sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1acc49fbc3420f3cc25d035ea0c239332e779d5f1bb2c6cd5a336688d32e3236 | MATLAB | 1,316 | 56 | function [d,dvar,dprime,h] = makeDprime(trials, goods, all_S,all_SU,all_index,event,sig,varargin)
% Inputs
% trials: {:,2} cell array of trials for each good neuron
% goods: subset of cells you want to use
% all S
% all SU
% all_index
% event
% varargin: defaults to signed d', add value to make unsigned
... |
5f99530e2fbbb142ce36b2a57986d0cc071bf9a29be00c58034b2b083e8fd876 | MATLAB | 1,316 | 18 | %-----------------------------------------------------------------------
% Job saved on 01-Apr-2016 11:17:08 by cfg_util (rev $Rev: 6134 $)
% spm SPM - SPM12 (6225)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
matlabbatch{2}.spm.stats.fmri_est.spmmat = cfg_dep... |
f9c892ec39db8c60f925f8fb3d20004695431bb33e0941b12b839e1e486d93ad | MATLAB | 1,316 | 44 | function CheckAssemblies( filenameCLUSTERS )
%CHECKASSEMBLIES( filenameCLUSTERS )
%
%
% === Jan Moelter, The University of Queensland, 2017 ===================
%
if( exist( filenameCLUSTERS , 'file' ) == 2 )
CLUSTERS_mat = load( filenameCLUSTERS );
[ ~ , filenameCLUSTERS_name , ~ ] = fileparts( fil... |
047ba2dbb6134526ac57636be60aec56b7b630fd5788f4bc0de416fa98fa3749 | MATLAB | 1,317 | 39 | function y = vl_nnconcat(inputs, dim, dzdy, varargin)
%VL_NNCONCAT CNN concatenate multiple inputs.
% Y = VL_NNCONCAT(INPUTS, DIM) concatenates the inputs in the cell
% array INPUTS along dimension DIM generating an output Y.
%
% DZDINPUTS = VL_NNCONCAT(INPUTS, DIM, DZDY) computes the derivatives
% of the block pro... |
19746eb3e1401b4f290046eca56de8921ceb6a2a8ac23a00d0961ca24cc0fd5f | MATLAB | 1,317 | 33 | function preprocess_nsd_structuralinspection(subjix)
% function preprocess_nsd_structuralinspection(subjix)
%
% <subjix> is 1-8
%
% write out some orthMID inspections of the T1, T2, EPI, SWI, TOF, DWI.
% setup
nsdsetup;
outputdir = sprintf('%s/ppdata/%s-structurals',nsddir,allnsdids{subjix});
outputdir2 = sprintf('%... |
c96904848675a8be5709d67854b9857dc0fb013c56eae399b19dc1cc7c28d714 | MATLAB | 1,317 | 41 | function varargout = tapas_physio_run_unit_tests()
% Executes all existing unit tests of PhysIO Toolbox
% NOTE: Unit tests are meant to test small, but critical nuclei of the
% code, such as numerical routines (convolution, PCA...)
% For more complex workflows (e.g. whole example scripts), use
% integ... |
ee3fde245d2e564f1b7438335a94a9ba1e8b58fd1345ceb4678f9e95ecbbf928 | MATLAB | 1,317 | 52 | function [pvec, pstruct] = tapas_hhmm_transp(r, ptrans)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2013 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% Lice... |
357c8b1ceb2cbf03d09a84ddef32a2ff3e5ada650d9b6a267057146afadbb495 | MATLAB | 1,318 | 45 | function nmri_write_dataset(fname, data, subject)
%nmri_write_dataset(fname, data, subject)
% Function to write a dataset to disk as .mat file
% we also generate some "smart" separate structs for fast access
% and deal with synchonising subject and data struct
%
% fname = filename
% data = fieldtrip data structure
% s... |
b3059e3b08a42f126f7b1405c96c3676230c98e9b8ff1179d2136ed711efa31b | MATLAB | 1,318 | 30 | %{
# general data about mesoscope scans
-> experiment.Scan
-> meso.Version
---
nfields : tinyint # number of fields
nchannels : tinyint # number of channels
nframes : int # number of recorded ... |
b57504d5692ba196265d9208de21d2aa901b4a17234537c3d584893c596c2d81 | MATLAB | 1,318 | 49 | function clear(obj)
% Recursively sets all non-MrCopyData-objects to empty([])
% to clear default values
%
% Y = MrCopyData()
% Y.clear(inputs)
%
% This is a method of class MrCopyData.
%
% IN
%
% OUT
%
% EXAMPLE
% clear
%
% See also MrCopyData
% Author: Saskia Bollmann & Lars Kasper
% Created: 2016-04-19
%... |
c10c9c45b35660d9e317d82aa7850113b964bc461cd78a0428e9c7acaabef878 | MATLAB | 1,318 | 65 | %% TE = readTEfromJSON(filenames)
%
% Input
% --------------
% filenames : json file fullname(s)
%
% Output
% --------------
% TE : echo times
%
% Description:
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 13 June 2018
% Date last modified:
%
%
function [TE] = readTE_dcm2niix_JSON(fil... |
ad22a341d1ee80c0477e54d682e40ecc4db479e8248800a26904464560095acb | MATLAB | 1,319 | 54 | function [umxSignal,umxReference]=runFastICA(source,reference)
options.savePath=[];
options.figName= '_runFastICA';
options.plotFigure=true;
% Make sure M is a row matrix
if iscolumn(source) && iscolumn(reference)
M=double([source reference]);
else
M=double([source' reference']);
end
% run fastICA
[icasig, ~... |
8f26c2c136a622bcb5a6ed1fcca0394dd0318a15f4cf5490cdde8f6765f413fe | MATLAB | 1,320 | 45 | function plot2axes_paraTimes(paraTimes, clrs, fillBand)
% plots into current axes vertical bands of paradigm times (RT, ...)
% paraTimes = 3D: clz x responseType x "channels" (or repetitions - channels in AA)
% clrs = colors
% if fillBand = 1, plots band = mean +/- SEM (over repetitions)
% if fillBand = 0, plots verti... |
9d7039c662b351427c190ee33009b4c878cc82130208b98f9687006f39629bde | MATLAB | 1,321 | 50 | function D=sim2dis(S)
%function D=sim2dis(S);
%
%PURPOSE
%
%To transform elements of a similarity matrix S into
%dissimilarities D by D=1-S.
%
%INPUT
%
%S (matrix) MxM similarity matrix whose elements must be in [-1,1],
% for example, absolute values of linear correlation coefficients.
%
%OUTPUT
%
% D (matrix) MxM... |
a0421ab8f3f23a119327fe2a9e9d5732758c045ae39e66b86f0d50c3480560e2 | MATLAB | 1,321 | 50 | function Out=svm_train(J,sFiles,img_dil,ind)
% INPUT:
% J: number of training subjects
% sFiles: a string variable with a list of name for the similarity data of
% all the training samples
% img_dil: 3-D image (matrix) comprises region of interest and its uncertainty zone
% ind: index of all subcortical voxels ... |
5df81b984aa4018b3025762157a42c542ec7c57f0cdf5feb1fba6b444ca9721d | MATLAB | 1,322 | 43 | function [dat, lab] = read_bham(filename)
% READ_BHAM reads the EEG data files as recorded by Praamstra in Birmingham
% the datafiles are in a particular ascii format
%
% [dat, lab] = read_bham(filename)
% Copyright (C) 2000, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
%... |
0c1c5477dbbb2573584498f6ad6d8aca1cdd8fd4cf623fc8c716ebb798cd0f58 | MATLAB | 1,323 | 37 | function varargout = covRQard(varargin)
% Wrapper for Rational Quadratic covariance function covRQ.m.
%
% Rational Quadratic covariance function with Automatic Relevance Determination
% (ARD) distance measure. The covariance function is parameterized as:
%
% k(x,z) = sf^2 * [1 + (x-z)'*inv(P)*(x-z)/(2*alpha)]^(-alpha)... |
8f82caa9ac28c0096d03e26757d5e7c0f3bab29c875249ec8665994f630fc849 | MATLAB | 1,323 | 49 | classdef Sum < dagnn.ElementWise
%SUM DagNN sum layer
% The SUM layer takes the sum of all its inputs and store the result
% as its only output.
properties (Transient)
numInputs
end
methods
function outputs = forward(obj, inputs, params)
obj.numInputs = numel(inputs) ;
outputs{1} =... |
a58da87bc572ea41b1d38e7b76c8f78d2c37d2530794cfd0b89068ead1895de0 | MATLAB | 1,323 | 27 | %% Working with events
eeglab_path = fileparts(which('eeglab.m')); % get EEGLAB path
[ALLEEG EEG CURRENTSET ALLCOM] = eeglab; % start EEGLAB
pop_editoptions( 'option_storedisk', 0); % Change option to process multiple datasets
EEG = pop_loadset( 'eeglab_data.set', fullfile(eeglab_path, 'sample_data')); % load data
%% ... |
1c6b88461f5788a8caa0284506cf8b57169a854ea846a738329e07bcf056a52e | MATLAB | 1,324 | 42 | %% processes matched_frames_aligned to provide a data structure used for model training
% Note that the model data files require marker label data, which we will
% just set to NaN here.
clear all; close all;
% paths to matched frames
dirname = 'Recording_day7_cafftwo_nopedestal';
basedir = ['.' filesep dirname filesep]... |
020ae63a50dcce38115c8c67a5d489ba7d7740ba955428a4a20421c9683c4859 | MATLAB | 1,325 | 51 | function cellvec = createCellVector(meshvar, cellval)
% this function creates a vector field based on the geometry and mesh
% size. For instance it can be used to create a gravity field.
%
% SYNOPSIS:
%
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:
%
% SEE ALSO:
% cellBoundary
% Copyright (c) 2012-2016 Ali Akbar E... |
58f65c518e9061daebed003a65626caf0b5cd9e3c8a28c83e99bf5426ddcde2e | MATLAB | 1,325 | 42 | function mat2ades(dat, fileName, Fs, chanlabel, chanunit, dattype, datunit)
% write in the current folder ADES and DAT files from matrix in MATLAB workspace
% data = matrix of data (nbchannel * time points) - the data have to be in microVolt
% fileName = string of the output files without extension ; the ades and dat ... |
8d89835eb79b3705b15eb0a78e2a41d6d661787cf1258cdd8beec5ed93a9d09b | MATLAB | 1,326 | 33 | function [encoderNet, decoderNet, options, ClusteringData, clustAssign] = create_VAE_model(handles)
options.imageSize = [128, 128, 1];
% Creates fixed frequency spectrograms
[ClusteringData, clustAssign, options.freqRange, options.maxDuration, options.spectrogram] = CreateClusteringData(handles, 'scale_duration', tru... |
f8c0c9a6b8c2d37568c41a5748a86c4b519cd793b2c11765d5ec6cff18a1f45a | MATLAB | 1,326 | 49 | classdef Sum < dagnn_bc.ElementWise
%SUM DagNN sum layer
% The SUM layer takes the sum of all its inputs and store the result
% as its only output.
properties (Transient)
numInputs
end
methods
function outputs = forward(obj, inputs, params)
obj.numInputs = numel(inputs) ;
outputs{1... |
8e44c3c0f89d11d5687b99dbc42e468766532d0da2548378b10781bf9ddbda9b | MATLAB | 1,327 | 47 | function getTriggers_carGame_rewsObst(params)
% determines & saves trigger times and class labels
% (c) Jiri, May16
display('triggering on rewards / obstacles ...');
%% per session: load, get trigger times and assign labels, save
for sess = 1:size(params.storage.analyzedSess,2)
t_trigger = [];
clz_label... |
e48eae4521415602bbea2749ea5699db4cfe50d182f584af8b52a10c50314a6a | MATLAB | 1,327 | 53 | function [GrpInfo, GrpNames] = GroupingInfo(spikeDetectedData)
% this function allows user to input information about groups/categories for the data
cd(spikeDetectedData)
GrpInfo = [];
%% how many types of groupings?
GrpNum = inputdlg({'How many group/category types? For example, if categories are age a... |
d0d587387f45e46be4b1e8a3b60b62af65bdb46fa9f740c01e1004d0a77c1566 | MATLAB | 1,328 | 48 | function LCMparam = osp_editControlParameters(LCMparam, key, value)
%% LCMparam = osp_editControlParameters(LCMparam, key, value)
% This function edits a set of control parameters saved as a struct.
%
% If the assigned value is '', the key is being removed.
%
% For now, this is relatively unsophisticated, i.e. th... |
0399075844bbe408a197c8bcdae536d0bffc5638e712218ff0377ef42c2b8e32 | MATLAB | 1,329 | 41 | function update_from_affine_matrix(this, ...
affineMatrix)
% Updates properties of MrImageGeometry from affine 4x4 transformation
% matrix
%
% Y = MrImageGeometry()
% Y.update_from_affine_matrix(affineMatrix)
%
% This is a method of class MrImageGeometry.
%
% IN
%
% OUT
%
% EXAMPLE
% update_from_affine_matrix... |
00a7128fa61c88968d53fd4c06d9ad397a613f600405af15e768ec61253681f8 | MATLAB | 1,330 | 59 | % op_leftshift.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_leftshift(in,ls);
%
% DESCRIPTION:
% Remove leading datapoints from the fid to get rid of 1st order phase
% errors.
%
% INPUTS:
% in = input data in matlab strucure format.
% ls = number of points to remove from the beginning of the f... |
50187ccc7decc01381ff343a8d75fd3032a7b46d4e6fa23f0230aace7324f274 | MATLAB | 1,330 | 55 |
load(...) % load TF maps
addpath('slanCM')
cmap = slanCM('haline',100)
frex = logspace(log10(0.01),log10(5),50);
srate=;
figure;
subplot(141)
contourf([1:size(powa,2)]./srate,frex,powa,100,'LineColor','none')
;set(gca,'YScale','log');colorbar;
caxis([0 .2*10^(-9)])
subplot(142)
contourf([1:size(pown1,2)]./srate,frex,... |
79045011d775a284f9bb176a0c7f411c054adfcb4c07b3e53a207888ca653e1d | MATLAB | 1,330 | 32 | % define
dirs = {'func1mm' 'func1pt8mm'};
res = {[1 1 1] [1.8 1.8 1.8]};
trs = [1 4/3];
% do it
for dd=1:length(dirs)
for subjix=1:8
% define
file0 = sprintf('%s/ppdata/subj%02d/%s/mean.nii.gz',nsddatadir,subjix,dirs{dd});
file0b = sprintf('%s/ppdata/subj%02d/%s/aseg.nii.gz',nsddatadir,subjix,dirs{dd})... |
eb3ef5a102fcb17a83146d76052d3e66c7b793edfacb1112f78107f131186f9f | MATLAB | 1,330 | 51 | function brewermap_plot()
% Simple plot of all ColorBrewer colorscheme nodes in one figure.
%
% (c) 2014-2020 Stephen Cobeldick
%
%%% Syntax:
% brewermap_plot()
%
% See also BREWERMAP CUBEHELIX LBMAP PARULA LINES RGBPLOT COLORMAP COLORBAR PLOT PLOT3 AXES SET
[scm,num,typ] = brewermap('list');
%
persistent cbh axh
%
xm... |
23bb47e9b50b11335c778db8480645a3d7cc08200372178263d8aa7d6957c315 | MATLAB | 1,331 | 49 | %% chi = myQSM(localField,mask,matrixSize,voxelSize,thres,b0dir)
%
% Description: compute QSM based on threshold-based k-space division (TKD)
% Ref : Wharton et al. MRM 63:1292-1304(2010)
%
% Input
% -----
% localField : local field perturbatios
% mask : user-defined mask
% matrixSize ... |
4e8c3599f66cf969f67c3ea69991b61499b034fce513b41d55f92c1c82fe1577 | MATLAB | 1,331 | 32 | %CustomDefaults - User-defined custom default values for function properties.
%
% The behavior of most FMAToolbox functions can be modified using optional
% property-value pairs, e.g. GetPositions returns position samples in different
% coordinate systems depending on the property 'coordinates'. Such properties
% u... |
6ffdd5e38c7d04adabcfa2dcc748179c676930c04445612fb51df1b27e72f267 | MATLAB | 1,331 | 54 | function [scaledImage, oldMin, oldMax, newMin, newMax]...
= scale(this, varargin)
% Scales to image to a given new (intensity) range (i.e. normalization)
%
% Y = MrImage()
% Y.scale(newRange)
%
% This is a method of class MrImage.
%
% IN
% newRange defines the new intensity range
% defa... |
e33b9106813b78ea1903324cec22e41750e382ddd7132c8cddb9e098faf4d33f | MATLAB | 1,331 | 38 | function [tf_idf_Rasterbin] = Ras_tf_idf(Rasterbin)
% TF-IDF normalization
% INPUT:
% Rasterbin: N-by-T spike matrix with only significant frames
% OUTPUT:
% tf-idf_Rasterbin: continuous matrix after tf-idf normalization
%
% The goal is to normalize the S_index array in such a way
% that it is only necessary ... |
1b3e1b9d98cbf2702fda41578c0b8c689be4e366bd62ce60e49a541d6aa9ffa7 | MATLAB | 1,332 | 49 | function play( obj, frames,trace_opt )
keys = fetch(obj);
for ikey = length( keys )
key = keys(ikey);
disp('Playing movie for');
disp(key);
tpr = tpReader(Scans(key));
if strcmp(fetch1(Scans(key),'scan_prog'),'MPScan')
gChan = getAlignedImagingChannel( tpr, 1 );
rChan = get... |
23d66f8f984892f98ff23088e5a54576d414fda2fbd72e42a80da7ee4459ec5a | MATLAB | 1,332 | 41 | function [lp,dlp] = priorInvGauss(mu,lam,x)
% PRIORINVGAUSS Univariate Inverse Gaussian hyperparameter prior distribution.
%
% Random sample from the distribution
% r = PRIORINVGAUSS (mu, lam)
%
% Compute log density at location x and first derivative (w.r.t. x)
% [lp, dlp] = PRIORINVGAUSS (mu, lam, x)
%
% ... |
c2f885a55199819da60ba00c5198603bc777c108b6495a21c91140e871945fc2 | MATLAB | 1,332 | 49 | function [hi, lo, mix, p] = wtcurves(A, varargin)
%block 1 is test block.
%block 2 = high adaptation block.
%block 3 = low adaptation block.
A.reward = convertreward(A.reward);
rvec = 1:5;
hi.wt = nan(1, length(rvec));
hi.er = nan(1, length(rvec));
lo.wt = nan(1, length(rvec));
lo.er = nan(1, length(rvec));
mix.wt ... |
f212b29aeab52f635fc84f0bfb2786c01d5d553932518040002ecd6c1854fe1a | MATLAB | 1,332 | 53 | function [b, er] = regress_latency_vs_delay(A, nback, z_arg, mixedblock)
if nargin<4
mixedblock = 0; % use all blocks by default
end
% filter outliers using all trials, not just the subset given
L = A.ITI;
thresh = [1, 99];
cutoff = [prctile(A.ITI,min(thresh)), prctile(A.ITI,max(thresh))];
fprintf('ITI filtered a... |
933931206e107e10a8583a4517a168cbc4c08d5196e040bc52c263fc7aafbc59 | MATLAB | 1,333 | 37 | function varargout = hlp_getresult(idx,f,varargin)
% Returns the Result-Idx's output of the function, given the supplied arguments.
% Results... = hlp_getresult(Result-Idx, Function, Arguments...)
%
% In:
% Result-Idx : index of the result (output) of the given function application; can also
% be a ve... |
cc6272653deeeb5d153aa5a45dfa5a25296969049a2f4399a6ee91ccb5dcadb0 | MATLAB | 1,333 | 30 | function [ensmat_in, enscells_in, nens, time_comp] = get_herzog_ens(raster, param)
% Gets the activation sequence and core-cells by Herzog's algorithm.
% INPUT:
% raster: <logical> N-by-T matrix with the raster, where N is the number of total neurons
% and T is the number of total frames.
% param: [optional] <s... |
4ebd1a5cdf526d48bdfaf4234f99cae34c3b26d23cf44e30614c7fbef01384c1 | MATLAB | 1,334 | 46 | function vec = tangent2vec(M, x, basis, u)
% Expands a tangent vector into an orthonormal basis in the Manopt framework
%
% vec = tangent2vec(M, x, basis, u)
%
% The inverse operation is lincomb (see below).
%
% M is a Manopt manifold structure obtained from a factory.
% x is a point on the manifold M.
% basis is a cel... |
eed43e633851b2a43ba81961e243606740cb1ade57db962cabdac67376fec712 | MATLAB | 1,334 | 30 | function [spikecountAve, spikecountraw, SCvar] = ...
MovieSpikecount(spiketrain, goodcell, imgPara, stimInd, StimTimeIndv,...
SpikeCount_Twindow, IgnoreTimeWindow)
StimNum = imgPara.stim_time/StimTimeIndv;
SpikeCountbin = SpikeCount_Twindow/0.001;
spikecountAve = []; spikecountraw = []; SCvar = [];
for n = 1:le... |
46b8b087408318faf9ab70769f602493808393ae44f6bcc998a2994a85a9e5d8 | MATLAB | 1,335 | 37 | function [logp, yhat, res] = tapas_gaussian_obs(r, infStates, ptrans)
% Calculates the log-probability of response y under the Gaussian noise model
%
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2012-2013 Christoph Mathys, TNU, UZH & ETHZ
%
% This ... |
4b161e30d9d6fab3eac91311e22a2dc4944727cb366142051ce5b049c589ca3d | MATLAB | 1,335 | 51 | function facevar = createFaceVariable(meshvar, faceval)
% this function creates a face variable based on the geometry and mesh
% size. For instance it can be used to create a gravity field.
%
% SYNOPSIS:
%
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:
%
% SEE ALSO:
%
% Copyright (c) 2012-2016 Ali Akbar Eftekhari
% See... |
0c33e5edceb05af41c055620cd016e5f3b56b04d7ea011adc25fb0e52bc0c30f | MATLAB | 1,336 | 48 | function [log2FC, y, txt1, txt2, txt3, stagescompared, stageslfc] =...
volcanoplot(MS, comparison, direction)
%input: comparison = 1 for diestrus vs proestrus
%3 for diestrus vs estrus
if comparison == 1
stagescompared = 'Diestrus vs. Proestrus';
stageslfc = 'Diestrus/Proestrus';
tx... |
16701419df8a8f34848c6b6131dcfad6047222769f114bd2b5ac81d82853335f | MATLAB | 1,336 | 62 | function[Xopt, Y] = testsimplexmatrices()
clear all;
rng(103)
n = 10;
k = 5;
Y = zeros(n,n,k);
for kk = 1:k
Y(:,:,kk) = randn(n,n);
Y(:,:,kk) = 0.5*(Y(:,:,kk) + (Y(:,:,kk))');
% Y(:,:,kk) = sparse(diag(diag(Y(:,:,kk)'*Y(:,:,kk))));
% Y(:,:,kk) = sparse(((Y(:,:,kk)'... |
a11093fb18b293d228a2469bf7e567c503158e1b5e698785bddc966b27a74de0 | MATLAB | 1,336 | 51 | %% [lambda,magn,tol,maxiter,Kernel_Sizes]=parse_varargin_SSQSM(arg)
%
% Description: parser for qsmFANSI.m
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 6 September 2017
% Date last modified: 26 September 2017
%
function [lambda,magn,tol,maxiter,Kernel_Sizes,b0dir]=parse_varargin_SSQSM(arg)
% functi... |
a616684af7a836d733aef4ed0c52abecaa40e9a30ac5cdf8301ff2094afebf60 | MATLAB | 1,337 | 36 | function indC = tapas_physio_check_get_xcon_index(SPM, cname)
% returns index of contrasts in SPM.xCon, whose name matches cname
% used to find existing contrasts in an SPM.mat
%
% INPUT:
% SPM - SPM.mat-file
% cname - name of contrast to be searched for (string)
% (works for incomplete names/patt... |
acfa78ef5fac639c97bec4c760a9b2a5290da8c96e0b6222bada8dead7a25703 | MATLAB | 1,337 | 50 | function y = centroid(M, x)
% Attempts the computation of a centroid of a set of points on a manifold.
%
% function y = centroid(M, x)
%
% M is a structure representing a manifold.
% x is a cell of points on that manifold.
% This file is part of Manopt: www.manopt.org.
% Original author: Nicolas Boumal, Dec. 30, 2012... |
d6028a01013ab1abfdc958b89152e87351f46319844fb027e1d3b78869914277 | MATLAB | 1,337 | 33 | function[] = osp_WriteBIDsTable(Table,OutLoc)
%% function[] = WriteBIDsTable(Table,OutLoc)
% Function for writing BIDs compliant tables.
%
% USAGE:
% WriteBIDsTable(Table,OutLoc,JSON)
%
% INPUTS:
% Table = Matlab table structure, including json fields in
% table properties
% ... |
dc0384cfa2ce543b31f93027f4c79b670e432957dd37ce8afd46bf00ac028d3a | MATLAB | 1,337 | 60 | function [outputArg1,outputArg2] = PlotSubjectRMSError_All(sn, TitleStr, lp_Color, hp_Color, bb_Color)
if ~exist('TitleStr','var')
% title parameter does not exist, so default it to something
TitleStr = ' ';
end
% --- RGB vector for grey
grey = 0.75*[1 1 1];
% --- means & standard deviation per azimuth ... |
0647a1f9a024e8fbc0b25c24435e803317266cdbb69f1a2edce53c9c1a2b5cdc | MATLAB | 1,338 | 44 | function X=parallelize(X,c)
%function X=parallelize(X,c)
%
%PURPOSE
%
%To multiply the columns of X by 1 or -1 as necessary so that the
%dot-products of column vectors of X are all positive (or zero)
%with respect to a reference vector c.
%
%INPUT
%
% X (matrix) of size dxN of N d dimensional vectors
% c (vector) ... |
14b50c26eeb95f5878bdadd7a889851ddd36e9dcb8dd213469f605382f1cb214 | MATLAB | 1,338 | 50 | function y = linspaceVector(start,stop,n)
%linspaceVector - Produce linearly spaced vector with multiple [start stop] points.
%
% Shorthand for a loop calling the colon operator for each [start stop] pair:
%
% y = [];
% for i = 1 : length(start)
% y = [y;(start(i):n(i):stop(i)).'];
% end
%
% USAGE
%
% y = lin... |
4ced76c35e72bff297777e0508e701e0aa76f37fc8febccb1152ca6053f71bf4 | MATLAB | 1,338 | 43 | function test_suite = test_setDirections %#ok<*STOUT>
% (C) Copyright 2021 CPP visual motion localizer developers
try % assignment of 'localfunctions' is necessary in Matlab >= 2016
test_functions = localfunctions(); %#ok<*NASGU>
catch % no problem; early Matlab versions can use initTestSuite fine
... |
a02b742f687048062900089a2348e5bf5c28d7c34920172ea2e3b3231ccf4a4d | MATLAB | 1,339 | 42 | function [w, state] = adadelta(w, state, grad, opts, ~)
%ADADELTA
% Example AdaDelta solver, for use with CNN_TRAIN and CNN_TRAIN_DAG.
%
% AdaDelta sets its own learning rate, so any learning rate set in the
% options of CNN_TRAIN and CNN_TRAIN_DAG will be ignored.
%
% If called without any input argument, retu... |
c43b94fccaed0897b67240a1281cef4a0acf24c5bfcd6b9869d480a09386fa0d | MATLAB | 1,339 | 34 | function [range, poly] = identify_linear_piece(x, y, window_length)
% Identify a segment of the curve (x, y) that appears to be linear.
%
% function [range poly] = identify_linear_piece(x, y, window_length)
%
% This function attempts to identify a contiguous segment of the curve
% defined by the vectors x and y that ap... |
14110b1debd46d39c81081f4f2e7cb2c32a0122e0c106c0a1a3b8a5e6576ab80 | MATLAB | 1,340 | 59 | % this is subj08
bet MRAangiogramDATECENSORED_121153TOF3Dmultislabs037a1001.nii.gz angio.nii.gz -f 0.25
cd ~/Dropbox/KKTEMP
%a = load_untouch_nii(gunziptemp('MRAangiogramDATECENSORED_121153TOF3Dmultislabs037a1001.nii.gz'));
a = load_untouch_nii(gunziptemp('angio.nii.gz'));
a = double(a.img);
skip = 3;
skip = 1;
[x... |
1dadde97ee81b848005535a54ae31f265482991ceef0b1e2e665c4cb084d06d9 | MATLAB | 1,340 | 47 | function [ match ] = nmri_match_structs( input, filters )
%function [ match ] = nmri_match_structs( input, filters )
% will check if a struct (e.g. subject) matches with filter, allows to
% recurse
items=fieldnames(filters);
match=true;
for i=1:length(items)
if match && isfield(input,items{i})
% we have it, so... |
60ff8cc60efa2a09b079f892c6f4cb53bf096a86938f135b20b9a9347241620f | MATLAB | 1,341 | 45 | function [output_file]=Load_CSV_from_blender(csv_file, data_file, START_TIME, END_TIME)
% Once the blender output (the traced lines) are exported into .csv files,
% below involves importing the .csv files back into matlab,
% splicing the traces together, and calibrating the curves to fit the channels.
addpath(fullf... |
a9ef171301449fba2a0994f3fc6c7bcbb868f04ee3871d3b76f065fcf5b078d1 | MATLAB | 1,341 | 32 | % Input/output functions (including batch handling) for FMAToolbox.
%
% NOTE
%
% Although individual data files can be handled by these 'low-level' functions,
% it is generally easier to use <a href="matlab:help SetCurrentSession">SetCurrentSession</a> and related <a href="matlab:help Data">Get...</a> functions
% ... |
e3b639b7bde40bfb651c2d38dc98ad85283fb7383bb463cc4e59a0637228faca | MATLAB | 1,341 | 39 | function notDefined = ieNotDefined( varString )
%
% notDefined = ieNotDefined( varString )
%
% Author: ImagEval
% Purpose:
% Determine if a variable is defined in the calling function's workspace.
% A variable is defined if (a) it exists and (b) it is not empty.
%
% notDefined: 1 (true) if the variable is not defined ... |
b2c602cb71c0187d66862162a5f422c981151eb834f8c1cdb7df69d3abca0a86 | MATLAB | 1,342 | 31 | function [pvec, pstruct] = tapas_hgf_ar1_transp(r, ptrans)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2012-2013 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Publi... |
3a7b74d22f42df5451c033e6e18d8fea09d7813b4d1397e7ef9d30bcfe5e5656 | MATLAB | 1,343 | 39 | %% Constants
startTime = [-31000, -21000, -11000, -7000 : 1000 : -1000];
endTime = startTime + 2000;
timewindows = [startTime', endTime'];
numDataset = size(timewindows, 1);
basepath = 'D:\Data\Lobster\Lobster_Recording-200319-161008\Data';
filelist = dir(basepath);
workingfile = regexp({filelist.name},'#\S*','match'... |
752b9a8b6074e718dafd591ef6eab40c806c9177bf08e850e0cb0578d9e678c0 | MATLAB | 1,343 | 42 | function [y_sum,y_mean] = tapas_logsumexp(x)
%% -------------------------------------------------------------------------------------------
% [y_sum,y_mean] = tapas_logsumexp(x) takes the values in x, exponates
% them, then takes the sum over the column, and finally applies the natural logarithm.
% The calculation us... |
1fcff73a986950960930cbbfdfbe4e132fc3ba78a089bcad9c0f6b2dea5d5bbf | MATLAB | 1,345 | 46 | %% 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
% ... |
592c629d0d06657c5f5c2c4e6e3b07663c967e17ead4ee9d150208ebc226d132 | MATLAB | 1,345 | 48 | function [indic, nms, condf] = string2indicator(str,varargin)
%[indic, nms, condf] = string2indicator(str,varargin)
%
% Takes a cell vector of string labels and returns an indicator matrix
% Optional argument is a cell vector of strings for which values to match.
%
% Examples:
%[indic,nms] = string2indicator(CL{1}(1).... |
8fd26ac68cc814c2621fc99678d5c4b3d92e1c63ce424b885d3be6717ba41dc4 | MATLAB | 1,345 | 47 | function [lar_out] = lar_statistic(hsi_img,tgt_sig,bin_img,bg_ems)
%
%function [lar_out] = lar_statistic(hsi_img,tgt_sig,bin_img,bg_ems)
%
% Least Angle Regression Statistic
%
% inputs:
% hsi_image - n_row x n_col x n_band hyperspectral image
% tgt_sig - target signature (n_band x 1 - column vector)
% bin_img - bin... |
17a6776c622083f2cc89f61594980615309df9595c043f34f70d2774547d4e83 | MATLAB | 1,346 | 39 | function [Mdl] = run_LogReg(params)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% run_LogReg returns Mdl structure including function handles of fit,
% predict and score functions for logistic regression.
%
% Arguments:
% params: Structure including following hyperparameters:
% lam... |
6ad5c6dd56152b4ee1fc1294caa3296c7661fdf4a43da07086f6df789f76d288 | MATLAB | 1,346 | 39 | function [Mdl] = run_LinReg(params)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% run_LinReg returns Mdl structure including function handles of fit,
% predict and score functions for linear regression.
%
% Arguments:
% params: Structure including following hyperparameters:
% lambd... |
9bf3231203afa41183d4c89a12d35bd8a553c3c52ba6a9e851eb87235175beb1 | MATLAB | 1,346 | 31 | function [pvec, pstruct] = tapas_hgf_ar1_mab_transp(r, ptrans)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2012-2013 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General P... |
c1af58611d6d6919d538d41f9d003b9bd03eb5c46c66094e9576a4b41ba02f15 | MATLAB | 1,346 | 59 | function openedge=surfedge(f,varargin)
%
% openedge=surfedge(f)
%
% find the edge of an open surface or surface of a volume
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2007/11/21
%
% input:
% f: input, surface face element list, dimension (be,3)
%
% output:
% openedge: list of edges of the specifie... |
36e1adbfe5dfa11cfa84fc24f87a7315be973b088ee70d9c7eaff5685c4aa6a0 | MATLAB | 1,347 | 47 | %% 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
% ... |
6d6c77baa5a014899c0bcd9cf709fc3ce743eb7d74f3cd4aa98b3ceee4911a09 | MATLAB | 1,347 | 42 | function varargout = tapas_physio_run_integration_tests()
% Executes all existing integration tests of PhysIO Toolbox
% NOTE: Integration tests are meant to check complex workflows, e.g., whole
% example scripts
% For smaller, but critical nuclei of the code, such as numerical
% routines (convolution,... |
c5fb9406df954b69d01632ba81103670186c097be299c4854cd5878c59e42a30 | MATLAB | 1,347 | 58 | function [ctmf_out,cluster_img] = ctmf_detector(hsi_img,tgt_sig,n_cluster)
%
%function [ctmf_out,cluster_img] = ctmf_detector(hsi_img,tgt_sig,n_cluster)
%
% Clutter Tuned Matched Filter (ctmf)
% k-means cluster all spectra, make a matched filter for each cluster
%
% inputs:
% hsi_image - n_row x n_col x n_band hypers... |
110ffbb186c04b1205fbee923d2d58025f2fa04ab06898ef6de0315b4c36c485 | MATLAB | 1,348 | 25 | function data = BIS(data)
%data = BIS(data)
%This function combines RTs and PC into a combined measure termed 'Balanced
%Integration Score' (Liesefeld, Fu, & Zimmer, 2015, JEP:LMC, 41, 1140-1151;
%Liesefeld & Janczyk, in press)
%the input data contains the field 'rt' and 'pc'
%the function calculates BIS ... |
62f8b6aed5ed9cc64a75011b0ec817b7d1da35245544613bc867e3661016f34d | MATLAB | 1,348 | 57 | clear all
close all
clc
%% add functions to path
addpath('../fcn/');
%% load data
load data/structural_connectivity.mat
load data/coordinates.mat
load data/brain_states.mat
%% rescale sc matrix
a = sc;
a = a/eigs(a,1);
a = a - eye(length(a));
%% define input matrices
% beta controls the decay rate
beta = 0.15;
n = ... |
fedc2085de8587f4e833af74c6b1a452f4c881d94cb29add8f4d7727355f016c | MATLAB | 1,348 | 77 | function [err,CondNum] = CompCondNum (N_tasks, N_basis, Task, N_TR, polort)
%
% [err,] = CondNum ()
%
%Purpose:
%
%
%
%Input Parameters:
%
%
%
%Output Parameters:
% err : 0 No Problem
% : 1 Problems
%
%
%
%Key Terms:
%
%More Info :
%
%
%
%
% Author : Gang Chen
% Date : Wed Aug 20 15:46:08 EDT 2003
% ... |
493390cc33557ffe51c9c273dc5033c7bca9b15ff7fd06ff00c66a16f06dd352 | MATLAB | 1,349 | 81 |
%% === compare timings for CHOL
R = 20; % number of repeats (to increase accuracy)
nn = 1:1:200;
K = length(nn);
time = zeros(K,3,R);
ops = zeros(K,1);
fun = {
@(a)mmx('chol',a,[]),...
@(a)mmx_MMKL('chol',a,[]),...
@(a)mmx_C('chol',a,[]),...
@(a)ndfun('chol',a)
};
names =... |
9cf84bff4defb3ba52a3223ab1566a0e29e97f38586c33dd498133bbee93eddb | MATLAB | 1,349 | 47 | function make_contrasts_main()
% Figure 3 contrasts identified from SPM.xX.name.
%% USER SETTINGS
spmMat = 'D:\path\to\MRI_project\firstlevel_model1_public\sub-001\SPM.mat';
spmDir = 'C:\path\to\spm';
addpath(spmDir);
spm('Defaults','fMRI');
spm_jobman('initcfg');
load(spmMat,'SPM');
names=SPM.xX.name;
n=numel(names... |
9d7783fbc8cac4fadb8f4f036b780d190ef7d605ae675a6f62dce0dc621f58e0 | MATLAB | 1,349 | 54 | function f = fig_make(varargin)
% creates figure based on aguments in varargin{1}, ..., varargin{end}
% returns its handle 'f'
% default (no arguments): full screen figure
% usage examples:
% f = fig_make('fig_W',18.3, 'fig_H',14);
% f = fig_make;
% (c) Jiri, Mar20
%% settings: backgroud color (bkgclr)
bkgclr = 'w';... |
aba9e5cdae53780ce3afece803b70310b94ce405dc8f66404d1708d2b4daa849 | MATLAB | 1,349 | 50 | function this = save(this)
%saves MrSeries in different file formats
%
% MrSeries = save(MrSeries)
%
% This is a method of class MrSeries.
%
% IN
% parameters.save.format
%
% OUT
%
% EXAMPLE
% save
%
% See also MrSeries
% Author: Saskia Klein & Lars Kasper
% Created: 2014-07-02
% Copyright (C) 2014 Institut... |
1cd2578dedaca494dc86f9d5814850b695293cabf5009dea0bb1d56f206c7786 | MATLAB | 1,350 | 55 | function h = imshow_phase(f, vs, z, slice, palette)
if nargin < 5
palette = 'hsv';
end
if ischar(palette)
palette = str2func(palette);
end
if isa(palette, 'function_handle')
palette = palette(2^10);
end
if nargin < 4
slice = 3;
end
dim = [size(f) 1 1]... |
3d8a55ded355fe9db90141b4f996bd36276f6e35b7f5aa419faa1bc4052ffee5 | MATLAB | 1,350 | 37 | function loadAndFilter(params, dataStruct)
% loads & filters data stored in session cache files
% required structure 'dataStruct' with fields (ex.):
% dataStruct =
% D_field: 'tracker'
% signalType: 'xVel'
% excludedChnls: []
% dataProcessing: {'bp_loPass' 'norm2std'}
% saveNa... |
90b72c241dc1eb7e01f6b239f54d85faceae3d844d86096f093d2f69151319ac | MATLAB | 1,350 | 45 | function params = apply_parameter_changes(params, param_changes)
% APPLY_PARAMETER_CHANGES - Apply user-specified parameter modifications
%
% H1 Line: Modify default parameters with user specifications
%
% Syntax:
% params = apply_parameter_changes(params, param_changes)
%
% Description:
% Updates parameter structu... |
0306c44994d6c063350deb53821b7a694b669578ce49a618e9a34bc7172cc9d3 | MATLAB | 1,351 | 54 | %% Generate Figure 6c
clear; clc;
set_participant_information
% Set hemisphere to analyze
hemi = 'lh'; % Change to 'rh' for right hemisphere
% Load the pre-processed beta values
% Path to change
betable = readtable(['/oak/stanford/groups/kalanit/biac2/kgs/projects/babybrains/mri/code/morphology_allparameters/REVIS... |
455a3bcb2e610870bc263a5489b8761b7fe7ae9f1f5d40d818249083e6ce15a6 | MATLAB | 1,351 | 53 | function [rho pval ts] = circ_corrcc(alpha1, alpha2)
%
% [rho pval ts] = circ_corrcc(alpha1, alpha2)
% Circular correlation coefficient for two circular random variables.
%
% Input:
% alpha1 sample of angles in radians
% alpha2 sample of angles in radians
%
% Output:
% rho correlation coefficient
... |
950141ea0387d69561851a619166f06edd6ccb817be44c3290d23043337ca948 | MATLAB | 1,351 | 50 | function stdshade_sorting(amatrix, astd, alpha,acolor,F,smth)
% usage: stdshading(amatrix,alpha,acolor,F,smth)
% plot mean and sem/std coming from a matrix of data, at which each row is an
% observation. sem/std is shown as shading.
% - acolor defines the used color (default is red)
% - F assignes the used x axis (def... |
48dcb671b9baef79e9298e5719f760c65c167221793cf0724dd8ea97e73d8da6 | MATLAB | 1,352 | 38 | function this = undo(this, doDeleteLastStep)
% restores previous processing step status of MrSeries, with optional deletion
% Y = MrSeries()
% Y.undo(doDeleteLastStep)
%
% This is a method of class MrSeries.
%
% IN
% doDeleteLastStep false - last step is kept for possible restore
% true ... |
a9d470079c23653cbddac7882973f2efd4ab042652aaa2c4ab9422b294a97ef2 | MATLAB | 1,352 | 37 | % Please cite this paper if you use any component of this software:
% D. Cunefare, L. Fang, R.F. Cooper, A. Dubra, J. Carroll, S. Farsiu, "Open source software for automatic detection of cone photoreceptors in adaptive optics ophthalmoscopy using convolutional neural networks," Scientific Reports, 7, 6620, 2017.
% Rele... |
eb598fd6fca2e3967f75dfc9e2fafadf105b969e65f0945b56ac991d4ff7c083 | MATLAB | 1,352 | 44 | function [ Ep ] = tapas_rdcm_empty_par(DCM)
% [ Ep ] = tapas_rdcm_empty_par(DCM)
%
% Creates an empty valid parameter structure for a given DCM
%
% Input:
% DCM - model structure
%
% Output:
% Ep - parameter structure
%
% -------------------------------------------------------------------... |
4a9123549cedcac0d15a3685c519117735d687000cd1b3a9ff9a08bfe811844a | MATLAB | 1,353 | 41 | % R2 - Calculate coefficient of determination (R^2)
% Computes R^2 between measured and estimated time series.
%
% Syntax
% r2 = R2(measured, estimated)
%
% Input Arguments
% measured - Measured time series [time x 1]
% estimated - Estimated time series [time x 1]
%
% Output Arguments
% ... |
6c865057167623d6208e64daad39cc72ea28efc97348996b46b4b49a5f8bc94c | MATLAB | 1,353 | 31 | function [pvec, pstruct] = tapas_ehgf_ar1_binary_transp(r, ptrans)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2012-2020 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU Gener... |
99bf6912ebed31734ecd9286f8ec49c7d43ab1cdd38143441b7252cad5144860 | MATLAB | 1,353 | 51 | function plot_fig4d()
tau = 2.5;
pcatches = [0.15, 0.2, 0.25];
dt = 0.1;
maxT = 30.; % approximately top 99 prctile given our task delay distribution
bins = 0.5:dt:maxT;
mycolor = {'#BCBEC0', '#6D6E71', '#231F20'};
kappa = 0.1;
D = 0.85;
R = [5,10,20,40,80];
figure;
set(gcf, units='inches', renderer='painters', ...
... |
d0115db5420e8a2583ff31f674602fb4cdb7714229cc408521dd0707fe74cb6d | MATLAB | 1,353 | 54 | function [m] = read_pulse(fname)
% [m] = READ_PULSE(fname)
%
% Reads a matrix from a file in the binary format written by
% write_binary_matrix() in miscmaths (FSL library)
%
% See also: write_pulse (for binary matrices), load (for ascii matrices)
if (nargin<1),
disp('??? Error using ==> read_pulse');
disp('Not... |
fb73606688422e735e7078c7c96fd495e4e0958adc8513b82341668ed528b1e9 | MATLAB | 1,353 | 42 | function this = apply_deformation_field(this, fileNameDeformationField, varargin)
% Applies a previoulsy estimated deformation field
%
% Y = MrImage()
% deformation_field = MrImage;
% Y.apply_deformation_field(deformation_field)
%
% This is a method of class MrImage.
%
% IN
% MrImage object containing the deforma... |
19bd501bc10ea19f04dbac0fc98db1e8e31bc087e0b313321bad3c4653e444c7 | MATLAB | 1,354 | 36 | function crf = tapas_physio_crf(t)
% cardiac response function, as described in
%
% Chang, Catie, and Gary H. Glover. �Effects of Model-based Physiological
% Noise Correction on Default Mode Network Anti-correlations and Correlations.�
% NeuroImage 47, no. 4 (October 1, 2009): 1448�1459. doi:10.1016/j.neuroimage.20... |
1f678873b296e288ede61adff4b6a9d3fa5d908d266741b27c0b446f9c5d53ab | MATLAB | 1,354 | 54 | function varargout = semplotGrouped(x,y,color,smooth,solid)
%semplot - plot mean (line) +/- s.e.m. (shaded area) of a matrix "y"
% semplot(x,y,color,smooth)
%
% Copyright (C) 2026 by Ralitsa Todorova
%
% SEE ALSO shadedErrorBar
%
% This program is free software; you can redistribute it and/or modify
% it under the te... |
a118c00cb9841883d3a970dbb8dccd69d9b4c07ca3110db08b211872f128775e | MATLAB | 1,354 | 49 | function [ subject, data ] = nmri_redefine_trials( cfg, subject, data )
%[ subject, data ] = nmri_redefine_trials( subject, data )
% Will redefine trials (using fieldtrip) and take care of markings /
% vigilance scoring, etc...
%
% 06/2018 by NF
data2=ft_redefinetrial(cfg,data);
% now rebuild the trialmarkin... |
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