sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
051a5ae86851bc66dd2e9a0fda0a30d9fbda5217f3efdc518526e41f5fa1e016 | MATLAB | 3,114 | 121 | classdef AffineGridGenerator < dagnn_bc.Layer
%DAGNN.AFFINEGRIDGENERATIOR Generate an affine grid for bilinear resampling
% This layer maps 1 x 1 x 6 x N affine transforms to 2 x Ho x Wo x N
% sampling grids compatible with dagnn.BlilinearSampler.
% (c) 2016 Ankush Gupta
properties
Ho = 0;
Wo = 0;
en... |
c38fb8a0695bca0d456bc2ed63f3d3684c879cbebaf7b0a60893abbae8ba1e54 | MATLAB | 3,114 | 76 | function sero_pulseq_gui_recon
% Create the main figure
fig = uifigure('Position', [100, 100, 400, 300], 'Name', 'Recon of TWIX data');
% Persistent variable to store last used folder
persistent lastUsedFolder;
if isempty(lastUsedFolder)
lastUsedFolder = pwd; % Default to the current working directory
end
% Data ... |
982bf77158d4dff86c256c6770a158992c672de7888044a00b9bda525aa99dff | MATLAB | 3,115 | 95 |
%% This demo loads and pre-processes 3D time series of calcium imaging
% This part is specific for the properties of the time series and must be modified according to one's needs.
%% The second part (starting with "%% Select ROIs") uses the 3D time series to load a non-graphical user interface
% This part is based on... |
3cd16ce743d9d9651de1d8f5c231b99fa6c0e609740605042fa87fe59b5b5c2d | MATLAB | 3,116 | 79 | function [bestParam,bestParamScore,bestParamIdx] = get_bestParam(CVscore,candParamsIdx,paramGrid,metric)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% get_bestParam returns best parameter in parameter space according to
% given their CV scores.
%
% Arguements:
% CVscore: Matrix in whic... |
2e3d7a18231bc4d1fe73dadd3815419df0c7310f490968aeef2371afab3d9a48 | MATLAB | 3,118 | 111 | %% [pSWI,dSWI,swi_phase] = swi(magn,phase,filterSize,thres,m)
%
% Input
% --------------
% magn : image that combines with phase contrast, can be 3D/4D
% phase : phase map (in rad)
% filterSize : window length of Hamming filter
% thres : threshold used to create positive/negative phase contr... |
aa865b86cdc54c19dd8f65fd0600aa1da5f7cdbfb46915b0319e26f1c6a806ba | MATLAB | 3,118 | 85 | 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.
%
% This function is used to decode strings from the Base64 encoding specified
% in... |
599e63b755a9e0dbc52d2fd0611cc648ee40a43f7c90a468570814e0df4ca46b | MATLAB | 3,119 | 43 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 3;
matlabbatch{1}.spm.tools.physio.write_bids.bids_dir = {''};
matlabbatch{1}.spm.tools.physio.write_bids.bids_prefix = 'sub-control01_task-YOURTASK_run-1';
matlabbatch{1}.spm.tools.physio.log_files.vendor ... |
c971e2bf4e6766ad773477da46166b1eb81baf4863ae515c5fada1b88a82f0bd | MATLAB | 3,119 | 88 | function fear_coactComp_5Cells(basename,varargin)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
% basename='~/data/Fear/triple/booyah180430/booyah180430'
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
load([basicMeta... |
8b69dedd726506770856f4122763d2841faeb38e32e6096be9bcce8e3701c33d | MATLAB | 3,120 | 79 | % eegplugin_bva_io() - EEGLAB plugin for importing Brainvision
% .vhdr and .ahdr data files.
%
% Usage:
% >> eegplugin_bva_io(fig, trystrs, catchstrs);
%
% Inputs:
% fig - [integer] EEGLAB figure
% trystrs - [struct] "try" strings for menu callbacks.
% catchstrs - [struct] "... |
bc82dfc0ee27dbe5cd94a0d60d9179eb8492ad35d17247812cd746cfe6aabfa2 | MATLAB | 3,121 | 66 | function cutBaseline_stft(params, resp, triggers)
% gets preprocessed data: resp{sess} = [samples x ch]
% & struct triggers.
% sampleSessLabel: [3238x3 double] - triplets = [sample, sess, clz]
% timeSessLabel: [3238x3 double] - time in [s]
% eventDuration: [3238x1 double] - in [s]
% ... |
281ba467213e755728ed37669a1318bb18cbc8695a75feccf2c4bc2ef7145099 | MATLAB | 3,122 | 74 | function osp_onRightBasis( ~, ~ ,gui)
%% osp_onRightX
% Callback function on process click on left x voxel direction button.
%
%
% USAGE:
% osp_onRightX( ~, ~ ,gui);
%
% INPUT: gui = gui class containing all handles and the MRSCont
%
% OUTPUT: Changes in gui parameters and MRSCont are writt... |
92b7bd3bf3eeeb98a7ee3f42c9a5dfc3a9fba0ecab4a3a93fa4ae906efa9a490 | MATLAB | 3,122 | 74 | %% %%%%%%%% Do setup
nsdsetup;
%% %%%%%%%% Use nsd_mapdata to get betas into MNI space
% Ran on Aug 18 2019 (1-224) [includes restingbetas and going forward]
% Update on Sep 3 2019 (225-239).
% DEC 29 2019: update and run for nsdimagery√
% DEC 29 2019: update and run for nsdsynthetic
% define
nsubj = 8;
betadirs = ... |
f46c32a3543565b547afbeb2de808399be52e3dd38d8ab8f80137dedbf15f82f | MATLAB | 3,123 | 97 | close all
clear all
glusnf = 1;
load('Y:\users\zilan662\Glusnfr_spine_metadata\glusnfr_spine_bci\061324_glusnfrspinebci5\Baseline\baselineMask_1.mat')
frames_tmp_ = sbxgrabframe('Y:\users\zilan662\Glusnfr_spine\glusnfrspinebci05\061324_glusnfrspinebci05\061324_glusnfrspinebci05_000_000\061324_glusnfrspinebci05_000_00... |
1b109da167249ec23e9d5b3e71cd41f25b43c4889e1c6605beedc8abf67c68c0 | MATLAB | 3,124 | 84 | classdef ConfoundRegression < baseScaler
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% ConfoundRegression removes variance explained by the confounds from
% given data. Simply, a linear regression method is fitted on the each
% feature in a given data using confounds are pred... |
f429f15f2be8829c091db0a03cc5cc53d082c52202e5188dcca659b9e3a75eef | MATLAB | 3,124 | 73 | %% Makes a nice supplementary materials figure of the parameter recovery results
printFigFlag = 0; % set to 1 to print figure in 2 png and svg formats
% Load the results of the parameter recovery: parameters obtained by
% fitting synthetic data created with fitted parameters, with 1SD of noise
% added to the happiness... |
24c2fdf9c836925a5340d69d4c4a68bf352deb2a6d234cedab95cc45444c1e62 | MATLAB | 3,125 | 63 | clear all, close all % tidy up
n = 2350; x = 7*rand(n,1); xs = linspace(-0.4,8,200)'; opt = [];
xs(13:15) = xs(12); % mess with the test set
x(14) = x(15); x(17) = x(16); % mess with the training set
sn = 0... |
3669bbbf9bca97c9262f9f75da01db86a8729f7847e39787b65fc39da566ef42 | MATLAB | 3,125 | 109 | function [fh yMin, yMax] = tapas_uniqc_plot_image_diagnostics(Y,iDynSli,fh, yMin, yMax)
%plots abs and phase of specific dyn/slice of complex data, for different
%sets of coils, adjusts plot limits automatically
%
% [fh yMin, yMax] = tapas_uniqc_plot_image_diagnostics(Y,iDynSli,fh, yMin, yMax)
%
% IN
% Y ... |
5a8237487f428eaeada92ea2487e7bfc9c7ca48c3861df48255e1128aa04c391 | MATLAB | 3,126 | 66 | %% sepia_configuration_BFR
%
% Description: a script contains all the background field removal method names and related function names
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 11 March 2020
% Date modified:
%
% DO NOT change the variable name
% DO NOT change the order of the entities, add a ne... |
b68fbf0eac63e01b47a532c49663496d5fb1083025636bc9c052d23bb25b9a9c | MATLAB | 3,126 | 93 | function scatterHistDiff(x, y, xeb, yeb, colors)
% takes paired data x and y, optional arguments for errorbars around
% individual datapoints (see ploterr) and plots a scatterplot as well as a
% rotated histogram of the differences between the two.
% requires http://nl.mathworks.com/matlabcentral/fileexchange/22216-pl... |
f8e578c237b35453f60f3888251f0b6065896080658369d5dbf25027a61b19e5 | MATLAB | 3,126 | 102 | function B = doubly_stochastic(A, maxiter, mode, checkperiod)
% Project a matrix to the doubly stochastic matrices (Sinkhorn's algorithm)
%
% function B = doubly_stochastic(A)
% function B = doubly_stochastic(A, maxiter)
% function B = doubly_stochastic(A, [], mode)
% function B = doubly_stochastic(A, maxiter, mode)
% ... |
96f2a8a8397adc90ece2f81fb0a3506d331f6bdd191605789c2822981932b138 | MATLAB | 3,127 | 105 | function GenerateBIDSStructure(nSubs, nSes, dataTypes)
%% GenerateBIDSStructure(nSubs, nSes, dataTypes)
% This function generates a coarse empty BIDS structure that can be used to
% pre-sort imaging and MRS data into a structure than can be reasonably
% well BIDS-ified with tools like BIDScoin.
%
% USAGE:
% ... |
e1cf87f50c2be6c95ff227be4f79b69ddb941681fdb6e087ab16b4c7829a3edf | MATLAB | 3,127 | 119 | function imageRDMs(RDMs,varargin)
% imageRDMs(RDMs,varargin);
%
% Visualizes one or many RDMs, and uses the *.RDM fields for each structure
% can deal with a number of different input formats:
%
%
% Joern Diedrichsen 2015
%__________________________________________________________________________
% Copyright (C) 2010 ... |
690c7441ca3d98c2955da05f007daa95fd78935fedd6debb122451d1881f4ccc | MATLAB | 3,128 | 116 | function ons_secs = tapas_physio_preprocess_phys_timeseries(ons_secs, sqpar, doNormalize)
% Preprocess raw cardiac/respiratory time series (e.g. amplitude
% normalization, padding for acquisition duration)
%
% ons_secs = tapas_physio_preprocess_phys_timeseries(ons_secs)
%
% IN
% ons_secs raw time series (c(ardia... |
4af4e8c851234d1f5a35c3257397b6e823d3f0155745fd8827d83f4041f9326c | MATLAB | 3,129 | 78 | function varargout = printSVG(varargin)
% prints current figure to SVG file at (pretty much) same size as on
% screen. If
%
% INPUTS: 4 (all optional)
% - 1st argument: name, default = the one from figure
% - 2nd argument: file format, default = 'png'
% - 3rd argument: resolution, default = 300 DPI (irrelevant for ep... |
7819b40277ce76ad1ddf10dd4ec63bab194c204391ee38216209a3cb3885489d | MATLAB | 3,129 | 97 | function [fit,cfg] = fit_MixtureModelBias(x,data,bias,cfg)
% [fit,cfg] = fit_MixtureModelBias(x,data,bias,cfg)
%
% fit mixture model by minimising MSE
if nargin < 4
cfg = struct;
end
if ~isfield(cfg,'fitmean')
cfg.fitmean = false;
end
if ~isfield(cfg,'offset')
if isfi... |
106000e73bbbefd493422c6c395cb449e37a32a7496a7c6f89b944bf4a691210 | MATLAB | 3,130 | 78 | function varargout = printfig(varargin)
% prints current figure to tiff file at (pretty much) same size as on
% screen. If
%
% INPUTS: 4 (all optional)
% - 1st argument: name, default = the one from figure
% - 2nd argument: file format, default = 'png'
% - 3rd argument: resolution, default = 300 DPI (irrelevant for e... |
749bdf60248ab8ed27a475a6283e6c57c82677248bf2935fe1bbf2d2363a1473 | MATLAB | 3,130 | 78 | function [ts_ind,dataCell,codeEval] = TS_WhichProblemTS(opID,whatData,doPlot)
% TS_WhichProblemTS Lists the indices of the time series with bad values for a given opID
%
%---INPUTS:
% opID: the ID of the operation to investigate
% whatData: hctsa data source (default: 'raw'; cf. TS_LoadData)
% doPlot: plot some example... |
3a59447e42c416c2638330cc9661e2d38c710f7e4c5ef871c5a07cfe5673dccf | MATLAB | 3,131 | 69 | % BIDS_EXPORTER - BIDS export wizard, from raw EEG to BIDS
%
% Usage:
% >> bids_exporter; % create new study interactively
%
% Authors: Dung Truong and Arnaud Delorme, SCCN, INC, UCSD, July 22, 2024
% Copyright (C) Arnaud Delorme, 2024
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentati... |
fa010292cb2fb02c7ceb031e58c3952d7a42625301e58fe3e25e94c9330729c0 | MATLAB | 3,131 | 88 | %% h = sepia_handle_panel_qsm_STIiLSQR(hParent,h,position)
%
% Input
% --------------
% hParent : parent handle of this panel
% h : global structure contains all handles
% position : position of this panel
%
% Output
% --------------
% h : global structure contains all new and other h... |
1965af421bce82f0bddaa7db6a4f764a611188e67a78e8b343aed9f6c415dd53 | MATLAB | 3,134 | 77 | % (C) Copyright 2020 CPP visual motion localizer developpers
%This function creates a direction matrix A with
%events [0 180 270 90].
%Then it creates another direction matrix B such that the directions are
%paired (0,180) and (270,90)
%A and B are combined for their corresponding pairs
%The target matrix is also cre... |
918d45597b06f73b2ba8a57d65251d7bcb3f82c08f35fc9679adaeae48c6fce4 | MATLAB | 3,134 | 127 | % addpath('C:\CODE\GitHub\KiloSort\preDetect')
function WUinit=optimizePeaks(ops,uproj,Nchan)
nt0 = ops.nt0;
nProj = size(uproj,2);
nSpikesPerBatch = 4000;
inds = 1:nSpikesPerBatch * floor(size(uproj,1)/nSpikesPerBatch);
inds = reshape(inds, nSpikesPerBatch, []);
if ~exist... |
a404db32cd5c4d3ecff57beb69badbe22753a863a972ac339c2f3e5782268bce | MATLAB | 3,134 | 89 | % GETTEXT - This function prints a dialog box on screen and waits for
% the user to enter a string. There is a cancel button which
% returns a value of [].
% Usage:
% >> out = gettext(label1,label2,...,label7);
%
% Author: Colin Humphries, CNL / Salk Institute, La Jolla, 1997
% Copyright (C... |
65ca195149ff540c0ea0632b7c92f28afe3dcf95ada9d9d42ec6b2eea1ec8b90 | MATLAB | 3,135 | 102 | function [Q, iQ, q] = gn_scale_U(EUU, EZZ, A0, nA0, N, D, q0)
% FORMAT [Q, iQ] = gn_scale_U(EUU, EZZ, A0, nA0, N, D, q0)
% ww - W'LW
% > Must have been orthogonalised before.
% zz - Z*Z'
% > Must have been orthogonalised before.
% Sz - cov[Z]
% > Must have been orthogonalised before.
% n0 - Number... |
033e06e44ad7694b3214e82a5d9c849422047bb48732981563198e2c0146c381 | MATLAB | 3,136 | 79 | function [K,dK] = covProd(cov, hyp, x, z)
% covProd - compose a covariance function as the product of other covariance
% functions. This function doesn't actually compute very much on its own, it
% merely does some bookkeeping, and calls other covariance functions to do the
% actual work.
%
% Note that cov = {c... |
dd79992c6a7a4b63c4bf28f9c74fba9b6eb30d02d889aa925ebb254a71fbec01 | MATLAB | 3,136 | 58 | % LBFGSB Call the nonlinear bound-constrained solver that uses
% limited-memory BFGS quasi-Newton updates.
%
% The basic function call is
%
% LBFGSB(x0,lb,ub,objfunc,gradfunc)
%
% The first input argument x0 is either a matrix or a cell array of
% matrices. It declares the starting point for the s... |
8b10ce3c945a201bba35516bf22e4045f585739e2923a881137321f12da2a9af | MATLAB | 3,137 | 79 | function BF_ProgressBar(progressProp,PB_length,theChar,suffixText)
% Create/update a text progress bar.
%
%---INPUTS:
% progressProp: EITHER Text string to initialize ('new') or terminate ('close')
% OR Proportion progress (numerical)
% PB_length: Length of progress bar (in characters)
% theC... |
acf28f975c49fe1155e15e7be796cb4e7d54513a9724f9695526fbfbe5a3faa6 | MATLAB | 3,138 | 91 | function settings = sd_get_image_specs(layers, settings)
% SD_GET_IMAGE_SPECS Obtains information from images
%
% DESCRIPTION
% This function obtains information from images, including header
% specifics, transformation matrix, and slice dimensions and positions.
%
% SYNTAX
% [settings, p] = SD_GET_IMAGE_SPECS(lay... |
f7cfda2ee493f046b1386f87d37683e9f56425bf7f01e028921d7ced8aec413b | MATLAB | 3,139 | 94 | function [ni,canXform] = niftiApplyCannonicalXform(ni, canXform, phaseDir)
% Reorient NIFTI data and metadata fields into RAS space
%
% [ni,canXform] = ...
% niftiApplyCannonicalXform(ni, ...
% [canXform=mrAnatComputeCannonicalXformFromDicomXform], phaseDir=[])
%
% Inputs:
% ni: Nifti-1 data s... |
682e5523109875bb65dd72a96ad3a82cc546f370b715a799549f58be96b59540 | MATLAB | 3,140 | 78 | function plotPrePostStimFR(spikeData, allStimTimes, Params, figFolder, figName, Info)
%PLOTPREPOSTSTIMFR Summary of this function goes here
% Detailed explanation goes here
numStimEvent = length(allStimTimes);
numChannels = length(spikeData.stimInfo);
% Start the post-stim window after the blanked artifa... |
6a098dd6ca6a870596c226a07abc21a53deae14a93ee2eb7035547427619e246 | MATLAB | 3,140 | 90 | function [refShift, refFWHM] = fit_OspreyReferencing(dataToFit)
%% [refShift, refFWHM] = fit_OspreyReferencing(dataToFit)
% Calculates the reference shift and full-width half-maximum (FWHM) of a
% spectrum according to the LCModel algorithm. The algorithm is described in:
% S.W. Provencher, "Estimation of met... |
4fa03790ddc69a1a540dae75245a7d8d79a4cb1e7bc241b94f35c976aa92d666 | MATLAB | 3,141 | 94 | function callBoxDeleteCallback(rectangle,evt)
% Only do anything if the face was selected, not the markers
if ~strcmp(evt.SelectedPart, 'face')
return
end
hObject = get(rectangle,'Parent');
handles = guidata(hObject);
clicked_tag = str2double(get(rectangle, 'Tag'));
switch evt.SelectionType
case 'right' % d... |
58fc3a629bc13a4b3e9ff43b2bad1ad7be1f9e63bee5a863dc6c432a8de1705d | MATLAB | 3,141 | 77 | function out = DN_OutlierTest(y, p, justMe)
% DN_OutlierTest How distributional statistics depend on distributional outliers.
%
% Removes the p% of highest and lowest values in the time series (i.e., 2*p%
% removed from the time series in total) and returns the ratio of either the
% mean or the standard deviation of... |
6dbc5de732607469d04000e46717bd1c6b206e6e01edcb808c3a93d38c3e2935 | MATLAB | 3,141 | 78 | % STD_ADDVARLEVEL - add design variable level
%
% Usage:
% >> [STUDY] = std_makedesign(STUDY);
% >> [STUDY] = std_makedesign(STUDY, designind);
%
% Inputs:
% STUDY - EEGLAB STUDY set
% designind - [integer > 0] index (number) of the new STUDY design {default: all}
%
% Author: Arnaud Delorme, Instit... |
babad73f847642373e2ea48f5da6cd9d0781f0fb8b5f2d9cfbf6dd3dbccd8cba | MATLAB | 3,141 | 97 | function density_image(varargin)
% function density_image([fname],[radius],[threshold],[plot types])
%
% tor wager, 4/19/03
%
% This function plots line graphs, a montage, and a surface rendering
% of a density map image, thresholded at a level you choose
%
% fname: must be an analyze image file containing dens... |
452927af15f32f839acead071deda7bf354e4ab5da32f137fcdeb4a7bb1cff4a | MATLAB | 3,142 | 102 | function FigureS14(datadir, codedir)
%FigureS14 Wait time curves without threshold have qualitatively similar
% context effects, but longer average wait times.
% datadir = directory of dataset
% codedir = director of code
%% Set up paths
s = pathsep;
pathStr = [s, path, s];
onPath = contains(pathStr,...
coded... |
f132de88949c0f568704cbfd5205b017ea53d01d58a5acb55ed96eff8f84b74f | MATLAB | 3,142 | 74 | % this function detects potential malware in the current folder and subfolders
%
% Author: A. Delorme, October 2013
% Copyright (C) Author: A. Delorme, October 2013
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribution and use in source and binary forms, wit... |
d81bbcce2dc318e1454c5586f969b6095add54f88a86ac29806c35ba2a363cf1 | MATLAB | 3,143 | 63 | %clear; clc;
morph_path = '/oak/stanford/groups/kalanit/biac2/kgs/projects/babybrains/mri/code/morphology_allparameters/';
addpath(morph_path)
% Set participants
subj = {'bb02_mri0_mask', 'bb02_mri3_mask', 'bb02_mri6_mask', 'bb04_mri0_mask', ...
'bb04_mri6_mask', 'bb05_mri0_mask', 'bb05_mri3_mask', 'bb05_mri6_mask... |
e325083f5343cc860dd682bbb081c8b49cfc51560642548f0734692c9f56ea78 | MATLAB | 3,143 | 74 | %% Cortical Input (CI)
%
% Copyright 2025 Laura Schmid
% Permission is hereby granted, free of charge, to any person obtaining a
% copy of this software and associated documentation files (the
% “Software”), to deal in the Software without restriction, including
% without limitation the rights to use, copy, modify, ... |
a46543000939225f55711ae59540d5a506df7f28b89633eae4cd0d53684e6e50 | MATLAB | 3,145 | 102 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% normalizeValues.m
%
% Normalizes the input values to range between the minValue and maxValue
% provided. Returns the values in type 'double'
%
%--------------------------------------------------------------------------
%
% function values... |
4c8d7d059c24ad3b6c58e5ffa67d216f4f3640cc62280193637aaa61deceb432 | MATLAB | 3,146 | 74 | %{
vis.Movie (lookup) # movies used for generating clips and stills
movie_name : char(8) # short movie title
---
path : varchar(255) #
movie_class : enum('mousecam','object3d','madmax') #
original_file : varchar(255) ... |
112ee73a2a9c8fcb205285aa5d5519ac5de309554edcaa57df50caa92ec1cc57 | MATLAB | 3,148 | 104 | function [b, tau, er, exp_t_1_coeff, stats, bestfit, bint] =...
regress_latency_vs_rew(A, nback, plotarg,...
z_arg, hit_arg, blk_arg, varargin)
%regress latency to cpoke against rewards, a la Wang/Uchida 2013.
%also fits exponential. cmc 12/2/20
%inputs: A struct. If you give it the S struct, will convert it to... |
a8e906da0a6dc2fd99533eac093cb8767139605b744ea192d58ab67103ad8fcf | MATLAB | 3,148 | 113 | %% ms SEI text: reaction times (RT_all) & right-wrong answers (RWM)
% (c) Jiri, Nov23
%% settings (v30)
% subjList = msSEI_getSubjList('SEI_withRS');
% pathBeg = 'F:\dox\ms_switch_EI\data\v30_stft_baseRS_bip\switchin_EI_IE_bip';
%% settings (v31)
subjList = msSEI_getSubjList('SEI_all');
pathBeg = 'F:\dox\ms_switch_EI... |
d116d2878dc241cd96de624f9ae3a4056c0d4ffa62403b593ef94216859682b4 | MATLAB | 3,148 | 110 | function plotResBlock(res100)
%it's always attention RIGHT (the left have been flipped)
fx = 2:2:45;
e11=1;
e12=5;
e21=7;
e22=11;
fTheta1 = 3;
fTheta2 = 7;
fAlpha1=8;
fAlpha2=12;
fBetaLow1=14;
fBetaLow2=24;
fBetaHigh1=25;
fBetaHigh2=35;
thetaFW = squeeze(nanmean(res100.fwdB(:,fx>=fThe... |
f8dd32088ac95bda42478bc1f356756e8ca1597604bd70e0e7ba139f7d3acf92 | MATLAB | 3,148 | 102 | %January 2025 SW: Script that reads out a portion of the eye and reads the average
%brightness over time from a tiffstack (frames), RED LASER USED, fiber
%implant in the brain, 1, 2.5, 5, 7.5, 10 mW
%darkness
%red stack : 1-4134
%%
clc;clear all;close all;
%% CHANGE ACCORDINGLY
% %DARK
tiffFilePath1 = 'C:\Users\... |
31ee82816e2f49cbd4fe74123c5f50e4a1419ebdd1d30f6b3bd491de026812b0 | MATLAB | 3,149 | 84 | % POP_COPYSET - Copy the current EEG dataset into another dataset.
%
% Usage:
% >> ALLEEG = pop_copyset(ALLEEG, index1); % pop-up
% >> [ ALLEEG EEG CURRENTSET ] = pop_copyset(ALLEEG, index1, index2 );
%
% Inputs:
% ALLEEG - array of dataset structure
% index1 - input dataset number
% index2 - inde... |
59e3d75b17e6e9e569312b57138cf90ac62db9770913288ba108dd310d5ae47d | MATLAB | 3,149 | 89 | % pop_icflag - Flag components as atifacts
%
% Usage:
% EEG = pop_icflag(EEG, thresh)
%
% Input
% EEG - EEGLAB dataset
% thresh - [7x2 float] array with threshold values with limits to include
% for selection as artifacts. The 6 categories are (in order) Brain, Muscle,
% Eye, Heart, Line ... |
a36bdef3b131236a4db07dd2e72d339f1ada753c2c446af46463c9b225d98cb5 | MATLAB | 3,149 | 110 | classdef nntest < matlab.unittest.TestCase
properties (ClassSetupParameter)
device = {'cpu', 'gpu'}
dataType = {'single', 'double'}
end
properties
currentDevice
currentDataType
randn
rand
zeros
ones
toDevice
toDataType
range = 128
end
methods (TestClassSetup)
... |
8a55bc3ad1b239dffd1a022f426ef2f29feec4e3675bec1e34d6afeeb1acb0ad | MATLAB | 3,151 | 57 | % For the process of DSC-MRI
% Youjie Wang, 2025-07-26. wangyoujie2002@163.com
% params
toolbox_dir = '/this/is/for/nipype/dsc_mri_toolbox'; % path to the DSC-MRI toolbox
DSC_info = niftiinfo('/this/is/for/nipype/pwi_path');
load('/this/is/for/nipype/aif_conc.mat', 'aif_conc'); % aif_conc should be a vector of AIF ... |
214940e13f5605210f35892bd93280e4fef6add88a7544f9f7550cd31fabb29a | MATLAB | 3,152 | 105 | function [Xsol] = Test_nonlinear_eigenvalue_problem(L, k, alpha)
% Minimize total energy minimization nonlinear eigenvalue problem.
%
% function [Xsol] = Test_nonlinear_eigenvalue_problem(L, k, alpha)
%
% L is a discrete Laplacian operator,
% alpha is a given constant, and
% k corresponds to the smallest eigenspace sou... |
b64157d84d1d0630cf8b7ade0ec4ce186363b93d72174ae32f1913ff80a27be4 | MATLAB | 3,152 | 73 | function pheno_resid = resid(pheno_file, ids_file, covar_file)
% Args:
% pheno_file: a file with phenotypes to residualize (lh.pial.0.fsaverage3.csv)
% - no header
% - columns contain phenotypes (no other columns)
% ids_file: a file with imaging ids (vertex_subjectlist)
% ... |
fc7c8e26de1b736af843f299b3157e5b168e0b254906064e3405b034ff531ca4 | MATLAB | 3,154 | 115 | % windows() - Symmetric window functions
%
% Usage:
% >> h = windows(t, m);
% >> h = windows(t, m, a);
%
% Inputs:
% t - char array 'rectangular', 'bartlett', 'hann', 'hamming',
% 'blackman', 'blackmanharris', 'kaiser', or 'tukey'
% m - scalar window length
%
% Optional inputs:
% a - scalar or vector wi... |
56059356ce09907fd99a82fef45c1d7921d4335bc24df0ffab2bc663f8522041 | MATLAB | 3,155 | 81 | function getTriggers_emoReco_timesLabels(params)
% extracts trigger times and class labels
% saves to session cache files
% (c) Jiri, Nov16
n_selected = 0; % number of selected trials
n_total = 0; % number of all trials
for sess = 1:size(params.storage.sessionCacheFiles,2)
t_trigger = [];
clz_... |
d3344b14d098bd569f3e0f526f61d3383ef2af1e82bf2b9a3e9795444133df92 | MATLAB | 3,155 | 85 | echo off;
% EEGLAB_OPTIONS - handle EEGLAB options. This script (not function)
% set the various options in the EEG_OPTIONS file.
%
% Usage:
% eeglab_options;
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, 2006-
% Copyright (C) Arnaud Delorme, SCCN, INC, UCSD, 2006-
%
% This file is part of EEGLAB,... |
2f382d4c6ce421bc79d1463da05c6d09f27600a1efea02c89803568d5da64668 | MATLAB | 3,156 | 113 | function [myelin, C1, C2, C3, tau] = Setup_Agents( ...
myelin, borders, sizing)
% SETUP_AGENTS
%
% Initialises agent populations (C1, C2, C3) and constructs the myelin
% structure, including oligodendrocyte grouping and state variables.
%
% INPUTS:
% myelin - myelin structure from Setup_Simulation
% borders -... |
6b29f1a201de5ed42a3bfcd4a297ac678ade3ea0b9428013c3ab2fc61c4f06e8 | MATLAB | 3,156 | 81 | function net = cnn_mnist_init(varargin)
% CNN_MNIST_LENET Initialize a CNN similar for MNIST
opts.batchNormalization = true ;
opts.networkType = 'simplenn' ;
opts = vl_argparse(opts, varargin) ;
rng('default');
rng(0) ;
f=1/100 ;
net.layers = {} ;
net.layers{end+1} = struct('type', 'conv', ...
... |
7c957179ecca8138e8e62b1136ffe81291bd421561f0f8363a9bbbeac6b91764 | MATLAB | 3,156 | 96 | function res = permutation_null_spin_correlated_genes(img_data)
% PERMUTATION_NULL_SPIN_CORRELATED_GENES(IMG_DATA) performs permutation testing to examine
% whether imaging profiles associate with gene expression profiles, based
% on the null-brain model (where random genes were selected from
% brain-expressed genes).... |
a2e701b2e7430ebfc556e5f4bb479d6cba6487cc2a98091956359273b8e4c794 | MATLAB | 3,156 | 125 | function r = save_mgh(vol, fname, M, mr_parms)
%
% save_mgh(vol,fname, M, <mr_parms>);
%
% M is the 4x4 vox2ras transform such that
% y(i1,i2,i3), xyz = M*[i1 i2 i3 1] where the
% indicies are 0-based
%
% mr_parms = [tr flipangle te ti]
%
% See also: load_mgh, vox2ras_0to1
%
%
%
% save_mgh.m
%
% Ori... |
b33839f3ad35a364082bb4779b34692b8e121285e80d8a52949acd722edea523 | MATLAB | 3,157 | 94 | function PlotLinkage(linkage,varargin)
%PlotLinkage - Plot network clustering obtained e.g. by FCA analysis.
%
% USAGE
%
% PlotLinkage(linkage,<options>)
%
% INPUT
%
% linkage network similarity matrix obtained using <a href="matlab:help FunctionalClustering">FunctionalClustering</a>
% <options> ... |
02fe06a45cb8bfdc02e69c730fe7d0510b37d8c3a8e24ba17b88109480c633d2 | MATLAB | 3,158 | 98 | clc;
clear;
atlas = cifti_read('C:\Users\lihon\Desktop\abcd_study\atlas\Schaefer\Schaefer2018_400Parcels_17Networks_order.dlabel.nii');
atlas_parcel = atlas.cdata;
atlas_label = unique(atlas_parcel(atlas_parcel>0));
num_parcel = length(atlas_label);
% load regional brain development (RBD) index patterns
K = 3;
cen_... |
ed2509b124ef1032498a127cf97b70bf660a051e017b9ecb8cb89070ff50e772 | MATLAB | 3,158 | 134 | function dbcluster_glass_plot(newcl,mycol,varargin)
% dbcluster_glass_plot(newcl,colors,[select by field],[cell vector of conditions to select])
% tor wager
% newcl = clusters structure, output of database2clusters.m
%
% Creates 3 views of glass brain with points in each cluster plotted
% in different symbols
%
% Needs... |
0f114fbab583e0213d555b393c2250f0a8c8d9b73d7b76a0f2c89e40c048943c | MATLAB | 3,159 | 98 | function organiseTsvMtMst
% it is a mini function to
% to change the trial type
% the originial tsv files have the trial types named "motion"
% we change it to motion_right or motion left depending on the aperture
% position
deleteSuffix = 1;
% add bids repo
bidsPath = '/Users/shahzad/GitHubCodes/CPP_BIDS';
... |
84ad6a4b423c7b6474faa18156ffc361762ed46dbdf2de0471d88a5d6b36d17a | MATLAB | 3,159 | 86 | %% [chi] = Wrapper_QSM_iLSQR(localField,mask,matrixSize,voxelSize,algorParam, headerAndExtraData)
%
% Input
% --------------
% localField : local field map (tissue fields), in Hz
% mask : signal mask
% matrixSize : size of the input image
% voxelSize : spatial resolution of each dimension of the data... |
fc68da6f86723c7c204ed7625479f62962b4ab7aa5dad96493f3e827bd9791cc | MATLAB | 3,160 | 102 | function res = fit_models(D_list, cfg, with_interactions)
% FIT_MODELS Run regressions at global, rsn_pairs, nodewise
nLevels = numel(D_list);
res = struct();
for li = 1:nLevels
D = D_list{li};
levelName = util.get_level_name(D, 'fit_models');
% Fit model
T = aggregate_and_fit(D, cfg, with... |
5d49127087c9ed45ef161c87ceb2c4ccffeddc16bd10c4ea6b229cb5a04e2695 | MATLAB | 3,161 | 91 | function ri=rindex(dist,partition)
%function ri=rindex(dist,partition)
%
%PURPOSE
%
%To compute a clustering validity index called R-index to assist in
%selecting a proper number of clusters. Input argument
%'partition' defines different clustering results, partitions, of
%the same data. Clustering result that has a (l... |
b07cddebff2565ddda82193448373ee4da6df95c29100f4246dab0e2236e3204 | MATLAB | 3,161 | 75 | function [cpulse, verbose] = tapas_physio_get_oxy_pulses_filtered(c, t, ...
dt120, verbose)
% Determines peaks of pulse oximeter data after Gaussian and high pass
% filtering, thresholding and assuming maximum heart rate (minimum peak
% distance)
%
% [cpulse, verbose] = tapas_physio_get_oxy_pulses_filtere... |
15964d050204dad66efcce1553a8f941a434276278250dafc7935a05b2d8881a | MATLAB | 3,162 | 103 | function xtfce=surfing_clustertfce(node2area,nbrs,x,dt,showprogress)
% Treshold-free cluster enhancement (TFCE) for volumes and surfaces.
% Yields a score (e.g. t-value) to each node, that is higher if the node
% is either part of a small but strong cluster, or a weak but large cluster
%
% XTFCE=SURFING_CLUSTERTFCE(... |
ee4ebb0467a41474e6c3ecbd9763b6678440f3b8ae5d348ac2e882b53ec3d16f | MATLAB | 3,165 | 78 | function ProcessData_Figure4(datadir, codedir, savedir)
%ProcessData_Figure4 - Process raw data saved under datadir such that it can be plotted by PlotFigure4.
% INPUTS:
% datadir - Local directory where 'Golden_Nature/RawData_Figure4.mat' from Zenodo was saved
% codedir - Local directory where code (e.g., publishe... |
34783ba8d1f837fe7866ca3a1ea835f627232d49f49e7de579d141f93d2574b2 | MATLAB | 3,166 | 87 | % Script demo_reslice
% ONE_LINE_DESCRIPTION
%
% demo_reslice
%
%
% See also
% Author: Saskia Bollmann & Lars Kasper
% Created: 2019-11-27
% Copyright (C) 2019 Institute for Biomedical Engineering
% University of Zurich and ETH Zurich
%
% This file is part of the TAPAS UniQC Toolbox, which is... |
833a1cf48c4b6c5eae81107f844d9cddbb84619e18ff66a2bc7f0a4b3c934eb0 | MATLAB | 3,166 | 85 | function [] = load_files ()
%%load_files Input experimental files and analysis parameters to WormTracker3000.
% Users can:
% Select an XSLX file containing an index/parameter tab and an XY coordinate tabs
% Select an XSLX file containing XY coordinates and input parameters
% using a GUI
% <Fut... |
d371c08055dd2305cd30a8874a68bc131bddbf54d16e7a513856cc5223b4704a | MATLAB | 3,166 | 93 | function [outputImage, varargout] = apply_spm_method_per_4d_split(this, methodHandle, varargin)
% Applies SPM-related method of MrImageSpm4D to a higher-dimensional MrImage ...
% splitting data into 4D chunks executing SPM method for each split separately
% before recombining the image
%
% Y = MrImage()
% [newY, ou... |
16631aac923750dc5638f20d7dbf781be3ad7073ab08c8eb17ea11829f5fc643 | MATLAB | 3,169 | 105 | function Xsol = nonlinear_eigenspace(L, k, alpha)
% Example of nonlinear eigenvalue problem: total energy minimization.
%
% function Xsol = nonlinear_eigenspace(L, k, alpha)
%
% L is a discrete Laplacian operator,
% alpha is a given constant, and
% k corresponds to the dimension of the least eigenspace sought.
%
% Thi... |
e0a2a518845afd55ee62aa238f3257b597eaf96f2081d039eaf4a02d5050f131 | MATLAB | 3,169 | 82 | %% get_set_bfr_lbv(h,mode,input)
%
% Input
% --------------
% h : structure contains all handles of SEPIA
% mode : 'set' - extract information from GUI to config file
% 'get' - extract information from config file to GUI
% input : if mode is 'set' then input should be fid
% ... |
5359ea9eeb4dc8c85c3465cf6ef7ad8c769f839f027734b268e2b37018cb76be | MATLAB | 3,170 | 104 | % EEG_EMPTYSET - Initialize an EEG dataset structure with default values.
%
% Usage:
% >> EEG = EEG_EMPTYSET;
%
% Outputs:
% EEG - empty dataset structure with default values.
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
%
% See also: EEGLAB
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, arno@sa... |
ad979e43928f61c54024bad028e0b6b0db1766e783a79a29ee9bbba3321f42ae | MATLAB | 3,171 | 87 | function fear_cueTrigTripleAct_optMeanShift(basename,varargin)
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
param.binSize=0.02;
param.halfWindow=5;
param.varName='cueTrigCoactChamber';
param.saveFile=[basicMetaData.AnalysesName '-cueTri... |
51a0c3409759dc3a9a7175a039b4fef129d7e560ef27117bbeb5501bbbfaf108 | MATLAB | 3,172 | 122 | function bandPassMovieChunk(h5Path,bpFilter,varargin)
%% mocoMovies
% SYNTAX
% [mov_corrected,mov_shifted,summary]=mocoMovies(movie,movie4shifts)
%
% HELP:
% Perform motion correction from the green movie, which contains the best blood vessel contrast
% and applies shifts on the red movie. Requires Normcorre on the... |
60725bae1ca330757e61d28589e512878eeb361ac50c742a70982467a56f8ad0 | MATLAB | 3,173 | 85 | function [sbc, fpe, logdp, np] = ARFIT_arord(R, m, mcor, ne, pmin, pmax)
%ARORD Evaluates criteria for selecting the order of an AR model.
%
% [SBC,FPE]=ARORD(R,m,mcor,ne,pmin,pmax) returns approximate values
% of the order selection criteria SBC and FPE for models of order
% pmin:pmax. The input matrix R is the upp... |
ba5724192ad5f5da0f4c4871882d7b6f0251cfa402855b5a9ac62e1105ddb2ab | MATLAB | 3,173 | 80 | function handleCurrentFigure(fileName, userOptions)
% handleCurrentFigure(fileName, userOptions)
%
% handleCurrentFigure is a function which will, based on the preferences set in
% userOptions, save the current figure as a .pdf, a .ps or a .fig; either
% leaving it open or closing it.
%
% fileName --- The name... |
17fbf927e76feb1b274308da5c54e2bde6cc8845728d4a6f45a70a99a21e00f5 | MATLAB | 3,174 | 75 | function [sc, sf, si, nsel, fsel] = surfing_subsurface(c, f, i, r, n2f)
% Generates a sub-surface with nodes from a surface that are within a
% certain radius (Euclidian distance) from a center node.
%
% [SV, SF, SI, NSEL, FSEL] = SURFING_SUBSURFACE(C, F, I, R[, N2V])
% INPUTS:
% C: 3xN coordinates for N no... |
a0f4f8cb3cb089a3d35a250db4bc822c407e410dac5ac98785278bc1df9d5c20 | MATLAB | 3,174 | 88 | % Main script for laminar projection of SANDI maps onto cortical surfaces
% using FreeSurfer mri_vol2surf with 5% cortical depth increments
%
% Reference:
% Lee H, ..., Huang S, Communications Biology, 2026
%
% Requirements:
% - FreeSurfer installed and configured
% - FreeSurfer recon-all completed
% - Valid FreeSurfe... |
26261ed7a7c60ffd9ab34bb016ff81167d57c36f6891173fe86785d71adff039 | MATLAB | 3,175 | 106 | function FuncHomoConn(NCore)
% path = '/home/NCPL09/Desktop/MRIDATA/ReseachPlan/Autism/analysis_fun/FunImgARWCSF'
% outdir = '/home/NCPL09/Desktop/MRIDATA/ReseachPlan/Autism/analysis_fun/tongji/FHC'
path=uigetdir;
outdir=uigetdir;
sublist = dir (path)
[TMSPath, fileN, extn] = fileparts(which('TMStarget.m')) ;
[mhea... |
76847e068958251b580971e7889b6ccf722811163b6c362c5a47d5775d789093 | MATLAB | 3,175 | 60 | % -Performs re-reference to average potential that is defined as the
% average potential across all the channels INCLUDING the initial
% reference channel which is usually unipolar-in that case, the average
% is calculated as sum(EEG.data,1)/... |
963df3d521f60def9e63f09e2be26a4d0cb3d216fe994bbd2f7551b6841e4194 | MATLAB | 3,175 | 69 | function [HeatMapMatrix, ThresholdMatrix, DeviationsCount] = PlotDeviationMatrix(Subject,ReferenceCohort,FullTitle)
% --- Deviations in azimuth specific RMSErrors between subject and control
% --- group, normalized by the standard deviation of the control group's std
% --- across subjects
RMSE_deviation_lp = (Subject.... |
0afe11e2f0d601f63f38543980184d748c3fcda6825b155c459e9b502b7460c9 | MATLAB | 3,178 | 74 | function ssMerged = mergeStructures( ssDest, ssSource )
% mergeStructures selectively create and update fields in ssDest with those in ssSource, recursively
% Merge tree-like structures in much the same way as files are
% copied to destination folders, overwriting values where they exist.
%
% ... |
b01118cc55975fada6946ce9a922b62939e207a522f2db7f8addb3dcd3521e4e | MATLAB | 3,179 | 77 | function [IDX,C,SUMD,K]=kmeans_opt(X,varargin)
%%% [IDX,C,SUMD,K]=kmeans_opt(X,varargin) returns the output of the k-means
%%% algorithm with the optimal number of clusters, as determined by the ELBOW
%%% method. this function treats NaNs as missing data, and ignores any rows of X that
%%% contain NaNs.
%%%
%%% [IDX]=k... |
0da00680a1c02d3cec3e9688a00076dfeea462a5ae4b7e1dfbc5e8a1f179ec23 | MATLAB | 3,180 | 83 | %% SummarizeSessionData
% load Unit data and summarized into session data
ClassifyUnits;
clearvars -except Unit
%% Load Other Data
BNBResult = load('D:\Data\Lobster\BNB_Result_fullshuffle.mat');
DistanceResultPath = 'D:\Data\Lobster\FineDistanceResult_syncFixed_May';
%% Make into a table
Sessions = table(...
u... |
0ef77996bdf527ca4d0dc0e49300330db773e4ba5b4b2db5049f78cc1cd61da2 | MATLAB | 3,180 | 133 |
%2D inputs
N = 2;
alpha = 1; %leak term
% Parameters
T = 100; % Number of time steps
num_targets = 8; % Number of peripheral targets
radius = 5; % Radius of the movement (distance from center to targets)
center = [0; 0]; % Center location
curve_strength = 0.2; % Strength of the curvature (perpendicular of... |
6b5022276d148dd8d8760b9cf14c92b993d6b17d77cef463546ddb32a20350d0 | MATLAB | 3,180 | 98 | %% Figure 1 main
YOURDATAPATH = '';
%% Panels A-C use mouse 1
mouse = 'cfa17';
session = '200825';
[R, M, config] = loadData(mouse, session, 'R', 'DLC3', YOURDATAPATH);
% Lock data for trajectories
config.preT = -100;
config.postT = 100;
config.tBase = 10;
eventNames = {'liftTimeDLC', 'grabTimeC'};
goodTrials = ~isna... |
8c8766fa143e32d02f091c2830fe5ac0728e4f178a733291f1b066848282e2ba | MATLAB | 3,183 | 67 | function [Es, Ed, delta_s] = pipelineCompareStaticDynamicEnergy(time_series, control_node, window_size)
% Pipeline of Compare static and dynamic control energy
% use staticMiniEnergy.m and dynamicMiniEnergy to calculate the control
% energy.
% This pipeline include:
% 1. random select the start point and ... |
3f9509f0b6dfa6105c8f7a96140c1ea5c7dea374d1f6029596924f7d843cdefe | MATLAB | 3,184 | 90 | function combinedObject = combine(this, combineHandle, tolerance)
% Combines properties or outputs of methods applied to objectArray data
% into a new object
%
% Y = MrCompare()
% combinedObject = combine(this, combineHandle)
%
% This is a method of class MrCompare.
%
% IN
% combineHandle property of the object... |
69f114cabd106617dd6821f66845f9bd0b57da88273cba7c44f14c5c186025ab | MATLAB | 3,184 | 73 | function p = HT_IndependenceTests(y, theTest)
% HT_IndependenceTests p-value of a hypothesis test of serial independence.
%
% These tests ask whether the temporal ordering of the time series carries
% structure: the null hypothesis is that successive values are independent (no
% serial dependence). Unlike the tests... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.