sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d18cd3b25625a2f95bda71bfaef7a3deb7eb10df50ddb2f68eae432e6f0a482e | MATLAB | 3,662 | 104 | function [X,electrode,err]=ea_mapelmodel2reco(options,elspec,elstruct,side,resultfig)
err=0;
load([ea_getearoot,'templates',filesep,'electrode_models',filesep,elspec.matfname,'.mat'],'electrode')
A = [electrode.head_position,1;
electrode.tail_position,1
electrode.x_position,1
electrode.y_position,1]; % ... |
d50756c16b744943288eee96facfe1632cc220240177a66a3c1c66ae2615ef28 | MATLAB | 3,662 | 108 | function [periods,in] = Threshold(x,criterion,threshold,varargin)
%Threshold - Find periods above/below threshold.
%
% Find periods where samples lay above or below a given threshold. Optionally,
% keep only periods of sufficient duration and ignore brief interruptions.
%
% USAGE
%
% [periods,in] = Threshold(x,c... |
3398951e5ec85b3ccfd487fa3aa9c3e9d6f9612f7d86a9f8e708b8ea29f6b6a4 | MATLAB | 3,664 | 100 | % UPGMA: Unweighted pair-group hierarchical cluster analysis of a distance
% matrix. Produces plot of dendrogram. To bootstrap cluster support,
% see cluster().
%
% Usage: [topology,support] = upgma(dist,{labels},{doplot},{fontsize})
%
% dist = [n x n] symmetric distance matrix.
% ... |
fdfb3954a93ecc754052776f357f123ec6fab7e363da3c6addaceaf89e9c2699 | MATLAB | 3,665 | 97 | function [filtered_data, mu_gauss, std_gauss, summary] = filterLognormalGaussian(data, sigma_cut, makePlot, alpha)
% Fits Gaussians and filters NSC or fraction data
if nargin < 2 || isempty(sigma_cut), sigma_cut = 2; end
if nargin < 3, makePlot = true; end
if nargin < 4, alpha = 0.01; end
% --- Convert input t... |
16e0fbc08a363eca7f7b712bc0b14695252e840b42a29f92a6b6c2a76c2b2362 | MATLAB | 3,667 | 92 | function [boxedImage, boxedImageMeasure] = boxImage(inputImage, boxSize, intstMeasureFlag)
%BOXIMAGE: split cells into boxes, divide an image up into blocks is by using mat2cell().
%
%SYNOPSIS: [boxedImage, boxedImageIntst] = boxImage(inputImage, boxSize, intstMeasureFlag)
%
%INPUT: inputImage : (matrix) image ... |
db66ca51ff6d74b54515cac58ce76802f72590fcbd44f76448f922125b01a7dd | MATLAB | 3,669 | 91 | %needs LFP, run_times, timesync
chspershank=64;
fpass1=0;
fpass2=200;
for shank=1:8
exp_dir=get_exp(animal);
% load(strcat(exp_dir, '\stimuli\', animal,'_VRtimesync.mat'));
load([exp_dir '\LFP\' animal '_shank' num2str(shank) '_LFP.mat'], 'LFP'); %loads LFP
% load(strcat(exp_dir, '\stimuli\', ... |
d04d544cc266e9ba7fc506ffa009e996c644a8dd8fed2364a95b70c965252cc0 | MATLAB | 3,670 | 90 | function [RegPara, handles, imageinfo, figuretitlename, continueflag, w, fext]...
= get_imageinfo(handles, k, RegPara)
continueflag = 1;
[imagefolder, imagefilename, fext] = fileparts(handles.Datalist{k});
RegPara.imagefolder = imagefolder;
RegPara.filename = imagefilename;
savename = handles.savenamelist{k};
figur... |
2163b734a2a996c72666dd44895b412cb9de95c1c014465d03edccf8add8a452 | MATLAB | 3,671 | 132 | function plot_hypnogram(stages, varargin)
% Plot a hypnogram. Scores can either be a sleepstages struct or a nx1
% array where n is the number of epochs and each row contains stage
% information for that epoch. If an array is used, argument 'EpochLength'
% can be specified as epoch length in seconds (Default = 30)
%%
%... |
c44d4f2407760c63e73222226be342ac82e97444d13a79d7eb8f12a6a9f15700 | MATLAB | 3,671 | 117 | function AdjustAxes(f,varargin)
%AdjustAxes - Adjust axes limits for all subplots
%
% USAGE
%
% AdjustAxes(f,<options>)
%
% f optional figure handle (default = gcf)
% <options> optional list of property-value pairs (see table below)
%
% ===================================================... |
609eb8a3ed1649babfb946b8e827742a8848b26b32923d263655da610b71709d | MATLAB | 3,672 | 70 | something= [dyn1l1p0a_nk1r_bioall.tt (([mean(dyn1l1p0a_nk1r_bioall.FLUX,2)-tmpfix*0.05,...
mean(dyn1l1p0b_nk1r_bioall.FLUX,2)-tmpfix*0.16,...
mean(dyn1l1p0c_nk1r_bioall.FLUX,2)-tmpfix*0.15,...
mean(dyn1wh1_nk1r_bioall.FLUX,2)]-1)*100)];
... |
050fe3bdc5f58ac40d8b764d2dfb5c187755802317d1d7165a0000e479158819 | MATLAB | 3,673 | 102 | % 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... |
97cd99d0d85a562dc8a4c8ce744cd7a1201262801937fe80734d176e61699115 | MATLAB | 3,673 | 83 | function [allow, scores, cdfs] = isiQuality(unit1times, unit2times, tmin, tmax, tref, Fs)
% ISIQUALITY Computes statistical measures of refactory period quality.
% [allow, scores, cdfs] = isiQuality(unit1times, unit2times, tmin, tmax, tref, Fs)
%
% Returns a boolean specifying whether the refractory period sta... |
84d83879b57fdb464f069ccce19de2a7cbe30595c331380fa4745322081cdd23 | MATLAB | 3,674 | 94 | function [fibsvalBin, fibsvalSum, fibsvalMean, fibsvalPeak, fibsval5Peak, fibcell] = ea_discfibers_calcvals_cleartune(vatlist, fibcell, thresh)
% Calculate fiber connection values based on the VATs and the connectome
prefs = ea_prefs;
if ~exist('thresh','var')
thresh = prefs.machine.vatsettings.horn_ethresh*1000;
... |
e59974344c17f2e394655720768c25b2df923fac2a5de351ae68c7ae61dfae8b | MATLAB | 3,674 | 69 | function [S,f,Serr]=mtspectrumtrigc(data,E,win,params)
% Multi-taper event triggered time-frequency spectrum - continuous process
%
% Usage:
%
% [S,f,Serr]=mtspectrumtrigc(data,E,win,params)
% Input:
% Note units have to be consistent. See chronux.m for more information.
% data (single channel) -- require... |
b92db6c903c2ab9fbfcd9c17b1fc7a581b97b8a661f89e63426ffc97738c3f0c | MATLAB | 3,676 | 85 |
figure(1)
subplot(211)
plot(dyn1l1p0a_new.tt,([mean(dyn1l1p0a_new.FLUX,2),...
mean(dyn1l1p0b_new.FLUX,2),...
mean(dyn1l1p0c_new.FLUX,2)]-1)*100)
axis('tight'), grid('on'), tmpax=axis; axis([-4 44 tmpax(3:4)]);
ylabel('LDF (CBF; %)'), xlabel('Time (s)'),
dofontsiz... |
6c36918be883f1005848f0e8aee3c1a5ce22464e9eeffc1846cb8a97c31dbe0f | MATLAB | 3,677 | 94 | % rejtrend() - detect linear trends in EEG activity and reject the
% epoched trials based on the accuracy of the linear
% fit.
% Usage:
% >> [rej rejE] = rejtrend( signal, winsize, maxslope, minR, step);
%
% Inputs:
% signal - 3 dimensional signal (channels x frames x trials)... |
785751a8d1a40a43aaee571fa74912fda5dea2a9e5784d1deb93a217681aa7d9 | MATLAB | 3,677 | 93 | function [Obj] = SOFAsave(filename,Obj,varargin)
%SOFASAVE
% [] = SOFAsave(filename,Obj,Compression) creates a new SOFA file and
% writes an entire data set to it.
%
% filename specifies the name of the SOFA file to which the data is written.
% Obj is a struct containing the data and meta
% data to be... |
9bacc970b86a2a20769c11d73c1ec73cf2a0bafa30fc1e8ccd49fd8cf4b5f8e9 | MATLAB | 3,677 | 94 | function [faces, vertices, vertexColors, data] = ea_readMz3(filename)
%function [faces, vertices, vertexColors, data] = readMz3(fileName)
%inputs:
% filename: the nv file to open
%outputs:
% faces: face matrix where cols are xyz and each row is face
% vertices: vertices matrix where cols are xyz and each row a vertex... |
a8ccab5825cf15423497d9234ec72b1ce5c5769e1b87a2ca1b13f0db8aed6b14 | MATLAB | 3,677 | 116 | function [z_irm,z_ibm,t] = applyIdealMasks(xt,xi,nfft,hop,fs)
%APPLYIDEALMASKS Calculate and apply ideal masks via STFT
%
% Z_IRM = IOSR.BSS.APPLYIDEALMASKS(XT,XI) calculates the ideal ratio mask
% (IRM) and applies it to the mixture XT+XI, where XT is the target
% signal and XI is the interference signal. The I... |
e82c5d8bc5680585372e73b94ea205103d1f34710a3c1174690c41ba7c0b8be4 | MATLAB | 3,678 | 87 | % std_mergeclust() - Commandline function, to merge several clusters.
% Usage:
% >> [STUDY] = std_mergeclust(STUDY, ALLEEG, mrg_cls, name);
% Inputs:
% STUDY - EEGLAB STUDY set comprising some or all of the EEG datasets in ALLEEG.
% ALLEEG - global EEGLAB vector of EEG stru... |
cc302f032e9d59983d00619050e926cbe84c879affa173c6d885c99cb3963465 | MATLAB | 3,679 | 91 | classdef CondColocPt2Pt2BlobProcess < ImageAnalysisProcess
% A concreate class for measuring conditional colocalization between 3 images
% Anthony Vega 09/2014
%Adapted by Jesus Vega-Lugo (May, 2019) to run conditional colocalization
%
% Copyright (C) 2021, Jaqaman Lab - UTSouthwestern
%
% This file is pa... |
e61c3c0c70e6c2691a292b7db6745bc5a7adf85a76b2d1be602f27efc502baf9 | MATLAB | 3,685 | 92 | % imagesclogy() - make an imagesc(0) plot with log y-axis values (ala semilogy())
%
% Usage: >> imagesclogy(times,freqs,data);
% Usage: >> imagesclogy(times,freqs,data,clim,xticks,yticks,'key','val',...);
%
% Inputs:
% times = vector of x-axis values
% freqs = vector of y-axis values (LOG spaced)
% data = matr... |
dd8a1f6d277970b2e0dd77aca6a111c25faa41c91db392a20698b3b0a5649a97 | MATLAB | 3,686 | 118 | function [R, t, corr, error, data2] = icp2(data1, data2, res, R0, t0, tri)
% [R, t, corr, error, data2] = icp2(data1, data2, res, tri)
%
% This is an implementation of the Iterative Closest Point (ICP) algorithm.
% The function takes two data sets and registers data2 with data1. It is
% assumed that data1 and data2 a... |
fd9cb74381a9991fb5800945349eae4c1eb8e7b1de85f1ae99b4239534848c88 | MATLAB | 3,687 | 113 | % spec() - power spectrum. This function replaces psd() function if the signal
% processing toolbox is not present. It uses the timef() function.
%
% Usage:
% >> [power freqs] = spec(X);
% >> [power freqs] = spec(X, nfft, fs, win, overlap);
%
% Inputs:
% X - data
% nfft - zero padding to lengt... |
c617d28765394374c349132141f2c55c14459d4b5c231299acb5c9aba4588de1 | MATLAB | 3,688 | 107 | function [data,extra] = palm_ciftiread(varargin)
% Provides limited support for reading CIFTI files
% (surface only) using the wb_command as the backend.
%
% [data,extra] = palm_ciftiread(filename,temp_prefix,wb_command)
%
% Inputs:
% - filename : Filename of the CIFTI (surface only, dtscalar).
% - temp_prefix : (Op... |
daf6a9415d6aae51740e4a7436aef950673f13bbe3f4ebdfe3098f253bbb22f4 | MATLAB | 3,688 | 101 | % setfont() - Change all the fonts properties of a figure.
%
% Usage:
% >> newdata = setfont( handle, 'key', 'val');
% >> [newdata chlab] = setfont( handle, 'key' , 'val', ... );
% >> [newdata chlab] = setfont( handle, 'handletype', handletypevalue, 'key' , 'val', ... );
%
% Inputs:
% handle - [gcf,gca... |
b92067b6789827672183873a3867d30cae5f559ac3b106eb9f4bdd1fb249d583 | MATLAB | 3,689 | 85 | %% LaBGAScore_pdm_regenerate_reports.m
%
% *USAGE*
%
% Regenerates c2a-style reporting (overview montage, labelled region table,
% regioncenters montage) for PDM analyses that have already been run, reading
% the written PDM*.nii rather than refitting. Each bootstrap takes over an
% hour, so refitting purely to improve... |
f0bd4aa407cbea9a6dcdf710a913528724291009edb071a10771ffe29d926ee2 | MATLAB | 3,695 | 148 | function CCF = parseCCF(varargin)
% parseCCF
%
% Parses an XML CCF file.
%
% Nick Halper
% support@blackrockmicro.com
% Blackrock Microsystems
% Version 1.1.0.0
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Version History
%
% 1.0.0.0:
% - Initial release.
%
% 1.1.0.0: Janua... |
65b20ea4a67a0d11021f90d7b3cb76331545c2dc83fd18ce5cbb36a1df593f18 | MATLAB | 3,696 | 117 | function cpSummary = couplingsum(coupling, srate, samples)
% Summarize coupling features. Calculates coupled and uncoupled density,
% coupling phase, and coupling strength. circStats toolbox required to
% calculate average phase and coupling strength
%
% Required inputs:
%
% coupling: A structure containing coupling da... |
818a7b608be954c95162ef5be9212e198b54d471dbf06b37cb9fc8e28b6b69ee | MATLAB | 3,697 | 115 | % fillcurves() - fill the space between 2 curves
%
% Usage:
% h=fillcurves( Y1, Y2);
% h=fillcurves( X, Y1, Y2, color, transparent[0 to 1]);
%
% Example:
% a = rand(1, 50);
% b = rand(1, 50)+2; b(10) = NaN;
% figure; fillcurves([51:100], a, b);
%
% Author: A. Delorme, SCCN, INC, UCSD/CERCO, CNRS
% Copyright ... |
8581c9045edf6e488090d17f8de3a80ceb2c76bd0a396a24bf2386f2aba88632 | MATLAB | 3,697 | 130 | % 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... |
dd2cc778f651e91db9ba346634ab856d24bf7857fea46b5901e0b033da4e4ffb | MATLAB | 3,697 | 114 | % pop_readsegegi() - load a segmented EGI EEG file. Pop up query
% window if no arguments.
% Usage:
% >> EEG = pop_readsegegi; % a window pops up
% >> EEG = pop_readsegegi( filename ); % no pop-up window
%
% Inputs:
% filename - first EGI file name
%
% Outputs:
% EEG ... |
3a0e37fbdcc2ef4dc256c79c2c55e66395e85c0c6273f035f4e987866b2ae5a1 | MATLAB | 3,698 | 109 | % Date: 05-10-2026
% export_two_layer_instr_lesion_results_to_excel.m
% Description: Export two-layer one-modality (instr) lesion-result .mat files
% from trained_models/two_layer_models_wo_inh_feedforward/lesion_results into
% a single Excel workbook with one sheet per .mat file.
%
% Each sheet contains three columns:... |
4bfcbdba528a9275b72fdcb62c683f09a0734ca54702ce2964e11cd33ee32555 | MATLAB | 3,700 | 100 | function fig = draw_surface_bluewhitered_gallery_dull(surface_to_plot, data_to_plot, hemisphere, medial_wall, with_medial)
% draw_surface_bluewhitered_gallery_dull.m
%
% Draw multiple data on surface using blue-white-red colormap for
% negative-zero-positive values with dull plot lighting
%
% Inputs: surface_to_plot : ... |
1548ebb68fd0824fa88dcbaed54f45afc25e86e1a19f8adc906d5314fd7251b6 | MATLAB | 3,703 | 130 | function CFAT
% clinic frequency analysis main function
% Version 1: fisrt build in 02 Dec. 2021
% Updata on 11 Mar. 2022
% Updata on 18 Oct. 2022
% Updata on 30 Dec. 2022: Add permutation&bootstrap for cluster correction.
% Which need updata later: Add permutation of cluster correction for
% Chisquare. # 10:20 30 Dec.... |
173bb4877febcb5e33657ad854394ce9f7a83fda31db75b1a8fef886a271443b | MATLAB | 3,703 | 110 | % chancenter() - recenter cartesian X,Y,Z channel coordinates
%
% Usage: >> [x y z newcenter] = chancenter(x,y,z,center);
%
% Optional inputs:
% x,y,z = 3D coordintates of the channels
% center = [X Y Z] known center different from [0 0 0]
% [] will optimize the center location according
%... |
74bfa5650d197831c80911e573cc1076692162778363c3c61e924bec23372d72 | MATLAB | 3,705 | 102 | % [data, names] = loadData(filename)
% Load one of several formats of data expected from a recording with either:
% Doric (csv), Multifiber (csv), Inscopix (csv), XLS files, or Axon (abf).
%
% [data, names] = loadData(filename, sheetName)
% [data, names, sheetName] = loadData(filename, sheetNumber)
% If the file... |
0fa3a4fd7df40a3c59f3a47eac84a211b95da53907e03ec46ebf447c45342363 | MATLAB | 3,708 | 114 | function h = PlotRepeat(X,Y,pattern,varargin)
%PlotRepeat - Plot repeated (tiled) copies of the data.
%
% USAGE
%
% h = PlotRepeat(X,Y,pattern,<options>,<options2>)
%
% X abscissae
% Y ordinates
% pattern 'xxy','xyy' or 'xxyy' depending on repeated axes
% <options> ... |
52e6896d71cc0b0c7786e6711927c174f0fa2031f8e17bf08dcd7a632c229bad | MATLAB | 3,708 | 89 | function T2_simulation(seg_file, T2_star_file, M0_file, T2_uniform_file, R2_file)
% Load the NIfTI segmentation file
seg_img = load_untouch_nii(seg_file);
seg_data = double(seg_img.img);
% Define the region values lookup table
region_values = [57.46, 41.47, 50.44, 44.07, 71.71, 47.255, 56.62,... |
9bc5380cb4d096ddaaf779b2ab1771a5c063021343406be8278b9695c4bef59f | MATLAB | 3,710 | 72 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Create meshes for a sphere inside a cubic domain
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% preparation
% you have to add the path to iso2mesh toolbox
% addpath('/path/to/iso2mesh/toolbox/'... |
8e4ed8369422838189c7570ca8f0ff9e5e75e23fe5a9ed57f63629d6973d4bd9 | MATLAB | 3,712 | 67 | function centroid = centroid_extraction_sphere(sphere_coords, annotfile)
%
% Usage:
% centroid = centroid_extraction_sphere(sphere_coords, annotfile)
%
% Description:
% Extract centroids of a cortical parcellation on a surface sphere (authors:
% @frantisekvasa, @saratheriver)
%
% Inputs:
% sphere_coords (d... |
dc0e6a861189525226b0f0625fd799dbfc2a7f4d54bf3e9dbc1efb0e48e5fc79 | MATLAB | 3,712 | 103 | function transforms = ea_ants_nonlinear_coreg(varargin)
% Wrapper for ANTs 3-stage nonlinear coregistration
fixedimage = varargin{1};
movingimage = varargin{2};
outputimage = varargin{3};
if nargin >= 4 && ~isempty(varargin{4})
normsettings = varargin{4};
else
umachine = load(ea_prefspath('mat'), 'machine');
... |
fd2cb854139982f217bf26909f51999c9288c188df48359d2bce0b2a7dbe0a04 | MATLAB | 3,712 | 142 | % PAD_NII: Pad the NIfTI volume from any of the 6 sides
%
% Usage: nii = pad_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be padded from which side.
%
% option.pad_from_L = ( number of voxel )
% option.pad_from_R = ( number of voxel )
% option.pad_from_P ... |
12c6f2b6ffceb835e32660730aefcdf1f274eca6c7131d37b6a11e94952d14a2 | MATLAB | 3,713 | 97 | function [intervals,indices] = ExcludeIntervals(intervals1,intervals2,varargin)
%ExcludeIntervals - Exclude intersecting intervals.
%
% Given two lists of intervals, exclude from the first list those intervals
% that intersect with one or more of the intervals in the second list.
%
% USAGE
%
% [intervals,indices]... |
18f3265543afdfafc6c7accd10fff9130fa488e70d148ac1257769db7ee67fe2 | MATLAB | 3,713 | 141 | % PAD_NII: Pad the NIfTI volume from any of the 6 sides
%
% Usage: nii = pad_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be padded from which side.
%
% option.pad_from_L = ( number of voxel )
% option.pad_from_R = ( number of voxel )
% option.pad_from_P =... |
7548fb9ce6b23844f72dfb29876571b9dc27c019d3596abb6be5465daf4490c9 | MATLAB | 3,714 | 128 | function [Ygreen, Yred] = makeStacks5D_ndk(folder)
% This function will make 4-dimensional stacks from 5-dimensional data.
% 5D data: x, y, z, t, c
% Volume imaging time series with two color channels.
%make 5D stacks
Ygreen = []; Yred = [];
chan = {'ChanA_0*.tif', 'ChanB_0*.tif'};
for c = 1:2
files = jdi... |
7dd39ad916202b29e7878a530c311b181348b67442230b2bef309f502eb40ab7 | MATLAB | 3,719 | 122 | function M = Array2PagedMatrix(A)
%Array2PagedMatrix - Transform an N-dimensional array into a paged matrix.
%
% Vertically concatenate all pages in the array, and add N-1
% columns listing the subscripts for all dimensions except the
% second dimension (which is implicit, since it becomes the
% second dimension o... |
08d1aef38d91d05101c73b43e7403f780e7c84ebb6e2e33d82b301616882c56c | MATLAB | 3,720 | 126 | function [slope, idx, info] = scaling_region(d, fs, opts)
%SCALING_REGION Automatic linear scaling region of a divergence curve.
%
% [slope, idx, info] = nonantest.scaling_region(d, fs)
%
% d is the average line divergence curve (LyE_R column 3), fs the sample
% rate. Returns the fitted slope in natural log units... |
ffaa09be44a6b59317aa44d6c045a9b6b87acf602655dda077482aca30694115 | MATLAB | 3,720 | 69 | function [S,f,R,Serr]=mtspectrumtrigpt(data,E,win,params,fscorr)
% Multi-taper time-frequency spectrum - point process times
%
% Usage:
%
% [S,f,R,Serr]=mtspectrumtrigpt(data,E,win,params,fscorr)
% Input:
% data (structure array of one channel of spike times;
% also accepts 1d c... |
5801494ea348e9d7940ace67b58774ad1447357a83605af0ce3f8ca7543e1007 | MATLAB | 3,723 | 80 | function [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params)
% Helper function to convert structure params to variables used by the
% various routines - also performs checks to ensure that parameters are
% defined; returns default values if they are not defined.
%
% Usage: [tapers,pad,Fs,fpass,err,trialave,para... |
4bcf28f5f0a822bdbd108d20fef494384921bf98c050e1e18bed0ebf13b6382e | MATLAB | 3,725 | 122 | function bb_gradient_plot(data, varargin)
%
% Usage:
% bb_gradient_plot(data, varargin)
%
% Description:
% Stratify parcellated data according to the BigBrain gradient
% (authors: @caseypaquola, @saratheriver)
%
% Inputs:
% data (double array) - vector of data
% Parcellated data.
%
% Name/value pairs... |
a6e5c14713f981a8ad9951c311efa2ee09c35a7b89ae00e67b8811cbb3f937e7 | MATLAB | 3,725 | 83 | % function [tracksFeatIndxCG,tracksCoordAmpCG] = pairwiseSegTracks(tracksFeatIndxCG,tracksCoordAmpCG,segmentMerge,segmentSplit)
%
% Copyright (C) 2022, Jaqaman Lab - UTSouthwestern
%
% This file is part of SMI-FSM.
%
% SMI-FSM is free software: you can redistribute it and/or modify
% it under the terms of the GNU Gen... |
1919f8416dd3d63ab95f351ca40ff354936fbb990371c01443d71f2aa1b9a155 | MATLAB | 3,726 | 139 | function [slope integral] = Pr2Radon(varargin)
% computes max projection line, using radon transform, on Pr matrix
if nargin == 1
Pr = varargin{1};
plotting = 0;
elseif nargin == 2
Pr = varargin{1};
plotting = varargin{2};
end
Pr(isnan(Pr)) = 0;
theta = 0:.5:180;%0:.5:180;
[R xp] = radon(Pr,theta);
y(... |
10139daddcb3da813c90356e95360d15389090d37c9ccb8cc4b0833efca77bcd | MATLAB | 3,727 | 112 | function [spectralPower, freqs] = fun_spectral_power(data, srate, varargin)
% Obtain estimates of power spectral density (PSD) in EEG data using the pwelch
% function. The default settings obtain PSD estimates on the temporal
% derivative of the data using a Hamming window (5 seconds long, 50%
% overlap)
%
% Required i... |
b0906fdad73d56dc881415dae06c71f4e062a5b1424549380ddc3bff70474a9f | MATLAB | 3,727 | 117 | function [x,m,e] = RunningAverage(X,Y,varargin)
%RunningAverage - Compute running linear or angular average.
%
% Computes the running average of y=f(x). Variable y can be linear or circular
% (use radians). The error bars are standard errors of the mean for linear
% data, or 95% confidence intervals for circular data.... |
007b0062dcf05414e4f859fa28b6bcc36c5b9f9d11333f72c32f17cdb4ce7ac8 | MATLAB | 3,728 | 89 | function [fibsvalBin, fibsvalSum, fibsvalMean, fibsvalPeak, fibsval5Peak, fibcell] = ea_sweetspot_calcvals(vatlist, cfile, thresh)
% Calculate fiber connection values based on the VATs and the connectome
disp('Load Connectome...');
load(cfile, 'fibers', 'idx');
prefs = ea_prefs;
if ~exist('thresh','var')
thresh =... |
10b5d522d87bb0df3543c929169705f58c8dbfb5522cd2d3a431a543f5ddba1b | MATLAB | 3,728 | 85 | function [trials] = crossValidateDiet(cfg,T,perturbations,intervene_matrix,data,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 biological... |
5cea4cdc95cd996f9e2118fb5bc213e7d4747a86db7a21e6ecb4fc96bccdbb71 | MATLAB | 3,730 | 123 | function out = globalBaselineCV(X, Y, C, opts, kind)
% globalBaselineCV Cross-validated global-signal baseline.
%
% out = globalBaselineCV(X, Y, C, opts, kind)
%
% Companion to the in-sample global-signal baseline that every pipeline
% already reports. The in-sample version fits fitlm/fitglm on all subjects
% ... |
78740ac475def33a4e42905446d69ff96ec9de5576adab68874d68b36cfc459f | MATLAB | 3,730 | 75 | function [corr_lasso,corr_select,corr_L2,rms_lasso,rms_select,rms_L2] = computeDietTrialTrajectories(T,perturbations,trials,densities,intervene_matrix_filtered_merge,experimentBlocks)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems model... |
a367275dcf53a03377226723402eb97733b813f1f000302f65115c3a2edd6bb5 | MATLAB | 3,731 | 114 | % anova1rm_cell() - compute F-values in cell array using repeated measure
% ANOVA.
%
% Usage:
% >> [FC dfc] = anova2rm_cell( data );
%
% Inputs:
% data = data consisting of PAIRED arrays to be compared. The last
% dimension of the data array is used to compute ANOVA.
% Out... |
f31f0ffb2c092ba63032d5ef96621e157753097d6a32ca8c6fddb987ee02f2a4 | MATLAB | 3,731 | 94 | function varargout = add(tree,uid,type,parameter)
% XMLTREE/ADD Method (add childs to elements of an XML Tree)
% FORMAT vararout = add(tree,uid,type,parameter)
%
% tree - XMLTree object
% uid - array of uid's
% type - 'element', 'chardata', 'cdata', 'pi' or 'comment'
% parameter - property name ... |
5fb72127c32884a036435f6261734c2ceabc429ce7160c1757e425c709c01703 | MATLAB | 3,732 | 78 | function [S,f,R,Serr]=mtspectrumpb(data,params,fscorr)
% Multi-taper spectrum - binned point process
%
% Usage:
%
% [S,f,R,Serr]=mtspectrumpb(data,params,fscorr)
% Input:
% data (in form samples x channels/trials or a single vector) -- required
% params: structure with fields tapers, pad, Fs, fpass, err, t... |
210dc9565e1892f76ed7d6f4dc12253512982cb8768aad99ed1f4cdad3fe5dfc | MATLAB | 3,739 | 115 | function version=ea_getvsn(com, num)
% This function simply exports the version of the current Lead
% distribution. For updates please see lead-dbs.org
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% ... |
744761b82bb86705dd2f1d37a3dfca9130e6540e2b10ef0fcf6bf9c1b7f6cd7d | MATLAB | 3,739 | 84 | function [node,elem]=meshresample(v,f,keepratio)
%
% [node,elem]=meshresample(v,f,keepratio)
%
% resample mesh using CGAL mesh simplification utility
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2007/11/12
%
% input:
% v: list of nodes
% f: list of surface elements (each row for each triangle)
% keep... |
1bb868cf525038f551c4d8a0f4e55f4a6e9a52f0cf09e37bbcd0c209538f4429 | MATLAB | 3,742 | 102 | function [assign, confidence] = CBIG_IndCBM_wta(surf_labels, vol2surf_fc, topX)
% [assign, confidence] = CBIG_IndCBM_wta(surf_labels, vol2surf_fc, top)
%
% This function use winner-take-all to assign labels to the cerebellum.
% For each cerebellar voxel, this function first identifies the X highest
% correlated surfa... |
7dbb0139ccea29c980ba1c0001c9133e8cc359bcddab70e876efe32acca3b35f | MATLAB | 3,743 | 69 | function [S,f,Serr]=mtspectrumtrigc(data,E,win,params)
% Multi-taper event triggered time-frequency spectrum - continuous process
%
% Usage:
%
% [S,f,Serr]=mtspectrumtrigc(data,E,win,params)
% Input:
% Note units have to be consistent. See chronux.m for more information.
% data (single channel) --... |
5a79b83c94b7ed0c3ef4aac0e68bd0f0c03ede098a1c4013535844d149da83c5 | MATLAB | 3,744 | 117 | function events = GetEvents(selection,varargin)
%GetEvents - Get events.
%
% USAGE
%
% events = GetEvents(selection,<options>)
%
% selection optional list of event descriptions; see examples below
% <options> optional list of property-value pairs (see table below)
%
% ===========================... |
b2bb3d7d2268b740d0d5aa4ad1b66c7e29f02030d426c6a707a7df1bf7f29598 | MATLAB | 3,745 | 116 | function output = GetCustomDefaults(current,property,value)
%GetCustomDefaults - Get custom default value for a given function property.
%
% This is an 'internal' function used by FMAToolbox. You should not need
% to use it, unless you are developping new functions for this toolbox.
%
% See Example below.
%
% WARN... |
2e7685582edc1a02306bbb0cc69680f2d31323cf48ad33f8ab710b071e9957a5 | MATLAB | 3,746 | 98 | % Name: Robert Kim
% Date: 05-12-2023
% Email: robert.f.kim@gmail.com
% fnc_task_neus.m
% Description: Identify task-selective (anti-DMS vs. pro-DMS) neurons in a
% trained one-modality (instr) RNN. The function generates random trials,
% averages each unit's firing rate over a stimulus-aligned window, and uses
% a Wil... |
ecb9e1fb0828211e926c5a8cc93a829c53c51bbd979b9cd46c66f926bb9e41cd | MATLAB | 3,746 | 109 | function varargout=xmlwrite_xerces(varargin)
%XMLWRITE_XERCES Serialize an XML Document Object Model node using Xerces parser.
% xmlwrite_xerces(FILENAME,DOMNODE) serializes the DOMNODE to file FILENAME.
%
% The function xmlwrite_xerces is very similar the Matlab function xmlwrite
% but works directly with the ... |
97596e410a0f84633dbb01f2b77b731b6a47a05f62a67fba44f510f244543485 | MATLAB | 3,748 | 104 | function handles = dan_stage_epoch(handles, stage)
% Assign a sleep stage to an epoch
%%
% Authors: Dan Denis
% Date: 2021-07-14
%%
% Get the current epoch number
epochIdx = str2double(get(handles.current_epoch_number, 'String'));
% Set sleep stage as a number
if stage == 0
handles.psg.stages.s1.stages... |
1a3cc5cfb03c40aa12104cb997c1352c8704cb9d664bd9bb8cd95d90ce10a892 | MATLAB | 3,750 | 63 | % General-purpose data processing and statistical tests for FMAToolbox.
%
% Bins and histograms.
%
% Accumulate - Accumulate repeated observations.
% Bin - Assign each input value a bin number between 1 and N.
%
% General Statistics.
%
% sem ... |
226fea16bd49bf5c573cbf1aab933942209209451214cd4bfb8b9d37ecbef202 | MATLAB | 3,750 | 75 | function [tmat,postopct] = ea_getrawct2preniimat(options,inverse)
% Gets the transformation from options.prefs.rawctnii_unnormalized to
% options.prefs.prenii_unnormalized and extracts the transformation matrix
%
% Returns: transformation matrix in LPI- (= RAS+)
%
% 2018, Andreas Husch, University of Luxembourg, Intenv... |
072e16c307feb1d9fdf44503864cd3e18d20770860652374338b8d985ee02745 | MATLAB | 3,752 | 97 | clear; clc;
%% Load and process experiment data
% data location
path_root = getenv('DECIDENET_PATH');
path_beh = fullfile(path_root, 'data/main_fmri_study/sourcedata/behavioral');
path_jags = fullfile(path_root, 'data/main_fmri_study/derivatives/jags/samples');
fname_beh = 'behavioral_data_clean_all.mat';
fname_meta =... |
6ed8dd4f13d3c112c7411cfb2772eed0c5b58179a7c7c7e54a4cb49142b9afe3 | MATLAB | 3,753 | 109 | function res = on_off_de(params,inputs,initcond)
% This function generates a vector of intensity values over time for one
% half of the PB to a sequence of single-modality experience (either AF or
% OF). It can handle PFNpc offset responses if given the correct
% parameters (see 'script_20240404.m')
% 'params'... |
b1acedd511cacaee3f17d9bfaa63a3db89cfb97832c4a729bf728e3d4f6dfcf7 | MATLAB | 3,753 | 113 | function [cY,mY,ng] = motion_metrics(Y,bnd,batch_size,var_name)
% computes several metrics for the quantitative assessment of the registration
% INPUTS
% Y: registered time series in a loaded or memory mapped array
% bnd: number of pixels to be exluded to avoid NaN effects
% ... |
a7b9dec1072df26db27ca410f18cfa8a6a6c8ee88b25a7e1d61122a83fb428ef | MATLAB | 3,754 | 96 | function [] = register_rois2(sourceFolder, otherFolders, FOV)
HEIGHT = FOV(1);
WIDTH = FOV(2);
clipAmount=0;
files = fullfile([sourceFolder; otherFolders(:)],'MC_Video.tif');
N_files = length(files);
templates = NaN(HEIGHT,WIDTH,length(files));
for i_file = 1... |
1f68c0b20a8861408b32b4a89c73f6346a93541d334a824efdbdf8cc7bac3246 | MATLAB | 3,756 | 132 | % matsel() - select rows, columns, and epochs from given multi-epoch data matrix
%
% Usage:
% >> [dataout] = matsel(data,frames,framelist);
% >> [dataout] = matsel(data,frames,framelist,chanlist);
% >> [dataout] = matsel(data,frames,framelist,chanlist,epochlist);
%
% Inputs:
% data - input data... |
6d86a955608b59feca679b21155654335d0c83a408771f37eabbb13de835cc54 | MATLAB | 3,757 | 91 | function ea_unified_save_model(obj, ExternalModelFile, ss_val, ff_val, nm_val)
exportedAnything = false;
% we want to define the model outside of cross-validation
if ~exist('obj.explorer.patientselection','var') % patsel can be supplied directly (in this case, obj.patientselection is ignored), e.g. for cr... |
2ee63b3382037ac2c8b450a53843803bd3fbe27e22a5736c2f31dedd006248c6 | MATLAB | 3,759 | 86 | function []=CBIG_gwMRF_write_cifti_from_annot(lh_annot,rh_annot,output_name,nparcels,lh_fslr_orig,rh_fslr_orig)
% [] = CBIG_gwMRF_write_cifti_from_annot(base_folder)
%
%This script writes files from freesurfer annot format into HCP cifti
%format. It has dependencies on CBIG, Workbench and Fieldtrip. Further it
%also n... |
43ea8b35ddc617198330e522a04271001b8f2235251e7487b8d38cd90d337b76 | MATLAB | 3,759 | 98 | % pop_snapread() - load an EEG SnapMaster file (pop out window if no arguments).
%
% Usage:
% >> [dat] = pop_snapread( filename, gain);
%
% Graphic interface:
% "Relative gain" - [edit box] to compute the relative gain, fisrt look at
% the text header of the snapmater file with a text editor.
% ... |
5c4c1c4cc8b34cc30c3eb48c8a7610a589963bd2cc938654fcd32689be7c0dfc | MATLAB | 3,760 | 111 | function obj = export(obj, varargin)
% export Export gramm plot to vector or bitmap image
%
% Example syntax: gramm_object.export('file_name','my_figure','export_path','./test/','file_type','pdf')
% export() must be called after a draw() call and will save the plot to
% file using the specified 'name',value options:
% ... |
d551bb059dd96948638bb327325d602f7f0875eeae96e96a129f0d04bdeecde1 | MATLAB | 3,762 | 62 | % plugin_installstartup() - install popular toolboxes when EEGLAB starts
%
% Usage:
% >> restartEeglabFlag = plugin_installstartup; % pop up window
%
% Outputs:
% restartEeglabFlag - [0|1] restart EEGLAB
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Oct. 29, 2013-
% Copyright (C) 2013 Arnaud Delorme, SCCN, INC, UCS... |
6ff415198972e54324fd0a0ad82b568fde0a599c3a07b88dea9aefae9fcf62d2 | MATLAB | 3,764 | 138 | function output = err(n,maxit,pmax,family)
if n==0
output.n=0;
output.fatal=false;
output.msg='';
else
switch family
case 'gaussian'
output = err_elnet(n,maxit,pmax);
case 'binomial'
output = err_lognet(n,maxit,pmax);
case 'multinomial'
ou... |
b59b450175ceaa1e2e864e623abf441a1280f28a0764cf2d87b555773669c9ca | MATLAB | 3,765 | 107 | %% NPS SUBREGION NAMES
% -------------------------------------------------------------------------
posnames = {'vermis' 'rIns' 'rV1' 'rThal' 'lIns' 'rdpIns' 'rS2_Op' 'dACC'};
negnames = {'rLOC' 'lLOC' 'rpLOC' 'pgACC' 'lSTS' 'rIPL' 'PCC'};
%% CONDITIONS
% ------------------------... |
b23922395d508e536ee4e7dae99d9726556dcbf0059814ff1b7e37e81eca131a | MATLAB | 3,766 | 81 | function contours = getContoursMap2D(smoothGrid, gridMask, xB, yB, thresholds, contourSmooth, method)
% Compute contours for thresholded values of a 2D map of scalar values
% thresholds is an array of desired percentile values for thresholding the map
% contours is a 1 x length(thresholds) struct array of XY contour po... |
27be9c2694866dcbafb92360e4329462418d760d6bd892b2976eb65a16fb7b7e | MATLAB | 3,768 | 70 | fprintf(1,'Executing %s at %s:\n',mfilename(),datestr(now));
ver,
try,
if isempty(which('spm')),
throw(MException('SPMCheck:NotFound', 'SPM not in matlab path'));
end
[name, version] = spm('ver');
fprintf('SPM version: %s Release: %s\n',name, version);
fprintf('SPM p... |
41d6d7c9baaa07b14e9bf6897f36e4482e3375417a9f4022e1852417d8643e69 | MATLAB | 3,771 | 118 | % listdlg2() - listdlg function clone with coloring and help for
% eeglab().
%
% Usage: same as listdlg()
%
% Author: Arnaud Delorme, CNL / Salk Institute, La Jolla, 16 August 2002
%
% See also: inputdlg2(), errordlg2(), supergui(), inputgui()
% Copyright (C) Arnaud Delorme, CNL / Salk Institute, arno@s... |
84161eb2105fa4ccbba16d45112e74e0812f9bde1c654d1aeadb6dbad3f3f6b6 | MATLAB | 3,771 | 115 | function pvals = palm_gamma(G,mu,sigsq,gamm1,rev,prepl)
% Return the p-values for a Gamma distribution, parameterised by
% its first three moments.
%
% pvals = palm_gamma(G,mu,s2,gamm1,rev)
%
% Inputs:
% - G : Statistics for which p-values are to be computed.
% - mu : Distribution mean.
% - sigsq : Distribution... |
b90d6b4d558a2145c745ff12075cb4c67370cd780a0c72e5ee9f97f12f808f12 | MATLAB | 3,772 | 98 | classdef VButtonBox < uix.ButtonBox
%uix.VButtonBox Vertical button box
%
% b = uix.VButtonBox(p1,v1,p2,v2,...) constructs a vertical button box
% and sets parameter p1 to value v1, etc.
%
% A vertical button box lays out equally sized buttons from top to
% bottom.
%
% See also... |
2fc403584c5ac9f1d430ed1adfaa15e3af27231fae00c506a15a2ebf3ecf8735 | MATLAB | 3,773 | 146 | function [cimat,reldist,mat]=ea_sample_cuboid(varargin)
% This function samples image points alongside a trajectory specified.
% usage: [cimat,~,mat]=ea_sample_cuboid(trajvox (trajectory in voxel space),options (regular lead options struct),volume_to_be_sampled_from,interpolation_mode (see spm_sample_vol),width_of_samp... |
1528ae29e1029fb710b2c4feb38c153ccbf62408c6d6354cbe854db6192e6c91 | MATLAB | 3,775 | 104 | function h=ea_heatmap2surface(nii,surface,sides,colormap,opts)
% surface can be a char (smoothed/full) or a cell pointing to rh and lh
% .mz3 surface files.
if ~exist('nii','var')
nii=[];
end
if ~exist('opts','var')
opts.posvisible=1;
opts.negvisible=1;
end
if ~exist('surface','var')
surface='smoothed';
e... |
6845cce8ca58663034e80a61327011193cab034fb6720ff22ff8f4a951f29385 | MATLAB | 3,777 | 119 | function [s,f,t] = stft(x,nfft,hop,fs)
%STFT Calculate the short-time Fourier transform of a signal
%
% S = IOSR.DSP.STFT(X) calculates the short-time Fourier transform (STFT)
% of signal X using 1024-point segments in steps (hops) of 512 points. S
% is a series of one-sided FFTs of size [N,K] where N is the num... |
c6f8855812e96329048cb53ba517b822e4ecb08ebcf6fda9a348e59c539d656e | MATLAB | 3,778 | 95 | function I = bfGetPlane(r, varargin)
% BFGETPLANE Retrieve the plane data from a reader using Bio-Formats
%
% I = bfGetPlane(r, iPlane) returns a specified plane from the input
% format reader. The index specifying the plane to retrieve should be
% contained between 1 and the number of planes for the series. Give... |
2325d303c0f3f1775d90b2c52a11878085e74cde1a44e7e2fcc4b2c2f33c3294 | MATLAB | 3,780 | 117 | function AlignTsp2Whl_All(varargin)
% USAGE
% AlignTsp2Whl_All('parameters','values')
%
% Inputs:
% SIMPLEST THING TO DO: call AlignTsp2Whl_All()
%
% WARNING: it is assumed that the root folder name and the final merge name are the same. If not, use
% the 'mergename' option. Typically the root folder... |
f744142bedeadcd8a39fd2c464f59f5966215bcb88ecd2fc3fbf7c43299cee40 | MATLAB | 3,780 | 114 | function [ structout ] = bz_CollapseStruct( structin,dim,combine,NEST )
%structout = CollapseStruct( structin,dim,combine,NEST ) Combines elements in a
%structure array
%
%INPUT
% structin struct(N).fields structure array with N elements where each
% of the N elements has the same fields and field st... |
3a8176a3a5056e76ee1ed2ba36ef4a5dc3f017178626ac652cbbfa85878c7cca | MATLAB | 3,781 | 107 | function ea_update(varargin)
% lead update
local=ea_getvsn('local');
web=ea_getvsn('web');
if strcmp(local,'Unknown') % full update
update=1;
elseif strcmp(local,web) % no update
update=0;
else % incremental update
update=2;
end
if nargin
if strcmp(varargin{1},'force')
update=1;
else
ret... |
88ca646e9d921156f27c75584d2344704fa0ae3000081f7ab0bccc1607aa1dc5 | MATLAB | 3,788 | 84 | %% Set-up Model
visang_rad = 2 * atan(27/2/34);
Ecc = visang_rad * (180/pi); % diameter
Ecc = Ecc/2; % radius
ApWidth = [size(ApFrm,1),size(ApFrm,2)];
% Which pRF model function? (default = prf_gaussian_rf)
Model.Prf_Function = @(P,ApWidth) prf_gaussian_rf(P(1), P(2), P(3), ApWidth); % Which pRF model function?
Model.N... |
05fce07445703407392038a7324e4226a8adb85a58b6bade30b1ab159c7f283b | MATLAB | 3,791 | 93 | function labels = watershed_algorithm_all_par_cifti(edgemetrics, ...
minimametrics, stepnum, fracmaxh, neighbors, minh, maxh)
%Label initial markers with unique value
labels = zeros(size(minimametrics), 'single');
if ~exist('minh', 'var') || isempty(minh)
minh = min(edgemetrics(:));
end
if ~exist('maxh', 'var... |
bc184d261295edd2d0052a6b193c224d31402a43dd6b48e67d4420ca49f2c5d3 | MATLAB | 3,792 | 89 | % 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... |
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