sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
7ac03944fde52c5706bf4df5ced5143d5c63018f0b720235adea39379f77751a | MATLAB | 12,468 | 164 | function [warped] = warp_apply(M, input, method);
% WARP_APPLY performs a 3D linear or nonlinear transformation on the input
% coordinates, similar to those in AIR 3.08. You can find technical
% documentation on warping in general at http://bishopw.loni.ucla.edu/AIR3
%
% Use as
% [warped] = warp_apply(M, input, met... |
d02df8a7914de1de21fcde8b167799107c2f41faa7c0b61a7d53979cac445dc3 | MATLAB | 12,486 | 319 | %% Using the atlas object for Region of Interest (ROI) analyses
%% About the atlas object
% An atlas-class object is a specialized subclass of fmri_data that stores
% information about a series of parcels, or pre-defined regions, and in
% some cases the probalistic maps that underlie the final parcellation.
%
% Some ... |
0d2142f72f0436c76c04c0f643e4ba53d6a707b7e17515e0145940a163d56fad | MATLAB | 12,505 | 366 | % THIS SCRIPT RUNS BETWEEN-PERSON CONTRASTS
% Assuming that groups are concatenated into contrast image lists.
% Requires DAT.BETWEENPERSON.group field specifying group membership for
% each image.
% --------------------------------------------------------------------
% USER OPTIONS
% USER OPTIONS
% This is a standard... |
e558b9d7743c84d7ffef11e87ad89f09f4edcc45879eead99d5f3412c96c5410 | MATLAB | 12,526 | 308 | function [h,p,cr,ca] = TestRemapping(control,repeat,test,varargin)
%TestRemapping - Test if firing fields remap (or shift) between two conditions.
%
% To test for random remapping between a control and a test condition, we
% first estimate for each place cell the absolute field shift between the two
% conditions, a... |
ab91db1ec571956064f7eee1da67f73bd2ca2376aced29ff1c177f6e60c13c98 | MATLAB | 12,535 | 326 | function [PCmean,PCstd,PCmax,PCmin,N] = perceptualCentroid(x,fs,varargin)
%PERCEPTUALCENTROID Perceptual spectral centroid
%
% PCMEAN = IOSR.AUDITORY.PERCEPTUALCENTROID(X,FS) calculates the spectral
% centroid of signal X, sampled at FS, with respect to mel-frequency.
%
% The algorithm first calculates the sp... |
3058c08cb2da063950adaa5b0ad9447a4a3a8bc14adc8797fcb23ca18dfd92fc | MATLAB | 12,554 | 317 | function [M_final,shifts_g,template,options,col_shift] = normcorre_batch_even(Y,options,template)
% online motion correction through DFT subpixel registration
% Based on the dftregistration.m function from Manuel Guizar and Jim Fienup
% INPUTS
% Y: Input data, can be already loaded in memory as a... |
852c25c2e9bb63980eb6db9b5c2c424657a549a91d7df29df23c148d5e65822e | MATLAB | 12,573 | 102 | %EEGLAB group processing (STUDY) functions (studyfunc folder):
% <a href="matlab:helpwin compute_ersp_times">compute_ersp_times</a> - Computes the widest possible ERSP/ITC time window,...
% <a href="matlab:helpwin neural_net">neural_net</a> - Computes clusters using Matlab Neural Net toolbox.
% <a href="... |
124347a9ddc7bc279cda02447bb011acb8e5c41b0f503438207ed79b491b0bc7 | MATLAB | 12,575 | 344 | function [placeFieldStats] = bz_findPlaceFields1D(varargin)
% [placeFieldStats] = bz_findPlaceFields1D(firingMaps)
% Find place fields from 1D firing maps. Reads the output of bz_firingMapAvg
%
% INPUTS
%
% =========================================================================
% Properties Values
% ... |
3906bcc1fd4143880aca26ca05339ce0094dc4852596b027b4343213c5dbf452 | MATLAB | 12,582 | 106 | %Miscelaneous functions not used by EEGLAB graphic interface (miscfunc folder):
% <a href="matlab:helpwin abspeak">abspeak</a> - Find peak amps/latencies in each row of a single-epoch data matrix...
% <a href="matlab:helpwin arrow">arrow</a> - Draw a line with an arrowhead.
% <a href="mat... |
63cf8dbdeba9d8486500f64316312af0f782c4dced374ddd5a6ba4480c3a84e8 | MATLAB | 12,583 | 342 | %% 3-D volume visualization
%% About volume visualisation
%
% Creating 3-D renderings of brain data and results can help localize brain
% activity and show patterns in a way that allows meaningful comparisons
% across studies.
%
% The CANlab object-oriented tools have methods built in for rendering
% volume data on br... |
6cbfc7f5ecb8c5a476666cc07f414d20e33f87c03e81554919cfd3fd533a4c22 | MATLAB | 12,593 | 229 | % pop_importevent() - Import events into an EEG dataset. If the EEG dataset
% is the only input, a window pops up to ask for the relevant
% parameter values.
%
% Usage: >> EEG = pop_importevent( EEG ); % pop-up window mode
% >> EEG = pop_importevent( EEG, 'key1', 'value1', ...);
%
% Gr... |
33b9d34c7b426f4304e30f09c34c7a989d5bc787c11aebe455012f6219c9543d | MATLAB | 12,606 | 251 | % pop_autorej() - perform automatic artifact epoch detection and rejection
%
% Usage:
% >> [EEG, rmepochs] = pop_autorej( EEG, 'key', 'val');
%
% Inputs:
% EEG - input EEG structure where epochs have been extracted.
%
% Optional inputs:
% 'threshold' - [float] Threshold limit for detection of extremely la... |
36d11472992187de25107e11421ed473eac9fd028ed5ed414adf308100764cf1 | MATLAB | 12,609 | 314 | classdef ea_sweetspot < handle
% ROI class to plot niftis on lead dbs resultfig / 3D Matlab figures
% example:
% figure; pobj.openedit=1; ea_sweetspot([spm('dir'),filesep,'toolbox',filesep,'OldSeg',filesep,'grey.nii'],pobj); a=light; axis('off','equal')
% A. Horn
properties (SetObservable)
... |
47d670848d7ab089fb3fb02b185685c32dd69bd205ec312c82bad6b1c59933da | MATLAB | 12,610 | 321 | function varargout = ea_normsettings_ants(varargin)
% EA_NORMSETTINGS_ANTS MATLAB code for ea_normsettings_ants.fig
% EA_NORMSETTINGS_ANTS, by itself, creates a new EA_NORMSETTINGS_ANTS or raises the existing
% singleton*.
%
% H = EA_NORMSETTINGS_ANTS returns the handle to a new EA_NORMSETTINGS_ANTS or t... |
6cdf2c00344f04e3ca4cbc6b9bf2a40d8215b3c940956310ec8ccbc7dfebc32e | MATLAB | 12,624 | 379 | function ConvertPhyKilo2Neurosuite(basepath,basename,ks_basepath,varargin)
% Converts Phy1 and kilosort1 or Phy2/kilosort2 output files into
% klusters-compatible fet,res,clu,spk files. assumes a 16bit .dat,
% .xml file is present in "basepath" (home folder) and that they are named
% basename.dat and basename.xml... |
2196911718444332d1bdac055effb6d270d0f292e43794d04f5fae29c2985fb5 | MATLAB | 12,629 | 314 | classdef ea_sweetspot_hemi < handle
% ROI class to plot niftis on lead dbs resultfig / 3D Matlab figures
% example:
% figure; pobj.openedit=1; ea_sweetspot_hemi([spm('dir'),filesep,'toolbox',filesep,'OldSeg',filesep,'grey.nii'],pobj); a=light; axis('off','equal')
% A. Horn
properties (SetObservable... |
51f1c2e598902b3dd88baa1a6ea067a4cb1fdc3a8ce6a19ae6ad8db86f444fdd | MATLAB | 12,644 | 294 | %% Create schematic of correlation plot
clear; clc;
% Load model parameters
loadparam;
% Compute grid spacing
dx = topology.L / topology.Nx;
fig = figure;
fig.Position = [100, 100, 520, 500];
ax = gca;
set(ax, 'color', 'white');
axis off;
hold on;
xticks([]);
yticks([]);
xlim([0 topology.L]);
ylim([0 topology.L]);... |
933cd1a01615748ac74251eff842d9a1d1e279f9115069334f15032bc98d2d2f | MATLAB | 12,652 | 329 | % pop_saveset() - save one or more EEG dataset structures
%
% Usage:
% >> pop_saveset( EEG ); % use an interactive pop-up window
% >> EEG = pop_saveset( EEG, 'key', 'val', ...); % no pop-up
%
% Inputs:
% EEG - EEG dataset structure. May only contain one datase... |
c0fce2601a79a45ed2374ca579608132718a610a2aafe4a84ccd54ba8c82a0bf | MATLAB | 12,657 | 454 | function shim = cvx_sdpt3( shim )
% CVX_SOLVER_SHIM SDPT3 interface for CVX.
% This procedure returns a 'shim': a structure containing the necessary
% information CVX needs to use this solver in its modeling framework.
global cvx___
if ~isempty( shim.solve ),
return
end
if isempty( shim.name ),
fname = 's... |
deebda29b4590210dfa40ff71d0440d309fb6e9f7d3ee9d7d9214c39631ea164 | MATLAB | 12,675 | 258 | function eps2pdf(source, dest, crop, append, gray, quality, gs_options)
%EPS2PDF Convert an eps file to pdf format using ghostscript
%
% Examples:
% eps2pdf source dest
% eps2pdf(source, dest, crop)
% eps2pdf(source, dest, crop, append)
% eps2pdf(source, dest, crop, append, gray)
% eps2pdf(source, de... |
9aa834c244bf849801ac806013bb20f252cdae8a2937aa7afaa889a51745f71a | MATLAB | 12,680 | 326 | function X = palm_miscread(filename,useniiclass,tmppath,precision)
% Read various scalar data formats based on the file extension.
%
% X = palm_miscread(filename,useniiclass,tmppath,precision);
%
% filename : File to be read.
% useniiclass : True/False. Use the NIFTI class when reading
% NIFTI files. I... |
509d18a131d5d345c131723bbf99f2b06447e1e263a1e92dde9567717f4c5ff6 | MATLAB | 12,698 | 341 | function [coords_mm,trajectory,markers] = ea_refinecoords(options)
%% Refine the fiducial markers following TRAC/CORE reconstruction
% Last Revision: 18/05/2018
% Thushara Perera (c) 2018 Bionics Institute
% Input:
% - lead dbs options struct
% Output:
% - refined reconstruction is saved to file using ea_save_r... |
92d3f36c605a7dfa93dc36c07621774db61628fa62bce9263a181ed715cd14e9 | MATLAB | 12,719 | 330 | function [M_final,shifts_g,template,options,col_shift] = normcorre_batch_even(Y,options,template)
% online motion correction through DFT subpixel registration
% Based on the dftregistration.m function from Manuel Guizar and Jim Fienup
% INPUTS
% Y: Input data, can be already loaded in memory as a 3D
% ... |
f14d0dee3fae4589f9d01754bbd766e1f78de55d6693a4b60e5293427d03ef07 | MATLAB | 12,743 | 323 | % std_pac() - Compute or read PAC data (Phase Amplitude Coupling).
%
% Usage:
% >> [X times logfreqs ] = std_pac(EEG, 'key', 'val', ...);
% Inputs:
% EEG - an EEG dataset structure.
%
% Optional inputs:
% 'components1'- [numeric vector] components in the EEG structure used
% for spec... |
5910f90c5eaf4072ef6f9fd680a95348a0cfab972de38a5581ff083b2bf241d2 | MATLAB | 12,748 | 267 | function cm_data=viridis(m)
cm = [[ 0.26700401, 0.00487433, 0.32941519],
[ 0.26851048, 0.00960483, 0.33542652],
[ 0.26994384, 0.01462494, 0.34137895],
[ 0.27130489, 0.01994186, 0.34726862],
[ 0.27259384, 0.02556309, 0.35309303],
[ 0.27380934, 0.03149748, 0.35885256],... |
7486d84073dd8f8bd5c0f50b9fcfef5d3af887fca937d94e009287a8ba47e70c | MATLAB | 12,752 | 308 | function varargout = ea_oss2optimizePAM(varargin)
% Wrapper for OSS-DBS simulations.
% By Butenko and Li, konstantinmgtu@gmail.com
if nargin==2
S=varargin{1};
options=varargin{2};
elseif nargin==3
S=varargin{1};
options=varargin{2};
hFigure=varargin{3};
elseif nargin==1 && ischar(varargin{1}) % ret... |
97ea68040889512f672a1aa45e159ce0c307004b6a97927272f301960de1b03b | MATLAB | 12,773 | 265 | function [pCompareTtestR,pCompareTtestL,outlierIndx1,outlierIndx2] = compareSigIndCellsMVRG(testResults1,testResults2,pSigTtest1,pSigTtest2,spekLabelBase, smLabelBase)
%COMPARESIGINDCELLSMVRG compares multivariate regression results for two
%groups of cells, each population
%
%SYNOPSIS: [pCompareTtestR,pCompareTtestL,... |
4f77ecd7cfc873113af68d2ed685cf6bca9e08eaba92d1c0edb1a6a1f12fc463 | MATLAB | 12,803 | 425 | function SANDIinput = investigate_exchange_effectes_NEXI_SANDI_RicianNoise_forGUI(SANDIinput, fig_axes)
%% 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_SHr... |
8cb77114033a1c5d1b9741dc4c83c1420b42c7e02c5e7db9d210db1ad34c6aa5 | MATLAB | 12,812 | 373 | function [x y pos trials map mapping] = getBehavEvents_with_Z(pos,bins)
if pos(1,1) == 0 & size(pos,2) < 6
%% old code for LED tracking
pos = [pos(:,2:5),pos(:,1)];
% assumes colomns 1/2 and 3/4 match
scatter(pos(:,1),pos(:,2),'.r')
hold on
scatter(pos(:,3),pos(:,4),'.b')
axi... |
1db016ea4fe002b6fa0f99779ed6108e7f0b589c97c6ac5849a9056e1042ce8a | MATLAB | 12,819 | 401 | function editor(tree)
%XMLTREE/EDITOR A Graphical User Interface for an XML tree
% EDITOR(TREE) opens a new figure displaying the xmltree object TREE.
% H = EDITOR(TREE) also returns the figure handle H.
%
% This is a beta version of <xmltree/view> successor
%
% See also XMLTREE
%___________________________... |
cf74f26bc9c99424054e0442a86ceff2679db2753298bc3412a833917c627677 | MATLAB | 12,833 | 368 | function R = LaBGAScore_dep_report(repodir, varargin)
%
%
% *USAGE*
%
% Generates the dependency documentation for a repository: which external
% functions each script calls, which repository each of those lives in, and
% where static analysis could not give a definite answer.
%
% Writes three files into the repository... |
0378f7a88952837357e4790bd90d9f3b8ce2740f8f0d745b0c69e15b60cbba79 | MATLAB | 12,861 | 278 | % Name: Robert Kim
% Date: 05-11-2023
% Email: robert.f.kim@gmail.com
% visualize_cebra.m
% Description: Plot CEBRA-3D trajectories for a chosen two-layer one-modality
% (instr) RNN. Reads <cebra_dir>/<model_prefix>_*_cebra.mat (e.g. intact,
% I->I lesioned, I->E lesioned, etc.) and renders one trace per trial in
% 3-D... |
804fb072045296d5cf58df94211da28a4cb17755e3f8f2e656a4699ccb6fb993 | MATLAB | 12,889 | 266 | function DECODING_RESULTS = create_confusion_matrices_and_MI(cv, YTe, all_predicted_labels, DECODING_RESULTS)
% A method to create confusion matrices for the zero-one loss and normalized rank results.
% A confusion matrix is a matrix in which the columns express the true class label
% and the rows express the pred... |
af7578deae2e58adc86da3c0416c553f9712697788c31c092612aaa0e80951a2 | MATLAB | 12,890 | 317 | function [X,Z,eCm,eCx,Y,imov,ifix,isdiscrete,istwotail] = palm_misspart(M,C,meth,my,mm,mcar,rmethod)
% Partition the model for missing data, generating all the sub-models
% that can later be subjected to NPC.
%
% Usage:
% [X,Z,eCm,eCx,Y,Pidx,isdiscrete] = palm_misspart(M,C,meth,my,mm)
%
% Inputs:
% M : Design ... |
dfd659f423c2b93b21e2ff610d58df76691f0835466ee65f4e2367185a54f560 | MATLAB | 12,894 | 380 | function [SleepScoreMetrics,StatePlotMaterials] = ClusterStates_GetMetrics(...
basePath,SleepScoreLFP,motion,overwrite,varargin)
%StateID(LFP,thLFP,EMG,sf_LFP,sf_EMG,figloc,WSEpisodes)
% Detailed explanation goes here
%
%This function calucates the metrics for state scoring (EMG, Slow Wave
%Power, Theta). It uses... |
e2b0c2a96dc90af69342b6989c8984a74881b9d3ddeb07536ee1e315a8cabb80 | MATLAB | 12,907 | 361 | % This version was derived from the original version by Pestilli and Caiafa.
% Copyright (2015), Franco Pestilli (Indiana Univ.) - Cesar F. Caiafa (CONICET)
% email: pestillifranco@gmail.com and ccaiafa@gmail.com
% https://github.com/francopestilli/life available under
% https://github.com/francopestilli/life/blob/mast... |
12f325fea8c23d58fcf70239084c64b16ec32d414d6a35747559c8b3b88f80a9 | MATLAB | 12,931 | 275 | function [positionDecodingBayesian] = bz_positionDecodingBayesian(varargin)
% USAGE
% [] = bz_positionDecodingBayesian()
%
% INPUTS
%
% spikes
%
% behavior
%
% plotting
%
% saveMat
%
% OUTPUTS
%
% positionDecodingBayesian cellinfo struct with the following fields
% .UID
% ... |
9ad208a1b5f458f717b3cf7dbb6bca8ea7cc0d22eeb3ba4f366bba97a07e5931 | MATLAB | 12,952 | 336 | function [RPVrate, RPVfraction, overestimateBool, estimatedTauR] = fractionRPviolations(theseSpikeTimes, theseAmplitudes, ...
tauR, param, timeChunks, RPV_tauR_estimate)
% JF, get the estimated fraction of refractory period violation for a unit
% for each timeChunk
% ------
% Inputs
% ------
% theseSpikeTimes: nSpi... |
0e527de818718f611f0d7d440b9c30c66534d4bc730ced8b3142a61d7931dc81 | MATLAB | 12,958 | 339 | % eegplotgold() - display EEG data in a clinical format
%
% Usage:
% >> eegplotgold('dataname', samplerate, 'chanfile', 'title', yscaling, range)
%
% Inputs:
% 'dataname' - quoted name of a desktop global variable (see Ex. below)
% samplerate - EEG sampling rate in Hz (0 -> default 256 Hz)
% 'chanfile' - file of ... |
e9253f3066129e50558f517b2ca1ab6568e08fefffe46a1cfe4e70e372527a3f | MATLAB | 12,967 | 276 | function [pSigTtest, outlierIndx, randResult, mvrgCoefStruct] = explainIndCellsMVRG(testResults, spekLabelBase, smLabelBase, sigThreshInput)
%EXPLAININDCELLSMVRG displays multivariate regression results for individual cells and pick out outlier cells
%
%SYNOPSIS: [pSigTtest, outlierIndx, randResult, mvrgCoefStruct] = e... |
3469b7b0755fa778687cd60ae2a05c2115b335cd3d5fc599af01ee6e5e1d7b52 | MATLAB | 12,974 | 415 | function ea_segment_electrode(~,~,options,resultfig,onoff)
directory=[options.root,options.patientname,filesep];
if options.native
switch options.subj.postopModality
case 'MRI'
elnii = options.subj.coreg.anat.postop.ax_MRI;
case 'CT'
elnii = options.subj.coreg.anat.postop.CT... |
1566900ac8bc8fda9b07ad28130a87bd7fae33e61e8def71e66e15121d172044 | MATLAB | 12,978 | 272 | function res = FBmodel7(gust_res,p_PFNd,p_PFNv,p_PFNpc,p_PFNa,inits,heatmaps,plt)
% This function will generate sinusoidal bumps in an eight-column space for
% the compass/EB and in the PB and FB (for PFNs). It takes parameters
% previously determined from fitting for timecourses of PFN calcium
% intensity and b... |
36661b76bd1ff942b32be06318c404ed354139c28056b5d5e5be34fee1068a54 | MATLAB | 12,991 | 291 | % pop_reref() - Convert an EEG dataset to average reference or to a
% new common reference channel (or channels). Calls reref().
% Usage:
% >> EEGOUT = pop_reref( EEG ); % pop up interactive window
% >> EEGOUT = pop_reref( EEG, ref, 'key', 'val' ...);
%
% Graphic interface:
% "Compute averag... |
ace619b752f3f888aea1b956c9869a382024b75819d44ba15044b47add6f9980 | MATLAB | 13,038 | 396 | % phasecoher() - Implements inter-trial amp/coherence using Gaussian wavelets.
% Returns same data length as input frames.
% Plots results when nargin>6. Outputs have flat ends
% at data indices [1:halfwin] and [frames-halfwin:frames].
% Usage:
% >> [amps,cohers ] = pha... |
6a79fd504c3a12003bf2eebe151465568bdac338a1f665a28af0febb3d026dee | MATLAB | 13,043 | 343 | function [d_min, varargout] = p_poly_dist(xp, yp, xv, yv, varargin)
%p_poly_dist Find minimum distances from points to a polyline or to a
% closed polygon.
%
% Description:
% Compute the distances from each one of a set of np points p(1), p(2),...
% p(np) on a 2D plane to a polyline or a closed polygon. Polyline is
%... |
698f74e9d83d9feb184df47ffb84a4e905686ff9e012dde61223fd7c9b1d2f7a | MATLAB | 13,047 | 434 | function [gridness, phi_v_cor, auto_corr, d] = Gridness2(self, cel, varargin)
% Calculates the original gridness score of 'cel'. Continuizes all epochs.
%
% ARGUMENTS
%
% cel 1x2 vector indicating tetrode index and cell index
%
% RETURNS
%
% gridness a number indicating gridness score
% period... |
baf137104c9d853a8b9b210b9235000dd335a20244772bbe15ac190110104aa9 | MATLAB | 13,049 | 283 | function [sigRes] = multiCompareAnovaIndCellsMVRG(testResultCellArr,pSigTtestArray,outlierIndxArr,spekLabelBase, smLabelBase, displSpacing)
%MULTICOMPAREINDCELLSMVRG: compares multivariate regression results for multiple groups of cells by ANOVAN, sorted by motion types and SM property
%
%SYNOPSIS: [sigRes] = multiCom... |
d4ffdc1242e2d31e5034309a14fd1b29bbf7232b9a7c7042500510332eb8eae1 | MATLAB | 13,049 | 282 | % inputgui() - A comprehensive gui automatic builder. This function helps
% to create GUI very quickly without bothering about the
% positions of the elements. After creating a geometry,
% elements just place themselves in the predefined
% locations. It is especial... |
f78d8c00d4d8e210b68d40b09a3e3defceaf9cc69cb461056d26156ecb6844a1 | MATLAB | 13,069 | 431 | % binica() - Run stand-alone binary version of runica() from the
% Matlab command line. Saves time and memory relative
% to runica(). If stored in a float file, data are not
% read into Matlab, and so may be larger than Matlab
% can handle owing to memory limitations.
% Usa... |
15030fcc199b5ea9e34d3747f6e6a3fb59d01306dbc2128562b3550b7c0d0698 | MATLAB | 13,077 | 313 | function alltrialstimecourse_multi(headpath,fileexpnum)
%use this one when the data has been analyzed before and saved.
%compare adjacent ROIs for activity differences
cd('extracted2')
savefilename=strcat(fileexpnum,'_analysis2');
load(savefilename);
cd(headpath);
%make a picker in here to select the ROI you want to l... |
f68a4230d4eb184418d085c885f106813c28ff4e907496922c06b614b3fb8a8c | MATLAB | 13,086 | 271 | function [ results ] = plot_pass_index( varargin )
import CMBHOME.PASS_INDEX.*;
ip = plot_pass_index_parser(varargin{:});
p = pass_index_parser(varargin{:});
for i = fields(p.Results)'
eval([i{1} ' = p.Results.' i{1} ';']);
end
for i = fields(ip.Results)'
eval([i{1} ' = ip.Results.' i{1} ';']);
end
for i = f... |
68e86c2c2023a8b3a3ce4821f7829519fed5a121b330b67c72076bf98992ad33 | MATLAB | 13,145 | 348 | % metaplottopo() - 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.
%
% Usage:
% >> axes = metaplottopo(data, 'key1', 'val1', 'key2', 'val2')
%
%... |
0bcdb58e35bdf1189ce56761fd58b81d3231cedf6c7bfef30409b61c53ac1f0c | MATLAB | 13,148 | 288 | function [soAll, soSummary, params] = fun_slow_oscillations(data, chans, srate, varargin)
% Slow-oscillation detection. Automatically detects slow oscillaiton events on
% multi-channel EEG data and returns each detected event plus their
% parameters.
%
% Required inputs:
%
% data: A channel x timepoints array, filtered... |
1dc007e15fea8c924a860df99a7d4cc14546d8b6019bf0acbf71bef6e5bc02e0 | MATLAB | 13,176 | 330 | % plotcurve() - plot curve(s) with optional significance highlighting.
%
% Usage: >> plotcurve(times, data, 'key1', 'val1', 'key2', val2' ...);
%
% Required inputs:
% times - [float] vector of time indices
% data - [float] data array, size of [n x times]. If n>1 several
% curves are plotted (unless 'plot... |
a8b68eb3dca3ad5035bdbde9a49a5be80de9e0d4a5bbbf4a7c5c6acf08bc3af4 | MATLAB | 13,183 | 295 | function [settings,fibersFound] = ea_prepare_fibers(options, S, settings, outputPaths, source_i)
% Preprocess fibers: warp to native (if neccesary), remove those far away
% from the stimulating contacts and too short to allocate axons.
% By Butenko and Li, konstantinmgtu@gmail.com
arguments
options % Lead-DBS ... |
e1a50f102a06dd25ed0b879f32645e742dcf760528ac2a9de88219444f535907 | MATLAB | 13,209 | 365 | function CVerr = cvglmnet(x,y,family,options,type,nfolds,foldid,parallel,keep,grouped)
%--------------------------------------------------------------------------
% cvglmnet.m: cross-validation for glmnet
%--------------------------------------------------------------------------
%
% DESCRIPTION:
% Does k-fold cros... |
81b33106804b4eae31fd33e190aeb478fc5d207b707cd62042f175d96311ec3e | MATLAB | 13,216 | 292 | function M_final = apply_shifts(Y,shifts,options,td1,td2,td3,col_shift)
% apply shifts using fft/cubic or linear interpolation
% INPUTS
% Y: Input data, can be already loaded in memory as a 3D
% tensor, a memory mapped file, or a pointer to a tiff stack
% shifts: calc... |
f8dc6a1d91bfb4d4dfcfea62e231ab105946cac1092b4960d458cb4ef3f377c0 | MATLAB | 13,227 | 357 | function obj=stat_smooth(obj,varargin)
% stat_smooth Display a smoothed estimate of the data with
% optional 95% bootstrapped confidence interval
%
% Arguments given as 'name,value pairs:
% - 'method': Which method to use for the smoothing. Available methods are:
% - 'eilers' (method from Eilers 2003, defau... |
7dc649462581a864f7c223f7e258eb85009bfe1f9184f8e0eeabdded3196ce97 | MATLAB | 13,235 | 306 | function M_final = apply_shifts(Y,shifts,options,td1,td2,td3,col_shift)
% apply shifts using fft/cubic or linear interpolation
% INPUTS
% Y: Input data, can be already loaded in memory as a 3D
% tensor, a memory mapped file, or a pointer to a tiff stack
% shifts: calculated ... |
87ad8840f795d3c5eb9105673a04b340f69f0c7cef6bb85918e5ed0e5da21780 | MATLAB | 13,236 | 257 | % std_dipoleclusters - Plots clusters of ICs as colored dipoles in MRI
% images (side, rear, top and oblique angles possible)
%
% std_dipoleclusters(STUDY,ALLEEG,'key1',value1, 'key2',value2, ... );
%
% Inputs:
% STUDY - EEGLAB STUDY set
% ALLEEG - vector of the EEG datasets included in the STUD... |
d1db81a4674f145d661dedc3f063d161a8f75953d77d50c6023ef713faee3e6f | MATLAB | 13,240 | 159 | function summary_stats = load_summary_stats(disorder)
%
% Usage:
% summary_stats = load_summary_stats(disorder)
%
% Description:
% Outputs summary statistics for a given disorder (author: @saratheriver)
%
% Inputs:
% disorder ({'22q', 'adhd', 'anorexia', 'antisocial', 'asd', 'bipolar', 'depression', 'epilepsy',... |
1c9f4ac5d5a0d88faeb70651eaf95344e49863c71322c6aaca1fb340a58bac44 | MATLAB | 13,268 | 320 | % makehtml() - generate .html function-index page and function help pages
% composed automatically from formatted Matlab function help messages
%
% Usage:
% >> makehtml(list, outputdir);
% >> makehtml(list, outputdir, 'key1', val1, 'key2', val2, ...);
%
% Input:
% list - (1) List (cell arra... |
37b05b35a9bf8cdf9c74b6a3c224e952c3c92d50b11bc47aefacb7a64da848d2 | MATLAB | 13,269 | 370 | %% a01_EphyReplot_acrossSU_SM.m
% Read "mXX_SU_population_rwX.mat"
% for IPS analysis
%%%%% Version History
% v2: 02/15/2024
% - support different reward condition
% v1: 01/20/2025
% - read NEV file and plot all units together in each single trial
% Liang-Yin
clear all; close all;
%% Parameters
path2data = p... |
81c89a267e6d6b1302a9c1eeda57a4a4914850a1da90c2592f8cd6c384dafbc2 | MATLAB | 13,274 | 333 | function ea_ptspecific_atl(options)
if startsWith(options.atlasset, 'Local atlas: ') % manually installed atlas coded with this prefix by lead-dbs.
return
end
troot=[options.earoot,'templates',filesep];
aroot=[ea_space(options,'atlases'),options.atlasset,filesep];
proot=[options.root,options.patientname,filesep];... |
4d42f9cfea22076b75a0561ec6b12a8c52102b233ce60bcc6bdf9e7647e6d048 | MATLAB | 13,301 | 389 | function fit = fit_meta_d_mcmc(nR_S1, nR_S2, mcmc_params, fncdf, fninv, name)
% fit = fit_meta_d_mcmc(nR_S1, nR_S2, mcmc_params, s, fncdf, fninv)
%
% Given data from an experiment where an observer discriminates between two
% stimulus alternatives on every trial and provides confidence ratings,
% fits meta-d' using MCM... |
c880fde2bf54024533426aef6da0631599db77a9d2bfd885147476b65dad5452 | MATLAB | 13,310 | 395 | %% e1_corr_patterns.m
%
%
% *USAGE*
%
% This script calculates, thresholds, and plots correlation maps
% between all pairwise combinations of condition or contrast images using
% the searchlight approach, calling the CANlab function
% searchlight_correlation() under the hood
%
% Run this script headless from the Li... |
584c5b5a7cc5ee401b391116050c178317966b74e7728cbf342e3842524a3e6c | MATLAB | 13,313 | 310 | %% a_set_up_paths_always_run_first.m
%
%
% *USAGE*
%
% Always run this first before you run any other CANlab_help_examples
% second-level script. This script
%
% # runs LaBGAScore_prep_s0_define_directories (if rootdir/githubrootdir are
% not already in the workspace) to set study-specific root/code/github
% direct... |
704feff08301e4a8ed49cce78e341446c7f02cdb5cf375f00c774235e236e9d5 | MATLAB | 13,315 | 231 | % Computational model of visual-vestibular interaction in Purkinje cells of
% the primate cerebellar nodulus and ventral uvula (NU), and the code that
% generates panels B-D of Figure 4 of the paper cited below.
%
% -------------------------------------------------------------------------
% CITATION
% -----------... |
5e67cf8bbfc53b99eb95b70c48fc4626c1d6c30cebdada1cb3c5e9f1f61c62f4 | MATLAB | 13,319 | 284 | function prefs = ea_prefs_default(patientname)
% determine preferences here. For filenames, the variable 'patientname' can
% be used in string-handling. This variable will be a string with the same name as the patient
% folder.
if nargin == 0
patientname = '';
end
% load loaded prefs (-> prefs.lp)
try
load([e... |
921bd02e82d050bd2e0a458ff3658b1a0c924064ef2396d11845044a608b50a0 | MATLAB | 13,344 | 360 | %%*****************************************************************************
%% sdpt3: solve an semidefinite-quadratic-linear program
%% by infeasible path-following method on the original problem
%% or the 3-parameter homogeneous self-dual model.
%%
%% [obj,X,y,Z,info,runhist] = sdpt3(blk,At,C,b,O... |
fecc7ed64595794fbe57f34b87ba915534c5d0338dfc9ba75c8b0debeb674341 | MATLAB | 13,363 | 385 | % eeg_topoplot() - plot scalp map
%
% eeg_topoplot( vals, chanlocs, 'key', 'val');
%
% Input:
% vals - values, one per channel
% chanlocs - channel structure, same size as vals
%
% Optional inputs:
% 'colormap' - colormap. Possible colormaps are 'blueredyellow', ...
% 'yellowredblue', 'bluere... |
dfd02efc2f6a5808819b2ba67ed0df8e86254caaea653199e1a52afb84419b17 | MATLAB | 13,365 | 365 | function saveas(this,filename,format)
% Save GIfTI object in external file format
% FORMAT saveas(this,filename,format)
% this - GIfTI object
% filename - name of file to be created [Default: 'untitled.vtk']
% format - optional argument to specify encoding format, among
% VTK (.vtk,.vtp), Collada (... |
d7871dc974b8347dd4845e19b85c4a193d5e56262f4b2157d4d628a241db74b6 | MATLAB | 13,381 | 357 | % pop_loadbci() - import a BCI2000 ascii file into EEGLAB
%
% Usage:
% >> OUTEEG = pop_loadbci( filename, srate );
%
% Inputs:
% filename - file name
% srate - sampling rate
%
% Outputs:
% OUTEEG - EEGLAB data structure
%
% Author: Arnaud Delorme, CNL / Salk Institute, 9 July 2002
%
% See... |
62f99e1ef98febdaa91d17a974951e62cb8081c214d9c1001a6f8691b71e1eb5 | MATLAB | 13,410 | 295 | %% prep_1_set_conditions_contrasts_colors.m
%
%
% *USAGE*
%
% This script defines DAT.conditions, DAT.contrasts, DAT.colors (and
% optionally DAT.between_condition_cons) - the core design specification
% consumed by every later script - and saves them, together with DSGN and
% standard paths, to image_names_and_setup.m... |
dcd26637b16829b03f073915eba7230681ff02a499b5d29a2df80db6a7f074fd | MATLAB | 13,413 | 320 | function ea_unified_draw(obj,vals,fibcell,usedidx) %for cv live visualize
%function draw(obj,vals,fibcell)
% re-define plainconn (since we do not store it)
%this is all based on which tool is selected
%match draw tool with field name
if strcmp(obj.drawTool,'sweetspotmapping')
flag2tool = 'sweetspotmapping';
if ... |
abde970d7ddb17686a8f04e8f9d091b324dd25cf0231f5d642c4dabbe2c65aa0 | MATLAB | 13,419 | 404 | % timefrq() - progressive Power Spectral Density estimates on a single
% EEG channel using out-of-bounds and muscle activity rejection
% tests. Uses Matlab FFT-based psd().
% Usage:
% >> [Power,frqs,times,rejections] = timefrq(data,srate,subwindow);
% >> [Power,frqs,times,rejections] = ..... |
becb60034b187582d603034941ae0059835149b792a9780e5eab95eb3074f3ce | MATLAB | 13,447 | 423 | function cs_fmri_conseed_matrix(dfold,cname,sfile,cmd,writeoutsinglefiles,outputfolder,exportgmtc)
tic
% if ~isdeployed
% addpath(genpath('/autofs/cluster/nimlab/connectomes/software/lead_dbs'));
% addpath('/autofs/cluster/nimlab/connectomes/software/spm12');
% end
if ~exist('writeoutsinglefiles','var')
... |
7ab24aa7844f5a837e62215531e4213272dc8e74d9768c95ae906f4b9aa321a0 | MATLAB | 13,479 | 463 | %% Create and plot design matrices
%%
% Create and plot your own design matrix easily using CANlab tools!
% Note: This also requires SPM software functions
%
% These functions are useful for design simulations. They use the following
% core functions, which may also be useful to use separately if you are
% doing simul... |
8fadfab20c7be5e19221550c435084a36a534124f99fea3445dd2a5dff70ff1b | MATLAB | 13,500 | 315 | function [output, Greg] = dftregistration_min_max_3d(buf1ft,buf2ft,usfac,min_shift,max_shift,phase_flag)
% function [output Greg] = dftregistration(buf1ft,buf2ft,usfac);
% Efficient subpixel image registration by crosscorrelation. This code
% gives the same precision as the FFT upsampled cross correlation in a
% small ... |
b5815924071ab970d1b68b7c503012d7130a3ba79fa59e92a04ab4ba5721e9ca | MATLAB | 13,501 | 359 | function bz_ConcatenateDats(basepath,deleteoriginaldatsbool,sortFiles)
% bz_ConcatenateDats - Concatenate raw .dat files found in a session folder
% - for intan type recordings
%
% ALGORITHM OUTLINE: looks for .dat files in a folder (or in subfolders) to
% concatenate together. The concatenation happens via system c... |
4c48985c52b54db4bbf8f655b61be14cb07ea1cf755d33182fb4f42ee713310f | MATLAB | 13,559 | 252 | function outputStruct = runSmactinAggMovExplain(tassm,matchindx,smactinFlag, propSpk, propSm, ...
maxNumPropVect, mvrgAggMatFlag, cutOffInput, outlierParam, spekLabelBase, smLabelBase, sigThreshInput)
%RUNSMACTINAGGMOVEXPLAIN takes data matrices of SM - speckles pairs, perform MVRG on them, and report statistical s... |
aa3770796174e51709edec0b5dae5e2ecdaf9412550cbd8accf76a5b56eb9904 | MATLAB | 13,571 | 411 | function [ results ] = infieldness(varargin)
% Reflects how "in field" an animal is along its trajectory.
%
% ARGUMENTS
% cel n x 2 vector like [tetrode index, cell index]. If
% unassigned, uses self.cel. If has more than one cell,
% all returns are as cell arrays with... |
1cecfe6747bdf449bd33b52f34e54f2de5d1a9442b099c15cb2e2a6031e810b0 | MATLAB | 13,593 | 442 | function dimord = getdimord(data, field, varargin)
% GETDIMORD
%
% Use as
% dimord = getdimord(data, field)
%
% See also GETDIMSIZ
if strncmp(field, 'avg.', 4)
field = field(5:end); % strip the avg
data.(field) = data.avg.(field);
data = rmfield(data, 'avg');
end
if ~isfield(data, field)
error('field "%s" ... |
957477b6b2967ce6bc6490fb3e8590431a05178d9220198f0c90f97dea890c99 | MATLAB | 13,607 | 436 |
% -------------------------------------------------------------------------
% Downloaded 10.08.2018 from:
% http://www.columbia.edu/~bsm2105/type2sdt/archive/index.html
% Author: Brian Maniscalco
% Contact: brian@psych.columbia.edu
% 10.08.2018: OKF added calculation for type 1 c to the results
% NOTE FROM ... |
b7ec97a71d082781dbbe5084845fb2bb29aad270fd686ba2978f666d5f6315fb | MATLAB | 13,641 | 460 |
function maps = computeParameterMaps(ftr,M);
idxmask = ftr.user.S2(:,:,:,2)>0;
% kernel for gathering values withtin original DWI-voxel
osamp = (ftr.trackParam.params.p_wid);
osamp = osamp/M;
st = max(ceil(osamp/2),1);
ker = ones(osamp,osamp,osamp); %ker = ker /... |
a40df6faae07294ca5c3ba39e678dc4eddec0b476916df50e87b01dc92bfc0ca | MATLAB | 13,646 | 333 | % pop_resample() - resample dataset (pop up window).
%
% Usage:
% >> [OUTEEG] = pop_resample( INEEG ); % pop up interactive window
% >> [OUTEEG] = pop_resample( INEEG, freq);
% >> [OUTEEG] = pop_resample( INEEG, freq, fc, df);
%
% Graphical interface:
% The edit box entitled "New sampling rate" contains the fre... |
4d8b80c93d52d290a7c99c1e3afb989d3556db192de1d1ee570a6c0f2e76f860 | MATLAB | 13,648 | 267 | function [pval ClusNum] = Clinc_permtest_heatnum(DATtemp1,DATtemp2,NUM1,NUM2,Lab,V,VoxelDirPermcluster,Dmasked)
% Lab: 1 voxel, 2 ROI
pths = which('Clinc_permtest.m');
[pth,fil,nam] = fileparts(pths);
if Lab==1 %
if isempty(dir([pth,filesep,'permtest_clust']))
mkdir([pth,filesep,'permtest_clust']);
els... |
7b4108dbde1e76458659c3df0263b6a3bb0653dd57a28b6798c4e41fd6398e62 | MATLAB | 13,654 | 454 | function clustered = direcClus_fix_bessel_bsxfun(x,k,d,noruns,lambda,p,mInit,epsilon,flagCorStop, max_iter, assignment_flag)
% clustered = DirClus(x,k,d,noruns,lambda,p,mInit,epsilon,flagCorStop)
%
% NOTE: This is a modified version of Danial Lashkari's original code direcClus.m,
% which can be found here:
% ... |
9436a13e12c6972a4cd63dd4c029ed06abd9bf175516dba53e44acd4f2f9fbdc | MATLAB | 13,668 | 372 | % pop_mergeset() - Merge two or more datasets. If only one argument is given,
% a window pops up to ask for more arguments.
% Usage:
% >> OUTEEG = pop_mergeset( ALLEEG ); % use a pop-up window
% >> OUTEEG = pop_mergeset( ALLEEG, indices, keepall);
% >> OUTEEG = pop_mergeset( INEEG1, INEEG2, keepa... |
750b771c4462a1e0c45f132f5542ba3428d390f5d71f3ab725dc01fbd1d2dba9 | MATLAB | 13,675 | 320 | function [ hListbox, jListbox, jScrollPane, jDND, permOrder] = reorderableListbox( ...
varargin )
%REORDERABLELISTBOX Create reorderable listbox.
% REORDERABLELISTBOX, by itself, creates a listbox in the current figure
% whose contents can be reordered by clicking and dragging items, and
% returns a handle to... |
b3edf26e8ad79933eb9d6d96f18f3a0870b028736b29ca09f6583e1c9344ffd6 | MATLAB | 13,688 | 302 | function [PL]=ea_calc_vatstats(resultfig,options,hmchanged)
% Calculate VAT stats (atlas intersection and volume)
% Stimulation information w.r.t the VTA will also be stored in stats.
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Be... |
b46617d84cf5ef054d3a4d69ba3191ca6a24bd6290e6ce9f89005e5b3bc88669 | MATLAB | 13,729 | 369 | classdef ea_roi < handle
% ROI class to plot niftis on lead dbs resultfig / 3D Matlab figures
% example:
% figure; pobj.openedit=1; ea_roi([spm('dir'),filesep,'toolbox',filesep,'OldSeg',filesep,'grey.nii'],pobj); a=light; axis('off','equal')
% A. Horn
properties (SetObservable)
niftiFilenam... |
879a37acfeb83e2c583842f2c006a6d1d1376d25d0f8d03d3a0bd94e97a55940 | MATLAB | 13,730 | 365 | function saveas(this,filename,format)
% Save GIfTI object in external file format
% FORMAT saveas(this,filename,format)
% this - GIfTI object
% filename - name of file to be created [Default: 'untitled.vtk']
% format - optional argument to specify encoding format, among
% VTK (.vtk,.vtp), Col... |
de14290da290405ede101ccf0b4637cf2027f747eb899ad7d858e0a1f2e15b94 | MATLAB | 13,741 | 267 | function cm_data=RdBu(m)
cm = [0.403921568627451 0 0.121568627450980
0.420234922908265 0 0.121780198586831
0.436093693351309 0 0.122121857680585
0.451507029581573 0 0.122593654786499
0.466483444818097 0 0.123195754618115
0.481031040567280 0 0.123928429963463
0.495157670291367 0 0.124792052969246
0.508871058866449 0 0.1... |
299f20b4f20cb8a6db0821817f9b36b6c6f7abff51ac59a342249d6dfa4d521a | MATLAB | 13,743 | 267 | function cm_data=RdBu_r(m)
cm = [0.0196078431372550 0.188235294117647 0.380392156862745
0.0283230993458890 0.197952412883611 0.398602525810859
0.0372992099145506 0.207543660101164 0.416224146840473
0.0461011759889104 0.217009699714168 0.433254817111962
0.0540166421641391 0.226351215333237 0.449694340499403
0.0611887383... |
920831bd951603e7cc94b226268290b0d9a5c5914f116333c02faa4fd30d2864 | MATLAB | 13,745 | 365 | classdef (CaseInsensitiveProperties = true) functionalBoxPlot < ...
iosr.statistics.functionalPlot
%FUNCTIONALBOXPLOT Draw a functional boxplot
%
% Use this class to plot a functional boxplot [1]. A functional boxplot
% considers each function as a single observation. The order statistics
% are calculate... |
091dcc0af8509e59b83b7abf425613189be3765b8d82a579626f3cf94d97e540 | MATLAB | 13,771 | 284 | function saved_binned_data_file_name = create_binned_data_from_raster_data(raster_file_directory_name, save_prefix_name, bin_width, sampling_interval, start_time, end_time)
% This function takes the name of a directory that contains files in raster-format
% and creates data that is in binned-format data that contain... |
d4edd2f7620d4c26441bebc29715f64c8a734f863825f17f6d1a2ebec3775d9f | MATLAB | 13,772 | 430 | function Browse(parameter1,parameter2)
%Browse - Interactively browse the data in one or all subplots in a figure.
%
% USAGE
%
% Browse(figure,'on') % enable browsing for this figure
% Browse(figure,'off') % disable browsing for this figure
% Browse('on') % enable browsing for all new figures
% ... |
fdbb088c053219139dbbda3918e8cc1b10ae31f7a528c1ec45571f5030efbfb6 | MATLAB | 13,774 | 276 | function saved_binned_data_file_name = create_binned_data_from_raster_data(raster_file_expression, save_prefix_name, bin_width, sampling_interval, start_time, end_time)
% This function takes the name of a directory that contains files in raster-format
% and creates data that is in binned-format data that contain the... |
716cb40d5e7d1dc41a0f6837734e137d40c75f125b018326c62354b66da852b9 | MATLAB | 13,779 | 405 | function analysisResults = analyzeByGroup(aggregatedResults, swTestPath, compareGroup, outputFile, options)
% ANALYZEBYGROUP Full Statistical analysis using file created from
% aggregateTrackingResults with normality testing.
%
% Load compiled tracking results from aggregateTrackingResults,
% run Shapiro-Wilk normali... |
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