sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2776a50d5e961ecd394634077ce618ad32401438d3631a1907c5edfd3730ae4e | MATLAB | 4,512 | 166 | function hdr = load_nifti(niftifile,hdronly)
% hdr = load_nifti(niftifile,hdronly)
%
% Loads nifti header and volume. The volume is stored
% in hdr.vol. Columns and rows are not swapped.
%
% Handles compressed nifti (nii.gz) by issuing a unix command to
% uncompress the file to a temporary file, which is then deleted.
... |
62483eae3b2b58a1000f041fe30cd2c59e791981f213d1d544172283b1fed395 | MATLAB | 4,512 | 110 | % Enter the values for the variables required for the ICA analysis.
% Variables are on the left and the values are on the right.
% Characters must be enterd in single quotes
%
% After entering the parameters, use icatb_batch_file_run(inputFile);
%% Modality. Options are fMRI and EEG
modalityType = 'fMRI';
%% Output ... |
edb6f06c40ae7c68eabb834f5fbb64c92d5135f5dfbe91042010c705a8e95419 | MATLAB | 4,512 | 175 | function options=ea_defaultoptions(varargin)
try
options=varargin{1};
catch
options=struct;
end
if ~isfield(options,'normalize')
options.normalize=0;
end
if ~isfield(options,'endtolerance')
options.endtolerance=10; % how many slices to use with zero signal until end of electrode estimate.
end
if ~is... |
967247704f49b87fe72c38cba61745390a0101aa01dd4ec15c02549e1504d6e9 | MATLAB | 4,519 | 115 | % dipfit_gridsearch() - do initial batch-like dipole scan and fit to all
% data components and return a dipole model with a
% single dipole for each component.
%
% Usage:
% >> EEGOUT = dipfit_gridsearch( EEGIN, varargin)
%
% Inputs:
% ...
%
% Optional inputs:
% 'com... |
8076bedff60dce460f4baf7063b8ca1f0ea7be5fac5eeec4b6fc932ef1b855fb | MATLAB | 4,523 | 127 | function [t,wr,w] = widelen(xc,zc,y0, dx,dz,dy0,d2y0, maxt,pars,K)
% [t,wr,w] = widelen(xc,zc,y0, dx,dz,dy0,d2y0, maxt,pars,K)
%
% WIDELEN Computes approximate wide-region neighborhood step length.
% Does extensive line search only if it pays, that is the resulting
% rate will be at most twice the best possible rate, ... |
b308af717f9a48bc03ac1487831c68ba2bddf3ae79b1bb091955240d843e2ae4 | MATLAB | 4,526 | 120 | function [t,peaks] = SineWavePeaks(sineWave,varargin)
%SineWavePeaks - Find peaks (or troughs) in a sine wave.
%
% Find the peaks (or troughs) in a sine wave. The algorithm can either determine
% the mid-points between the zero-crossings, or the zeros of the derivative of
% the signal. This assumes a minimum of 10 sam... |
7d244117fada91b47711f1033dcaa1b443db53bf84a061b5989a8c9fd7ed6d7c | MATLAB | 4,527 | 121 | %% Left Turns
% TO DO THIS, YOU NEED TO RUN THE CONTENT OF COMPUTETURNBOUTS2.M
Lturns = {}; leftPB = []; rightPB = []; turnLdata = []; PBcols = [];
trials = []; flies = [];
count = 1;
for k = [1,2] % for these trial types
A = allflies([allflies.trtype]==k);
for n = 1:length(A)
if length(A(n).t... |
2416d6746f113e6b4b4a636228cd7bf9fe53554d268bce136e4b21f40596d859 | MATLAB | 4,529 | 112 | % Name: Robert Kim
% Date: 05-14-2023
% Email: robert.f.kim@gmail.com
% fnc_task_neus_two_layers.m
% Description: Identify selectivity classes for the two-layer instruction-DMS
% RNNs. Crosses task selectivity (anti vs. pro) with stimulus selectivity
% (stim1 = +1 vs. stim1 = -1) using Wilcoxon rank-sum tests, then sor... |
3a8fe8430588b8ce63fdad7c9f38e150df9462cb05c4a184ba2e5f0c6d8abf44 | MATLAB | 4,534 | 133 | function [str, sts] = ea_gencode_rvalue(item)
% GENCODE_RVALUE Code for right hand side of MATLAB assignment
% Generate the right hand side for a valid MATLAB variable
% assignment. This function is a helper to GENCODE, but can be used on
% its own to generate code for the following types of variables:
% * scalar, 1D... |
2b365a8d1c32be1ff7e55bb591e662ad9f6969bffc375e08cc07672c6a82ad88 | MATLAB | 4,540 | 119 | function call_stampresp(handles)
mainfig_pos = get(handles.mainfigure, 'Position');
clear trace_stamp_pool trace_num_all ttlabel_pool
for k = 1:length(handles.datafilename)
handles = loadtrace(handles, k);
framestamp = handles.framestamp{1};
stampinfo = handles.stampinfo{1};
if handles.plotRawdff == 0 &... |
d10a6286c42109b232d94fd642e26f97a4f3a82f117c7c389b5cc35f096b028a | MATLAB | 4,541 | 106 | %% Replay estimation using place field (Bayesian decoding)
x_bin_pf_include = (sum(x2_rate_map,2) > 0);
x_tb_include = (sum(x2_sync_e_tb) > 0);
x2_p_sp_bin = zeros(n_bin_maze,n_tb);
for i_tb = 1:n_tb
if x_tb_include(i_tb)
x_sce_tb = x2_sync_e_tb(:,i_tb);
for i_bin_maze = 1:n_bin_maze
... |
fb89da1f826017ff284296c90bd57320c2f6d0aff812dc4fe889267d6a20babc | MATLAB | 4,541 | 104 | function plotSubpopTroughs(allROIs, subpopGMMs, method, names)
% Compute the vector connecting the multivariate Gaussians from each
% subpopulation of the clustered area-specific GMMs, project all
% hard-clustered cells onto the vector and plot their smoothed
% distributions
if nargin < 3
method = 'logistic';
end
... |
1a95abfa6ea1a38b49d8fb9a7ea1116e1346c8d287f93a4fca42a3c2406259fa | MATLAB | 4,543 | 84 | % SBM Matlab utilities
% Last updated: 10-07-2006
%
%
% DATATOOLS [Matrix manipulation, signal processing and statistics]
% alignwaveforms - Finds best alignment of waveforms to a reference
% buttersimple - Fixed order Butterworth digital filter design
% cmtm - Coherence function est... |
1d78680e8e56d088d753afc0c6addefcfbcacec1547f2f0dc94d437502d84f0a | MATLAB | 4,549 | 130 | %%*******************************************************************
%% schurmat_sblk: compute Schur complement matrix corresponding to
%% SDP blocks.
%%
%% symm = 0, HKM
%% = 1, NT
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
... |
3a0da1ecc3988ec0f4eb7e1cbb01641f789539f030032acff36b81b377747fde | MATLAB | 4,549 | 111 | function [evf, how] = LaBGAScore_firstlevel_find_events(BIDSdir, sub, stem)
% LaBGAScore_firstlevel_find_events Resolve one run's events.tsv by BIDS inheritance.
%
% evf = LaBGAScore_firstlevel_find_events(BIDSdir, sub, stem)
% [evf, how] = LaBGAScore_firstlevel_find_events(BIDSdir, sub, stem)
%
% Returns the fu... |
f809d81f6805798ff3e6680bcd1af1f6135d27c4edbc180be6382fab3de03e4a | MATLAB | 4,549 | 160 | % eeg_eventhist() - return or plot histogram of event or urevent field values.
% If NO output args, plots the histogram. If the field values
% are not numbers or strings, no histogram is computed.
% Usage:
% >> figure; eeg_eventhist(EEG.event,'field',bins); % plot histogram... |
dbc9c1e0f9b606f94df9272f71297d02650c3752332ae0cf98913ba823d4a013 | MATLAB | 4,551 | 98 | function CBIG_hMRF_generate_premultiplied_matrix(output_dir, lh_fmri_fullpath_txt, rh_fmri_fullpath_txt, mesh_type,...
censor_file_fullpath)
% CBIG_hMRF_generate_premultiplied_matrix(output_dir, lh_fmri_fullpath_txt, rh_fmri_fullpath_txt, mesh_type,...
% censor_file_fullpath)
% This function generates the premulti... |
2fd199881e78fc05b2bb2fc59dc1c6d802c4a42796108e0aac24f5d02fb21c9d | MATLAB | 4,553 | 153 | function pop( depth, clearmode )
%
% Determine the index of the problem to be cleaned up
%
global cvx___
if nargin < 2,
clearmode = 'clear';
end
if isempty( cvx___ ),
cvx_global
return
end
p = depth.index_;
if p > length( cvx___.problems ),
return
end
%
% Determine the indices of the variables, constraints, et... |
5063fa1b3b0bd9f444b618af36c96a568d4c9fb6acb6d90e6d6b80a5f1abff17 | MATLAB | 4,553 | 69 | function matlabbatch = batch_job_3T_dual(b)
%-----------------------------------------------------------------------
% Job saved on 15-Jan-2022 18:39:57 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%% Re... |
5745e28688ee9e2f1e821cbbb43186afcb281ca52f73d7962b32898fb7151705 | MATLAB | 4,553 | 149 | %% Example 1 of applying topic models to images
% Illustrates the "bars" example as discussed in Griffiths, T., & Steyvers,
% M. (2004). Finding Scientific Topics. Proceedings of the National Academy of Sciences, 101 (suppl. 1), 5228-5235.
%
% This program creates a dataset of 500 images, each containing 25 pixe... |
2d4140a5e1e680a1512204e54d710c6c44aa441b79f3a71a003278ac6f6794bc | MATLAB | 4,558 | 88 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
2a5fcb3b03c363710c468e48af6a4d33f2f202e7db1e743ff318ca37c11cb00a | MATLAB | 4,560 | 100 | % Graph Algorithms
%
% Searching through a graph
% bfs - Breadth first search
% dfs - Depth first search
% astar_search - Heuristic astar graph search
% breadth_first_search - Breadth first search with visitors
% depth_first_search - Depth first searc... |
96a07a53cb5a6e87947dac1c4de527a5eb2f5d3ff89c5264be8fb13c09bb4226 | MATLAB | 4,562 | 124 | function [asymParam,asymFlag] = asymDeterm2D3D(positions,alpha)
%ASYMDETERM2D3D estimates the asymmetry in a scatter of positions
%
%SYNPOSIS [asymParam,asymFlag] = asymDeterm2D3D(positions,alpha)
%
%INPUT positions: n-by-2/3 array of positions (x,y,[z]).
% alpha : Alpha-value for determining the thresh... |
2ddbafcc14698893053ef9f24b7c43b00d8d8d322a99094eb70920c974896bcb | MATLAB | 4,567 | 172 | function [] = view2vws(ax, filename, part_renderers, fix_daspect, part_tags)
%VIE2VWS Saves current view in a views file for LaTeX media9 package.
%
% See also FIG2U3D.
%
% File: view2vws.m
% Author: Ioannis Filippidis, jfilippidis@gmail.com
% Date: 2012.06.10 - 2012.07.16
% Language: MATLAB R2... |
1cdcaf77750cc1d8841511a0ee8d4268ac9cf34ebcdedf620c66760af0f5055d | MATLAB | 4,568 | 147 | %% A02_Read_decoding_outcome.m
% Need to run "DCNdecodingsSVM.py" on python first!
%
% Liang-Yin
clear all; close all;
%% Load data
path2decodeResult = fullfile(pwd,'DCN_decoding_result');
path2save = fullfile(path2decodeResult,'Outcome'); mkdir(path2save);
cd(path2decodeResult);
fstruct = dir('data_DCN_unit*.... |
e6d973db6045b3e020ab5dd290be36d55ba030c0894ddd222286a42957496e4f | MATLAB | 4,570 | 151 | function [count, edges, mid, loc] = histcn(X, varargin)
% Purpose: compute n-dimensional histogram
% function [count edges mid loc] = histcn(X, edge1, edge2, ..., edgeN)
%
%
% INPUT
% - X: is (M x N) array, represents M data points in R^N
% - edgek: are the bin vectors on dimension k, k=1...N.
% If it is a scal... |
3854473b6e50dae096ddc04e6abe7cc6c4ba30ddcb7891915d61731383bd6cb8 | MATLAB | 4,571 | 89 | function [S,f,varS,C,Serr]=mtspectrumsegc(data,win,params,segave)
% Multi-taper segmented spectrum for a univariate continuous process
%
% Usage:
%
% [S,f,varS,C,Serr]=mtspectrumsegc(data,win,params,segave)
% Input:
% Note units have to be consistent. See chronux.m for more information.
% data (single channel) -... |
19f02a4819f84ce514be437b4ac64e234e6ee41220c99fdb7f127e570291d9e4 | MATLAB | 4,574 | 143 | % Elmore delay sizing for a straight wire (GP)
% Boyd, "Problems in VLSI design" (Lecture)
% Written for CVX by Almir Mutapcic 02/08/06
%
% We consider the problem of finding optimal width profile
% for a straight wire segmented into N parts. We want to
% minimize the Elmore delay, subject to limits on wire width
% and... |
630471edd214a89101390790bfacf7edb1b208a21c22028bbfacf43776bb85ac | MATLAB | 4,578 | 93 | function [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)
% Multi-taper coherency matrix - point process times
%
% Usage:
%
% [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)
% Input:
% data (structure array of spike times with dimension channels) - required
% ... |
cacef17ec66a0c21a84c203928a04d00b828ed947bd65d44dde54045633f9789 | MATLAB | 4,580 | 111 | % Enter the values for the variables required for the ICA analysis.
% Variables are on the left and the values are on the right.
% Characters must be enterd in single quotes
%
% After entering the parameters, use icatb_batch_file_run(inputFile);
%% Modality. Options are fMRI and EEG
modalityType = 'fMRI';
%... |
ca3a772cac10759c9cbe7e1e18c52d2d3699191e4a139fa2e1984da931f9aa23 | MATLAB | 4,581 | 114 | % %function [xml, rxml] = LoadXml_old(FileBase)
% %loads the xml file using xmltools_olds (have to have it in the path)
% % rxml returns it's original layout - very messy structure but contains all
% % the xml file contents.
% % xml - is the ouput structure which is backwards compatible to LoadPar
% % output, so you ca... |
40010e818cf089cc85190ac9ce4493a50969160019382ea9e58e9d9e755064ca | MATLAB | 4,584 | 151 | function [varargout] = rdir(rootdir,varargin)
% Lists the files in a directory and its sub directories.
%
% function [D] = rdir(ROOT,TEST)
%
% Recursive directory listing.
%
% ROOT is the directory starting point and includes the
% wildcard specification.
% The function returns a structure D similar to the ... |
9df098e9728ee6382277e42188fdd0d947d81ecef038ca95348d161bc11c9f20 | MATLAB | 4,584 | 108 | function [d,vfrm] = updtransfo(x,z,w, dIN,K)
% [d,vfrm] = updtransfo(x,z,w, dIN,K)
%
% UPDTRANSFO Updated the Nesterov-Todd transformation using a
% numerically stable method.
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Rom... |
2ed81a7e8d44a3b1506bc3cf06c0163470100fc10efb67c2fe010bfde1c74645 | MATLAB | 4,585 | 132 | function x = DBGetVariables(query,varargin)
%DBGetVariables - Get all variables that match given criteria.
%
% Get variables and related information such as code used to generate them.
%
% This is mostly useful to get information about the variables (who stored
% them, when, which code was used, with what parameters, ... |
315b260740431156eb3098768e82de174a9ffbd1b19b87f58a88539330275bc7 | MATLAB | 4,585 | 122 | function PlotIntervals(intervals,varargin)
%PlotIntervals - Plot vertical bars or rectangles to show interval limits.
%
% Given a list of intervals [start stop], draw a green vertical bar at
% the beginning of each interval, and a red vertical bar at the end of
% each interval or a grey rectangle representing the inte... |
ffbb9ce37f285c02ac325d46d0da00ec955eb5a3f7a865972b756faee5293681 | MATLAB | 4,585 | 117 | function p_tau = CBIG_MMLDA_association_factor_tau_wrapper(out_dir)
% CBIG_MMLDA_association_factor_tau_wrapper(out_dir)
%
% Investigate association between factor loadings and tau loadings.
%
% Input:
% - out_dir : output directory. The output will be some forest plots.
%
% Example:
% CBIG_MMLDA_association_fact... |
c54605101ab900c0c9a74ea7ba967fd483f8ffbb1c1030e001e6f3b71287aeda | MATLAB | 4,588 | 181 | function [shaders, materials, modifiers] = shaders_materials_modifiers(v, f, c, t)
% File: shaders_materials_modifiers.m
% Author: Ioannis Filippidis, jfilippidis@gmail.com
% Date: 2012.06.24
% Language: MATLAB R2012a
% Purpose: mesh shaders, materials and modifiers
% Copyright: Ioannis Filippidis... |
8c6f6ad43d8f74fd5e21b364d09ace5915e9eb790e80e1fe8b019bfe70f45aa2 | MATLAB | 4,591 | 140 | % Digital circuit sizing for an inverter chain (GP)
% Boyd, Kim, Patil, and Horowitz, "Digital circuit optimization
% via geometric programming"
% Written for CVX by Almir Mutapcic 02/08/06
%
% We consider a chain of N inverters driving a load capacitance CL.
% The problem is to find optimal scale factors for the inver... |
d2209a3dbb301abb0f8479040c94048618e8185d67fa5d84912bf57c6c803911 | MATLAB | 4,592 | 148 | %%*******************************************************************
%% randsdp.m : creates random feasible SDP problems with various block
%% diagonal structures.
%%
%% [blk,Avec,C,b,X0,y0,Z0] = randsdp(dense_blk,sparse_blk,diag_blk,m,feas,solve);
%%
%% E.g.
%% randsdp([32 20],[10 5],100,10,feas,sol... |
22ddc9d677ccd3aaf3b510021976d63bec987fc8605c743f600714cb0b874140 | MATLAB | 4,594 | 125 | %LoadBinaryChunk - Load data chunck from an open binary file.
%
% USAGE
%
% data = LoadBinaryChunk(fid,<options>)
%
% fid file id (obtained via fopen)
% <options> optional list of property-value pairs (see table below)
%
% ====================================================================... |
a7332416d83b0eb320f3fc83fb6005ad485aab9050b165cef7098cc758b8b9aa | MATLAB | 4,596 | 109 | function [Y, carry] = filterm(B, A, X, carry)
%FILTERM One-dimensional digital filter (memory efficient).
% Y = FILTERM(B,A,X) filters the data in vector X with the filter
% described by vectors A and B to create the filtered data Y. The
% filter is a "Direct Form II Transposed" implementation of the s... |
aacb5c1af72e26ee9319754415692bac2177fdb083abcf7c488ce4c97c163f1c | MATLAB | 4,596 | 142 | function [status,interval,index] = InIntervals(values,intervals,varargin)
%InIntervals - Test which values fall in a list of intervals.
%
% USAGE
%
% [status,interval,index] = InIntervals(values,intervals,<options>)
%
% values values to test (these need not be ordered)
% intervals list of (start... |
976c021d7c3cf425b651739ed6c58c79add4c53a916e1bd0d7854148330a502c | MATLAB | 4,597 | 114 | function postprocess_write_files_for_stability_analysis_output(...
filename_prefix, N, outname_format, species_names, cutoff, doKeystone, ...
num_perturbations)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome... |
de979031cb620e71165271d4ea5d9b55f4214c212110cc51b6b844e37136e04b | MATLAB | 4,598 | 62 | addpath bva-io-master/
addpath (genpath('eeglab2022.1/'));
eeglab
datasetName = './ds005284/';
behav_data = tdfread([datasetName, 'participants.tsv']);
sub = behav_data.participant_id;
data = cell(1,size(sub, 1));
for subi = 1:size(sub, 1)
subjectName = sub(subi,:);
disp (subjectName)
input_folder = [dat... |
09e27aa78cb85457e941678b13da618a48892427949ec4d556efc88fdd6b83b3 | MATLAB | 4,599 | 101 | function spikes = ss_energy(spikes)
% SS_ENERGY Interface energy based cluster similarity computation.
% SPIKES = SS_ENERGY(SPIKES) adds an interface energy matrix to a
% spike-sorting object in SPIKES.HIERARCHY.INTERFACE_ENERGY.
%
% The energy similarity matrix is calculated by applying an exponential
% ... |
3e7775b83e924b06c6c873e194e7ba06a09e38446fa80a51127eeeb458d86add | MATLAB | 4,599 | 125 | typeArray = [allflies.trtype];
for i = 1:16
inds{i} = find(typeArray==i);
end
%% for flight bout onsets and also correlating flight intensity with neural
boutlengthsecs = 4;
fbl = boutlengthsecs * 100;
allbouts = {}; leftPB = []; rightPB = []; leftmickey = []; rightmickey = [];
trials = []; fliesinclu... |
d411395131d7af06adc0d5518553ffcc8e15bcb749ca7e78d3015601b3f24e30 | MATLAB | 4,602 | 111 | function [events,trigger] = triggerevents(trace, trigger, pre, post, gap)
%TRIGGEREVENTS Extracts data samples before/after a trigger signal.
% E = TRIGGEREVENTS(X, TRIGGER, PRE, POST), where X is an M x 1 vector
% and TRIGGER is a length M vector with P 0->~0 transitions, returns a
% P x (PRE+1+POST) matrix ... |
b4f67024555e0c7adff947aa9de4e3b8fa1d5135417ff6ddd26c8b74023f082b | MATLAB | 4,603 | 133 | function splitNSxPauses(fileName)
% splitNSxPauses
%
% Opens and splits an NSx file in smaller pieces, timewise.
%
% Use splitNSx(fileName)
%
% All input arguments are optional. Input arguments can be in any order.
%
% fileName: File name of the file that needs to be split.
% DEFAULT: The user will... |
6d250f8c8058c9cf476f0bf00d7c8a0fa799cfe2f067a3b517756acf09c6fe5b | MATLAB | 4,605 | 185 | % qrtimax() - perform Quartimax rotation of rows of a data matrix.
%
% Usage: >> [Q,B] = qrtimax(data);
% >> [Q,B] = qrtimax(data,tol,'[no]reorder');
%
% Inputs:
% data - input matrix
% tol - the termination tolerance {default: 1e-4}
% noreorder - rotate without negation/reord... |
3a146631e898452a112b2e761a10566a3861f90a460284822c400f68b1049f72 | MATLAB | 4,606 | 134 | %% LaBGAScore_prep_s2_smooth.m
%
%
% *USAGE*
%
% This script unzips fMRIprep output images, smooths them, zips the
% smoothed images, and deletes all the unzipped images again.
%
% Script should be run from the root directory of the superdataset, e.g.
% /data/proj_discoverie
% The script is generic, i.e. it does not re... |
7c9cbe012ce8ec0180e5700dd0da2205dc4e5c73a6c24585e968921b2f921b01 | MATLAB | 4,606 | 182 | % This script just gives some examples of how the code can be used
load('surface_data.mat')
load('example_data.mat')
%% Accentuate plotted data
surface.vertices = lh_inflated_verts;
surface.faces = lh_faces;
vertex_id = lh_HCPMMP1;
data = zscore(lh_HCPMMP1_gene_pc1);
cmap = turbo(256);
data_label = 'Gene PC1';
... |
0b96b90a076e168d2f70b8afe1b054151794a6e6499e10f1f0824ba5916b7f12 | MATLAB | 4,607 | 110 | function S = GetMD5_helper(V)
% GetMD5_helper: Convert non-elementary array types for GetMD5
% The C-Mex function GetMD5 calls this function to obtain meaningful unique data
% for function handles, java or user-defined objects and sparse arrays. The
% applied processing can depend on the needs of the users, therefore i... |
c0e450fb9ce3972c1fdb9324fe4d411742fdfb28f13a9a90177761e3619760d6 | MATLAB | 4,607 | 95 | function [dS,t,f]=mtdspecgrampb(data,movingwin,phi,params)
% Multi-taper derivatives of time-frequency spectrum - binned point process
%
% Usage:
%
% [dS,t,f]=mtdspecgrampb(data,movingwin,phi,params)
% Input:
% Note that all times can be in arbitrary units. But the units have to be
% consistent. So, if E is in sec... |
cacaefffd6a327bc615ec90fe69a7a03ec98234eb72b8a2568c236f685555250 | MATLAB | 4,608 | 128 | function bad_frames = LCN12_analyze_headmovement_PET(rp_file,threshold_translation,threshold_rotation)
% bad_frames = LCN12_analyze_headmovement_PET(rp_file,threshold_translation,threshold_rotation)
%
% This routine displays overall displacements as
% function of scan (time).
% A log file is created with all results.
... |
ab04db61b33b4e8b15990ca99f4669057522e7a592ce93819358852ed82d2086 | MATLAB | 4,610 | 94 | function [dS,t,f]=mtdspecgramc(data,movingwin,phi,params)
% Multi-taper derivative of the time-frequency spectrum - continuous process
%
% Usage:
%
% [dS,t,f]=mtdspecgramc(data,movingwin,phi,params)
% Input:
% Note that all times can be in arbitrary units. But the units have to be
% consistent. So, if E is in secs... |
10842c58c27d2206a4a35c5f2bf7c50e5a179f534f56b1abcae4d79055b3bdc7 | MATLAB | 4,612 | 105 | %% Extracts the convex hull of the brain out of a CT image
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dept. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicne
% 2015 - 2017
% mail@andreashusch.de, husch.andreas@chl.lu
function [convHullBrainMask, roughBrainMask] = extract... |
e79bdff998b8fb3cc0eb3a7cfb2486e7c6e932001ad759dbcc81d75dc0c2ca36 | MATLAB | 4,612 | 135 | % sbplot() - create axes in arbitrary subplot grid positions and sizes
%
% Usage: >> axis_handle = sbplot(v,h,index)
% >> axis_handle = sbplot(v,h,[index1 index2])
% >> axis_handle = sbplot(v,h,[index1 index2],axprop,..)
% >> axis_handle = sbplot(v,h,[index1 index2],'ax',handle,axprop,..)
%
%... |
5d7c74afd5afaf137a52cefcf58bee4b1adfc2f90519632d8bc06607e10005e5 | MATLAB | 4,613 | 127 | function ea_get_PCA_graphs(data, var_names, pcapath)
% Plots diagnostic graphs that help to interpret the PCs and to choose
% how many of them to retain for the fiberfiltering analysis
%
% data : a matrix with the data used, one variable per column, one
% line per observation
... |
1c4b436536114d540c90380ccaa72c90989113d92dbf2af6074d39a13d1880a1 | MATLAB | 4,614 | 134 | function [ints, idx, MinTimeWindowParms] = ClusterStates_DetermineStates(...
SleepScoreMetrics,MinTimeWindowParms,histsandthreshs)
% can input histsandthreshs from externally if needed... ie via manual
% selection in stateeditor
%% Basic parameters
% Min Win Parameters (s)
if exist('MinTimeWindowParms','var') && ~... |
935bfa7cfaecca635f79a50297f5b82defa73114a9e5f9544f14d35a3fc08fcc | MATLAB | 4,615 | 125 | function trainedML = train_MLP_matlab(database_train, params_train, n_layers, n_neurons, n_MLPs, SANDIinput)
% Train a Multi Layer Perceptron regressor for SANDI fitting
%
% Author:
% Dr. Marco Palombo
% Cardiff University Brain Research Imaging Centre (CUBRIC)
% Cardiff University, UK
% 4th August 2022
% Email: palom... |
ac201bb677bab75e12a7851ded1e0dd966fdd88de5266799e7bfeadfe45616f1 | MATLAB | 4,618 | 159 | function [R, dR, field, rm, peaks] = DistanceFromField(self, cel, strict, plot, peaks)
% returns the minimum distance from field centers.
% corresponds to root.x and root.y.
%
% may program this so dR is derived from the root.vel vector in case the
% kalman is there. for now, I will convolve with a gaussain of std 2bi... |
c3756703c8e333dd1cafef3402692593e7801dea52bb1625a5779d012941f7e6 | MATLAB | 4,618 | 134 | function [d pred] = shortest_paths(A,u,varargin)
% SHORTEST_PATHS Compute the weighted single source shortest path problem.
%
% [d pred] = shortest_paths(A,u) returns the distance (d) and the predecessor
% (pred) for each of the vertices along the shortest path from u to every
% other vertex in the graph.
%
% ... = ... |
83d7fa709c7d5eecb53d310a1215f3e9dfc4d3101688ec6830a2e2a6fec4415b | MATLAB | 4,621 | 142 | function [vatFibScoreBin, vatFibScoreSum, vatFibScoreMean, vatFibScorePeak, vatFibScore5Peak] = ea_discfibers_vtascore(vatlist, atlas, side, posneg, threshold)
% Calculate VAT fiber connection scores based on the discfiber atlas
if ischar(vatlist)
vatlist = {vatlist};
end
disp('Load discfiber atlas...');
load(atl... |
39903a2b3b7c44737e4103c9574830ce54d199e7ab8a2189660f9b671fe37710 | MATLAB | 4,622 | 120 | % subsref() - index eegdata class
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Nov. 2008
% Copyright (C) 2008 Arnaud Delorme, SCCN, INC, UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; e... |
e35279ac5bbcaf6e664330ff547fd58e1a4f21114275f7787ff0ee368789606a | MATLAB | 4,622 | 151 | function palm_hemisplit(varargin)
% Split back bh into lh and rh for files that have previously
% been merged with palm_hemimerge.
% Output file names have prefix "lh" and "rh".
%
% palm_hemisplit [-v #vtx] [-f #fac] <files>
%
% Wildcards are accepted.
%
% -v <nV> : Specify the number of vertices for the left hemispher... |
e3abbf53bf9f216b21f69c6fb439409dd1647bb1075c5780bcbac68282bf3fb5 | MATLAB | 4,624 | 98 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
219100f0633bb8326464585c3c0fc8ee1c1eb0be32e15dea72bafbbfc6ab9acd | MATLAB | 4,626 | 167 | function [vertices, edges, line_colors] = create_marker_lines(h, type)
% File: create_marker_lines.m
% Author: Ioannis Filippidis, jfilippidis@gmail.com
% Date: 2012.06.14
% Language: MATLAB R2012a
% Purpose: create linesets for markers which are not points
% Copyright: Ioannis Filippidis, 2012-
... |
6bf777c14e9868096692203f24cb6a83af290042085e8ccf5c897562c6a9005b | MATLAB | 4,630 | 175 | function plotexample_LFPs(animal)
load('W:\bad_chans_table.mat');
bad_chans = table2cell(bad_chans_table);
if strcmp(animal,'3xTg1-2')==1
load('F:\Ephys Analysis\VLSE neuro 4-4 - HPC2\probe_data\ECHIP512_3xTg1-2.mat')
else
load('F:\Ephys Analysis\VLSE neuro 4-4 - HPC2\probe_data\ECHIP512.mat')
... |
ed6afd8965a7e6e9e91448f9555942bf84554cc117d285242aa3dc32b092eff7 | MATLAB | 4,631 | 122 | function [spectrum,f,s] = MTPointSpectrum(times,varargin)
%MTPointSpectrum - Compute point process spectrum by multi-taper estimation.
%
% The spectrum is computed using the <a href="http://www.chronux.org">chronux</a> toolbox.
%
% USAGE
%
% [spectrum,f,s] = MTPointSpectrum(times,<options>)
%
% times ... |
80021ccbea30888d0287963005dfe851f3e1ff389e9a2d8b419d9236b245a4aa | MATLAB | 4,632 | 135 | function trackMoments = calcTrackMoments(coordinates,standardDevs,...
momentOrders,maxLag)
%CALCTRACKMOMENTS calculates the order^th moments of a track (MSD when order = 2)
%
%SYNPOSIS: trackMoments = calcTrackMoments(coordinates,standardDevs,...
% momentOrders,maxLag)
%
%INPUT coordinates : nTP-by-nD array of ... |
726adb7216dc2ee9404e30faefdd109c8fde2e37af1f724a40eb8e2d038dcf43 | MATLAB | 4,634 | 139 | % ttest2_cell() - compute unpaired t-test. Allow fast computation of
% multiple t-test using matrix manipulation.
%
% Usage:
% >> [F df] = ttest2_cell( { a b } );
% >> [F df] = ttest2_cell(a, b);
% >> [F df] = ttest2_cell(a, b, 'inhomogenous');
%
% Inputs:
% a,b = data consisting of UN... |
98aa5cb4d2a32da1ae10b841c4136bede4ec5e290c52af63b42b67b52d5911f1 | MATLAB | 4,635 | 133 | function [f, pp] = make_plot2_swarm2(plot_an, plot_aw, colL, colR, markerSize, markerAlpha, jitterWidth, null99_an, null99_aw)
% make_box_plot2 : swarmchartを使った簡易ヒゲなし箱ひげ図
% MATLABのswarmchart関数でデータをプロットし、Q1-Q3を太い線で表示、中央値を〇で表示します。
% null distributionの99%ラインを点線で表示します。
% ※ MATLAB R2020b以降が必要です
%
% 入力:
% plot_an... |
49759f41b877a448e40a1cb1e9bbcc6728664786473388ddda570be8f7f57e3d | MATLAB | 4,636 | 174 | figtitlebase = 'BucknerLab rsFMRI Cosine Similarity';
image_set_name = 'bucknerlab'; % keyword for named set to pass into load_image_set
[mapset, netnames] = load_image_set(image_set_name);
mycolors = seaborn_colors(length(netnames));
k = length(DAT.conditions);
myfontsize = get_font_size(k); % This is a function... |
7fc9bb8b8678a097c3aa2fe2eccb5e5f0c657d4017bbc7fb42b03a8339cde86e | MATLAB | 4,637 | 171 |
% Version 26/06/2026
% Authors: Alessandro Petrini and Davide Pierangeli
% -------------------------------------------------------------------------
% This script is provided as a reference implementation of the digital
% backend used in the high-dimensional photonic neural network implemented
% in the manuscr... |
f6654a3838313014ac8da2f81c6bebc8707b193f0547576be7b89c57717fca78 | MATLAB | 4,637 | 116 | function [Sc,Cmat,Ctot,Cvec,Cent,f]=CrossSpecMatpb(data,win,params)
%
%
% Multi-taper cross-spectral matrix - another routine, this one allows for multiple trials and channels
% Does not do confidence intervals.
% Also this routine always averages over trials - binned point process
%
% Usage:
%
% [Sc,Cmat,Ct... |
aae4a0c3e5e0abbe3852767b6177ecaf901b2e8ce97c741105eb685b11959a1a | MATLAB | 4,641 | 159 | function CutDatFragment(fname,timeperiod,RenameOriginalsAsOrig)
% Creating a new dat file from a fragment of an original dat file
% INPUTs
% fname: filepath/name of original dat
% timeperiod: start and stop of file fragment to keep, in seconds
% RenameOriginalsAsOrig: [optional] - specifies naming convention for new vs... |
d20b59284e13439c1efdbb4bea47a9db22d57ad2052d3765dfe2572a6a07e58d | MATLAB | 4,647 | 177 | % Script that runs dynamic perimeter model shown in Figure S4 for a
% specific parameter choice
% Adapted from Troost et al., 2023
%% RUN SCRIPT for SOP Weighted Lateral Inhibition Model
%% Dynamic perimeter driven by Activated Delta
clear; close all; clc;
%% Model setup
model.ratio = 'rho';
model.zone = 'Gaussia... |
f0cb722acce129355da9ea483dc40565bfb3f75f16882dc7769b9d0c6b330da9 | MATLAB | 4,647 | 154 | %% Draw neural field model
clear; clc;
loadparam;
% Create function for surface
f = @(x, y) 1-2*(x.^2+y.^2);
% Create surface mesh
Nx = 41; % 41 x 41 grid
x_coord = linspace(-0.5,0.5,Nx);
y_coord = linspace(-0.5,0.5,Nx);
[X, Y] = meshgrid(x_coord, y_coord); % Generate grid data
Z = f(X,Y); % Calculate Z values
% C... |
0b0f132a4965f25ffeb35d968ab89a68881416377e91f23a1c328db15b44ce93 | MATLAB | 4,649 | 127 | % this script reads all the spike timestamp and a/d info from a plx file into matlab
% variables.
% Open a plx file
% this will bring up the file-open dialog
StartingFileName = '';
%StartingFileName = 'c:\plexondata\NSSample.plx';
%StartingFileName = 'c:\plexondata\au101602a.plx';
[OpenedFileName, Version, Fre... |
9dea56d430c33bb9a31177cc78a276efdac8e582e7e92e8372857f4df8ab62b4 | MATLAB | 4,650 | 143 | classdef Grid < uix.Grid
%uiextras.Grid Container with contents arranged in a grid
%
% obj = uiextras.Grid() creates a new new grid layout with all
% properties set to defaults. The number of rows and columns to use
% is determined from the number of elements in the RowSizes and
% Colum... |
dd531f413138424f80e8932ba1233ec63f1492e0fabdb79f9233918bd6762e98 | MATLAB | 4,654 | 122 | function [curve,stats] = FiringCurve(samples,spikes,varargin)
%FiringCurve - Compute firing curve (e.g. for a head direction cell).
%
% Compute firing curve (e.g. for a head direction cell, or a place or grid cell
% on a linear track), as well as occupancy and spike count curves. Optionnally,
% curve statistics can... |
e8ea3d61c0ad39025aa311021be489db53fadbbcac430032e2e19cc5786a08aa | MATLAB | 4,655 | 130 | function [y,dx,k, r] = wrapPcg(L,Lden,At,dense,d, DAt,K, rb,rv,cgpars, y0)
% [y,r,k, DAy] = normeqPcg(L,Lden,At,dense,d, DAt,K, b, cgpars, y0,rhs)
%
% WRAPPCG Solve y from AP(d)A' * y = b
% using PCG-method and Cholesky L as conditioner.
% If L is sufficiently accurate, then only 1 CG-step is needed.
% In general, pro... |
1a6cd183fd8642f3d9eae813d79238b0d45b629c2ae009a353afeabfbe2c7720 | MATLAB | 4,659 | 147 | function wtcsig=wtcsignif(mccount,ar1,dt,n,pad,dj,s0,j1,mother,cutoff)
% Wavelet Coherence Significance Calculation (Monte Carlo)
%
% wtcsig=wtcsignif(mccount,ar1,dt,n,pad,dj,s0,j1,mother,cutoff)
%
% mccount: number of time series generations in the monte carlo run (the greater the better)
% ar1: a vector contain... |
9033fd01cb20f4ab3748d20b43f7808e569e7507bbf7720f1d471c59fd752c04 | MATLAB | 4,660 | 89 | function [S,f,varS,C,Serr]=mtspectrumsegc(data,win,params,segave)
% Multi-taper segmented spectrum for a univariate continuous process
%
% Usage:
%
% [S,f,varS,C,Serr]=mtspectrumsegc(data,win,params,segave)
% Input:
% Note units have to be consistent. See chronux.m for more information.
% data (single ch... |
df01a9a8e8eb9ab1888948e9ab2c4fdd8496f5510b3cb2b2fefe449bc30959fd | MATLAB | 4,665 | 135 | function [rate_map, xs, ys, xdim, ydim, no_occupancy] = plot_rate_map(self, cel, suppress_plot, xdim, ydim, clims, mergeepochs)
% [rate_map, xs, ys] = root.plot_rate_map(cel, suppress_plot, clims)
%
% Plots spatial rate map for cell cel = [ tetrode, cell ] for all root.epoch
% (multiple epochs concatinated).
%
% Return... |
da121097e12380fea15be0b865ce7b2b4d73ad730985e162ab7ee546b8de1f6e | MATLAB | 4,666 | 125 | function [trackedFeatureInfo,trackedFeatureIndx,trackStartRow,numSegments,aggregStateMat] = ...
convStruct2MatIgnoreMS(tracksFinal,startFirstFrame)
%CONVSTRUCT2MATIGNOREMS converts tracks from structure format to matrix format, ignoring merges/splits.
%
%SYNPOSIS [trackedFeatureInfo,trackedFeatureIndx,trackStar... |
38e63a3ae9629df6c485320024182672c0fa865c659fc973a693ef3512550ae8 | MATLAB | 4,669 | 158 | function [pval table] = circ_wwtest(varargin)
% [pval, table] = circ_wwtest(alpha, idx, [w])
% [pval, table] = circ_wwtest(alpha1, alpha2, [w1, w2])
% Parametric Watson-Williams multi-sample test for equal means. Can be
% used as a one-way ANOVA test for circular data.
%
% H0: the s populations have equal m... |
ae57adefe3bc8bdc4e02158011673bddbf842c59682eeb4b49359e9f5b185d0e | MATLAB | 4,669 | 133 | function [total_count_norm,biomass_norm,scaleFactor,med_counts,med_biomass] = calcNorms(keep_species,data_counts,intervene_matrix_filtered,biomass,experimentBlocks)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome t... |
00e218e26d714d9bbdcd99803ab61e3449a0d6711c5eadd71d2e4dd8bf96a7eb | MATLAB | 4,671 | 93 | function [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)
% Multi-taper coherency matrix - point process times
%
% Usage:
%
% [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)
% Input:
% data (structure array of spike times with dimension channels) - required
... |
6bca4045cd14e8ffa3bf5f4e224287ec28a1a5fab639aebe709d88cd4e5cb1b5 | MATLAB | 4,676 | 127 | function [synchronized,indices] = Sync(samples,sync,varargin)
%Sync - Make sample timestamps relative to synchronizing events.
%
% Select samples that fall around synchronizing events, and make their
% timestamps relative to the synchronizing events. This can be used to
% build e.g. spike raster plots or successive ev... |
1513228c5d5ac24fce0551f663bb78bcf6cf2da19529e78cc9e35b1b8c5b5eec | MATLAB | 4,677 | 114 | function res = summarizeSlopeReduction(slopeA, slopeP, areaName)
%SUMMARIZESLOPEREDUCTION Quantify passive reduction of repetition-rate slope.
%
% slopeA: behavioral/active slope
% slopeP: passive slope
%
% Output includes:
% allChannels:
% mean slopes across all included paired channels
% activeEnhancementCh... |
83e74094853b64c2591a99620150da9b34369e7fb905545b7e01955cbce1ff1a | MATLAB | 4,683 | 139 | % angtimewarp() - Given two event marker vectors, computes a
% warping of the input angular time series so that its
% evlatencies match newlatencies. Values of the warped
% timeserie that falls between two frames in the original
% timeserie will be linearl... |
6fc1d3cde87b0f0689b25b9cd18893671aaee1fc108a74f0056852dc72bd1642 | MATLAB | 4,684 | 142 | %%% normalize & average MUA - THINGS dataset
% 2022 P. Papale fecit
clear all
addpath(genpath('\_code\code_utils_v2\'));
% constants
monkey = 'monkeyN';
datadir_gen = '\';
% chns to region
if monkey == 'monkeyN'
rois = ones([1 1024]); % V1
rois(513:768) = 2; % V4
rois(769:end) = 3; % IT
else
rois = on... |
acbed3a9eacca9bdee82fa8f0e4e72a3ec362425f6b49d32940abaacef143f74 | MATLAB | 4,685 | 87 | addpath('/dartfs-hpc/rc/home/m/f0042vm/software/spm12');
addpath(genpath('/dartfs-hpc/rc/home/m/f0042vm/software/canlab/CanlabCore/CanlabCore/'))
addpath(genpath('/dartfs-hpc/rc/home/m/f0042vm/software/canlab/Neuroimaging_Pattern_Masks/'));
%% Plotting Parcellations
% There are two ways to plot parcellations. One is b... |
a4645ed1f41e6c42d4b3eb9bd62de56f48ffc00796a2f6aeafa423ee81557972 | MATLAB | 4,688 | 122 | function [coord_snapped] = LeG_warp_hermes2010(~, elec, surf, GridDim)
% WARP_HERMES2010 projects the ECoG grid / strip onto a cortex hull
% using the algorithm described in Hermes et al. (2010,
% J Neurosci methods) in which electrodes are projected onto the pial
% surface using the orthogonal local norm vector to th... |
2dd86db618b10eb409be8b3f423421f6c60956069ea04f57f610183d2b958925 | MATLAB | 4,689 | 117 | function [interpolated,discarded] = Interpolate(samples,timestamps,varargin)
%Interpolate - Interpolate samples (positions, spikes, LFP, etc.) at given timestamps.
%
% Interpolate samples (positions, spikes, LFP, etc.) at given timestamps. As a special
% case, a point process can also be 'interpolated' by changing eac... |
1d75553d07ec62ae3c036b1e087d2da66836e3311cf11863eaecbfce4e88e60e | MATLAB | 4,690 | 142 | function [res, errStr]= morph_data(mask, kernelAy, kernelPos, OPStr, noVoxInKernel, forceKPos)
%function [res, errStr]= morph_data(mask, kernelAy, kernelPos, OPStr, noVoxInKernel, forceKPos)
%
% Funktion to apply any binary morphology kernel an binary images or 3D datasets.
%
% Input:
% -mask: mrStruct and schou... |
c76b93c74ece74054786735317757e7dd9bca9e28e70db7b54df44229f49820b | MATLAB | 4,692 | 115 | function ydata = tsne_p(P, labels, no_dims, max_iter)
%TSNE_P Performs symmetric t-SNE on affinity matrix P
%
% mappedX = tsne_p(P, labels, no_dims, max_iter)
%
% The function performs symmetric t-SNE on pairwise similarity matrix P
% to create a low-dimensional map of no_dims dimensions (default = 2).
% The matrix ... |
adb48a5b66dc3a7fcb3832ec753cc1e4d16fcc7646ece6a43e62e18b74295c44 | MATLAB | 4,693 | 116 | % vectdata() - vector data interpolation with optional moving
% average.
%
% Usage:
% >> [interparray timesout] = vectdata( array, timesin, 'key', 'val', ... );
%
% Inputs:
% array - 1-D or 2-D float array. If 2-D, the second dimension
% only is interpolated.
% timesin - [floa... |
e3af92ccb611f6565e5d5ce21fed8a33d6fb0816bf0f71818056d6926a11520f | MATLAB | 4,695 | 108 | % Name: Robert Kim
% Date: 05-14-2023
% Email: robert.f.kim@gmail.com
% one_modality_cebra.m
% Description: Plot example CEBRA trajectories for the one-layer,
% one-modality instruction-DMS (instr) RNN. This script loads a CEBRA
% embedding produced by cebra_for_matlab.ipynb and renders trajectories
% during the instru... |
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