sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f4ce152a6398b7b6b031860b60035a9d286d64de7d377c797f44005dc07ca9d0 | MATLAB | 1,229 | 41 | function [squares,quad,squares2,quad2,D]=nt_qca2(x,npcs,nsmooth)
%[square,quad,square2,quad2,D]=nt_qca(x,npcs,nsmooth) - maximize induced power using quadratic component analysis
%
% square: linear component closest to most repeatable quadratic component
% quad: most reproducible quadratic component
% square2: line... |
6ac32b49819043160349db9c0e5ae8d8bed8e838af6e05b7247607b46b71ee47 | MATLAB | 1,230 | 29 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2017 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
b01243de23e757f9e26d67b887e34143449dcb46a3f7ae9c3c4671cc286c295c | MATLAB | 1,230 | 29 |
function [MuseStruct_micro, MuseStruct_macro] = MuseMarkers_update_filepath(cfg,MuseStruct_micro, MuseStruct_macro)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% function readMuseMarkers
%
% Crawls and searches through patient- and recording-directories to
% extracts marker timings (t... |
1bb61148988382e9b92849653e741c1a500bfde539f0927b03b226c377f3cbc6 | MATLAB | 1,231 | 23 | function [configs] = simulation_configs()
% Simulation configs, file for handling of paths to toolboxes.
% ---------------------------------------------------------------------
% Copyright (C) 2023 Simon R. Steinkamp, Iyadh Chaker
% This program is free software: you can redistribute it and/or modify
... |
f8233bfe6253a70475fc1cdedc8b03040031a3c02e6d54bf8cf225f832bc3dfa | MATLAB | 1,233 | 34 | %mask = '/dcl02/lieber/ajaffe/SpatialTranscriptomics/LIBD/spatialDLPFC/Images/Liebert_Institute_OTS-20-7748_rush_posterior_2_nuclei.mat';
%jsonname = '/dcl02/lieber/ajaffe/SpatialTranscriptomics/LIBD/spatialDLPFC/outputs/NextSeq/DLPFC_Br3942_post_manual_alignment/outs/spatial/scalefactors_json.json';
%posname = '/dcl... |
28cc9d63a601b3fdaeca1e9134cb567a59b5f5e31675767928546061e9c8265f | MATLAB | 1,234 | 35 | function smoothedV = CBIG_Smooth3DVolumeWithMask(V, mask, outside_mask_type, method, filter_size, arg)
% smoothedV = CBIG_Smooth3DVolumeWithMask(V, mask, outside_mask_type, method, filter_size, arg)
% outside_mask_type = SMOOTH => Everything outside the mask is smoothed ignoring the mask.
% outside_mask_type = SAME =>... |
c6dfee8ea1a086ed3cbaaa2cbbce082dac830cdfa1ddb0258cc616acb3e4d9de | MATLAB | 1,234 | 46 | function x=nt_sns_cluster(x,nneighbors,cluster_size)
% y=nt_sns_cluster(x,nneigbors,cluster_size) - sensor noise suppression within clusters
%
% y: denoised matrix
%
% x: matrix to denoise (time * channels * repeats * ...)
% nneighbors: number of channels to use in projection
% cluster_size: target cluster si... |
15a19cb3f6af3e7572b60030053951a83cf56179819904b13f5173b3e8d639d1 | MATLAB | 1,236 | 37 | function [modified_results] = normalise_to_zero(results_to_plot)
% if size(results_to_plot, 1) < 9 || size(results_to_plot, 2) < 6
% error('The matrix must have at least 9 rows and 6 columns.');
% end
% Number of rows and columns
[numRows, numCols] = size(results_to_plot);
% Check... |
d2331c665aa7981c7a445cef206a8e5e31455fc8acde61c1576279a3ea90e5d7 | MATLAB | 1,243 | 48 | function out = ctflop(in)
% OUT = CTFLOP(IN)
% Simple function to permute between a Mx3 color table and
% a Mx1x3 image. This allows tools which only support images
% to conveniently handle color tables. This can also be done
% using permute(), but ctflop() provides a succinct and readable
% way to e... |
d27e3aca1af836b2ab861a277b3329da24bacf1e064da19d2f0f20850c744842 | MATLAB | 1,251 | 28 | %% Demo 6 - Linear mixed model with random slopes
% Subjects often differ not just in their baseline but in how strongly a treatment
% affects them - something repeated-measures ANOVA cannot express, but random
% slopes can. Shown on the sleepstudy dataset (lme4; Belenky et al. 2003):
% reaction times of 18 subjects ac... |
1d6d188c84250869cf67b09b5090ed5b12023486f6781e6ac41c9278bea5c397 | MATLAB | 1,252 | 57 | %
% varargout = estimateVarSize(varType, numE, unit)
%
% Description:
% estimate variable size
%
% Input:
% varType - type of variable, e.g. double
% numE - number of elements
% unit - unit of Byte
%
% Output:
% varargout - print to screen if no output, otherwise output the estimated size and uni... |
4df9cf4612d39fd1fff89855a031fe1cb21d55142a800c4b4e161aab3a632d27 | MATLAB | 1,253 | 26 | function dict_out = dictInitialize(dict_init, T, N)
% dict_out = dictInitialize(dict_init, T, N)
%
% Function to initialize a TxN sized dictionary. The columns of the
% dictionary are normalized to unit norm. If a matrix is fed in as the
% first input, that dictionary is just normalized (no random
% initialization ... |
a8a55e34bc15c858f8e013e048ac4b5f15680b8954d4a37652e4d40c3ba9f3cf | MATLAB | 1,253 | 25 | function [epoched_bs_around_AMs,epoched_bs_around_NAMs] = merge_file_BS_epoched(bs_to_tap_predictions, window,s_i)
BS = bs_to_tap_predictions(:,2);
epoched_bs_around_AMs_i = cellfun(@(BS,s_i) getepocheddata(BS, s_i.AMs, window), BS,s_i,'UniformOutput',false);
epoched_bs_around_NAMs_i = cellfun(@(BS,s_i) getepocheddata(... |
d08fbc024b3d0736dd45976ba43900a082ab963f4f9971b960e5863d4bb4c226 | MATLAB | 1,257 | 40 | function pairAng = pairwiseAngles(X, Y, dim, varargin)
%% Default arguments
if ~exist('dim', 'var') || isempty(dim)
dim = 1;
elseif ischar(dim)
varargin = [{dim}, varargin];
dim = 1;
end
%% Reshape input to be in the form of column vectors
Xdims ... |
73f6d0752238b51d33698652582cddb0788ff1a1764ce24def03780e564f26f8 | MATLAB | 1,259 | 36 | %
% BDP BrainSuite Diffusion Pipeline
%
% Copyright (C) 2019 The Regents of the University of California and
% the University of Southern California
%
% Created by Chitresh Bhushan, Divya Varadarajan, Justin P. Haldar, Anand A. Joshi,
% David W. Shattuck, and Richard M. Leahy
%
% This program is free sof... |
1461127d29b51e79753629bd03c7cc7b478026fe0d91ba009a928b6d94d92b8c | MATLAB | 1,266 | 52 | function InFormStitch(filename,O,P,fname)
% O{1} = 'DAPI';
% O{2} = 'Abeta';
% O{3} = 'pTau';
% O{4} = 'GFAP';
% O{5} = 'MAP2';
% O{6} = 'Lipofuscin';
%filename = '/dcs04/lieber/lcolladotor/with10x_LIBD001/Visium_IF_AD/processed-data/Images/InForm/VIFAD1_V10A27-004/20210204_Visium-IF_Scan1*component_data.tif';
myfil... |
4150a742fc3ac859eca15182c1c6136ba281ab8b1531c7750b2c710a6d8ec3dd | MATLAB | 1,270 | 47 | %% Compute the dominant eigenvalue using power iteration together with Rayleigh quotient iteration.
% http://cis.poly.edu/~mleung/CS4744/f04/CS4744f04Instruction.htm
% From http://cis.poly.edu/~mleung/CS4744/f04/ch04/PowerRayQuotF.m
function [eVector, eValue, converged, iterations] = dominantEigen(A, x, maxIter,... |
df9493a8fc4caf85d33ed7a527382692184c7eaa8989053a7bab75f4fb7aeb07 | MATLAB | 1,271 | 39 | function next = accumulate_slice(input, header)
matrix_size = header.encoding.encodedSpace.matrixSize;
function slice = slice_from_acquisitions(acquisitions)
disp("Assembling buffer from " + num2str(length(acquisitions)) + " acquisitions");
acquisition = acquisitions(end);
sl... |
15b6b43016366130f9beaf407cbd710540944d79a621734c7011d812f997aefc | MATLAB | 1,274 | 38 | % Returns the sorted order of elements in A, i.e. 1 corresponds to the smallest element and numel(A)
% corresponds to the largest element.
function order = sortorder(A, dim, asRank, varargin)
%% Default arguments
if ~exist('dim', 'var') || isempty(dim)
dim = find(size(A) > 1, 1, 'first');
end
... |
3f46b96bf3c8bb0f58a519f41c2e966cbbdf16b956f6bc32b333e6e0d952c8f8 | MATLAB | 1,276 | 45 | function rstd = robustSTD(data)
% robustSTD compute robust standard deviation
%
% usage: rstd = robustSTD(data)
%
% arguments: data - vector of numbers
% or array - operates along 1st dim
%
% outputs: rstd - robust standard deviation
%
%
% translated from lisp (statistics.lisp) to mat... |
5ac1bb29cf4baf54ed620d40dfef35fa425166c9a953770d371e6c483f274514 | MATLAB | 1,276 | 34 | %% BINNEDAVERAGE Computes the average y(x) in bins of x.
%
% Note that the first and last bins includes under/overflow in the case where xEdges is provided. If
% not, the Matlab histcounts() function is used to obtain optimal binning divisions.
%
function [yAverage, xCenters, yData] = binnedAverage(x, y, xEdges... |
a3a3d2bec14be56b23c461a21505e9016b31affe2bb71d9a6cf86bfe8f69632f | MATLAB | 1,276 | 33 | function insertion = createArgumentDefaults(hDocument, eventData)
%% Obtain inputs from function signature
[~,inputs] = parseFunctionSignature(hDocument);
tabSize = com.mathworks.services.Prefs.getIntegerPref('EditorSpacesPerTab');
tab = repmat(' ', 1, tabSize);
if ... |
54ade9fc0a464ebaf7b7dd053a41cc28ddb7915ab48f6c4abba57722acc29c6d | MATLAB | 1,279 | 42 | %%*******************************************************%%
%%% B1 map calculation
%%%
%%% Parameters of the Fermi pulse are based on mfc_bloch_siegert_v3e
%%% - PhaseDat: phase encoding the B1 amplitude
%%% - dwrf: off-resonance frequency in Hz
%%% - DurPulse: Fermi pulse duration in sec
%%%
%%% NC 03.01... |
095ead5a56468a29bda53afeacffa15d86530e782bfe15c906bbda867c711566 | MATLAB | 1,280 | 33 | function handle = cmap(axis, palette, colorRange, numColors, varargin)
colormap(axis, palette);
handle = colorbar('Peer', axis);
if ~isempty(varargin)
set(handle.Label, 'String', varargin{:}, 'Rotation', -90, 'VerticalAlignment', 'bottom');
end
% Set range of axis color mapping
... |
fb345a50f33d4b2102ed0d0ed998e39df10ad90671ad387f2d1d6357f60ba7ac | MATLAB | 1,284 | 36 | function generateTests()
% this function generates some test data to be used with the consistency
% tests. It is just a list of the testcases effectively
% the most basic dataset
simulate_data('tests/test_cases/test1','2AFC','binom','Blocks10_fix',100,'norm')
% test case without blocks
simulate_data('tests/test_cases... |
fc4d614b1b4dd4d499264be1c6b0aab9e295c828ca52ffba6013c7e0b4741349 | MATLAB | 1,285 | 45 | function compile_bfp(bfp_version)
restoredefaultpath;
addpath(genpath('../../src'));
bfp_bin_dir=sprintf('bfp_%s', bfp_version);
fid = fopen('bfp_version.txt', 'w');
fprintf(fid, bfp_version);
fclose(fid);
if exist(bfp_bin_dir,'dir')
rmdir(bfp_bin_dir,'s');
end
mkdir(bfp_bin_dir);
mcc -m -v bfp.m
% Compile auxi... |
d97afe92790a7ef3cdf9f8bbf62708c1398b329d8b404dde36b854c14be377d5 | MATLAB | 1,286 | 33 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2019 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% mo... |
e5c367910c6115385546acd2780e88c9c5689ad7b093ba352c949f0d574f7224 | MATLAB | 1,286 | 52 | % FASTCORR Fast calculation of Pearson's correlation coefficient for each pair of columns in X and Y
%
% Inputs
% ========
% X :
% Y :
%
% Outputs
% =========
% corrCoeff :
% pValue :
%
% Created : 04-Apr-2019 14:50:47
% Author : Sue Ann Koay (koay@princeton... |
4e0c95d6a9b16881fd5156ce8748277ebb2a499d70b788ae3039bdd8aab0a071 | MATLAB | 1,287 | 35 | %**************************************************************************
%
% Writing data to disk for later use. Developed for writing sensitivities
% acquired separately (s-map) for later use in unfolding.
% input: Structure with data field
% gadNoiseDir: Gadgetron store directory
% ... |
f95597cf2f79ee83d0e9dd57fea6746945e01766546e6fc4bdfd2969cc4eb4f1 | MATLAB | 1,289 | 35 |
%% load experiment info and set a few variables for analysis
clear
% load experiments and generic stuff
experiments = 'your function here';
repeatCalc = 0;
save_data = 1;
% folders to save various results
folder4power_ramps = 'to save power of ramps';
folder4stim_props = 'to load stimulation properties';
folderSM = ... |
6fa510dd06b882876cc0246b56c04c96f4a7e89035be2fd6bf32f505b229e9be | MATLAB | 1,292 | 53 | function CBIG_AverageCorrelationMatrixGeneral(output_file, varargin_text)
% Read a file list, average all mat files in the list and save output.
%
% CBIG_AverageCorrelationMatrixGeneral(output_file, varargin_text)
% Input:
% output_file : output file name
% varargin_text: input list name
%
% Ex... |
87039ce0832bc5124e1fac4ed31c05712aff41239798bba212fdb8f5d5184c3f | MATLAB | 1,292 | 45 | function FastPrintv2(prefix, filename)
%Original code by David J. Barker; Modified by
%Carissa A. Bruno for the Barker Lab at Rutgers University.
mydir=cd;
%create a "Figures" folder if one does not already exist.
if isfolder([mydir '/Figures'])==0
mkdir('Figures')
else
end
%To DO: If current directory=f... |
a9a90b3b9117e5b7c723b021992042ed231748ba3c25d531d8a5ad35f7e9f4ea | MATLAB | 1,292 | 36 | % Like mtimes(), except that slices (3rd and higher dimensions) are supported.
function C = mtimes3(A, B)
%% Check input sizes
szA = size(A);
szB = size(B);
if szA(2) ~= szB(1)
error('mtimes3:size', 'Number of columns (%d) of A must be equal to the number of rows (%d) of B.... |
0377ca155baf203a8153bb2e6230f9a00573d2421a760b6c45d40566755cbc35 | MATLAB | 1,294 | 48 | %% function to get bins that are included in analysis
function [fieldBins, fieldBinsUpsampled] = GetFieldBins(I, rate_thresh, peakRate)
I0 = I;
%% get bins that exceed rate threshold
Npeak = length(peakRate);
[peakRate, ~] = sort(peakRate, 'descend');
FieldX =[];
FieldY = [];
[r,c] = size(I);
for i = 1:Npe... |
fd12ad0ca5e2338ae4db55e0dea98807975271e0fd3c73e1d7d2d2070ac3ac59 | MATLAB | 1,297 | 30 | % extractDevAdlNmGenes.m
% Extract genes intersecting Developing mouse brain atlas & Mouse brain
% atlas which have no missing values
%% import data
load("geneInfoNonmissing.mat")
load('structureInfoTableOh2014Sorted.mat')
load('expEnergyMatrixOh_nonMissing_sorted_logEps2_zscore.mat')
load('connectionMatrixOhP005_sor... |
f7fc4090f1059521ea249acf36843bb6b7b55469b83a574fe21e4ff3973b82c0 | MATLAB | 1,298 | 55 | %%
%
function [varargout] = replaceTitle(varargin)
%----- Default values
if nargin > 0 && all(ishghandle(varargin{1}))
handles = varargin{1};
iOption = 2;
else
handles = [];
iOption = 1;
end
options = inputParser;
options.addRequired('expressi... |
e0694a7dc5cb5ed2e9705da4a2586cffe3536446d0bab21215671dae7a7fbe50 | MATLAB | 1,300 | 38 | %%
% Optimal smoothing amount for a smoothingspline, depending on the
% separation of data points.
%
function [smoothing] = optimalSmooth(sequence, reference)
% User provided value
if numel(sequence) == 1
delta = sequence;
% User provided sequence, calculate average separation
... |
3820e0499159fc25f8b17aeb4ff84bef9218ae4055ab560f7a9db23b3d902911 | MATLAB | 1,302 | 36 | function [data1, data2, inactive] = remove_inactive_bs(data1, data2, window_of_inactivity)
%% Removes segments where BS data may have been absent.
% Inactive BS data is defined as any sequence of x milliseconds or higher where the sum of the difference between the signals is 0.
%
% **Usage:** [data1, data2, inacti... |
593df350e0cf725dd1e15925ed3a68266536fbb5687666c8d5d9fcf8c641b51e | MATLAB | 1,302 | 46 | function I = gcmi_model_cd(x, y, Ym)
% GCMI_MODEL_CD Gaussian-Copula Mutual Information between a continuous and a
% discrete variable in bits based on ANOVA style model comparison.
% I = gcmi_model_gd(x,y,Ym) returns the MI between the (possibly multidimensional)
% continuous variable x and the discrete v... |
dbf7cf9e3f25f9a44163f0b3d8f7798db1d1956df6e2381053c67e46fa13be12 | MATLAB | 1,302 | 49 | % Example script for estimating a regression model
%
% Steve Fleming 2018
clear all
Ntrials = 100;
Nsub = 50;
c = 0;
c1 = [-1.5 -1 -0.5];
c2 = [0.5 1 1.5];
group_d = 2;
group_baseline_mratio = 0.8;
sigma = 0.5;
sigma_beta = 0.2;
gen_beta = 0.5;
cov = rand(Nsub,1)';
mcmc_params = fit_meta_d_params;
mcmc_params.estim... |
e43daf6043a7ad2890066ea44babe8c7d3ed3ed0bc3d19ffb756994e2e6afc62 | MATLAB | 1,303 | 36 | function smoothedV = ...
CBIG_AuthorTopic_FFTSmooth3DVolumeWithMaskPredfinedFFTKernel(V, ...
mask, fftK)
% smoothedV = ...
% CBIG_AuthorTopic_FFTSmooth3DWithPredefinedKernel(V, ...
% mask, fftK)
%
% Smooth a 3D volume using Fast Fourier Transform (FFT) with a predefined
% smoothing kernel and a mask
%
% Inp... |
50f3ca357c34748cd6b361ff7ab2565ae7ae350dc5c3f4859af792c886ed8930 | MATLAB | 1,305 | 48 | function [Delta490] = DeltaF(Ch490,Ch405,varargin)
% Smooth and process 490 channel and control channel data for fiber
% photometry.
%Inputs:
% 1--Ch490-GCamp Channel
% 2--Ch405-isosbestic control channel
% 3--Start time- Set a specific sample to start at
% 4--End time-specify a specific ending sample
if... |
4a1cb1d6eaadd23a7262dbb1b75617f431a1e3aa6b4778824b0fe7facff389f4 | MATLAB | 1,306 | 40 | function reorg_neighbors = CBIG_SPGrad_neighbors_exclude_medial(orig_neighbors, mask)
% reorg_neighbors = CBIG_SPGrad_neighbors_exclude_medial(orig_neighbors, mask)
%
% This script excludes medial wall vertices from the neighborhood structure and make
% the neighborhood vertices indices contiguous.
%
% Input:
% - ... |
5625970d295e22d6021893c671228a0be44ee581c82a6a087e39533e0e465a7e | MATLAB | 1,306 | 32 | function CBIG_AnalyzeDirectAndIndirectCorrespondence
% CBIG_AnalyzeDirectAndIndirectCorrespondence
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
indirect_count = MRIread('1000sub.FSL_MNI152.1mm.count_map.nii.gz');
indirect_vertex = MRIread('1000sub.FSL_MNI152.1mm.v... |
fc277279d12a5a78c69045c6f7823138fbda6377c71b838f78ae51eca890ee45 | MATLAB | 1,306 | 59 | close all; clear all; clc
addpath(genpath('/data/code/matlab'));
prepOutput;
%%%% PARAMETERS %%%%
% Database
database{1} = '/data/coord/tyr/tyrunits';
database{2} = '/data/coord/zen/zenunits';
% Data files
dataDir = '../data/cohLFP_TestJustPrintReal/500ms_5Hz_Target_-450:1000ms';
dataDir2 = '../data/cohLFP/_old2/5... |
fe8f1aff9ba791c075193d36d3f64f0bd9db75eb0cf05b60eca3c5a3bd3aa23a | MATLAB | 1,307 | 37 | function splitSlide_IF(fname,O)
img = load(fname);
%O = fieldnames(img);
%N = 4; %number of capture areas
disp(['The IF image has ',num2str(numel(O)),' channels'])
[y,~,~] = size(img.(O{1}));
tic
disp('Splitting whole slide into individual capture areas')
for i = 1:numel(O)
tic
I1.(O{i}) = img.(O{i})(1:roun... |
2d9d02c4b7d8cdf1ac353dfd418af7b1fc5adcebc334834a8ed974a996b20fe7 | MATLAB | 1,308 | 28 | %% Demo 3 - Two-way ANOVA (two crossed factors + interaction)
% Two crossed factors and their interaction are the classic two-way ANOVA, which
% a linear model reproduces exactly on a balanced design. Shown here on the
% ToothGrowth dataset (R base): odontoblast length of 60 guinea pigs given vitamin
% C by two deliver... |
03ecf0567f704120c45f4be62779a0eb2f609f8eb42c9d65ed4f7a660d68bbac | MATLAB | 1,309 | 50 | function CBIG_CreateRandomVarargin(num_subjects, num_randomness, varargin_txt, out_path)
% Create num_randomness list of files, each containing num_subjects names
%
% CBIG_CreateRandomVarargin(num_subjects, num_randomness, varargin_txt, out_path)
% Input:
% num_subjects : number of subjects
% num_r... |
551d19b3ef55e26059961c5ffc9828ad3ff2317f48bc53cbc5cbb28f2bf0a13b | MATLAB | 1,309 | 45 | function [modified_results] = normalise_to_zero_SAP(results_to_plot)
% if size(results_to_plot, 1) < 9 || size(results_to_plot, 2) < 6
% error('The matrix must have at least 9 rows and 6 columns.');
% end
% Number of rows and columns
[numRows, numCols] = size(results_to_plot);
% C... |
21700cd683095e27ec56b6f0e7b1fe705e3f059eaf047d20e0086af5b334af42 | MATLAB | 1,313 | 37 | function [idx,distmm] = spm_prf_find_voxel(XYZmm,PRF)
% Identifies the index of the voxel in the PRF with coordinates closest to
% those provided
%
% XYZmm - [3 x 1] vector of coordinates (mm)
% PRF - PRF structure
%
% idx - Index of the closest voxel
% distmm - Euclidean distance in mm of closest voxel to the tar... |
41766a15cfa199ff80b17c5bc69b00e9f27ce36cbd2e5b7fa38583076d2e376c | MATLAB | 1,314 | 49 | function [childrenIdListTxt] = extractChildrenIdListTxtFromIDAndPath(structureId,structureIdPath)
%% same process with ~~fromPath
load("MBStructureTreeData_raw.mat");
idListStr = strrep(structureIdPath,'/',',');
idListStr = strip(idListStr);
idList = str2num(idListStr).';
% i = 1
childrenCell = struct2cell(MBStruc... |
c65b19a6160a8e3f179397b550a126eeaef6d74bd0b4b6445cd66860116493bb | MATLAB | 1,319 | 44 | %% Difference of exponentials kernel, normalized such that the maximum probability is 1.
function f = differenceExponentials(t, tauRise, tauDecay)
%% Special cases
norm = tauDecay * tauRise^(tauRise/tauDecay) ...
* (tauDecay + tauRise)^(-((tauDecay + tauRise)/tauDe... |
18dfa324ab194ce2b078f7a340e7701a280dac9313d54a43c591c6b525cddca1 | MATLAB | 1,323 | 57 | function x=nt_demean2(x,w)
%y=nt_demean2(x,w) - remove mean of each row and page
%
% w is optional
%
% if w is a vector with fewer samples than size(x,1), it is interpreted as
% a vector of indices to be set to 1, the others being set to 0.
%
% NoiseTools
if nargin<2; w=[]; end
if nargin<1; error('!');end
if ~is... |
ccaac519dd3d8ae54a3d043d94b42853167f247561a511cacc0123b9757faec1 | MATLAB | 1,324 | 25 | function [r_colormap,g_colormap,b_colormap, y_colormap] = create_rgb_colormaps()
%% Create R, G, B colormaps for easier visualisation of IF images
% @author: pdzialecka
%%
r_col = [1,0,0];
g_col = [0,1,0];
b_col = [0,0,1];
r_colormap = [(linspace(0,r_col(1),256)'),(linspace(0,... |
b93b288239d281ad8b8de775e929e31d3baa50c6ea58c8c78dbbd99ec534d918 | MATLAB | 1,325 | 23 | %% load epoched event
path_upper = '/home/ruchella/non_attribute_movement_and_EEG/data/all_epochs';
all_epochs = load_EEG_checkpoints(path_upper, 'all_epochs', 'all_epochs', 'save_results', 0);
%% load EEG data
ancova = load_EEG_checkpoints('/home/ruchella/non_attribute_movement_and_EEG/data/ancova', 'ancova', 'ancova'... |
1fff873294092b45ff973bfe1c2b39ab8c0f9373a005fab52284bd266c7e45b2 | MATLAB | 1,326 | 44 | function [trigTimes, trigLengths] = jw_extract_trig_times(fname,thres,negative)
% JW_EXTRACT_TRIG_TIMES reads an incoming trigger and returns the event
% timings for when the trigger goes high
%
% Author: Jeffrey B. Wang <Jeffrey.Bond.Wang@gmail.com>
%
% Inputs:
% fname: Name of input .ncs file with the t... |
864a09a3b1fdbf88d52be90685fd8328eaabbcad5c14d4c6b16d70f963c7d6c9 | MATLAB | 1,326 | 37 | function corr_mat = CBIG_nancorr(s_series, t_series)
% Calculate correlation matrix between each column of two matrix where
% there could be nan values in the matrices.
%
% corr_mat = CBIG_nancorr(s_series, t_series)
% Input:
% s_series: T x N1 matrix, T is number of frames, N1 number of voxels
% ... |
1abe916338ba5c9821c976aacd97a76d526aa1ff2ca350ab846f0a9c1c92850a | MATLAB | 1,327 | 41 | function [figHandle, position] = makePositionedFigure(position, monitor, positionMode, varargin)
% Default arguments
if nargin < 2
monitor = 1;
end
if nargin < 3 || isempty(positionMode)
positionMode = 'OuterPosition';
end
% Get the screen coordinates to reference the figure positi... |
a029fdc688af9c4b7f9292628b411d93de549941918121a541a2b618e2dfca04 | MATLAB | 1,327 | 38 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2017 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
cf38b5e25b37af725aea0bc4affdb451362d7a315ed5443efb2ba74968cff500 | MATLAB | 1,327 | 46 | function outpict = ptile(inpict,szo,varargin)
% OUTPICT = PTILE(INPICT,OUTSIZE,{OFFSET})
% Create an image by repeating a smaller image to fill a specified geometry.
% This can be used for generating images from tileable pattern/texture images.
%
% INPICT is an image of any standard image class.
% multicha... |
6bc4ef9fd129dde062b6b74a241f4aea1893de2e9d3a58c3c957d62b494b8da7 | MATLAB | 1,329 | 38 | function cmapnew = ctshift(cmap0,stretchamt)
% CMAPNEW = CTSHIFT(CMAP,AMOUNT)
% Nonlinearly shift the content of a colormap toward one end or the other.
% This may be useful if trying to tailor a map to provide good feature
% contrast when the distribution of data is significantly asymmetric.
%
% CMAP is a ... |
73484161ac53399888e7c25c4cb8f9e5fb1744da1049064aedceef9e9d08c028 | MATLAB | 1,329 | 39 | function CBIG_AverageCorrelationMatrix(SUBJECTS_DIR, input_file, session_file, output_file)
% CBIG_AverageCorrelationMatrix(SUBJECTS_DIR, input_file, session_file, output_file)
% This function is specific to Thomas's project. Please use CBIG_AverageCorrelationMatrixGeneral
%
% Example:
% CBIG_AverageCorrelationMatrix... |
bfb46303f6be4be86a498dea1c191b4568cedacebdd565ca96135fc77ef6d2cb | MATLAB | 1,329 | 27 | % === main_parameter_setting.m ===
%% === Set pair data generation options ===
noiseLevel = 0.01; % define level of noise added to CCA pair data for computational stabilization
dataType = "PC"; % define data type for analysis;
dataDim = 50; % define PC dimensions being used in the analysis % define seed for noise
pa... |
5fe911453a84e7b00f0964068a52b74a27f980efcd4a3489007347bf7731a2a2 | MATLAB | 1,335 | 41 | % Create a long figure with the given aspect ratio but near the default plot area (width*height)
function fig = longfigure(aspectRatio, areaScale, varargin)
%% Default arguments
if nargin < 1 || isempty(aspectRatio)
aspectRatio = 4;
end
if nargin < 2 || isempty(areaScale)
if aspectRatio <... |
3d0743d987e23b4cfd3986899aa16ef68431a93f45f5f475548444359403756b | MATLAB | 1,337 | 39 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2017 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
d7536259c9980eb2b9694db440ba6e9cc1c2d52552397a4a55b55983b0da645e | MATLAB | 1,340 | 29 | %% function to calculate tuning curves for each cell in both context and to calculate Rayleigh's vector
function [RV, HDir_Rate, EventHDir] = Get_HDirTuning(EventTime, binned_HDir, HDirOccupancy,Nbins,binCenter,edges)
[Ncells, ~] = size(EventTime);
EventHDir = cell(Ncells,2); % heading direction during event for e... |
7e764edc4f7577beef23ca6bbc9d35a63e5aafefec98c3fb1e09efce44157182 | MATLAB | 1,341 | 54 | % Test script, compare with funciton hypergeom from symbolic math toolbox.
% Siyi Deng; 10-10-2013;
if exist('hypergeom','file') ~= 2
error('Requires the function HYPERGEOM from symbolic math toolbox.');
end
numTest = 1000;
a = randn(numTest,1);
b = randn(numTest,1);
c = randn(numTest,1);
x = randn... |
1c9958ec1cb71a84498005239392453471dd67b4790899dc4278acdfff5acb62 | MATLAB | 1,342 | 42 | function [s] = mstruct(varargin)
% MSTRUCT Makes a struct array with the given fields, each of which is
% initialized to an empty array.
%
% The size of the struct array can be specified as the first arguments,
% otherwise the default is [1 1]. Also an initial value (if different
% from [])... |
aae4493bc28b12ceb8e30f9083d566b6ec10f0fc5516c76b8fc0f9d0f6db1ca5 | MATLAB | 1,342 | 34 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2017 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
21b3d827d97ddb7e1e3c45304c57f39d177da7caf35b136327c1a61b3839b630 | MATLAB | 1,344 | 41 | function neighborhood_cell=CBIG_ComputeNeighborhood(hemi, mesh_file, radius, surf_type)
% neighborhood_cell=CBIG_ComputeNeighborhood(hemi, mesh_file, radius, surf_type)
% This function is used to find neighborhood vertices for each vertex
% within radius.
% Input:
% -hemi: 'lh' or 'rh'
% -mesh_file: Freesurf... |
b7ab2846f32529a398cf6d4cd4a7123c755cb390b1d204866e10e1c3d9f753bb | MATLAB | 1,344 | 41 | % Author: Woojae Jeong
%% Bad channel interpolation
if ~isempty(char(chan{:}))
% Process: Set bad channels
sFiles = bst_process('CallProcess', 'process_channel_setbad', sFiles, [], ...
'sensortypes', chan); % Specify bad channel names
% Process: Interpolate bad electrodes
sFiles = bst_proces... |
ef2cf67cc53ab61c1a9fb512f36c9a076bc3fc88861ab7e243cec44df0286bac | MATLAB | 1,344 | 43 | function X = chisquare_inv(P,V);
%CHISQUARE_INV Inverse of chi-square cumulative distribution function (cdf).
%
% X = chisquare_inv(P,V) returns the inverse of chi-square cdf with V
% degrees of freedom at fraction P.
% This means that P*100 percent of the distribution lies between 0 and X.
%
% To check, the a... |
4eefe1a0fd1b1d2e48b5f2867c5d70e452e5fcffb1a65d957d54e428ef80b74a | MATLAB | 1,345 | 43 | %% Gergely Tarcsay, 2022. Function to read Bonsai behavior data. Files are merged when multiple outputs are found (due to restarting the recordings for example).
function [pos, event] = ReadData(rootdir)
poslist = dir(strcat(rootdir,'\Pos*.csv'));
%if there is more than 1 position csv - merge them
pos = [];
... |
1d92bbf61bf49d5642f527a24c9c915952b1b802042073906c038c06e441e5ff | MATLAB | 1,347 | 35 | % Compute the standard deviation and confidence interval thereof using boostrapping
function [stddev, interval] = standardDeviation(data, numBootstrap, probability, w, dim, varargin)
if nargin < 3 || isempty(probability)
probability = [0.05, 0.95];
end
if nargin < 4 || isempty(w)
w ... |
676871757b4efa1425e5f525d46ca86858cae89360fb4ec13bbc7fc3c2f90a44 | MATLAB | 1,348 | 45 | %predefine port
function [error_type, pairs] = GetWrongChoice(event, reward_ports, Incorrect)
ports= ["W", "SW", "S", "SE", "E", "NE", "N", "NW"];
error_type = [0 0 0];
pairs = strings(length(Incorrect(:,1)),2);
for i = 1:length(Incorrect(:,1))
%% get correct port
msg = string(event{Incorrect(i,2),1});
msg_p... |
1d3a51341a2c98a532369b9fdd255dc9aaa42a4d8e82b79769ca6dde3e106c29 | MATLAB | 1,351 | 54 | function Q = randomFindRange(A, r, epsilon, randMatrix)
%% Default arguments
if nargin < 2 || isempty(r)
r = 10;
end
if nargin < 3 || isempty(epsilon)
epsilon = 1e-5;
end
if nargin < 4
randMatrix = [];
end
%% Initial values and stopping conditions
maxError2... |
24e2d26fa8e880fd2a5db7fdb850baaadf71decf499e4d24265b7457a92c1705 | MATLAB | 1,354 | 38 | function x=nt_sns1(x,nneighbors,skip,w,threshold)
% y=nt_sns1(x,nneigbors,skip,w,threshold) - sensor noise suppression
%
% y: denoised matrix
%
% x: matrix to denoise
% nneighbors: number of channels to use in projection
% skip: number of closest neighbors to skip (default: 0)
% w : weights (default: all on... |
4bac1318d182c77ea581198610d522be724b2f83061c3c6a20375a82046ed184 | MATLAB | 1,354 | 30 | %% Demo 7 - Linear mixed model on log-transformed response
% Strictly positive, right-skewed outcomes strain the constant-variance assumption
% of an ordinary linear model; one remedy is to model them on the log scale. Shown
% on the sleepstudy dataset (lme4) - the same reaction-time data as demo 6. The
% response is f... |
c0b82c4f958b707c525643fba7a9fcb81aa93c9b750e6de831886ceff5877919 | MATLAB | 1,355 | 64 | function [sbb, sww, icc] = CBIG_manova_cov(data)
% [sbb, sww, icc] = CBIG_manova_cov(data)
% Implemented as in Equation 3 of Amemiya 1985 (What should be done when an estimated
% between-group covariance Matrix is not Nonnegative Definite)
% WITHOUT correction for negative-definite covariance
%
% assume data = n x r x... |
c0e99eecdd802070aea76bdd5e97f84f6d01e0f44338e3e4a1412eeb79fbb40c | MATLAB | 1,358 | 37 | function PET_slurm_joblist
%find config script :
addpath (genpath('\\l2export\iss02.charpier\analyses\vn_preictal\scripts\EpiCode\projects\preictal'));
config = PET_setparams;
sc_version = '1.0.8';
fname = fullfile(config{1}.datasavedir,'spyking_circus_slurm_job_list.txt');
fid = fopen(fname,'w');
for ielec = 1:size... |
1c16bfd8d3edd6755373f521581f18ebceb7c961d30657bed9c1e34f4ae73aca | MATLAB | 1,360 | 39 | function [rastmat timevec] = mraster(trialspx,pre,post,varargin)
% function [rastmat timevec] = mraster(trialspx,pre,post,varargin)
%
% function generates matrix for raster plot from cell array 'trialspx' generated by mpsth.m
% works with ms resolution
%
% IMPORTANT: pre and post must be as large or larger than pre a... |
4906faae1c36d1571d662acf1ef8f1c8f039111ffa1f228b554a6f29322e0bd8 | MATLAB | 1,360 | 37 | function katia_slurm_joblist
%find config script :
addpath (genpath('\\l2export\iss02.charpier\analyses\vn_preictal\scripts\EpiCode\projects\preictal'));
config = PET_setparams;
sc_version = '1.0.8';
fname = fullfile(config{1}.datasavedir,'spyking_circus_slurm_job_list.txt');
fid = fopen(fname,'w');
for ielec = 1:si... |
1bc4341eb75505d32c85cda836a47fc3727ca916c250c7defba4fea38020291c | MATLAB | 1,364 | 54 | function [c,tw]=nt_tsxcov(x,y,shifts,w);
%[c,tw]=nt_tsxcov(x,y,shifts,w) - cross-covariance of X and time-shifted Y
%
%
% c: cross-covariance matrix
% tw: total weight
%
% x,y: data to cross correlate
% shifts: array of time shifts (must be non-negative)
% w: weights
%
% This function calculates, for each pair o... |
580ea3c496975c9ea982213e2555f2642e3f4472361d55b18a470eb0d4287409 | MATLAB | 1,364 | 39 | %TEMP Blue-pale-dark red colormap
%
% Examples:
% map = temp
% map = temp(len)
% B = temp(A)
% B = temp(A, lims)
%
% A colormap designed by Light & Bartlein for visualizing data such as
% temperature, with good contrast for colorblind viewers.
%
% The function can additionally be used to convert a r... |
8d7d7a6727420d800e4ec1c0163edc016961a76886754c8cb9d34751a7dd2d4a | MATLAB | 1,367 | 37 | function next = noise_adjust(input, header)
noise_matrix = [];
noise_dwell_time = single(1.0);
try
noise_bandwidth = header.acquisitionSystemInformation.relativeReceiverNoiseBandwidth;
catch
noise_bandwidth = single(0.793);
end
function f = scale_factor(acquisit... |
16d1cbde49fa831dfe843b4239d4e656bda4b6886a19af5f767ac3e1bd1b15ba | MATLAB | 1,369 | 46 | %% Creates a toolbar button that switches from one figure to another in a linked set
function linkfigures(handles, labels, icons)
% Default arguments
if nargin < 3
icons = repmat({fullfile(matlabroot, 'toolbox', 'matlab', 'icons', 'plotpicker-comet.png')}, size(handles));
end
for iFig = 1:nu... |
2fd73a5e9983cd57fa3b564af6c07a7dfd0fbe5e79d7ab39e22f3862965f793f | MATLAB | 1,372 | 32 | % BINOINTERVAL Binomial parameter estimates and confidence intervals using Jeffreys method.
%
% Usage:
% [phat,pci] = binointerval(x,n)
% [phat,pci] = binointerval(x,n,alpha)
%
% binointerval() computes the maximum likelihood estimate, phat, of the
% probability of success in a given binomial trial, based... |
6db150e790bfea3dda768a113d998554bd0a1e98cdb880a8aaa91ac503d6235f | MATLAB | 1,372 | 41 | classdef HoldoutSplit
properties
TrainMask (:,:) logical % [#Region,#Region]
TestMask (:,:) logical % [#Region,#Region]
Description string % explanation for split（e.g. 'RandomSplit_Seed42'）
end
methods
function obj = HoldoutSplit(trainMask, testMask, descrip... |
7c8e1a962be8964c2982f8f1909cb7eeceb9285b7bd1bfa755437ee21dba0f13 | MATLAB | 1,372 | 38 |
% Compute mean parametric maps averaged across all subjects
clear, clc, close all
%% Paths
path_batches = 'D:\Projects\2023_multib\MK_multi_b\Scripts';
cd(path_batches)
load('Table_demographics_biomarkers_2023_10_23.mat') % loads T_subjects
n_subjects = size(T_subjects,1);
path_stats_group ... |
50120cd4e36e4d146cbe5983b99108f39fb2e73643e8bc111da2f3250650cc01 | MATLAB | 1,379 | 70 | function varargout = memsize(invar,varargin)
% MEMSIZE(THING,{UNITS})
% convenience tool to calculate the memory footprint of an array or other variable
%
% THING can be a variable of any class
% UNITS specifies the output units (case-insensitive, default 'MB')
% 'B','KB','MB','GB','KiB','MiB','GiB' are ... |
f9ea87f407daa5e0b02cd8c98bf4e8f7a2c260de97e1d9b0443beb625fc1fbf9 | MATLAB | 1,381 | 45 | function outpict = dotmask(dotpict,gridpict,dotfill,dotsize)
% DOTMASK(DOTPICT, GRIDPICT, {FILL}, {DOTSIZE})
% Combines two images using an adjustable mask in the form of a grid.
% The pattern of square dots or grid lines is often visually-distinct
% enough against common image content, allowing di... |
bbdecd27cbb8725054c361e5819b04646d4da5252e86ab9fa6570779ce33b159 | MATLAB | 1,382 | 46 | function PRM2folder(animal, DATfolder_animal, PRMfolder)
if ~ exist(PRMfolder)
mkdir(PRMfolder)
end
filePattern = fullfile(DATfolder_animal, '*.dat');
DATfiles = dir(filePattern);
filePattern = fullfile(DATfolder_animal, '*.prb');
PRBfile = dir(filePattern);
str1 = strcat('experiment_name = ''', animal, '''');... |
98462bf11952adc534c0ef4c90784a679f4afb4639690c1fedf35bd5f176950c | MATLAB | 1,388 | 38 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2017 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
9a6c319e8cc5fe0deb7ebcc34a633311a8011387f8caa81531a097baaa64cf2b | MATLAB | 1,391 | 30 | % modify 3D annotation order
load('ANO100_ConMatIndOh_subCompManually_onlyRight.mat') %[DV,AP,LR]
load('gaussianCenterCoordList_subCompManually.mat') %[DV,AP,LR]
load('ANO100_majorRegion_onlyRight.mat')
[DVSize,APSize,LRSize] = size(ANO100_ConMatIndOh_subCompManually_onlyRight);
ANO100_onlyRight_LRAPDV_flipped = pe... |
8df6cdd0622e2823e080257b5e72606282c2ade76d4db632b55ea1f12185e194 | MATLAB | 1,392 | 40 | function unbinned = unbin(data, origLength, dim, wasSummed)
if nargin < 3
[~, dim] = max(size(data));
end
if nargin < 4
wasSummed = false;
end
original = size(data);
standardized = [ prod(original(1:dim-1)) ...
... |
1f26c0be2fabc29865af7bc881858130c7309cac82c6160d871e20112f9eb3c9 | MATLAB | 1,394 | 38 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2017 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
cb32a790213d0aedd7f39b1f3f213391e6a3a48e50bce029ceee1b2edee7b8e0 | MATLAB | 1,394 | 46 | function y=nt_resample_interp1(x,p,q,method)
%y=resample_interp1(x,p,q,method) - Resample using interp1 (no antialiasing)
%
% y: resampled signal
%
% x: data to resample
% p,q: resample to p/q original sampling rate (p,q can be non-integer)
% method: interpolation method [default: 'spline']
%
% From interp1:
% ... |
e5e785ba718bb81795a9cb49933ce56f253c95095bbe2393e7cf90429ef5f277 | MATLAB | 1,396 | 56 | function out = noisedither(img,ntype)
% NOISEDITHER(INPICT,{TYPE})
% Apply simple noise threshold dither to an I/RGB image
%
% INPICT is a 2-D intensity image
% if fed an RGB image, its luma channel will be extracted
%
% TYPE is the noise type (default 'blue')
% 'white' for noise with a flat pow... |
ff0886715a0c7e900b06a52bcd65fcbbb3734b8684b12ce4c4d01dfc3530db69 | MATLAB | 1,396 | 56 | function [count,prop] = countSpots(BW, R, tbl, posPath)
count = [];
prop = [];
O = fieldnames(BW);
nSpots = size(tbl, 1);
disp([num2str(nSpots),' Visium spots detected'])
disp('Building spot grid')
crow = round(table2array(tbl(:, 5)));
ccol = round(table2array(tbl(:, 6)));
mask = zeros... |
b0cad77b8dae92612caa239279ece0c5399fb946d360ecee3fef98d9aac347c2 | MATLAB | 1,397 | 74 | function [c] = vecchol(x)
%computes cholesky decomposition of matrix x, using explicit analytic definition if
%size(x,1) < n, otherwise use matlab chol-function
n = inf;
siz = size(x);
c = zeros(siz);
siz = size(x);
if numel(siz)==2
if siz(2)==1
% 1d response
c = sqrt(x);
else
c =... |
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