,632 | 438 | function [coef,alphas,offset] = fracridge(X,fracs,y,tol,mode,standardizemode)
% function [coef,alphas,offset] = fracridge(X,fracs,y,tol,mode,standardizemode)
%
% <X> is the design matrix (d x p) with different data points
% in the rows and different regressors in the columns.
% <fracs> is a vector (1 x f) of one or ... |
b03a9351b4edcc4800e54224e16753176ed27b90738a7fc23703a142340e4294 | MATLAB | 16,689 | 345 | %% ============================================================
% Threshold sensitivity analysis for PrL calcium-network pipeline
%
% Based on:
% - solve_calcium_PrL_Apr1_2026.m
% - calcium_data_PrL_SB_struct_clean.m
%
% What this script does
% 1) Runs the same PrL WT + Shank3 structured pipeline
% 2) Sweeps co... |
1ea4893641848cb20226fafa0a8301374cfb40e95dcdb61c859ccfc40f23ea07 | MATLAB | 16,692 | 310 | function [channel] = channelselection(channel, datachannel)
% CHANNELSELECTION for EEG and MEG labels
%
% This function translates the user-specified list of channels into channel
% labels as they occur in the data. This channel selection procedure can
% be used throughout fieldtrip.
%
% You can specify a mixture of r... |
db93f244afa1839124608a4555d0ee21e79c0e775a0668cafca7922d3f85e449 | MATLAB | 16,698 | 331 | function [propPerSmPerCellOutput, propStatsPerCellOutput, trackClassSizePerCellOutput, inputParam] = ...
collectSmPropByTracklets(combnPropPerTimeInt, prop2extract, indicesOfInt, figFlag)
%COLLECTSMPROPBYTRACKLETS: collect specified single-molecule property from combinePropPerTimeInt
%
%SYNOPSIS: [propPerSmPerCell... |
473bf44f1c16aa89cd0ed58e8e269bc9e3865ed9ba8d17dbcc2d6bc39baf255d | MATLAB | 16,700 | 269 | function [cm_data]=inferno(m)
cm = [[ 1.46159096e-03, 4.66127766e-04, 1.38655200e-02],
[ 2.26726368e-03, 1.26992553e-03, 1.85703520e-02],
[ 3.29899092e-03, 2.24934863e-03, 2.42390508e-02],
[ 4.54690615e-03, 3.39180156e-03, 3.09092475e-02],
[ 6.00552565e-03, 4.69... |
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