sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ff3cec7dfe10a9f8558edc52818dba49018db1416b80e0c193b29cfe5f5a617a | MATLAB | 2,615 | 82 | classdef debiasIntegrationTest < matlab.unittest.TestCase
%DEBIASINTEGRATIONTEST End-to-end test for petraToCT.debias.
%
% DESCRIPTION:
% Runs N4ITK bias correction (via 3D Slicer) on the small PETRA
% fixture and checks that an output NIfTI is written with
% sensible properties. Fil... |
57afe17d2acdd62f0c6c0eeacebb52a43762b9f99009d95a33f982d344822d23 | MATLAB | 2,616 | 101 | function [logp, yhat, res] = tapas_softmax_wld(r, infStates, ptrans)
% Calculates the log-probability of responses under the softmax model
% with phasic volatility exp(mu3) as the decision temperature and parameters
% accounting for win- and loss-distortion of state values.
%
% -----------------------------------------... |
8ebc6f3259f6975a3f55486a52330002ed4df11547e3d139418caed11523938f | MATLAB | 2,616 | 92 | function [cellofMats, uIdents] = repackData (identifiers, data)
%cellofMats = repackData (identifiers, dataCel)
%e.g. repackData (fbmm.szGenotype, fbmm.hist)
%takes a datastructure like fbmm, and repackages a data cell from one field
%into a nan-padded matrix held inside a cell, one for each identifier type.
% Reworke... |
3435eda7a544ee9a90f0442cfae1bce8999c8431706a1268fc5b156465ee9b47 | MATLAB | 2,617 | 99 | function [nbc, data, group_data] = Meta_NBC(MC_Setup, terms, test_images)
% [nbc, data, group_data] = Meta_NBC(MC_Setup, terms, test_images)
%
% You will need:
% Inputs: a folder of text files with term labels
%
% MC_Setup = a database saved from an MKDA meta-analysis
% terms = {'pain', 'working.memory', 'emotion'};
% ... |
ac39769977048915b31f8c40514f27f7f7a19fea5fe38429a5cb3b99bb823b04 | MATLAB | 2,617 | 68 | function [results100]=wavesAnalyzerAllFreqs(output)
nSbj=16;
for ss=1:nSbj
ss
data=load(['\sbj' num2str(ss) 'rawWaves.mat']);
if output(ss).data(1).leftRightFlag(1)==1
leftBlocks=1:2:10;
rightBlocks=2:2:10;
elseif output(ss).data(1).l... |
c813ae9d150e99e53d368f33756e1a13bec8e4279a1b54f2eace8b2067f4a453 | MATLAB | 2,617 | 86 | function status = IsInZone(positions,zone)
%IsInZone - Test when the animal is in a given zone.
%
% Test when the animal is in a given zone of the experimental setup (typically the
% firing field of a place cell).
%
% USAGE
%
% status = IsInZone(positions,zone)
%
% positions position <a href="matlab:help s... |
2ff9427276009f985472d8bed270be540db61a8e7a99507279d88612055ee81e | MATLAB | 2,618 | 68 | function fear_coactPartner(basename)
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
% load([basicMetaData.AnalysesName '-instReacZNCCG_sig.mat'])
load([basicMetaData.AnalysesName '-icaReacZNCCG_sig.mat'])
%%
for reacType=1%0:1
if re... |
0427c7e68f148f71d850111fbbf1a6df22b5c7ee2fc9fd6c187472c469837191 | MATLAB | 2,619 | 78 | function mra = modwtmra_custom(wpt, wavelet_type)
%(Inverse Stationary Wavelet Transform)
%
% Usage:
% mra = modwtmra_custom(wpt, wavelet_type)
%
% Inputs:
% wpt - (Bands x Samples x Channels) matrix
% Order: [W1, ..., WJ, VJ]
% wavelet_type - 'haar'
%
% Output:
% mra - (B... |
609516f4d1b50f6656c8dbb4056d9f1ab89b9f82760e16c3935b321072ee3caf | MATLAB | 2,619 | 64 | function [K,dK] = covSum(cov, hyp, x, z)
% covSum - compose a covariance function as the sum 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 = {cov1, cov2, ..... |
ea6916bb83acba775830dd04a372ae6adda5803244d1a8a3e14b25e9ea2a3f08 | MATLAB | 2,619 | 75 | function fear_tripleCCG_beh(basename)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
% 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.Ana... |
1ac4b2d974283c262aed8b57e3c0e1a4f637f20a0796547b2eff50a66a69a875 | MATLAB | 2,620 | 69 | function [SpikePhase,PhaseMean,MeanLength,Z,PVal,PhaseLock] = LFP_OffsetPhaseLock(LFPData,SpikeLoc,f1,f2,Fs,MaxLag,StepSize)
%% Calculate LFP phase in one frequency band for the spikes with a range of temporal offsets
%
% Inputs
% LFPData -- local field potential data for a single channel
% SpikeLoc ... |
95adaab8103f6866d31c3e157add698c1aa559b1621cbfb04e5ca5df77c85de2 | MATLAB | 2,620 | 67 | function x = spatialPattern(DIM,BETA)
% function x = spatialPattern(DIM, BETA),
%
% This function generates 1/f spatial noise, with a normal error
% distribution (the grid must be at least 10x10 for the errors to be normal).
% 1/f noise is scale invariant, there is no spatial scale for which the
% variance plateaus ... |
95dfc61a758b72db0a2f5a4aeae3e7a4761607d44da48ab0443b9e473214bb7e | MATLAB | 2,620 | 96 | function [exp_avg,exp_avg_null,z]=do_homogeneity(x,mskFile,parcelFile,gmFile,MM)
% Input:
% x: fMRI data matrix,dimension: time x number of all gray matter voxels
% mskFile: subcortex atlas in NIFTI (*.nii)
% parcelFile: random parcellation in NIFTI (*.nii)
% MM: number of randomizations
% Output:
% exp_avg: parcellat... |
d19321ab1350746c26fa2af1fc3df930f50a42e19f99237e3b523759c6fb3280 | MATLAB | 2,620 | 67 | % HLP_ARGSTRUCT2LINEARCELL - Linearize configuration output of arg_guipanel
%
% Usage:
% >> cellval = hlp_argstruct2linearcells( cfg );
%
% Inputs:
% cfg - output configuration structure from arg_guipanel
%
% Output:
% cellval - cell array of output values
%
% Author: Arnaud Delorme, SCCN & CERCO, CNRS, 2013-
%... |
0b0d706a3a93aeb74a6012a2b9ccce71552bb493ee3c90f7c07e3cb36d1b3b79 | MATLAB | 2,621 | 90 | %% unitTest.m
% This function performs a command line unit test based on the jobTesting.m file in the
% ci folder. All Osprey modules are tested in dependence of the
% included dataset. You can change the jobTesting.m file according to your desired
% needs. The results unittest class includes detailed informati... |
c9f855571092ab1577b382b742eb50b0be18c4463358e5c7d1c7e9764679f44f | MATLAB | 2,621 | 67 | function out = EN_CID(y)
% EN_CID Simple complexity measure of a time series.
%
% Estimates of 'complexity' of a time series as the stretched-out length of the
% lines resulting from a line-graph of the time series.
%
% cf. Batista, G. E. A. P. A., Keogh, E. J., Tataw, O. M. & de Souza, V. M. A.
% CID: an efficient ... |
ce00139affc56bd7649988ae6fa5b568b3d67313468e21135f5931aef28a8683 | MATLAB | 2,621 | 97 | function [outputs,summary]=template_function(arg1,arg2,varargin)
% One line short description
%
% SYNTAX:
% outputs=templateBFM(arg1) - use 1
% outputs=templateBFM(arg1,arg2) - use 2, etc.
% outputs=templateBFM(arg1,arg2,'option1',option1value,'option2',option2value) - use 2, etc.
%
% INPUTS:
% - arg1 - description
%
%... |
490a1500ca489e94f7512413c279b738655fc12e633c4a371778cdbd7d80cece | MATLAB | 2,622 | 64 | function [ylimit] = plot_cnm_struct(cnm_struct,Fs)
cnm_plot_options = CNMFSetParms;
cnm_plot_options.roi_color = colormaplines;
cnm_plot_options.plot_bck_image = true;
cnm_plot_options.thr_method = 'nrg';
cnm_dims = size(cnm_struct(1).shape);
num_comp = size(cnm_struct,2);
com_fov =... |
54c92154245e4fedcc6d35de09f53afdcd8b584fae5f3d2be1f9e00c7e511d70 | MATLAB | 2,622 | 87 | function dbcluster_point_table(cl)
% function dbcluster_point_table(cl)
% looks for Study or study field in clusters
% determines length, and looks for other fields of the same length
% uses specified fields in a particular order, then other fields
N = fieldnames(cl(1));
% reorder - reverse order, bottom rows are top... |
67b857980f78c64a16faa98f61ddd8c1037e08e4ca63e760992e288ae504da15 | MATLAB | 2,623 | 70 | function [d, d_shuff] = compute_dPrime(SU, alignto, wndw, trialtype1, trialtype2)
% Compute the dscriminability index (d') for trialtype1 versus trialtype 2.
% Shuffled d' is subtracted
% INPUTS:
% SU = struct of spiking info for a single recording session
% alignto = task event ('COFF' = trial start, 'SON' = LED... |
75153f5da5f4e06346429cf6ad08fcb2533d9b226ed3c3d43a7e73a448ce744f | MATLAB | 2,624 | 73 | function PlotExtendedData4(datadir, codedir)
%PlotExtendedData4 - Plots Extended Data 4.
% INPUTS:
% datadir - Local directory where ProcessData_ExtendedData4.mat was saved after running ProcessData_ExtendedData4
% codedir - Local directory where code (e.g., published/EstrousRPE/) was saved
%% Set up paths
s = pa... |
225df5dc9feada1a054353309ab6e14b361aa27cff8956a2ad7c6343eaa8e9dc | MATLAB | 2,625 | 80 | function res = plugin_urlsize(urlChar,method,params)
%URLREAD Returns the contents of a URL as a string.
% S = URLREAD('URL') reads the content at a URL into a string, S. If the
% server returns binary data, the string will contain garbage.
%
% S = URLREAD('URL','method',PARAMS) passes information to the server ... |
06529426909dfa4c2234a9364311f21d288e1cd9a0933e9fb7806c151a006528 | MATLAB | 2,626 | 69 | function c = tapas_unitsq_sgm_config
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Contains the configuration for the unit square sigmoid observation model for binary responses
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
3f503783947766f81df81599d612c4db57f36b0f1ff30e8e17f7adf5590cd6fd | MATLAB | 2,626 | 32 | % -stroke '#FFFFFF
% -strokewidth 2
% columnsxrows
% on surly
remap = [1 3 5 7 2 4 6 8];
for p=1:8
unix(sprintf('convert /home/stone-ext4/generic/Dropbox/nsddata/inspections/surfacevisualizations/subj%02dflat_curvature_subj%02d.png -gravity northwest -font FreeMono-Bold -fill black -pointsize 120 -stroke ''#eeeee... |
8175abda0754fa3c6795b2ba75b2ec527b0bf99f749318bdce92a0e7b837fa7a | MATLAB | 2,626 | 88 | function TractMS2Nii(ng1,ng2)
%% This function will
%% 1) summary the tract measures of all subjects into a single mat file
%% 2) idetify and exclude subjects who failed in tracking all 18 bundles
%% 3) translate the data containing eligiable subjects into nii.gz images
%% This is an necessory process before performi... |
cc5e401676135ccf7e975ec2b4767998947dd5d926513e513912a2bc50b34430 | MATLAB | 2,626 | 106 | function [fid, tree, dir] = fiff_open_le(fname)
%
% [fid, tree, dir] = fiff_open_le(fname)
%
% Open a fif file and provide the directory of tags
%
% fid the opened file id
% tree tag directory organized into a tree
% dir the sequential tag directory
%
% This is a modified version, specific for opening 'littl... |
1475cb1bb30474f82422c3dbba6b96ee6e2ab03729bc3b2610065a7668fa9a48 | MATLAB | 2,628 | 74 | function download_FANSI_toolbox()
% One-time setup: check whether FANSI-toolbox (https://gitlab.com/cmilovic/FANSI-toolbox)
% is available; if not, download the pinned commit into SEPIA_HOME/external/
% and register its path in SpecifyToolboxesDirectory.m.
%
% This script only runs when you call it explicitly - it is n... |
83a561759a068e66ad511d7945aa9561b27b2e33b0ed665ffbc3cbfb029bb8b6 | MATLAB | 2,628 | 73 | function kfold_inds = cvpartition_wrapper(ops)
%decides how to generate labels for cross-validation
%
%
if ops.kfold > 1
switch ops.cvtype
case 'ofc'
%use CV partition, but fit it into your current code
%decide on stratification groups. currently balance among trial behaviors
... |
b995476f82bf86fbe3a98fd9b76c1621a1135e04bceda070ae73c9591e64a320 | MATLAB | 2,630 | 74 | %% PETH_Scripts
output = loadAllUnitData();
%% Draw Single PETH
index = 15 ;
event = 'valid_IROF'; % ["TRON","first_IRON","valid_IRON","first_LICK","valid_IROF","ATTK","TROF"]
TIMEWINDOW = [-1000, 1000];
timepoint = getTimepointFromParsedData(output.BehavData{index});
% Generate spikes cell to feed in to the drawPET... |
f0ba912d804d9012701140ae171fed9c3ec09f267972f62a6dae652937945438 | MATLAB | 2,630 | 68 | function [chi2,actual,expected,colnames] = computechi2(studycount,totalstudycount)
% function [chi2,actual,expected,colnames] = computechi2(studycount,totalstudycount)
%
% 07.22.01 by Tor Wager
%
% computes a yes/no chi2, where #nos is total - #yesses
% can generalize to other things, L/R for example, but must give L o... |
5a13fcd815c802816ad54610584c7993afd44f57552724b4a3ecc80b84530869 | MATLAB | 2,631 | 69 | function [mergedImage, newDimLabel] = ...
merge(this, mergeDims, varargin)
% Merges multiple dimensions into one dimensions
%
% Y = MrImage()
% mergedImage = Y.merge({'echo', 't'})
%
% This is a method of class MrImage.
%
% IN
% mergeDims which dims should be merged into one dim
% can ... |
e30d642ce138154e0c79ab7bc005dada2edec4c637ace1d2f0d0e5f0991e1de5 | MATLAB | 2,631 | 96 |
function [ output mosaic ] = Orthoview( volume ,varargin)
%[ output_args ] = Orthoview( volume ,varargin)
% varargin{1} is the position of the slices
% varargin{2} is the range of the colorbar
% varargin{3} is the type of image 'normal','mip',proj
dims=size(volume);
if nargin>=2
if isempty(varargin{1})
... |
1ddb6fd7535e7db06f798b2013629f2da516c53df3525ca0e054dc1f4050ed2d | MATLAB | 2,632 | 77 | % --------------------------------------------------------------------
function Import_From_Ultravox_Callback(hObject, eventdata, handles)
[ultravoxName,ultravoxPath] = uigetfile([handles.data.squeakfolder '/*.txt'],'Select Ultravox Log');
if ultravoxName == 0
return
end
[audioname, audiopath] = uigetfile({
'*... |
5b8cc169d6f3ea338ffd5fd8aeedc3a977c101915bdfaae31acca04ed3509a66 | MATLAB | 2,632 | 74 |
USE_IMAGE_SPECTRA = false;
% setup paths
addpath('util');
addpath('Bullwinkle');
addpath('signature_detectors');
% load one of the campus images
load muufl_gulfport_campus_w_lidar_1;
if USE_IMAGE_SPECTRA
% load the target signatures
load tgt_img_spectra; % order: brown, dark green, faux vineyard green, pea... |
69395d92c80377b899a512e226e1b982fa7d74bef2968a7eb2025470b067e8fb | MATLAB | 2,632 | 65 | %% Demo of using 'axislabel_rotation'
% Orthographic, DataAspectRatio = [1 2 3]
figure;
axes('box','on','dataaspectratio',[1 2 3],'projection','orthographic');
xlabel('This is an x label')
ylabel('This is a y label')
zlabel('This is a z label')
h = rotate3d;
set(h,'ActionPostCallback',@align_axislabel)
%% De... |
8185dcaab427a9dfc5ef9d8337ec1899ef3adb2821cdc4f84741511dc3b1ced6 | MATLAB | 2,632 | 73 | function []=wavelet_transformation(Fs, time_ms, num_electrode, LP_Signal_fix, Downsample_rate, t1, t2)
%WAVELET_TRANSFORMATION Time–frequency analysis using continuous wavelet
%transformation
%
% INPUTS:
% Fs - Sampling frequency (Hz)
% time_ms - Time vector (milliseconds)
% n... |
cd5956a8ce05e26166750057b607f569427192486628e27b1439dc0b59ec5e61 | MATLAB | 2,633 | 74 | function osp_onSave( ~, ~,gui)
%% osp_onSave
% Callback function on save button click. Saves MRSCont.
%
%
% USAGE:
% osp_onSave( ~, ~ ,gui);
%
% INPUT: gui = gui class containing all handles and the MRSCont
%
% OUTPUT: Changes in gui parameters and MRSCont are written into the
% ... |
d9c827a4dbdc0f179fd4f2c889a48ffbe16a53fa25d4b543388c5ed7db85130d | MATLAB | 2,633 | 90 | %% unitTest.m
% This function performs a command line unit test based on the jobTesting.m file in the
% ci folder. All Osprey modules are tested in dependence of the
% included dataset. You can change the jobTesting.m file according to your desired
% needs. The results unittest class includes detailed informati... |
4e906c5131e90b153ac40e79e91e3d7140ce4fc749f49e27d3cc043b5eb6bebe | MATLAB | 2,634 | 77 | function preprocessing(mri_lst)
%
% Input: mri_lst <list of strings> list of fullpaths to MRI images to be
% preprocessed
%
% This function converts the MRI scan to nifti-fileformat, orients the input
% MRIs to the ACPC corrdinate system and creates an average MRI image (u... |
7f55fa5385419f61f0d0b7c6b091b8876b893cbd04f9a7406b524950cec71ab9 | MATLAB | 2,634 | 76 | function band_signal = modwtmra_single_band(wpt, wavelet_type, target_band)
% MODWTMRA_SINGLE_BAND - Reconstruct a single band from MODWT coefficients
%
% Optimized function to reconstruct only ONE wavelet band instead of all bands.
% Eliminates the need to allocate the full (Bands × Samples × Channels) MRA array.
%
% ... |
ed986363cc7837facb709d3b11ce866f597aee4416d09abb4351d0dce1704543 | MATLAB | 2,634 | 72 | % STD_FINDGROUPVARS - find group vars in STUY structure
%
% Usage:
% >>
%
% Inputs:
%
% Outputs:
%
% See also:
% pop_studydesign,
%
% Author: Arnaud Delorme
% Ramon Martinez-Cancino
%
% Copyright (C) 2014 Arnaud Delorme,
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the document... |
e26eff017f3c3c6c04192ed8f37c8adeaf4361ee7fa67b6eff23521b85571624 | MATLAB | 2,635 | 89 | %% ExportQMSHubHeaderIOWrapper(input,outputDir,b0_input,b0dir_input,voxelSize_input,te_input,flag)
%
% Input
% --------------
% input : either DICOM directory or NIfTI file fullpath
% outputDir : directory that store the output header file
% b0_input : user field strength input
% b0dir_inpu... |
0d132b05992070263046f33d581484e12d15872830045f3ca345d1814fe0f29e | MATLAB | 2,636 | 67 | clear all, close all
n1=10; n2=5; % number of data points from each class n1/n2
sc=1; % change the scale of the initial problem
% 1) draw data from two Gaussians
S1 = eye(2); S2 = [1 0.95; 0.95 1];
m1 = [0.75; 0]; m2 = [-0.75; 0];
randn('seed',17); rand('seed',17... |
5ae6eea482445c1f1d70fefd1942523ca526c146dab54434aa590bb19fc1f8f8 | MATLAB | 2,636 | 56 | % The file "LORETA-Talairach-BAs.csv" was downloaded from the LORETA-KEY
% website. It was convreted using this script to a Matlab source model file
% Original documentation:
% The file "LORETA-Talairach-BAs.csv" is plain text (ascii), but suitable for excel.
% On the first line are the column ... |
764bb834a79ad8b6b3177525322200b69ec6f1118cfd4077f09bcfcf8e0e61d3 | MATLAB | 2,637 | 100 | function FigureS7(datadir, codedir)
%FigureS6 - Alternative retrospective models fail to capture both fast
% and slow trial initiation time dynamics at block transitions.
% datadir = directory of dataset
% codedir = director of code
%% Set up paths
s = pathsep;
pathStr = [s, path, s];
onPath = contains(pathStr,... |
3f0771ae43529e060d3933c20b70efada673dcb35b17446c7c5d637760badd93 | MATLAB | 2,638 | 92 | function vl_testnn(varargin)
%VL_TESTNN Run MatConvNet test suite
% VL_TESTNN('option', value, ...) takes the following options:
% `cpu`:: true
% Run the CPU tests.
%
% `gpu`:: false
% Run the GPU tests.
%
% `single`:: true
% Perform tests in single precision.
%
% `double`:: false
% Perform tests in do... |
1f6e1971a8a27dd5a671f1f0929dfd57c846a99dd0313bcbd8ba4a4535a211a3 | MATLAB | 2,639 | 57 | function [AmpXCorr,Lags,MaxXCorrLag,AmpXCorrSig] = LFP_AmpXCorr(LFPData1,LFPData2,Fs,FreqBand,MaxLag)
%% Calculates the cross correlation of the amplitude envelope between two LFP channels in specified frequency band
%
% Inputs
% LFPData 1&2 -- LFP data from different regions to be compared
% Fs -- S... |
3de10e245ffef17a872173b55cda9998c31cb42b806f1ed53bff12bc7e4724dd | MATLAB | 2,640 | 88 | %% function save_nii_img_only(headerfilename,savefilename,images)
%
% Description: Wrapper script for saving with target image header
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 24 January 2017
% Date modified: 28 June 2020 (v0.8.0)
%
function save_nii_img_only(headerfilename,savefilename,img,data... |
7e03346894b45582a58131ad4d7245e3aab334b538cb2b816935edf52c0e65b7 | MATLAB | 2,640 | 92 | function Test_fixedrank_spectahedron()
% Test_fixedrank_spectahedron()
% The problem being considered here is the fixed-rank DSPCA
% All intputs are optional.
%
% This file is part of Manopt: www.manopt.org.
% Original author: Bamdev Mishra, July 11, 2013.
% Contributors: Nicolas Boumal
% Change log:
clear al... |
92c9092ffe5748f3298b9fb78348c96c8348348aebce71b72fe6d35b48de73ac | MATLAB | 2,640 | 103 | addpath('../../networktools')
%% load network data
NT = NetworkObj('../testing/linear2.net',struct('dim',2));
NT.interpolateEdgePaths(2);
NT.setCumEdgeLen();
%% load snapshot data
resdir = '../testing/';
runname = 'testfptCone';
filename = [resdir runname '.mesh.txt'];
MSH = MeshObj(filename);
snapfile = [resdir ru... |
a93ea6cfd3d72dfd1848cce98e8f53bc56c8c7e22e6f27e048261a0095270ec4 | MATLAB | 2,640 | 90 | %% Making the ensemble raster
load('/home/octodon/Documents/MATLAB/FastEnsDet/4exps/4_exps_6_conds_concatenated.mat')
nexps = 4;
templates = arrayfun(@(x) load(['v4_templates_exp_',num2str(x),'.mat']),1:nexps,'uni',0);
templates = {templates{1}.templates,templates{2}.templates,templates{3}.templates,templates{4}.templ... |
eb4d21eb31d403b4dfb6ae657a36171eb9e380d3a3ef45eb5b4a74f4313ffaf8 | MATLAB | 2,640 | 79 | function this = MrDataNd_constructor(this, testVariantsDataNd)
% Unit test for MrDataNd constructor with different input variants
%
% Y = MrUnitTest()
% run(Y, 'MrDataNd_constructor');
%
% This is a method of class MrUnitTest.
%
% IN
%
% OUT
%
% EXAMPLE
% MrDataNd_constructor
%
% See also MrUnitTest
% Author: ... |
52dfc502c09e26d1d4a9cd8ec959a6d3050b7eb8e9cdcbd349c50b9de4fada07 | MATLAB | 2,641 | 96 | %% Preprocessing script for AD_UCSF MEG data
% This script performs the following preprocessing steps:
% 1. Load raw MEG data
% 2. Resample data to 200 Hz
% 3. Detect and interpolate bad channels
% 4. Segment data into 2-second trials
% 5. Reject bad trials based on amplitude thresholding
% 6. Save the preprocessed dat... |
c408fddec633f290d0dd842fe1a60450409065f5bb90f8f31601db6134523386 | MATLAB | 2,641 | 63 | %VL_NNPOOL CNN poolinng.
% Y = VL_NNPOOL(X, POOL) applies the pooling operator to all
% channels of the data X using a square filter of size POOL. X is a
% SINGLE array of dimension H x W x D x N where (H,W) are the
% height and width of the map stack, D is the image depth (number
% of feature channels) and N... |
09de7ed31363eec2573b970eacfe0e795eef57b10c1f2fb29f2e2bbe3692cdac | MATLAB | 2,642 | 82 | % Script tapas_physio_example_multi_subjects(input)
% Shows how to generalize single-subject batch for all subjects
%
%
% See also tapas_physio_new
% Author: Lars Kasper
% Created: 2015-07-31
% Copyright (C) 2015 TNU, Institute for Biomedical Engineering,
% University of Zurich and ETH Zurich.
%
... |
21e74dcdcc55f77afb99e1da4393cd29b261e8f5321e20c1fb43a3e63b8e73a7 | MATLAB | 2,642 | 86 | function theta = generate_ori_map(Nx, Kc, varargin)
% GENERATE_ORI_MAP Orientation map generator (Kaschube et al., 2010, Eq. 20).
%
% Syntax
% theta = generate_ori_map(Nx, Kc, Name,Value, ...)
%
% Description
% Implements the orientation map synthesis from Kaschube et al. (2010) Supp.
% Materials, Eq. 20. Produc... |
c82b9f2495b719aba215229de19bbf8ecfa944b92538cd00e0edaf28eb61daee | MATLAB | 2,643 | 88 | function testviolinplot()
figure();
% One could use tiled layout for better plotting them but it would be
% incompatible with older versions
subplot(2,4,1);
% TEST CASE 1
disp('Test 1: Violin plot default options');
load carbig MPG Origin
Origin = cellstr(Origin);
vs = violinplot(MPG, Origin);
plotdetails(1);
% TES... |
e602e7068020344b132184d88745294c90c080a24122bc94bac839ed0eaf81d4 | MATLAB | 2,645 | 90 | %% unitTest.m
% This function performs a command line unit test based on the jobTesting.m file in the
% ci folder. All Osprey modules are tested in dependence of the
% included dataset. You can change the jobTesting.m file according to your desired
% needs. The results unittest class includes detailed informati... |
678b73ec76f1171105d08ec3566e78ace0a8221600e4c6a877d5914768429618 | MATLAB | 2,648 | 76 | function sortOrder = drawPeakSortedPETH(zscores, TIMEWINDOW, TIMEWINDOW_BIN, ax_hm, ax_hist, options)
%% drawPeakSortedPETH
arguments
zscores (:,:) double % vertical vector is one data. sorted horizontally.
TIMEWINDOW (1,2) double
TIMEWINDOW_BIN (1,1) double
ax_hm matlab.graphics.axis.Axes
ax_hist ... |
b05f3136adf2796dd6ad0d5cf19e301753dbd73889b8a73edfd46ef1c41158f0 | MATLAB | 2,648 | 76 | % osp_extract_three_plane_image_overlay.m
% Helge Zoellner, Johns Hopkins University 2021.
%
% USAGE:
% [three_plane_image] = osp_extract_three_plane_image(ImageFile, MaskFile);
%
% DESCRIPTION:
% Creates a SPM volume containing a voxel mask with the same dimensions
% as the SPM volume containing a structural image. Th... |
b9abf277d984511795e94b51567bb3ac3b88c9db38a35ef45106a968e2500c5d | MATLAB | 2,648 | 60 | function ccg_data = ccg_to_attributes_V1(ccg_output, flag)
ccg_types = ["ccg"];
for ccg_type = 1:length(ccg_types)
ccg_data_t = struct;
ccg_data_t.ccg_control = ccg_output.(strcat(ccg_types(ccg_type),'_control'));
ccg_data_t.ccg_jitter = ccg_output.(strcat(ccg_types(ccg_type),'_norm_jitter'));
ccg_data... |
a2c6d758569a4317647f0de0a483c2124b445c7e6b3afedba5090eb17956f830 | MATLAB | 2,649 | 79 | function outputImage = k2image(this, applicationDimensions)
% Computes image representation (scaled/circshifted FFT) of k-space per slice
% by applying transformKspaceToImage;
%
% Y = MrImage();
% k2imageY = Y.k2image(applicationDimensions)
% k2imageY = k2image(Y, applicationDimensions);
%
%
% This is a method of... |
c31915b705671f40427b9cd82879685f0f5bcdb45dac93957e997ef008b7c287 | MATLAB | 2,649 | 77 | function subgrad = getSubgradient(problem, x, tol, storedb, key)
% Computes a subgradient of the cost function at x, up to a tolerance
%
% function subgrad = getSubgradient(problem, x)
% function subgrad = getSubgradient(problem, x, tol)
% function subgrad = getSubgradient(problem, x, tol, storedb)
% function subgrad =... |
694cd7f3c98f134c586f13baf520be0785f9090797cc6f34223057cb990d6991 | MATLAB | 2,650 | 89 | function cl = pmap_threshold(pimg,searchmask,pt,varargin)
% cl = pmap_threshold(pimg,mask image,p-threshold,[image with values to extract])
%
% Threshold a p-value image (pimg) and display suprathreshold blobs
% Only display significant values included in the mask image (img2)
%
% p-threshold is the p-value threshold ... |
a7d7addd8e1342c3db9bdcab87c65359e80e22192ef4044d4dfc1a474704c24c | MATLAB | 2,650 | 94 | function im=mat2im(mat,cmap,limits)
% mat2im - convert to rgb image
%
% function im=mat2im(mat,cmap,maxVal)
%
% PURPOSE
% Uses vectorized code to convert matrix "mat" to an m-by-n-by-3
% image matrix which can be handled by the Mathworks image-processing
% functions. The the image is created using a specified color-map... |
839011bdf34ab455ba759d15d8f6e4bafeebbc430427f803610097cb6df00794 | MATLAB | 2,651 | 96 | function [RDMs,nRDMs]=unwrapRDMs(RDMs_struct)
% unwraps dissimilarity matrices of a structured array (wrapped RDMs) with
% meta data by extracting the dissimilarity matrices (in square or lower
% triangle form) and lining them up along the third dimension. (if they are
% already in that format they are handed back unch... |
da21757cfbc55a090c4297b0c76ff11dacc192d170bfc684c9ad472f17bc3112 | MATLAB | 2,653 | 68 | % Bang et al (2020) Private-public mappings in human prefrontal cortex
%
% Reproduces Figure 1-figure supplement 3
%
% The visualisation is based on the analytical approach developed in "Bang
% et al (2017) Confidence matching in group decision making"
%
% The visualisation is based on an example subject (subjec... |
29f9391c7d900ba92de3991fea8fef340bdd3905250177c29ab880d13eb21cbb | MATLAB | 2,654 | 81 | function fear_icaReacStrWake_optShfit(basename,varargin)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
param.templateSes=2;
param.threshold=25;
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
%%
param=parseParameters(... |
e18f7bfc8fb30d900322d1571b2630491b85714b4c8efc4ac50275cd5918045f | MATLAB | 2,654 | 73 |
function [rate,dt,nt,op,S0,M,ds,dif,tp,T,K,SName,Cb,clim,NameMask,unittime,unitconc, bounds,freq]=LoadParam(app)
% Extract selected tab title
Tab = app.TabGroup.SelectedTab.Title;
if strcmp(Tab,'Multiple Simulations')==1
% Extract values for multiple simulations
unittime=app.Units_2... |
11fe0e85e9a241bae493c2457343b9204a8f5fdea70d79ead4f1a7fc7e6f3a25 | MATLAB | 2,655 | 79 | %% save_json_sidecar(niiFilename, info)
%
% Input
% --------------
% niiFilename : full filename of the NIfTI output the sidecar describes
% ('*.nii' or '*.nii.gz'). The sidecar is written next to
% it with the same basename and a '.json' extension
% info : (optional) structur... |
30ac24231780586df7d399e12a1508fc952c510ae7ae003c7cd697cf6d45526c | MATLAB | 2,655 | 65 | function res = permute(obj, dims);
if length(dims) > 3
error('Max 3 dimensions for permutation');
elseif length(dims) == 2
error('Permutation with 2 dimensions: use transpose instead');
end
newFileName = mmo.getnewfilename;
copyfile(obj.dataFile, newFileName);
res = obj;
res.dimensions = obj.dimensions(dims)... |
9de9ee1299e5659b2ac2801f94655bdd33ca46363e789bd0ec99b934a71247be | MATLAB | 2,657 | 75 | function out = op_add_analysis_provenance(in,fields)
%% out = op_add_analysis_provenance(in,fields)
% This function adds analysis provenance to the the NIfTI header
% extension for NIfTI-MRS following the standard described in "Clarke WT,
% Bell TK, Emir UE, Mikkelsen M, Oeltzschner G, Shamaei A, Soher BJ, Wils... |
55439b74b5b6770af9d7e3e316e9cab3401272a2d7b6fac04006b1cd28ca4fae | MATLAB | 2,659 | 69 | % MEMMAPDATA - create a memory-mapped data class
%
% Usage:
% >> data_class = memmapdata(data);
%
% Inputs:
% data - input data or data file
%
% Outputs:
% data_class - output dataset class
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Nov. 2008
% Copyright (C) 2008 Arnaud Delorme, SCCN, INC, UCSD
%
% ... |
b90ee0f004420e714734a779056c29fe3fd0f2ce973fc09e02af29c1f5aee8a0 | MATLAB | 2,660 | 74 | function [] = plotBetasSwarm(beta, colors)
% This code reproduces the analyses in the paper
% Urai AE, Braun A, Donner THD (2016) Pupil-linked arousal is driven
% by decision uncertainty and alters serial choice bias.
%
% Permission is hereby granted, free of charge, to any person obtaining a
% copy of this software an... |
f0f881ad0aa6c4cd162d3311f6c45dfa551b2fade06898930967a1ce25f69df5 | MATLAB | 2,660 | 63 | % demonstrate usage of classification
%
% Copyright (c) by Carl Edward Rasmussen and Hannes Nickisch 2013-10-16.
clear all, close all
%% SAY WHICH CODE WE WISH TO EXERCISE
id = [1,1]; % use Gauss/Exact
id = [1,2; 2,2; 3,2]; % compare Laplace
id = [1,3; 2,3; 3,3]; % study EP
id = [1,5; 2,5]; % look into KL (takes quite... |
0f9170a59dc8a017038b38515616c2e56b25bf2de89274f959703c9d10eb8b3e | MATLAB | 2,663 | 102 | function [r,normr,nre,s] = reorth(Q,r,normr,index,alpha,method)
%REORTH Reorthogonalize a vector using iterated Gram-Schmidt
%
% [R_NEW,NORMR_NEW,NRE] = reorth(Q,R,NORMR,INDEX,ALPHA,METHOD)
% reorthogonalizes R against the subset of columns of Q given by INDEX.
% If INDEX==[] then R is reorthogonalized all co... |
8ad57b1072fb98db4189b93b4be6391cd141af0cbf90a63f3a922260612d83e6 | MATLAB | 2,664 | 79 | function [Px, F, T] = PSD_v1(signal, time, labels, setting)
% Function computes power spectral density (PSD) in dB from trials data for
% each channel.
% INPUTS===================================================================
% signal... EEG (time X channel X trials)
% time... time vector in seconds (time X 1 X 1)
% ... |
41ef6ed1b8d816dd3d159306e4e5feee10a49b82be67c97bca8ed6c612c31227 | MATLAB | 2,665 | 63 | %VL_NNPOOL CNN poolinng.
% Y = VL_NNPOOL(X, POOL) applies the pooling operator to all
% channels of the data X using a square filter of size POOL. X is a
% SINGLE array of dimension H x W x D x N where (H,W) are the
% height and width of the map stack, D is the image depth (number
% of feature channels) and N... |
89e65145f69c86c8433cd926a1482616208534a94d3531a72aa948b3f4038c09 | MATLAB | 2,665 | 63 | function samples = Sample(histogram, n)
% sample from distributions.
% EXAMPLE
% [h,t] = hist(spikes(:,1),resolution);
% samplespikes = t(Sample(h,1000));
% NOTE: multiple histograms may be provided in different columns of h.
%
% By Raly Todorova (2016), inspired by Dahua Lin's discretesample (2008)
if nargin<2
e... |
f2e1b08a5ce348fe4f6afa3feb2357f5577cdfb71d1545f08be5734e2cc1d6b2 | MATLAB | 2,665 | 68 | %{
# Reference map
-> mice.Mice
ref_idx : smallint # reference map index for each animal
---
-> experiment.Scan
pxpitch : double # estimated pixel pitch of the reference map (microns per pixel)
ref_table : varchar(256) # reference table
ref_map ... |
0cbecc874e7a139dcaba3bbcc68090b2d0bae39ff66cd4e577d914cb40b92160 | MATLAB | 2,667 | 65 | % createApertures
% Creates a stimulus and fixation apertures.
%
% Syntax
% [stimulus_aperture, fixation_aperture] = createApertures(p, w)
%
% Input Arguments
% p – structure containing scan parameters
% w – structure containing window parameters
%
% Output Arguments
% stimulus_aperture – stim... |
4c477fab71f0a5fbab09f809cebdacd64cde63a9acc8d3afe150ff9483a54f06 | MATLAB | 2,667 | 85 | % Script demo_smooth
% Shows smoothing
%
% demo_smooth
%
% See also
% Author: Saskia Bollmann & Lars Kasper
% Created: 2018-05-27
% Copyright (C) 2018 Institute for Biomedical Engineering
% University of Zurich and ETH Zurich
%
% This file is part of the TAPAS UniQC Toolbox, which is released
... |
ea4d12b00bdbeff6998ba8aaaf254dd0449ed64faaa7ac633bb5daa115074096 | MATLAB | 2,667 | 70 | function cleaned = RemoveArtefacts(lfp,times,varargin)
%RemoveArtefacts - Remove artefacts from local field potentials.
%
% Remove large deflections such as stimulation artefacts from local field
% potentials, i.e. flatten the data around the times of artefacts.
%
% USAGE
%
% cleaned = RemoveArtefacts(lfp,times,<o... |
5422da7607f373ebcbf868976692ef10a930b860e5eb226154061ee47e726fe8 | MATLAB | 2,670 | 79 | function OptimHistory = InflowAlgorithm_allparam(param0, flow, maxFlow, minFlow, maxPressure, ...
minPressure, ntp, nv, l, u, sc, irun,Qdat)
% Set up shared variables with OUTFUN
OptimHistory.x = [];
OptimHistory.fval = [];
%% Contrained optimization with gradient based method (sqp algorithm)
options=opti... |
d6d30495ad5570301cbe4bd92a3b598ac6307f7cd81dbe0684a03bcaca1765f0 | MATLAB | 2,670 | 87 | %Creado por Luisca Mayo09. Para hacer completamente objetivo el proceso de
%las ventanas de tiempo de cada pico y para facilitar la elección de los
%estados en el LLE.
%SRasRen() genera una matriz nXm donde n:Número de células; m:número de
%picos tomando cada pico como los cuadros con Sindex=1 del Sindex con
%1 frame... |
e871ae739791c2df66dc73e0de17b1d62ea5ad8a6f2799375a0e673157caed32 | MATLAB | 2,670 | 57 | % Scripts to remove residual B1 bias from T1 maps calculated with the
% MP2RAGE sequence correction of T1 estimations as sugested on:
% Marques, J.P., Gruetter, R., 2013. New Developments and Applications of the MP2RAGE Sequence - Focusing the Contrast and High Spatial Resolution R1 Mapping. PLoS ONE 8. doi:10.1371/jou... |
25f57eb750535d2fc72c3be855ae6e800dcd6a4efffe75394a05e10c15bd6c24 | MATLAB | 2,671 | 101 | function [err, Itrans] = AFNI_IndexChange (Info, Iorig, Direction, DispOrient)
%
% [err, Itrans] = AFNI_IndexChange (Info, Iorig, Direction, [DispOrient])
%
%Purpose:
% Change the AFNI Index system between the display's and AFNI's coordinate system
%
%
%Input Parameters:
% Info: The data structure output from Bri... |
abc81e08ec2648d951b6f4cc6996d9faf0e6eec332c269c6dbac3d393c710470 | MATLAB | 2,671 | 64 | % eegplugin_firfilt() - EEGLAB plugin for filtering data using linear-
% phase FIR filters
%
% Usage:
% >> eegplugin_firfilt(fig, trystrs, catchstrs);
%
% Inputs:
% fig - [integer] EEGLAB figure
% trystrs - [struct] "try" strings for menu callbacks.
% catchstrs - [struct] "catc... |
c2a57e2cee27a2698409b3f43101247859dfb3b569eed3b156ea4f339b59a028 | MATLAB | 2,671 | 94 | addpath(genpath(pwd));
LoadData;
load(fullfile( 'results', 'doseResponseData.mat'));
reproduceFig2 = 1;
% Simulated annealing algorithm is used to search a combination of odor and
% ORN order to best visaulize the heatmap.
if reproduceFig2
% Because SA is a stochastic algorithm, the result may be different for e... |
f95c13eb06f9ff303aa4550635dd4e148cff59a67ab4ce78e83fc534c43c43b8 | MATLAB | 2,671 | 66 | function [Q, R] = qr_unique(A)
% Thin QR factorization ensuring diagonal of R is real, positive if possible.
%
% function [Q, R] = qr_unique(A)
%
% If A is a matrix, then Q, R are matrices such that A = QR where Q'*Q = I
% and R is upper triangular. If A is real, then so are Q and R.
% This is a thin QR factorization i... |
0f1cee29e46b75b0adba628065635903d112adce46260011142bd91f4eec40f1 | MATLAB | 2,672 | 74 | %% [chi] = Wrapper_QSM_StarQSM(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 da... |
50304779a2581dd25e6b5114809265a99f808176c78a77dccc24cc79062ebaa2 | MATLAB | 2,672 | 78 | function [vonl2h,vonh2l,mindist]=surfing_lowres2vonoroi(c1,c2,f2,r)
% constructs a Vonoroi mapping on a high resolution surface, using a low
% resolution surface as seed points and geodesic distance measure.
%
% [L2H,H2L,D]=SURFING_LOWRES2VONOROI(CLOW,CHIGH,FHIGH[,R])
% INPUTS:
% CLOW: 3xNLOW coordinates for N n... |
5d6f128672b3c5cc4d92549755a59e6ca8b88df731758d7ebf693f5a41e6c192 | MATLAB | 2,672 | 54 | % Inference methods: Compute the (approximate) posterior for a Gaussian process.
% Methods currently implemented include:
%
% infGaussLik Exact inference (only possible with Gaussian likelihood)
% infLaplace Laplace's Approximation
% infEP Expectation Propagation
% infVB Variati... |
bdae41314b5c191963d12d86fd65385631002c96cf96a9e45c57c9ce368a2fd3 | MATLAB | 2,672 | 30 | % EEG_OPTIONS - eeglab option script
%
% Note: DO NOT EDIT, instead use POP_EDITOPTIONS or the menu
% /File/Maximize memory in EEGLAB gui
% STUDY and file options (set the first checkbox if you intend to work with studies)
option_storedisk = 0 ; % If set, keep at most one dataset in memory. This allows pr... |
a56dd91022665ff070dda04249ccd61474f74324af84f602514714f0c4d5e9c2 | MATLAB | 2,674 | 81 | function [nTestFailed, nTestTotal, testResults] = tapas_physio_test(level)
% Interface of PhysIO-Toolbox-specific test functions to global tapas_test
%
% [nTestFailed, nTestTotal] = tapas_physio_test(level)
%
% IN
% level Depth of testing required
% Approximate run time per level
% ... |
147a06c4e6334717bbb81c3afeb2508d99be78dececce1221242698c09e36d9d | MATLAB | 2,675 | 84 | function y = tapas_physio_read_physlogfiles_philips_matrix(fileNamePhyslog)
% reads out complete numerical matrix from SCANPHYSLOG-file
% Physlog file version 1: [nSamples,10]
% Physlog file version 2: [nSamples,11]
%
% IN
% fileNamePhyslog
% string, filename of SCANPHYSLOG-file
% OUT
% y [nSamples... |
865fef64d55e2654dbefa057198678dfdbcfc4f1f0ede3435a7c061c64e06dee | MATLAB | 2,675 | 74 | % NUMDIM - estimate a lower bound on the (minimum) number of discrete sources
% in the data via their second-order statistics.
% Usage:
% >> num = numdim( data );
%
% Inputs:
% data - 2-D data (nchannel x npoints)
%
% Outputs:
% num - number of sources (estimated from second order measures)
%
% R... |
91d23724d2c3ec768263e190aa1b38fa621300f4cab9e9c540c1bd176f508a52 | MATLAB | 2,675 | 91 | function X = tapas_uniqc_dicom_mosaic2image(pathDicom)
% Computes MrImage from Dicom-Folder with mosaic images (over slices), one
% image per volume
%
% X = tapas_uniqc_dicom_mosaic2image(pathDicom)
%
% IN
% pathDicom folder with mosaic-style *.IMA files
% OUT
%
% EXAMPLE
% tapas_uniqc_dicom_mosaic2image
%
% ... |
a693356fd4d46c72b6c703c8eda7e8e405d5b2a6c41556084aba31c412ebc60a | MATLAB | 2,675 | 82 | function plotChannel2Axes_complexBins(ampPhiBins, plotInfo)
% plots the tuning bins in: ampPhiBins [ampBin x phiBin]
% uses polar coordinates (amp x phi bins) for each channel
% complex predictor (e.g. 2D velocity), real response (e.g. high-gamma iEEG channel)
% axes position defined in 'plotInfo'
% ampPhiBins = 2D: [... |
277235d651f31c43a3c8b5ef29c225543adbd444aeb993d728957ba2ee8806b3 | MATLAB | 2,677 | 69 | function EEG = iclabel(EEG, version)
%ICLABEL Function for EEG IC labeling
% Label independent components using ICLabel. Go to
% https://sccn.ucsd.edu/wiki/ICLabel for a tutorial on this plug-in. Go
% to labeling.ucsd.edu/tutorial/about for more information. To report a
% bug or issue, please create an "Issu... |
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