sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4a7e716846dcb2ce16e817d4b89d20c771b8c7d3b8b497cb59d68945f641f481 | MATLAB | 3,345 | 83 | function [normtrace, baseline, sigma] = normtobaseline3(trace, percentile, window, nsigma)
% Normalize a trace to baseline in two steps:
% 1/ In a defined window, calculate the percentile value to be substracted.
% A large window (but still smaller than the total length of trace) allows
% to remove the slow drift o... |
5f99ccf8c2f70d200f753f2961589a42924c6947d75beabc6f26996008cb9eaf | MATLAB | 3,345 | 88 | function [t, wv] = LoadTT_Intan(fn,records_to_get,record_units)
%LOADTT_INTAN MClust loading engine for Intan data.
% LOADTT_INTAN loads Intan data and fullfils all requirement for
% Neuralynx loading engines (see MClust 3.5 documentation for details on
% MClust loading engines).
%
% Syntax:
% [T, WV] = LOA... |
05a60554d8571ba6277521cfd5475793e92fd99cb6aa68241c56c08e46dfe6c0 | MATLAB | 3,346 | 98 | function [mean_burst_amp,num_bursts,mean_burst_length] = BURST_ANALYSIS_W_SPECGM(bandpass_analysis,threshold_val,ts_data,band_edges,fs)
% Identify burst count and duration, as well as mean burst amplitude
% Input is the hilbert transformed amplitude values, and the amplitude
% threshold value for determining a bur... |
cce56cfa63ecfa5f67a15f244472bc3c9090088fdd4863566f42ef995b97036b | MATLAB | 3,347 | 111 | function x=randht(n, varargin)
% RANDHT generates n observations distributed as some continous heavy-
% tailed distribution. Options are power law, log-normal, stretched
% exponential, power law with cutoff, and exponential. Can specify lower
% cutoff, if desired.
%
% Example:
% x = randht(10000,'powerlaw',... |
c93552cf5c5cdf1e9142ceb251b6e891bf81231b0b753acb8d21e8ae5ff765ae | MATLAB | 3,349 | 74 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% pop_GEDAI plugin
% This EEGlab GUI is used to call the GEDAI denoising function, and select parameters
%
% [Generalized Eigenvalue De-Artifacting Intrument (GEDAI)]
% PolyForm Noncommercial License 1.0.0
% https://polyformproject.org/licenses/... |
66733498b58ec5a00b7acf8c298c7f44ac4f5fe8312c5a88dd93d977c13fd018 | MATLAB | 3,350 | 82 | function [] = fun_video_analysis(date)
% wrapped video_analysis_main into this function
%% single mouse tracking
% load DLC results and make into mat files
% ZZ 2022
% close all
%% select sessions to process
video_dir = 'C:\Data\videos';
proc_dir = 'D:\DeeplabcutProcData\matfiles';
figure_dir = 'D:\Deeplab... |
925d8742173746bbb15f88127c941869d8bbe233d7c096064b66a1a2757378ff | MATLAB | 3,350 | 102 | function MS = createMeshCylindrical2D(varargin)
% MeshStructure = buildMeshCylindrical2D(Nr, Ny, Lr, Ly)
% MeshStructure = buildMeshCylindrical2D(facelocationR, facelocationY)
% builds a uniform 2D mesh on a cylindrical coordinate:
% Nr is the number of cells in r (radial) direction
% Ny is the number of cells in y (ve... |
039481f1acef687a4cbe9e9334c68629c23f0db4cef0810c18f8ab454274f35e | MATLAB | 3,351 | 118 | function fear_detectOFFstates(basename,varargin)
% basename='~/data/Fear/triple/achel180320/achel180320';
%%
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
load([basicMetaData.Basename '.SleepState.states.mat'])
load([basicMetaData.Basenam... |
e1cfde4ab06c9275dd43c1955e981d9763d37d9b76f897e65da74f96d09bf7a9 | MATLAB | 3,351 | 47 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
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 ... |
1b6063e550c700300c194ec33423254c7d3fa6fe9117bf92e236d22526bcd53d | MATLAB | 3,352 | 66 | function [Gait_avg, ERDS, GPM, cycle_cnt, si] = gait_ersp(EEG_block, F_Rest,...
N_freq, f_axis, FWHM,...
gait_event,gait_timeNextHs, gait_event_order, varargin)
%UNTITLED Summary of this function goes here
% Detailed explanation goes here
%v1.2 Nadine Jacobsen, April 2022: added IC option
% add docume... |
d5427881791666d96d76f21221ed08f27e8aae5999518be5742e35d820f6604e | MATLAB | 3,352 | 119 | function plotHalfViolinByX(compiledData, eMeti, eMetl, X, lagIdx, Params, figureHandle)
%HALFVIOLINPLOTBYX Make half-violin by X, where X is either group or DIV
% eMeti : str
% name of the network metric, eg. 'ND'
% eMetl : str
% label of the network metric, eg. 'Node Degree'
% X : str
% ... |
d567d37525872b21b682ddd2a9b02c658baca329896a83f81b4bb638dad89698 | MATLAB | 3,353 | 87 | function w = window_func(name,m,param)
% Design a window for a given window function
%
% In:
% Name : name of the window, can be any of the following:
% 'bartlett' : Bartlett window
% 'barthann' : Bartlett-Hann window
% 'blackman' : Blackman window
% 'blackmanharris' : Blackman-Har... |
3488a2adeab5937e4d7645afc42c1a49f85dca281519410c1538c5ec600ce091 | MATLAB | 3,354 | 140 | function [] = plotNodeCartographyProportions(NetMet, lagval, FN, Params, figFolder, oneFigureHandle)
% Plot proportion of nodes belonging to each node cartography group
% Parameters
% ----------
% NetMet : structure
% lagval : int
% FN :
% Params : structure
% figFolder : path to directory
% absolut... |
11650387360e659b61d982ef659835d9af2abad0cac167746d2c11ae06dbfcf5 | MATLAB | 3,356 | 85 | % DFTFILT - discrete Fourier filter
%
% Usage:
% >> b = dftfilt(n,W,c,k,q)
%
% Inputs:
% n - number of input samples
% W - maximum angular freq. relative to n, 0 < W <= .5
% c - cycles
% k - oversampling
% q - [0;1] 0->fft, 1->c cycles
%
% Authors: Sigurd Enghoff, Arnaud Delorme & Scott Makeig,
% ... |
5d4447de9acdbbf13ead7644f4c05ee334898f7633d3b4fd1476cef04afd17cf | MATLAB | 3,356 | 65 | % extract eye positions for all animals, all sessions and all scans
% build a map, an element of the map represents the number of eye positions
% within a circle centered at the element
function BuildEyePositionClusterMap(radius)
% get lookup table to assign circle membership to eye positions
rv = preprocess.CirclesLo... |
e40b6e95d4de8127cd720cf71872a6f1cbe03acdffe62e208eafd644d6b4670d | MATLAB | 3,356 | 87 | function out = MD_Porta(x,numLevels)
% MD_Porta Porta's symbolic-dynamics word-type indices.
%
% Quantizes the time series into a small number of levels and classifies
% consecutive length-3 "words" of symbols by their pattern of variation:
% 0V -- no variation (all three symbols equal)
% 1V -- one variati... |
7b849dd7f67772ee78946f7813561cd6714ec717894cbb7e4f26f3a35d0dedc1 | MATLAB | 3,357 | 127 | classdef node < handle
% NODE Helper class for circularGraph. Not intended for direct user manipulation.
%%
% Copyright 2016 The MathWorks, Inc.
properties (Access = public)
Label = ''; % String
Connection = line(0,0); % Array of lines
Position; % [x,y] coordinates
Co... |
9d5f93fb8822440b5f97ec9cff9e14b48d9cee67bc1e9e3e2b24b7a64bbd6404 | MATLAB | 3,357 | 106 | 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 rbag patterns
K = 3;
cen_dir = 'C:\Users\lihon\Desktop\abcd... |
f9184e51eb6c832bc19c3c6d85c1410e1c7d531dde7f6160ac166b6eaf89a125 | MATLAB | 3,359 | 82 | function calcProjMatContrastsSubj_forPalm_Shirley(matFname, analysis_name , n_sub)
% save single subject contrusts of Tim's PCA projections analysis
spm_path = '/data/holly-host/smark/spm';
data_path = '/data/holly-host/smark/fmri_sub_preproc_dir';
addpath(genpath(spm_path));
util_path = fullfile(data_path,'alon_util')... |
717722ff72ce0fb3cece602ad0a9ad053a26f96e224204155d5bbc5c24fd619c | MATLAB | 3,360 | 97 | % bids_importjson - Import json file following BIDS key-based inheritance rule
% (https://bids-specification.readthedocs.io/en/stable/common-principles.html#the-inheritance-principle)
%
% Usage:
% curjsondata = bids_importjson(curFile, ext)
%
% Inputs:
% curFile - [string] full path to the cu... |
ec143d4cbd65786b8cbe472565f67488a464bea45a44af77d9c9b7d18736fa1b | MATLAB | 3,360 | 61 | function [deconv_sta_traces,noisy_sta_traces,speed_sta_traces,dist_sta_traces, sp_sta_traces,rawdeconv_sta_traces, deconv_baseline_mean,noisy_baseline_mean,raw_sta_traces] = get_var_df_stas(full_deconv_traces,full_noisy_traces,full_speed_trace,full_dist_trace,...
photo_test_frames,this_pre_frames,this_post_frames,... |
410940a77a8c325e3aaf82c7cbb1db66289f94608649ca4c684aba7b80d0bb3b | MATLAB | 3,361 | 60 | function osp_pop_corrOvQuant_Call(src,~,gui)
%% osp_pop_corrOvQuant_Call
% This function is triggered when the correlation quantification popup menu is changed. It refreshes
% the figure.
%
%
% USAGE:
% osp_pop_corrOvQuant_Call(src,~,gui);
%
% INPUT: src = handle of the fit tabs
% gui ... |
aa434a3662eec7edb53ead07fb8961e8df6da1bfec80d5788f8df140499bb0b1 | MATLAB | 3,362 | 111 | function fear_deltaTrigLFP(basename,varargin)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
load([basicMetaData.Basename '.pfcSlowWave.new.events.mat'])
load([basicMetaD... |
d37dd9f3f754b22d390c4ec3a5968813fe9dfe3bd8534dabed6857833aee9692 | MATLAB | 3,363 | 133 | % parse up the beliefs into a 2d discrete distribution, but from raw matlab
% file
function [output] = decode_parsedata_rawdat(fname,varargin)
% parse up the beliefs into a 2d discrete distribution, but from raw matlab
% file. a general form of dSTR_decode_parsedata that uses Maggie's curated
% dSTR data. does beleifs... |
fd994300ac0b923c2de0e0984e6e0ad5a9497f7f5adc9cd12fe888333d77f776 | MATLAB | 3,363 | 95 |
function [] = run_decoding_mlb_shuffle(dataname, savename, shuff_idx)
% for each shuffle, run code to decode
rng(shuff_idx) % which shuffle to do
%location of analysis codebase
codepath = '~/projects/constantinoplelab/Analysis/';
% add code paths
addpath(genpath(codepath))
addpath(gen... |
1b1eb10479e037dc8db6eb01ea7b5d1e6169804bc090f7adabab3aaf537f6780 | MATLAB | 3,364 | 113 | % RUNPCA - perform principal component analysis (PCA) using singular value
% decomposition (SVD) using Matlab SVD or SVDS
% >> inv(eigvec)*data = pc;
% Usage:
% >> [pc,eigvec,sv] = runpca(data);
% >> [pc,eigvec,sv] = runpca(data,num,norm)
%
% Inputs:
% data - input data ma... |
0dc11ee1dabd76269691ced6806fcfae47b6c9d5a2d54c262c55b700dd354f79 | MATLAB | 3,366 | 84 | function varargout = hlp_scope(assignments, f, varargin)
% Execute a function within a dynamic scope of values assigned to symbols.
% Results... = hlp_scope(Assignments, Function, Arguments...)
%
% This is the only completely reliable way in MATLAB to ensure that symbols that should be assigned
% while a function is ru... |
055d5050b693b2bee987ac11bc9bc27a347f7400dab8e3b192a5c17361dda67c | MATLAB | 3,367 | 76 | function [tsTime,masterTime,masterIDs] = TS_TotalCalcTime(whatData)
% TS_TotalCalcTime Total calculation time per time series, counting each master
% operation once.
%
% TS_CalcTime stores, for every operation (feature), the time taken to evaluate
% its *master* operation -- so all operations drawi... |
7b15fc5f2f98aee933a3c232f61532aa2b5a8825bef73d8af9e40eed232ed71c | MATLAB | 3,367 | 96 | function MS = createMeshCylindrical3D(varargin)
% MeshStructure = createMesh3D(Nr, Ntheta, Nz, Radius, theta, height)
% MeshStructure = createMesh3D(facelocationR, facelocationTheta, facelocationPhy)
% builds a uniform 3D mesh:
% Nx is the number of cells in x (horizontal) direction
% Ny is the number of cells in y (ve... |
34044dd4ef1a6a49be6bf876763c07039e54f7c432b5ec2ac811194a840b3596 | MATLAB | 3,368 | 88 | function data = removeLinesMovingWindow(data, lineNoise)
% Removes significant sine waves from (continuous) data using overlapping windows.
%
% Usage:
% data = removeLinesMovingWindow(data, lineNoise)
%
% Parameters
% data data in [N,1] (a single time column vector)
% lineNoise structure with va... |
38e2c0b896139eb89363937b1c3ca549008cc5f1b3efd87e935c967c0d6eeed7 | MATLAB | 3,368 | 101 | function [np_data] = np_readdata (filename, np_info, idx_begin, data_length, option)
%
% function [np_data] = np_readdata (filename, idx_begin, data_length, option)
%
% np_readdata reads data from a NEURO PRAX data file (*.EEG).
%
%
% Syntax:
%
% [np_data] = np_readdata(filename,idx_begin,data_length,'samples');
% ... |
1656cd10b0f1bfeebd6b130c257bf2ebf9b031e8cd27a8b14ab5786bf94d290a | MATLAB | 3,369 | 103 | % pop_firma() - Filter data using moving average FIR filter
%
% Usage:
% >> [EEG, com] = pop_firma(EEG); % pop-up window mode
% >> [EEG, com] = pop_firma(EEG, 'forder', order);
%
% Inputs:
% EEG - EEGLAB EEG structure
% 'forder' - scalar filter order. Mandatory even
%
% Outputs:
% EEG - filtered ... |
7bff15bd2d57437fabf92735977819c1e57f12da0f67e544c878badd6936a8cf | MATLAB | 3,369 | 93 | % SUBSREF - index eegdata class
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Nov. 2008
% Copyright (C) 2008 Arnaud Delorme, SCCN, INC, UCSD
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribution and use in source and binary forms, with or without
% modificati... |
f45184c3ab8f978e0f0234f3d082826edb1d2cdf7197a068cf1a621cad38cc69 | MATLAB | 3,369 | 119 | function [ testResult ] = tapas_ceode_testScript_cmc()
% [ ] = tapas_ceode_testScript_cmc()
%
% THIS IS A SCRIPT SOLELY FOR TESTING THE SPM/TAPAS SETUP. DO NOT CHANGE!
%
% Takes a synthetic dataset (3 population ERP model), and computes the
% predicted response for different integrators and levels of delays. The
% c... |
127d492cf521a8872094ad209e2ad1f07147559618e453d46a64284b83e5e575 | MATLAB | 3,372 | 132 | function [ hFig ] = nmri_schemaball_plot( metric, ref_surf, opt )
%[ hFig ] = nmri_schemaball_plot( metric, ref_surf, opt )
% will generate a schemaball plot from a metric, with some options
% opt.scale = number to scale the metric from -1 to 1, i.e. the maximal
% value. If not provided, will take abs-max... |
d0e105b2e79cd1b8c0dddb88956af71cbb630551ab6d007593347e9d582a2897 | MATLAB | 3,372 | 127 | function phiBC = cellBoundaryCylindrical3D(phi, BC)
% function phiBC = cellBoundary2D(MeshStructure, BC, phi)
% It creates the matrix of coefficient based on the BC structure provided
% by the user. It also generates the right hand side vector of the linear
% system of equations
%
% SYNOPSIS:
% phiBC = cellBoundary2D... |
456265e8ea1be55eb0ce91d2502cb64a221b7ffa119493c9c707527ac7f8fd8a | MATLAB | 3,373 | 84 | %% sepiatest.assert_output_contract(testCase, outputPrefix, suffix, expectations, maskFile)
%
% Description: asserts a set of non-numeric regression properties about
% SEPIA's output for one pipeline run:
% 1. each expected output NIfTI file exists
% 2. its BIDS-Derivatives-style JSON sidecar is present/absent exac... |
edbc827ec4a13474105e8d3ebb8dfdd7da89e29c45dc7ddb1026718f78ac1b43 | MATLAB | 3,373 | 101 | function normalized = NormalizeFields(fields,varargin)
%NormalizeFields - Normalize one or more firing fields in space and rate.
%
% For each field, interpolate space in [0..1] and normalize z values
% (typically, firing rates for place fields). Z values outside the fields
% should be set to zero (see example below... |
f078ffb93559d6d5e1bdd21fdb6bbfd523c34e9f1c232cbfa7e347e2265adc3b | MATLAB | 3,373 | 89 | function [diffObject, isObjectEqual] = diffobj(obj, input_obj, ...
tolerance)
% Sets all values of obj to [] which are the same in input_obj; i.e. keeps only the distinct differences in obj
%
% Y = MrCopyData()
% [diffObject, isObjectEqual] = diffobj(obj, input_obj, ...
% tolerance)
%
% This is a method of c... |
1a31f29458ae59f0115d957f90edbf5bb5f67e809ff4a3880af9998457f7f2e0 | MATLAB | 3,374 | 120 | function Z = inormal(varargin)
% Applies a rank-based inverse normal transformation.
%
% Usage: Z = inormal(X)
% inormal(X,c)
% inormal(X,method)
% inormal(X,...,quanti)
%
% Inputs:
% X : Original data. Can be a vector or an array.
% c : Constant to be used in the t... |
4d2e09b4d53e6e1711abc6c83149b138d37a8c0cfea1720ded9bc94ba778e050 | MATLAB | 3,374 | 88 | function angles = GetAngles(varargin)
%GetAngles - Get angles (from position samples).
%
% Angles are returned in radians (in [-pi,pi]). This function requires two
% or more LEDs (only the first two are used).
%
% USAGE
%
% angles = GetAngles(<options>)
%
% <options> optional list of property-value pairs... |
abe4c9427dbd3537463094ee6429715543e5d7dc50a7dc5cb1f81af142c8f6e8 | MATLAB | 3,375 | 100 | % EEG_HEDREMOVEUNICODE - remove unicode characters in HED strings.
%
% Usage:
% >> EEGOUT = eeg_hedremoveunicode(EEGIN);
%
% Input:
% EEGOUT - EEG dataset structure or array of structures
%
% Output:
% EEGOUT - EEG dataset structure or array of structures
%
% Author: Arnaud Delorme, SCCN/INC/UCSD, 2021
% Copyrig... |
fb3924f3cbac02d7ca4f657d8a41541f24ec5d0ae3581007d229f5104cf47c5b | MATLAB | 3,376 | 73 | set_up_paths_and_data_directories;
types = {'category', 'valence_arousal'};
num_types = length(types);
brain_atlas = load_atlas('canlab2018');
region_masks = {fullfile(folder_project, 'masks', 'HC_Julich.nii.gz'),...
fullfile(folder_project, 'masks', 'ERC_Julich.nii.gz'),...
select_atl... |
1d87d984fcbc30d2705cedec2efa6dad0448b60c92fbd25ac1132a120f67ac86 | MATLAB | 3,377 | 101 | % BLOCKAVE - make block average of concatenated data sets of same size
% Each data set is assumed to be of size (chans,frames).
% Usage:
% >> aveout = blockave(data,frames)
% >> aveout = blockave(data,frames,epochs,weights)
% Inputs:
% data = data matrix of size (chans,frame... |
b5cc58429ca7e0a7eed8d93b9a97786f5816fcbe751a6fbd15c06c2492f1557b | MATLAB | 3,377 | 101 | function dimsiz = getdimsiz(data, field, numdim)
% GETDIMSIZ
%
% Use as
% dimsiz = getdimsiz(data, field)
% or
% dimsiz = getdimsiz(data, field, numdim)
%
% MATLAB will not return the size of a field in the data structure that has trailing
% singleton dimensions, since those are automatically squeezed out. With t... |
8999eac61695e7d27c02b71eb59c6aef63a3c8482441ff9dd458fb12c0f32312 | MATLAB | 3,378 | 103 | function DataAnalysis( BASEdir )
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Wrote by David André Barrière 09th September 2022
% This function permit to create and launch non linear normalization
% (DARTEL), spatial smoothing and two sample Student' t-test comparison
% using SPM8 fun... |
7c04da0be6f320bcf9fb980d9f0b1b862392c7a281d714b51c2b20839eec530b | MATLAB | 3,379 | 102 | function plotZETAScores(modScores, thresh)
% Scatter plot containing cells plotted by log(p-value)
thresh = log10(thresh);
% Get logs of p-values for left and right
pval_L = log10(modScores(1,:));
pval_R = log10(modScores(2,:));
% Set NaN values to 0
pval_L(isnan(pval_L)) = 0;
pval_R(isnan(pval_R)) = 0;
pval_L(isinf... |
b4cc6ac52b6267aab9cc0615ee7b1a7cbd1704485e3f6e68a118cc9a8a81d8a0 | MATLAB | 3,380 | 96 | function [M, Mx, My, Mz] = diffusionTerm3D(D)
% This function uses the central difference scheme to discretize a 2D
% diffusion term in the form \grad . (D \grad \phi) where u is a face vactor
% It also returns the x and y parts of the matrix of coefficient.
%
% SYNOPSIS:
%
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:... |
54acd488c0b09ee28f17dd426ec36d33275e2013763cbae51dfd3c3050e57cc8 | MATLAB | 3,382 | 93 | function [theta_x,theta_y,theta_z] = axislabel_rotation_angle(h_a)
% This function computes the proper angles of x, y and z labels in order to
% align them to the direction of their axes.
% It can be used as part of an 'ActionPostCallback', which is a callback
% function of a rotate3d object.
% Each of the output... |
0f310a057c01fb0a4ad78addf63c5a85efe62137bddb31225a2999be6743957b | MATLAB | 3,383 | 95 | function [lfp,indices] = GetLFP(channels,opt)
%GetLFP - Get local field potentials.
%
% Load local field potentials from disk (unlike spikes or positions, LFP data
% is usually too large to keep in memory).
%
% USAGE
%
% [lfp,indices] = GetLFP(channels,<options>)
%
% channels list of channels to load (u... |
d4719c67fdc2563c6deb2d645eb5bd9e385ad0d2dadb4844a15228bc7dfc4647 | MATLAB | 3,384 | 83 | classdef segmentationSPMIntegrationTest < matlab.unittest.TestCase
%SEGMENTATIONSPMINTEGRATIONTEST End-to-end test for petraToCT.segmentationSPM.
%
% DESCRIPTION:
% Runs the SPM unified segmentation plus morphological
% post-processing on the small PETRA fixture, and verifies that
% ... |
0000c67a4d259babae6a7bf73578436ad27708c76d2d7bcd903878cb39fa56b5 | MATLAB | 3,386 | 130 | %RunBatch - Run a batch job. This should *not* be called directly.
%
% Run a batch job. This function is called automatically by the
% batch timer upon expiration of the required delay.
%
% USAGE
%
% RunBatch(timer,event,b)
%
% timer Matlab timer object
% event Matlab timer event type
% b... |
f665180ea10c00d87eefdb4f0b90ccd27099c3eb26a713111bc293e32bff7128 | MATLAB | 3,386 | 73 | function [imageSpm4DArray, selectionArray] = split_into_MrImageSpm4D(this, dimLabelsSpm4D)
% Splits high dimensional MrImage (>4) into array of 4D MrImageSpm4D
% objects to be used for SPM interfacing
%
% Y = MrImage(); % >4 dimensions
% imageSpm4DArray = Y.split_into_MrImageSpm4D(inputs)
%
% This is a method of cl... |
e1642d596c910cbd77bf9dd7ef51150d1be7297e19f364837fd6ab7f6c7ffd93 | MATLAB | 3,392 | 80 | % COMPVAR - project selected components and compute the variance of
% the original data they account for.
%
% Usage:
% >> [proj, variance] = compvar( data, wts_or_act, winv, components);
%
% Required Inputs:
% data - 2-D (channels, points) or 3-D (channels, frames, trials)
% data ... |
e817bb1e3ccdac04c4c88a39cd4e33704c953b2dbdd115c7751b962e04bddc83 | MATLAB | 3,392 | 98 | function [FIT3D,Residuals,b]=PolyFit_weights(Data3D,Mask,order,weights);
dim=size(Data3D);
%% for volume fitting
Indices = find(Mask(:,:,:));
[x1,y1,z1]=ind2sub(size(Data3D(:,:,:)),Indices);
% x1 = cast(x1,'like',Data3D);
% y1 = cast(y1,'like',Data3D);
% z1 = cast(z1,'like',Data3D);
if isempty(weights)... |
c6259ff63e3c7cb2ce18bb89df3665c6a3c5596e5f54f86ddc135337849ff8a3 | MATLAB | 3,394 | 79 | %% Load data
data_path = 'Y:\Alice\0012_NeuroGI\NeuroGI_ephys_data\2024-11_all_ex-vivo_experiments\20241115_ExVivo-09\';
load([data_path 'datafile0018.mat'], 'data')
%% Preprocess data
reorder = (1:32:128)' + (0:31);
reorder = reorder(:);
y = resample(double(data),200,2000);
y = highpass(y, 10, 200);
... |
e608dadb4e31dc59e8f7ccc86be4750879031e3b63a7e945d152c6011f2c001c | MATLAB | 3,394 | 110 | function tpl = set(tpl,action,varargin)
%TEMPLATE/SET Edit data stored in a Template object
% TPL = SET(TPL,ACTION,VARARGIN)
% ACTION 'root'
% ACTION 'unknowns'
% ACTION 'file'
% ACTION 'block'
% ACTION 'var'
% Copyright (C) 2003 Guillaume Flandin <Guillaume@artefact.tk>
% $Revision: 1.0 $Date: ... |
6a6fd072913c5d35dfae39ef339d7e4a544333e12b8d383e02d6f56fa622a53a | MATLAB | 3,395 | 123 | function df = cent_diff_n(f,h,n)
% df = cent_diff_n(f,h,n)
% Computes an n-point central difference of function f with spacing h.
% Returns a vector df of same size as f.
% Input f must be a vector with evenly spaced points.
% Input n must be 3,5,7, or 9.
% All three inputs are required.
%
% Differences for points near... |
cee4655a9abda3eac6f044060337e33e1f6b1c561b1be08b17bc5fa5f8d5a5ef | MATLAB | 3,395 | 104 | % INPUTDLG2 - inputdlg function clone with coloring and help for
% EEGLAB.
%
% Usage:
% >> Answer = inputdlg2(Prompt,Title,LineNo,DefAns,funcname);
%
% Inputs:
% Same as inputdlg. Using the optional additional funcname parameter
% the function will create a help button. The help message will be
%... |
e3dc28639024244ae340b5360c5e02d67e6605509ad16cd41eee4e8cb6ebc0d0 | MATLAB | 3,395 | 109 | function fear_pfcRipTrigIcaReac(basename,varargin)
% basename='~/data/Fear/triple/achel180320/achel180320';
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
load([basename '.basicMetaData.mat']);
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
%%
param.tWindo... |
6b3995203e92331a967afcfeaf5069d36b36a63aa4f2a95957e604219876b304 | MATLAB | 3,396 | 88 | function task_sPCA_sensor_condTogether(sii, PATH, cfg)
% perform spectral PCA à la Seeber
% - sii: vector of subject IDs to be processed
% - PATH: structure with all paths leading to diff processing steps
% generated in naj_neurCorGait_paths
% - cfg: structure with all processing variables generated in naj_ne... |
7a7aab3c079b600db3c83b4bec303e78c10c96a0933ced47ddba625bd4bdbdbc | MATLAB | 3,397 | 106 | function [t_incongruent, t_congruent] = findIncongruentTrials_Vio(S)
%Finds the index for the first REWARDED incongruent trial in a mix block
%and the most recent rewarded trial congruent with the adaptation block.
%input:
% S: S struct of neuropixels data
%output:
% t_incongruent:
% ltom: low to mi... |
4de59a8f3a71bc0aeae4425358d7fbae3f4833f9d879a22f30a7fd5ed2ca9ed9 | MATLAB | 3,400 | 66 | function [n, nfinal, neutZone]= quant_specific_co2(plotxvals, CportStdLoc)
%% quant_specific_co2
% includes additional analyses specific for for single-worm CO2 tracking assays
% that are done using a CO2 gradient.
%
% Currently, calculating number of worms that end in scoring regions, as
% well as time spen... |
c3bd541e0787a07bb692fd8b263cc30bdddc4eba944558aea5e0cad4a8a26a99 | MATLAB | 3,400 | 85 | %{
# RF map.
-> tune.DotRF
-> fuse.ScanSetUnit
---
response_map : blob # average response for each location
center_x : float # (fraction of x) center of receptive field on x, from Gaussian fits
center_y : float # (fraction of x) center of receptive field on y, from Gaussi... |
7cd9d6cd765661c237a671334f0c1c8febfe29d86ca3479a1961a9b7afb4797b | MATLAB | 3,402 | 101 | function varargout = preprocNonLinearOut(S, params)
% Usage: [Spreproc,params] = preprocNonLinearOut(S, params)
%
% Output nonlinearity on each channel of a model. Generally done BEFORE
% (zscore or other) normalization.
%
% Inputs:
% S : Stimulus or PreprocessedStimulus (STRFlab classes), or simple
% numeric... |
cecb42fecf97a69f6d537122232f6f90c3973061b2b79765cfd2199da3615c0f | MATLAB | 3,403 | 107 | function result = modvalidity(result,data,param)
%modified validation function for clustering, it calculates all the
%validity measures, so param.val is not needed
N = size(result.data.f,1);
c = size(result.cluster.v,1);
n = size(result.cluster.v,2);
v = result.cluster.v;
if exist('param.m')==1, m = param.m;else m = ... |
e21fdf591042de7aefa4748046f5a11add0b03b52fe5dbfc8903aabd717ea7e1 | MATLAB | 3,403 | 91 | %% Setup
do_followup_viz = true;
% To run this demo, you will need a stack of movie frames stored as a 4D
% (X x Y x Color x Time) array.
% If you have your own stimuli, you will need to modify this variable:
fname = 'nishimoto_2011_val_1min_uint8.mat';
% add relevant paths
if ~exist('preprocColorSpace_GetMetaParams'... |
1073c3a3d321445798e00e159a1bba92b60af94a06482d3a4466b8803e13f9b8 | MATLAB | 3,405 | 96 | function this = compute_stats(this)
% Compute statistical values for ROI per slice and in total volume
%
% Y = MrRoi()
% Y.compute_stats()
%
% This is a method of class MrRoi.
%
% IN
%
% OUT
%
% EXAMPLE
% compute_stats
%
% See also MrRoi
% Author: Saskia Klein & Lars Kasper
% Created: 2014-07-18
% Copyright... |
4358d999c23872bb9b4406044a871400e827f23b4f5eaa822dd21bdb5c8e69a7 | MATLAB | 3,405 | 126 | function [ data , regional_labels] = nmri_regional_timecourse( data, ref_surf, opt)
%[ regional_metrics ] = nmri_regional_values( full_metrics, ref_surf, opt )
% Will resample a full brain e.g. SUMA surface (1 value/vertex) metric
% into a regional metric (1 value / region)
% the regional information will be take... |
8de2c81b3622c92ad7042adb2035e04b882961bb67d3896d69511a8fb2f5cd22 | MATLAB | 3,405 | 106 | function [A] = spm_matrix(P, order)
% Return an affine transformation matrix
% FORMAT [A] = spm_matrix(P [,order])
% P(1) - x translation
% P(2) - y translation
% P(3) - z translation
% P(4) - x rotation about - {pitch} (radians)
% P(5) - y rotation about - {roll} (radians)
% P(6) - z rotation about - {yaw} (r... |
b11107b815d7750e0ce0eb7c90c776e01fdadd652446cd8d5329f084ac499dd2 | MATLAB | 3,405 | 86 | function download_HEIDI_toolbox()
% One-time setup: check whether the HEIDI_SEPIAready package is available;
% if not, download it into SEPIA_HOME/external/ and register its path in
% SpecifyToolboxesDirectory.m.
%
% This script only runs when you call it explicitly - it is not invoked
% automatically by sepia_addpath,... |
37702950c6f92251a67022396a7a290cce768fdea79e5bbbf9a87d8e8d420f5b | MATLAB | 3,406 | 98 | % Script demo_model_estimation_1st_level
% 1st level model specification and estimation
%
% demo_model_estimation_1st_level
%
%
% See also
% Author: Saskia Bollmann & Lars Kasper
% Created: 2018-05-04
% Copyright (C) 2018 Institute for Biomedical Engineering
% University of Zurich and ETH Zuri... |
81a9e1b2a871ca8d73424c18832fb8b78b35817feda59d1386f5a839a44446c8 | MATLAB | 3,409 | 134 | function figure4()
% Create public-facing Figure 4 panels.
%
% Inputs:
% 1. Thresholded No > Yes statistical map
% 2. Joined ROI/questionnaire CSV produced by roi_statistics.m
%
% Edit USER SETTINGS, then run:
% figure4
%% USER SETTINGS
spmDir = 'C:\path\to\spm';
noGreaterThanYesMap = [ ...
'D:\path\to\seco... |
8679f1cd75a245098ca8d2de37de67e7ed5952e3e0966af53afd90febe8af446 | MATLAB | 3,409 | 117 | function [indices,mask] = findcells(data,categories,active,pSI,pPF,combination,region)
% Options:
% old version (fast, no removal of highly correlated cells/boutons) = [indices,mask]
% new version (slow, with removal of highly correlated cells/boutons) = [indices_new,mask]
% Get indices of cells in a dataset tha... |
bae6e2e2c42ce3fa652dfe4d21710d44913b9f89ed2d8d8b5343e6aade7b1461 | MATLAB | 3,411 | 71 | function rhoBest = findCARArhoInSearchSpace(riskyHigh,riskyLow,EVsafe,ChooseRisky,rhoToTest,plotFlag)
%
% function rhoBest = findCARArhoInSearchSpace(riskyHigh,riskyLow,EVsafe,ChooseRisky,rhoToTest);
%
% This function finds the value of the risk aversion parameter rho that,
% under the CARA model, best fits the observe... |
0ab5c8413d442815b470b97265e2cbc4dd86a6aab08c51417cd3dbed9cc4adde | MATLAB | 3,412 | 128 | function [Y,Nsum] = moveavg(X,F,DIM)
%MOVING_AVERAGE Smooths a vector through the moving average method.
%
% Syntax:
% [Y,Nsum] = moving_average(X,F,DIM);
%
% Input:
% X - Vector or matrix of finite elements.
% F - Window semi-length. A positive scalar (default 0).
% DIM - If DIM=1: s... |
20c233e6d36a7c6f39f6de058d56dab0520472967e1cf7885b0fd0a4e08a9fe8 | MATLAB | 3,412 | 77 | function W = BF_TheilerWindow(y, spec, Nfrac)
% BF_TheilerWindow Resolves a Theiler-window specification to a number of samples.
%
% Neighbor-based methods (recurrence, dimension, Lyapunov, and nonlinear
% prediction estimates, ...) exclude candidate neighbors that are close in
% time to a reference point, since those... |
ae4e53c9daf07a6e4b3a4c1fe965334d29daab239d788615317226833631e9ac | MATLAB | 3,412 | 101 | function plot_fig1c(datadir)
% Plot time to initiate trial by block type for an example rat and all
% rats included in fiber photometry experiment (N = 16).
%
% INPUTS
% datadir: file path of data downloaded from Zenodo. Link to download can
% be found in README.
% load list of photometry rats and example rat
load(ful... |
d518a56de7ccf74e45ff1744bf3bec62f96e4ae6e9591bb7720c7276fe702cba | MATLAB | 3,413 | 109 | function info = mrs_readLcmodelTABLE( fileName )
% MRS_READLCMODELTABLE reads the important metabolites concentration from the
% LCModel output file (.table)
%
% info = mrs_readLcmodelTABLE( fileName )
%
% ARGS :
% fileName = name of LCModel ouput .table file
%
% RETURNS:
% info = information about quantified metabol... |
a1435a3dd4d6f0c2d6d1a646ba2850011d14869f64325f21bbd402ff1aca9e62 | MATLAB | 3,415 | 48 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
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 ... |
86428c99dbccb8af1ffcf75c93bd44d7122255373d60932278068cf0b9a7d748 | MATLAB | 3,417 | 95 | function SU = channelLocation_MD(S,SU)
%% Updates the SU to include the AP, ML, & DV of the electrode.
% Note that this assumes that the electrode goes straight up without changing
% the AP/ML. Because there is definitely some angle associated with implants,
% I widened the range of acceptable values for the LO from w... |
814dfc01948bc22225877f9a5a78a14c7e24e17c09816ac17eec8d0e7c03a78f | MATLAB | 3,418 | 100 | function [refShift, refFWHM] = fit_OspreyReferencingMM(dataToFit)
%% [refShift, refFWHM] = fit_OspreyReferencingMM(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... |
ab6cc0c84a423465dc4a4e64554a89062c9b56951ccaff691f358a467d02eee1 | MATLAB | 3,418 | 113 | function plot2ptraces(suite2pFolder, Params, fileName, fs, figFolder, oneFigureHandle)
%PLOT2PTRACES Summary of this function goes here
% Detailed explanation goes here
%% Set up figure
p = [50 100 700 550];
if Params.showOneFig
if isgraphics(oneFigureHandle)
set(oneFigureHandle, 'OuterPosition', p);
... |
bebffab0380a621c110e71bb51644b49d12d960b4e993a4924560421b0e2e700 | MATLAB | 3,419 | 81 | function [ensmat_in,enscells_in,raster,frates] = MakeEnsembles_fix_rate(ncells,fr,T,nens,ncellsperens,ntimesperens)
% Reference paper: Herzog et al. 2020 "Scalable and accurate automated method
% for neuronal ensemble detection in spiking neural networks"
% https://www.biorxiv.org/content/10.1101/2020.10.12.335901v1
... |
b425cd54c9aade2396bc1d99e471ef78fa8d810b078f80be88297b1403e65673 | MATLAB | 3,420 | 104 | function [pE, pC, x] = tapas_rdcm_spm_dcm_fmri_priors(A, B, C, D)
% Returns the priors for a two-state DCM for fMRI.
% FORMAT:[pE,pC,x] = spm_dcm_fmri_priors(A,B,C,D,options)
%
% options.two_state: (0 or 1) one or two states per region
% options.endogenous: (0 or 1) exogenous or endogenous fluctuations
%
% INPUT:
... |
bf62052e49a0c493c3b8db17ae648d6c52a253f35d48744e20c58a9d66e2047a | MATLAB | 3,420 | 107 | function linidxsrs=surfing_coords2linvoxelidxs(coords,voldef,dim,mask)
% maps coordinates to linear voxel indices
%
% I=SURFING_COORDS2VOXELIDXS(C,VOLDEF)
% INPUTS:
% C: A 3xN matrix or 3xPxQ array with (x,y,z) coordinates
% VOLDEF: Struct with fields .mat (4x4 voxel to coordinate transformation matrix
% ... |
ffffc9b5454fea32c06b99d21e1ae8841d6b86426150a69d6edcaab350bb505d | MATLAB | 3,420 | 101 | % fit_selectMetabs.m
% Georg Oeltzschner, Johns Hopkins University 2019.
%
% USAGE:
% basisSetOut = fit_selectMetabs(basisSetIn, metabList, fitMM)
%
% DESCRIPTION:
% This function loads the basis set functions for the metabolites
% that have a positive flag set in the structure metabList, which has
% previously been c... |
c15719615d349d93ccf717c90764eb575aebf6488f19c69f1a8a3648f11a2c0b | MATLAB | 3,421 | 111 | function [e, p, A, B] = PN_sampenc(y,M,r,justM)
% PN_sampenc Sample Entropy
%
%---INPUTS:
%
% y input time-series data
% M maximum template length (embedding dimension)
% r matching tolerance level
%
%---OUTPUTS
%
% e sample entropy estimates for m=0,1,...,M-1
% p probabilities
% A number of matches for m=1,...,M
% ... |
e92ae013ca3f49f7a9c4ad2b4119002c3c28f5537ef7e98d8b2b4b487209a1c7 | MATLAB | 3,422 | 109 | function Behavior_Only_Plots(ProcDataIT1_Rep,ProcDataIT2_Rep,ProcDataHC1_Rep, ProcDataHC2_Rep,ProcDataIT1_Lure,ProcDataIT2_Lure,ProcDataHC1_Lure, ProcDataHC2_Lure)
%% Behavior_Only_Plots
%{
This Code takes in the procdata files and extracts only the behavioral data
in order to generate a mean plot of monkey performanc... |
c1992ac1d84e9c7f4288877360d4e36d8a7f2ae8e5fa9a26fc9624f91ce380eb | MATLAB | 3,423 | 94 | function isObjectEqual = isequal(obj, input_obj, ...
tolerance)
% Sets all values of obj to [] which are the same in input_obj; i.e. keeps only the distinct differences in obj
%
% Y = MrCopyData()
% [diffObject, isObjectEqual] = isequal(obj, input_obj, ...
% tolerance)
%
% This is a method of class MrCopyDat... |
57bcedb1941dca44345870ac032a8a516be3e30ffc3d800e469c620be0c8fc3e | MATLAB | 3,426 | 100 | function [h,U2] = WatsonU2Test(group1,group2,alpha)
%WatsonU2Test - Test if two samples (circular data) have different means / variances.
%
% This non-parametric test assumes the data comes from a continuous distribution.
%
% USAGE
%
% [h,U2] = WatsonU2Test(group1,group2,alpha)
%
% group1 angles in rad... |
13ce5f63a744b235503a87a22e74e8201e5f0ad785f3eef82693b103aa5cf8e2 | MATLAB | 3,427 | 130 | function [WTOpt, WTMdl, BlkInf, Belief, Prior, Kappa] =...
GenerateSynthData_Bayes_priorUpdate(params, ratTrial,...
noise_arg, gen_arg, noise_params, updateParam)
%GenerateSynthData_Bayes - generates synthetic wait times
%for optimal Bayes model.
% Inputs:
% params - Parameter vector. [kappa_mi, kappa_hi, kap... |
9f67083cc6e5222feb675846f025fccf3f1b255539680bddda87f0e661630e89 | MATLAB | 3,427 | 95 | function niiv = niftiNi2Vista(nii)
%
% Transforms a NIFTI-1 structure to an old VISTASOFT nifti-1 structure.
%
% niiv = niftiNi2Vista(nii)
%
% INPUT
% nii - nifti-1 structure
%
% OUTPUTS:
% niiv - OLD VISTASOFT nifti-1 structure
%
% Web Resources:
% mrvBrowseSVN('niftiNi2Vista')
%
% Example:
% nii = make_nii(on... |
e539bccad57fbbc025d154a1ca9b6fb9d9c02e6198c7aca030931415285e743f | MATLAB | 3,428 | 93 | function [nidxs,vidxs]=surfing_randomsubspace_select(c1,c2,voldef,nodeidxs,roisize,itercount,linedef,progressstep)
% selects voxels and nodes randomly from the surface, for a fixed number
% of voxels
%
% [NIDXS,VIDXS]=SURFING_RANDOMSUBSPACE_SELECT(C1,C2,VOLDEF,NODEIDXS,ROISIZE,ITERCOUNT,LINEDEF]
%
% INPUTS:
% C1,C2 ... |
5deb80558465bb4873f5c62c170d819a3e10c323b0ddda94fed447881488b425 | MATLAB | 3,429 | 105 | function [fh, prop, MyColors] = tapas_physio_get_default_fig_params(...
verbose, convfac, xscale, yscale)
% set and return General settings for plots
%
% IN
% visibility 'on'/'off'; sets figure visibility when created
% convfac conversion factor (1...Inf) to scale size of text and
% ... |
e6dfc0b5cfb16f63884a4399777ad239cd9375326db2cf699a5014ba2bc5daf6 | MATLAB | 3,433 | 99 | function [pdd, pddnode, meanpdd] = dyn_pdd(data,sample,mindur,meanfreq)
% Computes the phase difference derivative (PDD) without pairwise
% leakage correction/pairwise orthogonalisation
%
% Tewarie et al., 2019 Tracking dynamic brain networks using high temporal
% resolution MEG measures of f... |
4ec5e973fc44f8636caaa869b40cefb639f203fe314d1e1042b4cfb065727cd1 | MATLAB | 3,434 | 87 | function out = CO_FirstCrossing(y, corrFun, threshold, whatOut)
% CO_FirstCrossing The first crossing of a given autocorrelation across a given threshold
%
% ---INPUTS:
%
% y, the input time series
% corrFun, the self-correlation function to measure:
% (i) 'ac': normal linear autocorrelation function. Uses CO_... |
a5c5c7483867ad2e521c014c4ed6f16d60f2b038b99a7dc6ceb2d4f741fe3f40 | MATLAB | 3,434 | 116 | function this = MrDataNd_split_epoch(this)
%Tests split_epoch by creating artificial trials for fmri_short example
%
% Y = MrUnitTest()
% run(Y, 'MrDataNd_split_epoch');
%
% This is a method of class MrUnitTest.
%
% IN
%
% OUT
%
% EXAMPLE
% MrDataNd_split_epoch
%
% See also MrUnitTest
% Author: Lars Kasper
... |
c93bc4878c018d59dbef501845c18c66021453865110d07de1edc3b333fd9f1a | MATLAB | 3,434 | 48 | matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
matlabbatch{1}.spm.tools.physio.write_bids.bids_step = 4;
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 ... |
0d25f8686580251dfac77db7bc9d8450b0ba0f0ac5da79eb9e2959b46e1c1ae2 | MATLAB | 3,437 | 81 | function [xk,crlbs] = createModelIVIM(data,parameter)
%% [xk,crlbs] = createModelIVIM(data,ModelFunction,parameter)
% This is the heart and soul of the optimization. This function takes
% the data, model function, and parametrization and translates them into
% appropriate loss and gradient functions
%
% USAGE:... |
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