sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6c73116f8f88f9e221f8479a3c47e330d946e794f44ec75a1d9508794ce04b57 | MATLAB | 3,437 | 112 | function [outputMap, mask] = ea_agreementmap(inputMaps, outputFileName, writeoutMask, mode, zz)
% Calculate agreement R-map
% mode can be 'mult' or 'sum', 'avg' or 'sum/avg0...x' which creates an average/sum map across pixels that agree in
% polarity for 0 to x cases. (avg0 for instance would just be the average
% map ... |
e2f8559eaa56e79be2e6d8c5d45ab41506f33a3a6118db10cf1f248bbfe4f1c7 | MATLAB | 3,437 | 81 | function [handles] = callBAPsubtract_master(handles, dataID)
if nargin<2
dataID = 1;
end
f_wait = waitbar(0.5, 'Auto processing Backpropagation removal');
scrsz = handles.scrsz;
handles = call_autoBAP(handles);
traceplot22(handles)
close(f_wait);
delete(f_wait);
if handles.openGUI==0
comIn = input('Start manual... |
631b2ed53f3344d3d1cc0a6a4b5870e0e337ea497bed405cad91ae5401431362 | MATLAB | 3,441 | 97 | function ClincFreq_CentPointForVolume_pre(INDIR,outdirCent,Para,spmjobdir)
[V,D,namelist] = Dynamic_read_dir_NIFTI_sparse(INDIR);
D(isnan(D)) = 0;
D(isinf(D)) = 0;
D = D>0;
inum = 1;
for isub = 1:length(namelist)
Du = reshape(full(D(:,isub)),V(1).dim);
Coninf = bwconncomp(Du);
nums = Coninf.NumObjects;... |
ce42b02616b5f726c77660d18158f231899d3a5850b9d69f6028c2feda9d74a7 | MATLAB | 3,441 | 105 | function [mask weight]=mesh2vol(node,elem,xi,yi,zi)
%
% [mask weight]=mesh2vol(node,face,Nxyz)
% [mask weight]=mesh2vol(node,face,[Nx,Ny,Nz])
% [mask weight]=mesh2vol(node,face,xi,yi,zi,hf)
% or
% newval=mesh2vol(node_val,face,...)
%
% fast rasterization of a 3D mesh to a volume with tetrahedron index labels
%
% aut... |
cfa4c807ea15df41b688138f92c275b168ecf7ede495fe30217b0afca8ecf2c5 | MATLAB | 3,441 | 87 | function [goodx,goody,goodz]=ea_export_templates(coords,trajectory,patientname,options,side)
% this function can export templates based on manual measurements of the
% electrode tips and is originaly based on ea_sample_cuboid.
% uses map_coords authored by Ged Ridgway
switch options.subj.postopModality
case 'MRI'
... |
ea9e61cf61f996373fcfb2eedac2628820ec3b2f5100d91239a12c6596227617 | MATLAB | 3,441 | 77 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
5345ea254213ece13248a73bd8f30d18a364ac15e568b0135443ce5d8ed61ca8 | MATLAB | 3,444 | 96 | function mStatus = startMotion(idx, grid, stepperHandles, panelHandles)
%
% Function:
%
global currentPositionX currentPositionY currentPositionZ
global pausePositionX pausePositionY pausePositionZ
global useEncoderX useEncoderY useEncoderZ
global surgIdx isPause isFinished isStop
mStatus = 0;%0-normal 1-... |
e52d02cc70ae05f94fe637fd109fda6d4f01521a2b6a86b70d301c2449234f3a | MATLAB | 3,446 | 92 | function RMSE = getRmse(X, y, varargin)
%GETRMSE Calculate the root-mean-square error between input data
%
% RMSE = IOSR.STATISTICS.GETRMSE(X, Y) calculates the RMSE of the inputs
% data where
%
% RMSE = sqrt( 1/N-D * SUM(err^2) )
% err = abs(X-Y)
%
% The input data X and Y can be vectors ... |
711a1f6121e7d1d23ae2038bd396263e7779c0542531574709e8fcf54dc70eb5 | MATLAB | 3,447 | 71 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
a1172cabf7ff0e0d4ff7685f883c92470c98b5b1c19e418cbaed3001b6d70ca7 | MATLAB | 3,449 | 109 | % gabor2d() - generate a two-dimensional gabor matrice.
%
% Usage:
% >> [ matrix ] = gabor2d(rows, columns);
% >> [ matrix ] = gabor2d( rows, columns, freq, ...
% angle, sigmaR, sigmaC, meanR, meanC, dephase, cut)
% Example :
% >> imagesc(gabor2d( 50, 50))
%
% Inputs:
% rows - n... |
5b838fa0a8467a33f04d77666482248aef3abe105116c4078af0fd615914c263 | MATLAB | 3,450 | 80 | function [handles] = callBAPsubtract_filt(handles, dataID)
if nargin<2
dataID = 1;
end
f_wait = waitbar(0.5, 'Auto processing Backpropagation removal');
scrsz = handles.scrsz;
handles = call_autoBAP_filt(handles);
traceplot22(handles)
close(f_wait);
delete(f_wait);
if handles.openGUI==0
comIn = input('Start man... |
b21987df0cb6cb2aa3a6f09f80038e9fe4d5fe64874083dcea3188735c0500d6 | MATLAB | 3,450 | 109 | function [N, wMean, wStdDev, p] = CBIG_MMLDA_characteristics_glm(prob, y, y_type)
% [wMean, wStdDev, p] = CBIG_MMLDA_characteristics_glm(prob, y, y_type)
%
% Analysis about factors effect on characteristics by using glmfit and hypothesis test.
%
% Input:
% - prob :
% N x K matrix, factor compositions... |
c859f0d683dcfc99023299a3c698fd0c9034e70f42fd1e313abfce423fa19ee5 | MATLAB | 3,451 | 91 | % varsort() - reorder ICA components, largest to smallest, by
% the size of their MEAN projected variance
% across all time points
% Usage:
% >> [windex,meanvar] = varsort(activations,weights,sphere);
%
% Inputs:
% activations = (chans,framestot) the runica() activations
% weights = ... |
05fb8cfaddd115cde649b367b01c450bc2ddb12e6e38d903614e32923de59096 | MATLAB | 3,452 | 105 | % Computing a sparse solution of a set of linear inequalities
% Section 6.2, Boyd & Vandenberghe "Convex Optimization"
% "Just relax: Convex programming methods for subset selection
% and sparse approximation" by J. A. Tropp
% Written for CVX by Almir Mutapcic - 02/28/06
%
% We consider a set of linear inequalities A*... |
91c8a3531829f63b42174d793d7bb977cf680b7b0b15d8ec7894ec025870db93 | MATLAB | 3,452 | 97 | % timewarp() - Given two event marker vectors, computes a matrix
% that can be used to warp a time series so that its
% evlatencies match newlatencies. Values of the warped
% timeserie that falls between two frames in the original
% timeserie will be linear ... |
9aa55a06cf57348ae402aea2828d5951b7a334eb76631401b8a1813cd1ea00ba | MATLAB | 3,452 | 73 | %% Generate mean and 95% CI for group-level ROC
Nsub = length(fit.d1);
ts = tinv([0.05/2, 1-0.05/2],Nsub-1);
if any(isnan(fit.obs_FAR2_rS1(:))) || any(isnan(fit.obs_HR2_rS1(:))) || any(isnan(fit.obs_FAR2_rS2(:))) || any(isnan(fit.obs_HR2_rS2(:)))
warning('One or more subjects have NaN entries for observed confid... |
6bedf99558e12d46b4631aee95277335d729061caf171f391ae2b295b4812524 | MATLAB | 3,454 | 90 | function [MI] = MutualInfo(CountsMat)
%MutualInfo calculates the mutual information between Y and {X1,...XN}.
% [MI] = MutualInfo(CountsMat) is the mutual information between the Y
% variable and the X variables considered as one vector valued variable
% {X1, ... XN}.
%
% Inputs
%
% CountsMat: An array that c... |
256635179fd8cf0517aee5f807daba4be87d93ab482eef45b635c3087627239a | MATLAB | 3,455 | 98 | for i = 1:length(leftmeansd{11})
if iscell(leftmeansd{11}{i})
figure;
for tr = 1:length(leftmeansd{11}{i})
subplot(1,length(leftmeansd{11}{i}),tr);
imagesc([leftmeansd{11}{i}{tr} rightmeansd{11}{i}{tr}]);
hold on; xline(8.5,'y','linewidth',2)
ca... |
67c359f0d8742bc098e2d5635413c6bb2b6e3644510567905a1de198c696f3ae | MATLAB | 3,457 | 90 | % Runs a two-sample t-test for a set of signature responses, for each
% contrast.
% Signatures, scaling, etc. are defined below.
%% USER OPTIONS
% -------------------------------------------------------------------------
mysignature = {'PINES', 'Rejection', 'VPS', 'VPS_nooccip'};
scalenames = {'raw'}; ... |
aa128e87033531c22b772b370c632145d567fdb47b377d419e24eb434468455f | MATLAB | 3,457 | 102 | function CBIG_pMFM_step6_SWSTD_state_main()
% This function is used to conduct the statistical analysis corresponding
% to figure 5D and 5E in the paper.
%
% There is no input for this function as it can automatically get the
% output file from previous step.
% There is no output for this function as it will generate ... |
1d73367d67b07bd448d6a1a608515a7d69ec9699c4c6a982a3208474578b8aed | MATLAB | 3,461 | 85 | function corr_array = compute_spont_corr(topology, dx, dt, hetparam_het, homparam, num_parcel_x, tol)
% Compute the SCF with reference point p, with given sigma_n
% Set tolerance if not given
if nargin < 7 || isempty(tol)
tol = 1e-7;
end
parcel_Nx = topology.Nx / num_parcel_x;
if mod(... |
08861c9f41bbf00ad25c34166fcedfa4878db5b8600bf2c0478eb3225cfdf74d | MATLAB | 3,463 | 106 | classdef Panel < uix.Panel
%uiextras.Panel Show one element inside a panel
%
% obj = uiextras.Panel() creates a standard UIPANEL object but with
% automatic management of the contained widget or layout. The
% properties available are largely the same as the builtin UIPANEL
% object. Whe... |
e6c877b67226f6c2975d89f942af6bbf894b2df7323cd2a5950acbb5dfb587c1 | MATLAB | 3,464 | 129 | %filtering script by Kathy Nagel 07/12/22
load('from0deg.mat')
plot(Trial')
load('from0deg.mat')
hold on; plot(Trial')
load('from0deg.mat')
hold on; plot(Trial')
close
hold on; plot(Trial')
close
load('from0deg.mat')
plot(Trial')
analyzeCalciumExperiment_newThor5D_roishift(pwd,'67A04_apr072022_f2e1',[],[]... |
ec0b22b3fb2cb6d2b2f5454e2ec165485b9d9bd510a48a4c6bc081aafa892a37 | MATLAB | 3,464 | 93 | function varargout=cbiQuaternionToHomogeneous(varargin)
% [M,R,T]=cbiQuaternionToHomogeneous( quatern, pixdim, qfac, qoffset )
% - OR -
% [M,R,T]=cbiQuaternionToHomogeneous( hdr )
%
% Computes the 4x4 homogeneous transformation matrix from quaternion coefficients quatern,
% voxel dimensions pixdim, coordinate system o... |
21b2fae332fcd1e9cb409c05e28ffdcd7660dc522a352c682b48074fde1b196c | MATLAB | 3,465 | 90 | % Runs a two-sample t-test for a set of signature responses, for each
% contrast. Also runs NPS subregions.
% Signatures, scaling, etc. are defined below.
%% USER OPTIONS
% -------------------------------------------------------------------------
mysignature = {'FAPS','VIFS','reddan'};
scalenames = {'raw'}; ... |
5e234b2372b47ba6b3414da8a618acf589b54cb498bbfdcd5b49f5f06401d2bf | MATLAB | 3,465 | 119 | %%*********************************************************
%% convertcmpsdp: convert SDP with complex data into one
%% with real data by converting
%%
%% C - sum_{k=1}^m yk*Ak psd
%% to
%% [CR,-CI] - sum ykR*[AkR,-AkI] psd
%% [CI, CR] [AkI, AkR]
%%
%% ykI = 0 for k = 1:m
%%
%% [bblk,AAt,C... |
ed2481b0341cce598c82f9429ed5d3c95abe68ea2ab1db50d1fa7eb760c6e8b0 | MATLAB | 3,466 | 103 | %%
clear
thedata = 'apr2623_f3e4';
trllength = 127; % in frames
% First, navigate to the folder containing the folders of data you want to
% concatenate.
% [a,b]=NDK_Motion_Correction5D_savecat(thedata,1,0);
[Xpix,Ypix,FrameRate,Zframes]=findkeyparams_newThor5D();
FrameRate=str2double(FrameRate)/Zframes
thepat... |
ed84aff9c3db4fdafe2807091c5f053b8cb82ca21991fd51fe5acdef5e5e5784 | MATLAB | 3,469 | 84 | function obj=geom_point(obj,varargin)
% geom_point Display data as points
%
% This will add a layer that will display data as points
p=inputParser;
my_addParameter(p,'dodge',0);
my_addParameter(p,'alpha',1);
parse(p,varargin{:});
obj.geom=vertcat(obj.geom,{@(dobj,dd)my_point(dobj,dd,p.Results)});
obj.results.geom_po... |
d92b4ff5693713ffe38316b54477234bf8f559ad0c13a89616e362f74f414dde | MATLAB | 3,471 | 78 | function jControl = findjobj_fast(hControl, jContainer) %#ok<*JAVFM,*JAPIMATHWORKS>
if double(get(hControl,'Parent'))~=0 % avoid below for figure handles
try jControl = hControl.getTable; return, catch, end % fast bail-out for old uitables
try jControl = hControl.JavaFrame.getGUIDEView; return,... |
54b5ce68d9ba8eca559b04ebd77a2b2174d48bef7932554337fc586e044a265a | MATLAB | 3,473 | 114 | function M = mz3_read(filename)
% Read MZ3-formatted data from disk
% FORMAT M = mz3_read(filename)
%
% filename - MZ3-formatted file name
% M - data structure
%__________________________________________________________________________
%
% MZ3 Format Specification:
% https://github.com/neurolabusc/surf-ice/tree... |
93f97bf026c58a7a56ba057fdc9cd08ed2987e7b5c72c5c9285d6b225b51460a | MATLAB | 3,475 | 78 | %% function GibbsSamplerAT
%%
% Runs the AT Gibbs sampler for the Author-Topic model.
%
% |[ WP , AT, Z, X ] = GibbsSamplerAT( WD,AD,T,N,ALPHA,BETA,SEED,OUTPUT )|
% will run the Gibbs sampler for the AT model on a bag of words sparse count
% matrix |WD| of size |W| x |D| (|W|=vocabulary size, |D|=number of do... |
a391388ad9babe53f1d298e16879c776821a97e88f89ea1c2417820b2060a07a | MATLAB | 3,476 | 78 | function [TE_all_xy,TE_all_yx, Phi_all, Syn_all, Red_all, AIS_all, Syn_Red_ratio, MI_all] = calc_PhiID_trial_based2(wave_itrials,target_time,past_tau)
[n_trials, n_channels, n_timepoints] = size(wave_itrials);
% past_tau = 10;
n_time= length(target_time);
TE_all_xy = zeros(n_time, n_channels, n_channels);
TE_a... |
6202c819608ded3cdd735fe471e5cd22ab4738ec3179cd1219fde563a8e1d4c1 | MATLAB | 3,480 | 109 | function varargout = ea_explorer_stats_1sampleweightedlinreg(varargin)
% Function to estimate a certain mass univariate test (see below) as used
% in explorer apps.
% - Expects valsin as V x N matrix where
% V is the number of
% voxels/streamlines... |
4e53a0b30fc850431e6d603ace1853fa4315ea3db923acde58fb457d20c91eb9 | MATLAB | 3,481 | 70 | % sleepDanalyzer montage script.
% chanList. A list of channel names and (optionally) channel coordinates.
% This should be an EEGLAB chanlocs struct. Alternatively you can read in a
% .txt file using the readlocs function (EEGLAB). If you wish to
% differentiate channel types (e.g. EEG, EOG, etc.) make sure to use t... |
8caeb2de76b310a125abd57cfb302ffa7ae77e226c592e4a20d88ffe3bdfc79f | MATLAB | 3,482 | 71 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
12f66d79461ad3073d89791e08a1bfce93852af20174d8730981c03181489386 | MATLAB | 3,484 | 113 | %ISOLATE_AXES Isolate the specified axes in a figure on their own
%
% Examples:
% fh = isolate_axes(ah)
% fh = isolate_axes(ah, vis)
%
% This function will create a new figure containing the axes/uipanels
% specified, and also their associated legends and colorbars. The objects
% specified must all be in th... |
68ac6ff93e096185cefaecbc0068792fffb1001603aba389be219d95584dd81b | MATLAB | 3,484 | 84 | % When you load any ANALYZE or NIfTI file with 'load_nii.m', and view
% it with 'view_nii.m', you may find that the image is L-R flipped.
% This is because of the confusion of radiological and neurological
% convention in the medical image before NIfTI format is adopted. You
% can find more details from:
%
% http... |
83931e4db58be25e96f273a72575a5b54a2e6e87867f62a02473075d52d2d449 | MATLAB | 3,485 | 74 | function newmarkers=ea_correctcoords(oldmarkers,trajectory,command,options)
newmarkers=oldmarkers;
grone=[0.1,0.5,3]; % step-sizes
switch command.Key
case 'uparrow'
try
trajvector=gettraj(trajectory,options.elside);
newmarkers(options.elside).head=oldmarkers(options.elside).head+gr... |
298be66390295f821afd99c2885d319346a806add3c19b64cec0c41b1c3eeb18 | MATLAB | 3,486 | 129 | function [tscounts, wfcounts, evcounts] = plx_info(filename, fullread)
% plx_info(filename, fullread) -- read and display .plx file info
%
% [tscounts, wfcounts] = plx_info(filename, fullread)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% fullread - if 0, reads only the file header
% ... |
38b40ea671a70ab24e9470fc4ea8b31b0a25636517a8f32a86d1041e1a9ec410 | MATLAB | 3,486 | 77 | function obj=set_color_options(obj,varargin)
% set_color_options() Set options used to generate colormaps and color
% legends
%
% Parameters:
% 'map': Set custom colormap. Available colormaps are:
% - 'lch' : default, supports lightness
% - 'matlab' : post-2014b default colormap (no lightness support)
% - '... |
5cd66ec29d92f5bbd639cbb275abf7fb8b36cc6b6e3d04a7df67c30470c513bd | MATLAB | 3,486 | 84 | function spike_alignment_batch_Axona(files)
% spike_alignment_batch
% function for alligning spikes detected outside wave_clus.
% INPUT: Matrix of spikes in an ascii file. Spikes must be grouped in a
% matrix called 'spikes' with a spike per row.
% OUTPUT: matrix of spikes alligned with the maximum in sample set by the... |
1e61a0a4bcba0b557f91bc74077c8ba889a1a90665db7e2de6311bd0ad7c52d2 | MATLAB | 3,487 | 87 | %% electrodePointCloudModelEstimate - extract skeleton points from given pointcloud and subsequently fit a polynomial
%
% PARAMETERS
% varargin{1} = pixelValues list got from reference image of the segmentation. When given used for intensity based
% weightig of cenroid calculation.
% varargin{2} = rever... |
9d64dc401585c74537fea55013c7fe7f5d027a069c404f83c306c7234bea6f2e | MATLAB | 3,487 | 119 | function y = poly_env( p, x )
%POLY_ENV Evaluate the convex or concave envelope of a polynomial.
% POLY_ENV( P, X ) uses a semidefinite program to compute the value of the
% convex or concave envelope of the polynomial represented by the vector
% P. The format of the vector P is identical to that required by POL... |
b54f8f3948a0a767781d3ea43743fbaa02b70f5cf55798fa5132e846a284d98c | MATLAB | 3,488 | 91 | function [OpenedFileName, Version, Freq, Comment, Trodalness, NPW, PreTresh, SpikePeakV, SpikeADResBits, SlowPeakV, SlowADResBits, Duration, DateTime] = plx_information(filename)
% plx_information(filename) -- read extended header infromation from a .plx or .pl2 file
%
% [OpenedFileName, Version, Freq, Comment, Tro... |
f9c799ecf83f4bc2cdf78a040502570c95b9f2373a68752c6a23df3a945c28ef | MATLAB | 3,488 | 141 | %% Animate geometric model
clear; clc;
% Load model parameters
loadparam;
dx = topology.L / topology.Nx;
dt = topology.T / topology.Nt;
ts = run_periodic(topology,homparam,hetparam_hom,stim);
% Create figure
f = figure;
sgtitle('Evoked Response - Geometric Connectivity')
f.Position = [300 100 650 600];
set(gcf, 'co... |
07c3f872392a0869f0e0b2ab91bdc7bd2a28341515f744abf60f62170a7d962b | MATLAB | 3,489 | 84 | function l = IsFirstAfter(timestamps,list,varargin)
%IsFirstAfter - Identify first item after each of a list of timestamps.
%
% For each element i of a list of test timestamps, find in a list of reference timestamps
% the first element j larger than i. Returns a list of logical indices (the elements of the
% test list... |
81abf5960ef0bcb4d9da2c45e8440135d6727abb92a0e80696435c2f9d0f4ede | MATLAB | 3,489 | 102 | function [sessionInfo] = bz_getSessionInfo(basePath,varargin)
%[sessionInfo] = bz_getSessionInfo(basePath) loads the sessionInfo metadata
%for the recording in basePath. basePath should be in the format:
% /whateverPath/baseName/
% a file basePath/baseName.sessionInfo.mat
% or basePath/b... |
a5a9f98117ba0c9a1eb60593193cbeef14700eecbeb0621e174dfb712dcfce31 | MATLAB | 3,489 | 90 | function data_out = Trinh_loadConditionData_usingendmarker(filename,eventtype,eventvalue,prestim,poststim)
%% load and cut condition data
% insert name of the file: filename, e.g., 'MUSICOM_001.vhdr'
% eventtype, e.g., 'Stimulus' or 'Trigger'
% eventvalue, e.g., 'S 1' in cell
% define how much to cut before and a... |
288c03ae466061f60c165a0678ab023a2f913ca28e6da1702043b658848626c5 | MATLAB | 3,491 | 133 | function CBIG_pMFM_step2_generate_FCD_schaefer()
% This function is the wrapper to generate parcellated time serises and FCD
% for Desikan parcellation
%
% There is no input for this function as it can automatically get the
% output file from previous step.
% There is no output for this function as it will generate th... |
8f9624114290a6e52eb8e6b4512ea8a593469354a9ca6ead52fc93c945b50c28 | MATLAB | 3,492 | 84 | function l = IsLastBefore(timestamps,list,varargin)
%IsLastBefore - Identify last item before each of a list of timestamps.
%
% For each element i of a list of test timestamps, find in a list of reference timestamps
% the last element j smaller than i. Returns a list of logical indices (the elements of the
% test list... |
2799796aa7b9e650e7ce7527ceb1570ac707bd1f5ddc72cfcbe5c4802b2decd0 | MATLAB | 3,493 | 114 | classdef HBox < uix.HBox
%uiextras.HBox Arrange elements in a single horizontal row
%
% obj = uiextras.HBox() creates a new horizontal box layout with
% all parameters set to defaults. The output is a new layout object
% that can be used as the parent for other user-interface components.
... |
b1cd70ace52a3fe0603abcc5443015c34227ed78c66c5393c36b5a0e25a340e2 | MATLAB | 3,493 | 99 | % eegplot2trial() - convert EEGPLOT rejections into trial and electrode
% rejections compatible with EEGLAB format.
%
% Usage:
% >> [trialrej elecrej] = eegplot2trial( eegplotrej, frames, ...
% sweeps, colorin, colorout );
%
% Inputs:
% eegplotrej - EEGPLOT output (TMPREJ; se... |
e0639d729097ffb30f534442821a2e01b1661eebace917df658dd560669e087a | MATLAB | 3,495 | 93 | function ea_exportb0(options)
b0threshold = 10;
disp('Export b0...');
bvals=load([options.root,options.patientname,filesep,options.prefs.bval]);
idx=find(bvals<b0threshold);
if isempty(idx)
matlab.desktop.editor.openAndGoToLine(which('ea_exportb0'), 3);
error(sprintf(['Exporting b0 image failed: b0 threshold... |
b6c41c602d279ba597afa199f4f1ba9fead533e08193b49c2ae22790e8e3b4b4 | MATLAB | 3,496 | 131 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
%% set parameters
% input parameters
subj = 'S01';
session = 1; % s1 or s2
num_layer = 20;
atlasFrom = 2; % 1:MNI152; 2:std141
switch atlasFrom
case 1
atlas = 'glasser360';
atlas_readname = ['Data.HCPMMP1.d... |
d71a2845f474035243085e257dcc562286106ce854997b1d8d77fed682f9d092 | MATLAB | 3,496 | 104 | function y = base64decode(x)
%BASE64DECODE Perform base64 decoding on a string.
%
% BASE64DECODE(STR) decodes the given base64 string STR.
%
% Any character not part of the 65-character base64 subset set is silently
% ignored. Characters occuring after a '=' padding character are never
% decoded.
%
% STR doe... |
298d1c66522a06041648c1a705f0e6ed5b15abfdd266d199421ed2dcac9bb177 | MATLAB | 3,498 | 129 | function [scaleFactor vid_ts vid_x vid_y headdir d_epoch] = dacq_pos(fname)
%[root.scaleFactor, root.ts, root.x, root.y, root.headdir, root.epoch] =
%dacq_pos(dataPath,prefix)
%
% Finds video file with the prefix "prefix" in folder "dataPath", and
% returns relevant spatial information for a CMBobject
% Bill 2012.06.2... |
8a192012f4698c31bec28470f33aec98262c02eb383730480f6404af5a9bbd9e | MATLAB | 3,498 | 114 | classdef VBox < uix.VBox
%uiextras.VBox Arrange elements vertically in a single column
%
% obj = uiextras.VBox() creates a new vertical box layout with all
% parameters set to defaults. The output is a new layout object that
% can be used as the parent for other user-interface components.
... |
634c3503fba7281f748984b16fed8016cfb622c1aa01fc8b49514f64c769ae22 | MATLAB | 3,499 | 109 | function f=showProj(stk,type,filtparms,scaleparms,wlev,fig_flag)
% Usage ... f=showProj(stk,type,filt,scale,wlev)
%
% filt=[gauss_smooth_wid medfilt_wid]
% scale=[x y z] in pixels
if ~exist('type','var'), type=[]; end;
if ~exist('filtparms','var'), filtparms=[]; end;
if ~exist('scaleparms','var'), scaleparms=[... |
b79895043eeb33fef6b8f1351ab7af66ffbc4d59bd7c01ab836ab384d540bf94 | MATLAB | 3,501 | 115 | function [maxsize,clstat,sizes] = palm_clusterd(X,y,thr,opts,plm,varargin)
% Compute cluster density statistics, for volume or surface
% data (vertexwise or facewise).
%
% Usage:
% [maxsize,clstat,sizes] = palm_clusterd(X,y,thr,opts,plm)
%
% Inputs:
% - X : Statistical map.
% - y : Modality index (of those stor... |
60ec85c703cd77e0aa9f61cad4516f5e97d8c985526aa3d0609c029038346964 | MATLAB | 3,502 | 94 | function till_creategridforelectrode(reco,side,space,options)
% clearvars -except reco side space
% options = ea_getptopts('/media/netstim/E/Till/Testsession/derivatives/leaddbs/sub-BiDirect3');
%% load electrode model
try
load([ea_getearoot,'templates',filesep,'electrode_models',filesep,options.elspec.matfname,'.m... |
23195a6ec42408ceba361b99959f1c23b9b437690e26771a8fce07361795068d | MATLAB | 3,503 | 77 | function [J_chrom, J_chrom_brain, pathlength_tot, pathlength_brain, J_chrom_full] = computeJChromBrain(model, epsilon_mm_uM, brain_nodes_idx)
% computeJChromBrain Compute normalized spectral Jacobians and pathlengths
%
% [J_chrom, J_chrom_brain, pathlength_tot, pathlength_brain, J_chrom_full]
% = computeJCh... |
9d15f262010c60a22debf383143a221ccb09053a52cec215b5a100c83eb5b2d4 | MATLAB | 3,504 | 98 | function C = convnsep(varargin)
%CONVNSEP N-dimensional convolution with separable kernels.
% C = CONVNSEP(H1,H2,...,A) performs an N-dimensional convolution of A
% with the separable kernel given by the outer product of the H1,H2,...
% such that the input vector Hk is convolved along the kth dimension o... |
a435b7f0402b2b1d4610be1cc072372deebecb36fc3c3db3d714dc9fdec73c22 | MATLAB | 3,505 | 125 | function [phasedev3 stddev]=LFPphasedev_running(animal,filtertype, refchannels, numloops)
exp_dir=get_exp(animal);
load([exp_dir '\LFP\' filtertype '\' animal, '_', filtertype, '_128power.mat']);
%LFP128 and PX
phasedev=[];
phasedev2=[];
phasedev3=[];
stddev=[];
load([exp_dir '\stimuli\' animal '_VRstatea... |
31cc02b8a6986492a3ee765a1f4ba8bf0003eda217c380d92f082529acfe6a99 | MATLAB | 3,507 | 111 | % Name: Robert Kim
% Date: 03-29-2023
% Email: robert.f.kim@gmail.com
% fnc_eval_model.m
% Description: Run a trained continuous-rate RNN forward on a given input
% sequence, optionally with a modified recurrent weight matrix (lesion sweep)
% and/or with specific units clamped during a stim epoch (perturbation).
% Retu... |
5061a1ff36808e1dc0114332eda3d7ca529c63bbc386198c0b5f38b911634bdd | MATLAB | 3,507 | 135 | function savejmesh(node,face,elem,fname,varargin)
%
% savejmesh(node,face,elem,fname,opt)
%
% export a mesh to the JMesh format
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2011/10/06
%
% input:
% node: input, node list, dimension (nn,3)
% face: input, optional, surface face element list, dimension ... |
82287c2545f94c8b1cf7694be3fb566b269c735e7c723eb0ea3c4d90e709a7d6 | MATLAB | 3,507 | 108 | function Z = palm_gtoz(G,df1,df2)
% Convert a G-statistic (or any of its particular cases)
% to a z-statistic (normally distributed).
%
% Usage:
% Z = palm_gtoz(G,df1,df2)
%
% Inputs:
% G : G statistic.
% df1, df2 : Degrees of freedom (non-infinite).
%
% Outputs:
% Z : Z-score
%
% If df2 = NaN and df1 = ... |
dcc1229a35e2c23c20001a7e16e179db0f3463a1de9af54da8f7fa414fcaaf39 | MATLAB | 3,508 | 91 | function result = cvglmnetCoef(object, s)
%--------------------------------------------------------------------------
% cvglmnetCoef computes coefficients from a "cv.glmnet" object.
%--------------------------------------------------------------------------
%
% DESCRIPTION:
% This function extracts coefficients at ... |
9a5570004e186f55178c1e641da672070a849bdc6bd5c2344416281de77a0308 | MATLAB | 3,509 | 78 | function [trials] = crossValidateCdiff(cfg,T,intervene_matrix,data_counts,species_names,BMD,experimentBlocks)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically rel... |
b52286d37e1a031bc29e5e4f20f82f6aa4fca5e55603ddb335b576b219b3ac22 | MATLAB | 3,510 | 95 | function spatial_information = SpatialInformation(self, cel, varargin)
% Computes the spatial information of a cell (bits/spike)
%
% Will return the spatial information score in bits/spike for
% tetrode cel(1), cell cel(2). Can return continuized epochs, or vectorizes
% multiple epochs. Note that if xdim and ydim are ... |
28f83518634c39fc9078f28fa2f61329ea0857d087c69bb272cb689f745864b6 | MATLAB | 3,512 | 116 | % MAKEFIR design an n-th order fir filter using firls
%
% H = MAKEFIR( FREQ, FS, N, BAND, TOL, X, FFUNC )
%
% FREQ - [ highpass lowpass ] frequencies (Hz)
% FS - sampling frequency (Hz); {1000}
%
% optional:
% N - order (number of samples); determined automatically if not specified
% BAND - 'low', 'high', 'ba... |
956e54c948ccafb1d716f62952c1483a529232ecb0579af34c72cd8a51682df8 | MATLAB | 3,512 | 127 | function averageOIS(fname,fps,ntr,noff,nper,nfa,zoomdn,basediff)
% Usage ... averageOIS(fname,fps,ntrials,offset,trialdur,desiredres,zoomdown,basediff)
if (nargin<8), basediff=[]; end;
if (nargin<7), zoomdn=[]; end;
if isempty(basediff),
do_norm=0;
else,
if abs(basediff)>0, do_norm=1; else, do_norm=0; en... |
6932d51677d26d2fb2c1d0eeb3f1b538effda88c5cf2a3d49f1aeff9cab5ffa0 | MATLAB | 3,517 | 116 | function PETHSpikes = bz_PETH_Spikes(events,varargin)
%% input parsing
p = inputParser;
addParameter(p,'basepath',pwd,@isstr);
addParameter(p,'cellnums',[],@isvector);
addParameter(p,'eventCategory','timestamps',@isstr);
addParameter(p,'eventNumber',1,@isvector);
addParameter(p,'secondsBefore',0.5,@isvector);
addPara... |
97e5302993ea99416bceb920f71d04fc2c8f79a2d88f764c4468794cd4aad201 | MATLAB | 3,517 | 82 | function [handles, ListOfImageNames] = listselectedfiles(handles)
ListOfImageNames = handles.Datalist;
if handles.datatype == 1
[filelist, filepath, cCheck] = uigetfile({'*.tif'; '*.tiff'},...
'Select Movies To Be Processed', ...
'MultiSelect', 'on');... |
b56653b62133fc3a98ca61913e191d76db9544871ef8aff4ab122d67980b2a8f | MATLAB | 3,517 | 128 | function z = plus( x, y, isdiff, cheat )
% Disciplined convex programming information for PLUS:
% Both terms in a sum must have the same curvature. Real affine
% expressions are both convex and concave, so they can be added to
% any nonlinear expressions. Complex affine (or constant)
% expression... |
b35302c02ae5b4614173b3adfd1f703a2a4245a95dac67ee5d48c4aa69805b10 | MATLAB | 3,521 | 72 | function dists = pairdist(X,varargin)
%PAIRDIST Computes a pairwise Euclidean distance matrix.
% DISTS = PAIRDIST(X) returns a symmetric positive definite matrix DISTS
% such that the DISTS(i,j) is the Euclidean distance between the vectors
% X(i,:) and X(j,:). X must be a real-valued matrix.
%
% DIST... |
c98e868653195329599fa498cb0fb5f90b040e266ce744d054a6df7276b9e5e6 | MATLAB | 3,521 | 95 | %% ============================================================
% WT Habituation: behavior-conditioned calcium AUC
%% ============================================================
clear; clc;
outdir = '/Users/rongsong/Library/Mobile Documents/com~apple~CloudDocs/Documents/tex/Simulation_Model_2026/matlab/tracking_data... |
34aed8bddb7b3c8e473ce6c6d22554a15f9c759bdef61cf84e335ebce556cb63 | MATLAB | 3,523 | 77 | grangerspctrm = eval(['grangerspctrm_', sourceArea, '2', targetArea, '_topo', topoArea]);
GC_tuning = eval(['GC_tuning_', sourceArea, '2', targetArea, '_topo', topoArea]);
chs2Avg = eval(['chs2Avg', topoArea]);
%% GC TFR
nCh = size(grangerspctrm, 2);
figure;
plotSize = mu.autoplotsize(nCh);
for cIndex = 1:nCh
mu.... |
8f1215df3dfa0f12bd1696f5f54e51b563b84a4df01aa0471dd6ef9651982176 | MATLAB | 3,523 | 145 | function y=myOISmap1(data,parms,sparms,tparms)
% Usage ... y=myOISmap1(data,parms,sparms,tparms_or_mask_apply)
%
% parms = [ntrials,nimtr,noff]
% stim_parms = [nimstim nskp]
% tc_parms = [thr mincthr maxcthr smw maskflag]
do_figure=1;
do_applymask=0;
if nargin<4, tparms=[]; end;
if nargin<3, sparms=[]; end... |
4eff49140f18d6ccef76a1300a8c4e9b49a4dd9841e59cfba9637823cf304e4b | MATLAB | 3,524 | 63 | function varargout=ea_normalize_spmnewseg(options)
% This is a function that normalizes both a copy of transversal and coronal
% images into MNI-space. The goal was to make the procedure both robust and
% automatic, but still, it must be said that normalization results should
% be taken with much care because all recon... |
ac44af6517aad4cb43880114eddebaba2c6227823a18776afa7ed4657407a555 | MATLAB | 3,525 | 111 | function [bc,E] = betweenness_centrality(A,varargin)
% BETWEENNESS_CENTRALITY Compute the betweenness centrality for vertices.
%
% bc = betweenness_centrality(A) returns the betweenness centrality for
% all vertices in A.
%
% [bc,E] = betweenness_centrality(A) returns the betweenness centrality for
% all vertices in ... |
daaef91741e0f5cd983ad525d90f853564b6021ad4176f37de6092b268de1782 | MATLAB | 3,526 | 96 | function newdata=struct2jdata(data,varargin)
%
% newdata=struct2jdata(data,opt,...)
%
% convert a JData object (in the form of a struct array) into an array
%
% authors:Qianqian Fang (q.fang <at> neu.edu)
%
% input:
% data: a struct array. If data contains JData keywords in the first
% level children, t... |
f30902e24293b53f111699875267fb7ed106ca139fbec058d760c08f48b97bde | MATLAB | 3,528 | 116 | % Digital circuit sizing (vectorized)
% Boyd, Kim, Vandenberghe, and Hassibi, "A Tutorial on Geometric Programming"
% Written for CVX by Almir Mutapcic 02/08/06
% (a figure is generated)
%
% Solves the problem of choosing gate scale factors x_i to give
% minimum ckt delay, subject to limits on the total area and power.... |
414816919ee9c8e15ac1986184ac644756875c73fe1f7e0b536edc04aab9c98f | MATLAB | 3,529 | 87 | function xSE = ent_xsamp(x,y,m,R,norm)
% xSE = ent_xsamp(x,y,m,R,norm)
% Inputs - x, first data series
% - y, second data series
% - m, vector length for matching (usually 2 or 3)
% - R, R tolerance to find matches (as a proportion of the average
% of the SDs of the data sets, usually ... |
db0242bbb5d03c55a8af79e741c158821937d95c6d1f83164682e0150545f5ff | MATLAB | 3,530 | 118 | function OUTPUT = openNSxHL(fname)
% openNSxHL
%
% Opens and reads an NSx file without the header information and returns
% the binary data. This can be used for specific applications that require
% this type of data, e.g. Klusters. Works with File Spec 2.1, 2.2 and 2.3.
% It does not support pauses at this time.
%
%... |
b75144840cbbf4c84bbec973e37438cbc89b7a3111781e90d8c86feb28cbb8de | MATLAB | 3,531 | 118 | function [data,eid,name] = DBGetValues(query,direction)
%DBGetValues - Group values for all variables that match given criteria.
%
% Concatenate individual values for all variables matching the optional query.
% Values must be scalars, vectors or matrices. Concatenation can be performed
% horizontally or vertically... |
0c2fd9d9815520dcad505be0a04e6b1ecd3ce5cb78b05c4b288858073205d55b | MATLAB | 3,534 | 103 | function [node,elem,face]=cgalv2m(vol,opt,maxvol)
%
% [node,elem,face]=cgalv2m(vol,opt,maxvol)
%
% wrapper for CGAL 3D mesher (CGAL 3.5 or up)
% convert a binary (or multi-valued) volume to tetrahedral mesh
%
% http://www.cgal.org/Manual/3.5/doc_html/cgal_manual/Mesh_3/Chapter_main.html
%
% author: Qianqian Fang (fangq... |
22e838f5c0f6b583ad41ae8479f933f44591fa61ad627a9d78588aafbe144ca6 | MATLAB | 3,534 | 92 | classdef CondColocGeneralProcess < ImageAnalysisProcess
%Concrete class definition to run general conditional colocalization
%Jesus Vega-Lugo December 2021
%
% Copyright (C) 2021, Jaqaman Lab - UTSouthwestern
%
% This file is part of conditionalColoc.
%
% conditionalColoc is free software: you can redistribu... |
eda7bfdd2208f48f40e3bf77ca1585e3c44376bc87175dfab12bcd85a75d28f1 | MATLAB | 3,535 | 93 | % std_fileinfo() - Check uniform channel distribution accross datasets
%
% Usage:
% >> [struct filepresent] = std_fileinfo(ALLEEG);
% Inputs:
% ALLEEG - EEGLAB ALLEEG structure
%
% Outputs:
% struct - structure of the same length as the ALLEEG variable
% containing all the fields in... |
fe6a63e6d913f4b8b9bfd4263c91a0959eed976ee48bd3a37c5d7b950a707484 | MATLAB | 3,535 | 72 | % std_pvaf() - Compute 'percent variance accounted for' (pvaf) by specified
% ICA component clusters. This function computes eeg_pvaf on each
% of the component of the cluster and then average them. See
% eeg_pvaf for more information. This function uses the
% Usage:
% ... |
185782716c87bf6647d872142060efa788b58bd0d3e7d2d1b990a2ffa486400b | MATLAB | 3,536 | 139 | %%*************************************************************************
%% mybicgstab
%%
%% [xx,resnrm,flag] = mybicgstab(A,b,M1,tol,maxit)
%%
%% iterate on bb - (M1)*AA*x
%%
%% r = b-A*xtrue;
%%
%%*************************************************************************
function [xx,resnrm,flag] = mybicgstab(A,b... |
4bcb70ef55d6583e15be3179953ba1d486ab24703686745c28201c4d88eb0bc0 | MATLAB | 3,537 | 149 | %%%%%%%%%%%%%%%%%%%
%% Zicheng Yang @CCMU
%%
%% Version: YZC 2021/5/9 calculate the correct rate
%%%%%%%%%%%%%%%%%%%
clear all;
close all;
% load files
actfile = 'x';
% parameters
Fs = 100;
Ts = 1/Fs;
correctCue =2;
pre_time = 3;
trial_time = 15;
ntrialpersess = 20;
isoneodorcase = false;
... |
38b314d9696954901c6648fe8f804dfc5fd13fa2fb47f8cacfab27f0132474fa | MATLAB | 3,541 | 101 | function [model, p_lr] = CBIG_ASDf_logReg_clusterBehavAssoc(cluster_idx, id_scoreGrp, ...
sub_info_file, behav_score_file, idx_score)
% [model, p_lr] = CBIG_ASDf_logReg_clusterBehavAssoc(cluster_idx, id_scoreGrp,
% sub_info_file, behav_score_file, idx_score)
%
% Performs logistic regression to compare ASD participa... |
6f95a8f1c281fd7ca532b58e2230b89a58d299210336bb38b5a5340745aab927 | MATLAB | 3,543 | 105 | % pop_loaddat() - merge a neuroscan DAT file with input dataset
% (pop out window if no arguments).
%
% Usage:
% >> OUTEEG = pop_loaddat( INEEG ); % pop-up window mode
% >> OUTEEG = pop_loaddat( INEEG, filename, no_rt);
%
% Graphic interfance:
% "Code signifying no event ..." - [edit box] reaction ... |
c77c27391714951800e62e3fa74adea6465c2ab567406f943f4b06db8a5f8847 | MATLAB | 3,544 | 87 | function [X,data] = kamada_kawai_spring_layout(A,varargin)
% KAMADA_KAWAI_SPRING_LAYOUT Use springs to compute a graph layout
%
% X = kamada_kawai_spring_layout(A) computes a layout for an undirected
% graph, connected graph by simulating a system of springs.
% [X,data] = kamada_kawai_spring_layout(A) returns extra dat... |
c1a2e8133a7458065cefc98d174f6859426ccc529dc7faf87dee05683988e94d | MATLAB | 3,546 | 127 | function averageOIS2(fname,fps,ntr,noff,nper,nfa,zoomdn,basediff)
% Usage ... averageOIS2(fname,fps,ntrials,offset,trialdur,desiredres,zoomdown,basediff)
if (nargin<8), basediff=[]; end;
if (nargin<7), zoomdn=[]; end;
if isempty(basediff),
do_norm=0;
else,
do_norm=1;
end;
if isempty(zoomdn),
zoomdn=... |
c2686aa1e1826fa10a5def9f83f115226727d833cb3129e15f36399342e45c2d | MATLAB | 3,546 | 101 | function [D,P] = all_shortest_paths(A,varargin)
% all_shortest_paths Compute the weighted all pairs shortest path problem.
%
% D = all_shortest_paths(A) returns the distance matrix D for all vertices
% where D(i,j) indicates the shortest path distance between vertex i and
% vertex j.
%
% For the Floyd-Warshall algori... |
7d5133dc4c86cdc906fe96f2ba5d8dcbf841b8a1cabe5f49727e8b07a7c45792 | MATLAB | 3,547 | 124 | function y = sincFilter(x,Wn,N,dim)
%SINCFILTER Apply a near-ideal low-pass or band-pass brickwall filter
%
% Y = IOSR.DSP.SINCFILTER(X,WN) applies a near-ideal low-pass or
% band-pass brickwall filter to the array X, operating along the first
% non-singleton dimension (e.g. down the columns of a matrix). The
% ... |
e4657c0ea9cbec2538e4b22fca0a87661392a6a9efc44b0ad5123e628e2a4fe0 | MATLAB | 3,547 | 119 | function [a, cb] = plot_cortical(data, varargin);
%
% Usage:
% [a, cb] = plot_cortical(data, varargin);
%
% Description:
% Plot cortical surface with lateral and medial views (authors: @MICA-MNI, @saratheriver)
%
% Inputs:
% data (double array) - vector of data, size = [1 x v]
%
% Name/value pairs:
% surface... |
ff69f6b81f36f35858ff90b88d4d5647964f4c8f2f84ca4908d529624305e8c9 | MATLAB | 3,547 | 106 | % Date: 05-10-2026
% export_instr2_task_lesion_anti_to_excel.m
% Description: Export two-modality one-layer lesion-result .mat files from
% trained_models/one_layer_models/instr2/task_lesion_anti into a single Excel
% workbook with one sheet per .mat file. This folder corresponds to the
% cue-fixed-to-mod1 analysis and... |
0b968a25a3830a37dd8e3cbe4f3d407bea1b0f4ba263e0ab1b41cad3f309ebba | MATLAB | 3,548 | 106 | % Date: 05-10-2026
% export_instr2_task_lesion_anti_to_excel.m
% Description: Export two-modality one-layer lesion-result .mat files from
% trained_models/one_layer_models/instr2/task_lesion_anti into a single Excel
% workbook with one sheet per .mat file. This folder corresponds to the
% cue-fixed-to-mod1 analysis and... |
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