sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4e58591746280dc7261e54adcf953ba478616f59b2f154ec44839301aafbd57e | MATLAB | 3,549 | 99 | function mono_res = bz_GetMonoSynapticallyConnected(basepath,varargin)
%% Method for estimating likelihood of monosynaptic connectivity based off of relative spike timing
% Based off of Stark and Abeles 2009 and verified for PYR -INT in English et al., 2017
% Assumes network synchrony is low frequency and that synapse... |
1469837730167cf1fe3177577baa404541a3d0351d6fe4552cbd8645ababa33f | MATLAB | 3,551 | 97 | function [itk_fwd_field, itk_inv_field] = ea_synthmorph(target_image, source_image)
% Wrapper to run SynthMorph and get ANTs-like transforms
%
% SynthMorph
%
fs_fwd_field = strrep(source_image, '.nii', '_fs_fwd_field.nii');
% Check Conda environment
condaenv = ea_conda_env('SynthMorph');
... |
e3f8428326abc503c394ab5a40b19d2da0bbce17030e5641865ab9bbe2e21dfb | MATLAB | 3,551 | 82 | % std_readspec() - load spectrum measures for data channels or
% for all components of a specified cluster.
% Called by plotting functions
% std_envtopo(), std_erpplot(), std_erspplot(), ...
% Usage:
% >> [STUDY, specdata, allfreqs, setinds, cinds] = ...
% ... |
c2976f7de91b5519634d5d0c8dfbfa25c8a8de3a5fc8c926bce8ae5465144849 | MATLAB | 3,552 | 76 | function ClincFreq_CalClinWeiLocation(INDIR,OutWeiLocdir,SetUpPara,Para,VolLab,ClincWei)
[V,D,namelist] = Dynamic_read_dir_NIFTI_sparse(INDIR);
D(isnan(D)) = 0;
D(isinf(D)) = 0;
D = D>0;
Dvol = sum(D)';
Dvole = sum(D,2);
IgV = Para.IgP;
indexs = find(Dvole>=(size(D,2)*IgV/100));
Dmasked = zeros(V.dim);
Dmasked(indexs)... |
64a78b7dc56b021f8906c4d053034fd8324b75ff158826a8aa6800ff45158774 | MATLAB | 3,554 | 128 | function [ INT,IDX_new ] = bz_IDXtoINT( IDX ,varargin)
%bz_IDXtoINT(IDX) Converts state indices to state on/offsets
%
%INPUT
% IDX: structure with fields: IDX.statenames
% (see buzcode wiki) IDX.states
% IDX.timestamps
% -or-
% [len x 1] vector ... |
9d426b1b618b6312e68dd58983c1bdfb2f601cc674bfa6c7e93d646a896a3905 | MATLAB | 3,554 | 95 | function options = ea_ensure_b0_coreg(options)
% EA_ENSURE_B0_COREG Ensure that a coregistration transform between B0 and T1 exists.
%
% This helper is intended to be called from the main pipeline (ea_autocoord)
% before any Lead-Connectome structural steps run. It is read-only with
% respect to options except for po... |
b9aac7f91e14726ec58b4682c471e1d92a8480f049b6ac29db059b29200b9b00 | MATLAB | 3,554 | 116 | function [fibers, idx] = ea_trk2ftr(trkFile, ref, saveFTR)
% Convert trk to ftr (fibers format in Lead-DBS)
%
% ref can be:
% 1 - Lead-DBS / MNI152 NLin 2009b Asym
% 2 - Choose a reference NIfTI file
% 3 - Interactively select ref type (1 or 2 above)
% [string] - Path of a NIfTI file defini... |
50a9c659f70afc2a64e52c818fb21af469ed1e3dba6ff8b17978ab88eac56021 | MATLAB | 3,555 | 108 | function [] = fig2idtf(filename,...
surface_vertices, faces, face_vertex_data,...
line_vertices, line_edges, line_colors,...
pointset_points, pointset_colors,...
mesh_tag)
%FIG2IDTF Save figure in IDTF format.
%
% usage
% ... |
4187add54027b56d9a51e75294f3e07c3d78fbaf4c6508306580ffb43411ffde | MATLAB | 3,556 | 76 |
function ft_struct = Trinh_happe_detectbadchannels(ft_struct,baby,flatline,corrnoise,specrej)
% rejects channels according to the HAPPILEE pipeline
% baby (1 on, 0 off) --> changes channel locations according to MUSICOM WP4
% (needs adaption for Biosemi as the function needs 3d coordinates). This
% can be achieve... |
57fd4e3b0a6aab00c616060fbc2975a76805c9d742bdf1280a2b83fe53dd2056 | MATLAB | 3,556 | 64 | %% PaCER - Precise and Convenient Electrode Reconstruction for Deep Brain Stimulation
%
% Andreas Husch
% Centre Hospitalier de Luxembourg (CHL), Dept. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine (LCSB)
% (c) 2016 - 2017
% mail@andreashusch.de, husch.andreas@chl.lu
function... |
34d57510568d57f558fcfe9881d9539be624f1e2a01df34022c9972d8ae5b435 | MATLAB | 3,560 | 91 | % Runs a two-sample t-test for a set of signature responses, for each
% condition.
% Signatures, scaling, etc. are defined below.
% created by @lukasvo76 from h2_group_differences_emosignatures.m, March 2021
%% USER OPTIONS
% -------------------------------------------------------------------------
mysignature = {... |
4de93494383cad717c67591497175fee19d97efd9933962af217e40480f3edf2 | MATLAB | 3,560 | 108 | function [posAlongDir,deltaPosAlongDir,prefDir] = projectCoordOntoDir(...
trackCoord,deltaCoord,centerCoord,prefDir)
%PROJECTCOORDALONGDIR reduces coordinates into their 1D projection along a line
%
%SYNPOSIS [posAlongDir,deltaPosAlongDir,prefDir] = projectCoordOntoDir(...
% trackCoord,deltaCoord,centerCoord,pre... |
b3818c0f9e36e7442da1a182403aaaa60350ac87578655d32ee36eee09e988e7 | MATLAB | 3,560 | 117 | % readlocsold() - Read electrode locations file in style of topoplot() or headplot().
% Output channel information is ordered by channel numbers.
%
% Usage: >> [nums labels th r x y] = readlocsold(locfile);% {default, polar 2-D}
% >> [nums labels th r x y] = readlocsold(locfile,'polar'); % 2-D
%... |
f91cea3ceecd2e051883263da8f41763301946696a9d1ada32188f3c28a88d68 | MATLAB | 3,562 | 71 | classdef CBIG_gwMRF_unit_test < matlab.unittest.TestCase
%
% Target project:
% Schaefer2018_LocalGlobal
%
% Case design:
% Schaefer2018_LocalGlobal already has unit test script, here
% we call its unit test script and automatically
% make judgement on whe... |
5378a887bda213d782bbaeec38e3cf436e1f0307515b84d0c66cf733ed8fb36a | MATLAB | 3,563 | 91 | % [labels, start, stop] = Boris.Aggregated.load(filename)
% Returns a list of events encoded with BORIS.
% Output:
% labels: 'behavior1', 'behavior2', ...
% start: [start1, start2, ...];
% stop: [stop1, stop2, ...]
%
% epochs = Boris.Aggregated.load(filename)
% Output:
% {'behavior1', [start1, stop1, ... |
61be3f66e0e73332175ecf9d0d96adf89e0d4eeaf9e0e9061bac7d8332b39ba6 | MATLAB | 3,565 | 95 | function ea_cvshowvatdmri(resultfig,directory,handles,selectedparc,options)
% get everything we need to know from handles:
if isstruct(handles) % called from GUI
vatmodality=get(handles.vatmodality,'String');
vatmodality=vatmodality{get(handles.vatmodality,'Value')};
vs=get(handles.vatseed,'String'); % don... |
7d642fb06b0f2ef9a46a84ce79d9a68d4cfd2f703be7a7821ab233033ef30d31 | MATLAB | 3,565 | 118 | function [U, S, V] = mySVD(X,ReducedDim)
%mySVD Accelerated singular value decomposition.
% [U,S,V] = mySVD(X) produces a diagonal matrix S, of the
% dimension as the rank of X and with nonnegative diagonal elements in
% decreasing order, and unitary matrices U and V so that
% X = U*S*V'.
%
% [U,S,V] = m... |
8c63d6f639a46f65997629f59f2d88c51298cef94b59b73c65f5aa1255e1c057 | MATLAB | 3,567 | 91 | function result = plugin_install(zipfilelink, name, version, forceInstall);
if nargin < 4, forceInstall = false; end;
result = 1;
% get plugin path
% ---------------
%version(find(version == '.')) = '_';
generalPluginPath = fullfile(fileparts(which('eeglab.m')), 'plugins');
newPluginPath ... |
df9b07ca477ec5275cea3d5282c9aef0e40d2b99576948145b4dda91603ea482 | MATLAB | 3,570 | 104 | close all;clear;clc
fs = 40;
pre = 20;
post = 50;
% % Select the folders to be analyzed
FolderList = uipickfiles;
%% Analysis
for i = 1:size(FolderList,2)
% Determine the current subfolder name
selected_path = FolderList{i};
cd(selected_path);
work_folder = selected_path(find(selected_path ... |
0ff90b7d028e3c42d1daaf30481634735f6886791e2382766c4ed3373a502ea1 | MATLAB | 3,571 | 68 | function CBIG_MMLDA_brain_behavior_zscore_to_doc(Z_brain, Z_behavior, rid, ind_out, plus_num, nfold, out_dir, out_name)
% CBIG_MMLDA_brain_behavior_zscore_to_doc(Z_brain, Z_behavior, rid, ind_out, plus_num, nfold, out_dir, out_name)
%
% Convert brain behavior zscore to documents used to run MMLDA.
% 1. Plus a number to... |
b68021a4ae29af8a91907332896054e654cd12f6c64493399f19dfab9e0cb94c | MATLAB | 3,571 | 76 | function [maxDrift_estimate, cumulativeDrift_estimate, median_spikeDepth, timeBins, spikeDepths_inChannels] = maxDriftEstimate(pcFeatures, pcFeatureIdx, spikeTemplates, ...
spikeTimes, channelPositions_z, thisUnit, param, timeChunks)
% JF, Estimate the maximum drift for a particular unit
% ------
% Inputs
% ------
... |
17e01ff7a3a9350a386389aac03db23554084942270646601ded8f51c33a01cd | MATLAB | 3,572 | 94 | function out = LaBGAScore_pdm_report_image(d, label, varargin)
% LaBGAScore_pdm_report_image c2a-style reporting for one thresholded brain map.
%
% Produces the overview montage, the labelled region table, and the
% regioncenters montage that second-level GLM results get from c2a, for a map
% that is ALREADY threshold... |
b2ce3caef5e1c8cd52462fb45ef65c2b4ae35fb6c3980c5c24295f5e150bc904 | MATLAB | 3,572 | 156 | % Philipp Berens
% CircStat: A Matlab Toolbox for Circular Statistics
% Submitted to Journal of Statistical Software
%
% Example 2
% An Application to Neuroscience
%
%
% In this example, we assess the orientation tuning properties of three
% neurons recorded from the primary visual cortex of awake macaques. th... |
33d761718435bbc8113726626964add789d5d9daf6a0a284fe904d0733ea9713 | MATLAB | 3,573 | 73 | function CBIG_ASDf_FC2doc_infFactorComp_wrapper(corrMat_ASD_path, corrMat_con_path, ref_path, sub_info_file, output_dir)
% CBIG_ASDf_FC2doc_infFactorComp_wrapper(corrMat_ASD_path, corrMat_con_path, ref_path, sub_info_file, output_dir)
%
% Wrapper function to compute Z-normalized, discretized FC (Z-normalization
% w.r.t... |
837a8160b7b9fc4c81f0d7d5f004280acd60220245f31cc08895482068e47046 | MATLAB | 3,574 | 72 | function [plx] = get_all_from_plx(fileName)
plx = [];
if (nargin == 0 | isempty(fileName))
[fname, pathname] = uigetfile('*.plx', 'Select a .plx file');
if isequal(fname,0)
error 'No file was selected'
return
end
fileName = fullfile(pathname, fname);
end
[plx.tscounts, plx.wfcounts,... |
f93e635d3eaaed8712507ed4483136ff873d05f2c88b0ffdbf8c28ec028ffa1f | MATLAB | 3,574 | 119 | % logimagesc() - make an imagesc(0) plot with log y-axis values (ala semilogy())
%
% Usage: >> [logfreqs,dataout] = logimagesc(times,freqs,data);
%
% Input:
% times = vector of x-axis values
% freqs = vector of y-axis values
% data = matrix of size (freqs,times)
%
% Optional Input:
% plot = ['on'|'off'] plot ... |
9f62cac3dab9716b5164d2fa60ef84e05e0feee4b71db425ecdd59caae180335 | MATLAB | 3,577 | 95 | function [trackCntOut] = getFsmTrackNum(qfsmPackPaths, frameRange)
%GETFSMTRACKNUM: output number of speckle track per movie from MPM of QFSM given directory of movie where QFSM was performed
%
%SYNOPSIS: [trackCntOut] = getFsmTrackNum(qfsmPackPaths, frameRange)
%
%INPUT : qfsmPackPaths : (nx1 cell) locations to n acti... |
d8ba41cad0370d300644e3aab9a05b3dbdcdb9a8514f0b3e505bbec0dc4d9411 | MATLAB | 3,577 | 136 | function CBIG_pMFM_step2_generate_FCD_desikan()
% This function is the wrapper to generate parcellated time serises and FCD
% for Desikan parcellation
%
% There is no input for this function as it can automatically get the
% output file from previous step.
% There is no output for this function as it will generate the... |
007061b421d1e7545343c429a50a15de08d893e51b5b2c8fa14cb9a8a907ce07 | MATLAB | 3,578 | 135 | function out = computeFluctuations(par, scenario_fun, proc, k)
% Compute stochastic fluctuations for:
% - total NSC number S = Q + A
% - active fraction f = A / (Q + A)
scenario = scenario_fun(par);
%% --- fixed time grid ---
% Variance propagation requires the full time-dependent trajectory.
dt = 0.05... |
54499dca26fa92647a38bbb165d9f91ceb8a79d2acf02c2fb0e7e0f99ef61422 | MATLAB | 3,578 | 84 | % When you load any ANALYZE or NIfTI file with 'load_nii.m', and view
% it with 'view_nii.m', you may find that the image is L-R flipped.
% This is because of the confusion of radiological and neurological
% convention in the medical image before NIfTI format is adopted. You
% can find more details from:
%
%... |
529fa886157127e85ef5cd4296b0fd65af2801ad35c6affec72a9cdc24a2475f | MATLAB | 3,580 | 92 | function SOFAstart(flags)
% SOFAstart
%
% SOFAstart adds all needed pathes and checks if we need the Matlab or Octave
% version of the API
%
% SOFAstart(0) or SOFAstart('silent') will suppress any message during the start.
% SOFAstart ('short') will show a short header only during the start.
% SOFA A... |
524ee16f6eaab148acc6f2c05e1917ae88d08782ff5ac851795662d68fed79e6 | MATLAB | 3,581 | 121 | function plot_brain_mesh_iso2mesh(p, e, brain_nodes_idx, overlay_brain, plot_cfg, varargin)
%PLOT_BRAIN_MESH_ISO2MESH Plot a brain mesh with optional nodewise overlay using iso2mesh.
%
% fnirspower.measpred.plot_brain_mesh_iso2mesh( ...
% p, e, brain_nodes_idx, overlay_brain, plot_cfg)
%
% fnirspower.measp... |
d89f9f73808dfebd1ee11b4c238a1c75cdacccd000b6461fa8f0552e4c5158dd | MATLAB | 3,582 | 146 | function [xmax,imax,xmin,imin] = extrema(x)
%EXTREMA Gets the global extrema points from a time series.
% [XMAX,IMAX,XMIN,IMIN] = EXTREMA(X) returns the global minima and maxima
% points of the vector X ignoring NaN's, where
% XMAX - maxima points in descending order
% IMAX - indexes of the XMAX
% XMIN ... |
d8d537c71db2554f860b93e2e5363d9da1302c0c23800336743de4523f5098b6 | MATLAB | 3,582 | 106 | function [d pred f]=astar_search(A,s,h,varargin)
% ASTAR_SEARCH Perform a heuristically guided (A*) search on the graph.
%
% [d pred rank]=astar_search(A,s,h,optionsu) returns the distance map,
% search tree and f-value of each node in an astar_search.
% The search begins at vertex s. The heuristic h guides the searc... |
eadd7fddb0bd5d35a9ed3cecec14b23710957c1c9db207377ec80e669e20dd82 | MATLAB | 3,582 | 96 | function spikes = ThresholdSpikes(amplitudes,factor,varargin)
%ThresholdSpikes - Post-hoc threshold correction for spike detection.
%
% USAGE
%
% spikes = ThresholdSpikes(amplitudes,factor,<options>)
%
% amplitudes [time, electrode group, cluster, amplitude] tuples
% e.g. obtained using <a... |
11e36eb2b15242ccb4d83b3dc3f5c98d9c31172610a73106eddace08957a00e8 | MATLAB | 3,583 | 94 | function [vatlist,FilesExist] = ea_discfibers_getvats(obj)
% Return list of VATs
numPatient = length(obj.allpatients);
vatlist = cell(numPatient*2,2);
FilesExist = zeros(numPatient*2,2); % also check if mirrored fields exist
modelLabel = ea_simModel2Label(obj.M.vatmodel);
disp('Construct VAT list...')
for sub=1:num... |
5d27b3e3b075621baf68198fd1ee06e1249950c14e3a75c8e41e6604a217258f | MATLAB | 3,587 | 73 | function [dS,f]=mtdspectrumc(data,phi,params)
% Multi-taper frequency derivative of the spectrum - continuous process
%
% Usage:
%
% [dS,f]=mtdspectrumc(data,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, win, t have to be in secs, ... |
d8a0bd6615da237c22e088c393886d471dad2ce79175476314081e9e750fc63d | MATLAB | 3,588 | 81 | function Y = filterzm(B, X)
%FILTERZM Zero-phase 1-D digital filter (memory efficient).
% Y = FILTERZ(B, X) filters the data in vector X with the FIR filter
% given by the vector B to create the filtered data Y, shifting the
% filter to give zero-phase delay. The process is equivalent to
% convolution... |
138351c87bb891a173e790556ff2c94e1c749fbaa2edd2d390ee4986a7685da9 | MATLAB | 3,589 | 100 | % 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... |
ed68b53ae174d0e867518ddca852e8e97201f4c9606f750e7795d096f31fa8d5 | MATLAB | 3,589 | 113 | % readegihdr() - read header information from EGI (versions 2,3,4,5,6,7) data file.
%
% Usage:
% >> [head] = readegihdr(fid,forceversion)
%
% Input:
% fid - file identifier of EGI datafile
% forceversion - optional integer input to override automatic reading of version number.
%
% Output:
% head - structure con... |
fb10d200a13769f835b7c40b7d66dc9815a2b82f48ffdb570a563969fba035ec | MATLAB | 3,589 | 89 | classdef CondColocPt2Pt2PtProcess < ImageAnalysisProcess
% A concreate class for measuring conditional colocalization between 3 images
% Anthony Vega 09/2014
%Adapted by Jesus Vega-Lugo (May, 2019) to run conditional colocalization
%
% Copyright (C) 2021, Jaqaman Lab - UTSouthwestern
%
% This file is part... |
c453e3b0188724bd5a62d94578c1205f6be528ae35605ff165a603f4f0c85a9a | MATLAB | 3,590 | 94 | % written by Yiyuan Han, Essex BCI-NE Lab, 05/03/2020
% It's just a modified version of multiClassPar for CFC
% Multi-class classifiers for each participant based on the CFC as the
% selected features
%% Only remain the participants with complete data in all of 4 classes
classes = ['O' 'H' 'W' 'S'];
bands = [0.... |
129ae07aff893d30032e38a679a689e110bf1fbb40cb24c6241c7d632431e0b1 | MATLAB | 3,591 | 94 | function fig = draw_surface_bluewhitered_gallery(surface_to_plot, data_to_plot, hemisphere, medial_wall, with_medial)
% draw_surface_bluewhitered_gallery.m
%
% Draw multiple data on surface using blue-white-red colormap for
% negative-zero-positive values
%
% Inputs: surface_to_plot : surface structure with fields
% ... |
1344254f46dd629680b9862182852cb7d887aa9fca48b10bb60ddb1859f486ac | MATLAB | 3,591 | 118 | function [line_resources] = populate_line_resource_str(line_vertices,...
line_lines, line_colors, n_resources)
%
% See also FACE_VERTEX_DATA_EQUALS_NPOINTS, VERBATIM.
%
% File: populate_line_resource_str.m
% Author: Ioannis Filippidis, jfilippidis@gmail.com
% Date: 20... |
e2c19d6106822ccc1f2fbd98d294919ed60d4c623e6625a1a953556f479927ac | MATLAB | 3,591 | 117 | function bz_LFPFromAbf(basePath,chanNums)
%assumes you are in or pointed to a directory containing subdirectories for
% various recording files from a single session
%
%INPUT
% Assumes presence of the following files:
% basePath/baseName.abf
% where basePath is a folder of the form:
% whateverPath/base... |
a23312041a252f297fa4ac7ba634cb5898765659002276459aae141a5faffe98 | MATLAB | 3,593 | 78 | % 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... |
0e72fba50fa1a85c9b5116790248a3ea8219c11a695d2101b168914fb8373e7b | MATLAB | 3,594 | 93 | function [Figs, Results] =...
scatterSignificance(Results, Counts, CondNames, Delta_t, clID)
%SCATTERSIGNIFICANCE takes the statistical results from the statTests and
%plots them against each other (conditions)
meanfr = cellfun(@(x) mean(x,2)/Delta_t, Counts, 'UniformOutput', false);
mxfr = cellfun(@max, meanfr);... |
0ede1a2294256490f6da65c80d3e41566acebe75fae5fa57684c2551fb860439 | MATLAB | 3,602 | 134 | function [r,p] = ea_bendcorr(X,Y)
% Computes the percentage bend correlation along with the bootstrap CI
%
% FORMAT: [r,t,p] = bendcorr(X,Y)
% [r,t,p,hboot,CI,H,pH] = bendcorr(X,Y,fig_flag,beta)
%
% INPUTS: X and Y are 2 vectors or matrices. In the latter case,
% correlations are computed c... |
75145bd650b03413d4917f1533344b8972900463f97310eb6f0ee18f5c3e24fa | MATLAB | 3,602 | 102 | % eegdrawg() - subroutine used by eegplotgold() to plot data.
%
% Author: Colin Humphries, CNL, Salk Institute, La Jolla, 7/96
% Copyright (C) Colin Humphries, CNL, Salk Institute 7/96 from eegplot()
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public... |
8cb0e8d9506d50973f1793c5da0391d6df97b87ff7ce19dd794b40c1d9d94707 | MATLAB | 3,602 | 101 | function [R, t, iter_err, reg_pointqueary] = ...
ICP_point_regRTbalance(reg_points, reg_pointqueary, ops)
% This is an implementation of the Iterative Closest Point (ICP) algorithm.
% Arguments: pointcloud - 3 x n matrix of the x, y and z coordinates of data set 1
% pointqueary - 3 x m matrix of the x, y... |
ddc9b504ab10d717a3b3b00376767d76d476c0d9a7034ff3a097e6d36c011a3e | MATLAB | 3,605 | 128 | function averageOIS3(fname,fps,ntr,noff,nper,nfa,zoomdn,basediff)
% Usage ... averageOIS3(fname,fps,ntrials,offset,trialdur,desiredres,zoomdown,basediff)
% this one does global division
if (nargin<8), basediff=[]; end;
if (nargin<7), zoomdn=[]; end;
if isempty(basediff),
do_norm=0;
else,
do_no... |
b84beb89d44c4cbca63f02bfa2880388dd99af8c8d1e3a70cd817043bf422439 | MATLAB | 3,608 | 71 | % sleepDanalyzer montage script.
% chanList. A list of channel names and (optionally) channel coordinates.
% This should be an EEGLAB chanlocs struct. Alternatively you can read in a
% .txt file using the readlocs function (EEGLAB). If you wish to
% differentiate channel types (e.g. EEG, EOG, etc.) make sure to use t... |
94a41187e593fedae83644ee8787d7c7d38787168dbe2d7d1244c7234305188e | MATLAB | 3,609 | 121 | % getallmenuseeglab() - get all submenus of a window or a menu and return
% a tree. The function will also look for callback.
%
% Usage:
% >> [tree nb] = getallmenuseeglab( handler );
%
% Inputs:
% handler - handler of the window or of a menu
%
% Outputs:
% tree - text output
% nb ... |
8090e46097cbe506b29a340178b17cded39db2c2a9272e583b655189ea102e4e | MATLAB | 3,611 | 106 | function unfreezeColors(h)
% unfreezeColors Restore colors of a plot to original indexed color. (v2.3)
%
% Useful if you want to apply a new colormap to plots whose
% colors were previously frozen with freezeColors.
%
% Usage:
% unfreezeColors unfreezes all objects in current axis,
% un... |
eb12947dd3ab010662b9f6a700de9d8c5b90f277bdd651522134825712d42070 | MATLAB | 3,611 | 118 | function [maxsize,clstat,sizes] = palm_clusterp(X,y,thr,opts,plm,fastpiv,M,psi,res,m,c,o)
% Compute cluster pivotal statistics, for volume or surface
% data (vertexwise or facewise).
%
% Usage:
% [maxsize,clstat,sizes] = palm_clusterp(X,y,thr,opts,plm)
%
% Inputs:
% - X : Statistical map.
% - y : Modality index... |
f1b0f5f884994b797911aaf692922bd0f9cb6793524f49f5fdccb66a8f6ef3f3 | MATLAB | 3,614 | 87 | % Example replay and relationship between weighted corr. and
% sequence likelihood for all candidates
load('result_example_1_8.mat'); % 8th replay candidate in the 1st block
load('result_w_Lseq2.mat'); % weighted correlation and L_seq for all candidates
%% Figures
% example replay candidate
subplot(3,4,2);... |
817e80280e314dc1d07b332aed8eb051c15e615718daa1a44d29c8ef3553967d | MATLAB | 3,615 | 147 | function [psgOUT, scoresOUT] = fun_subset_data(psgIN, scoresIN, ar, varargin)
% Subset a continuous dataset in artifct free segments of either a
% particular sleep stage or a defined set of epochs.
%
% Required inputs:
%
% psgIN: A danalyzer psg structure
%
% scoresIN: A danalyzer sleepstages struct or an array of sle... |
798f832b8a930d2a7be823f8140fbca2af2831676e86953618309f2c7f8302ee | MATLAB | 3,616 | 142 | function [ CONDXY ] = ConditionalHist( X,Y,varargin)
%[CONDXY] = ConditionalHist(X,Y) Calculates the conditional probabilty
%of Y given X
%
%INPUT
% X
% Y
% (options)
% 'numXbins' (default: 50)
% 'numYbins' (default: 50)
% 'Xbounds'
% 'Ybounds'
% 'Xbinoverlap' (default: 1)
% 'minX' (default: 25)... |
3435b24cc5fd9febcaf027624ba269d0eda789db6705319af4ee0d07555790fd | MATLAB | 3,617 | 105 | %%controls across animals
ControlAll=[];
allnames={
'Tser4883_res_cfr4.mat'
'Tser5198_res_cfr3.mat'
'Tser5205_res_cfr3.mat'
};
groupname='ControlAll';
all_rr1a_micronsC=[];
all_rr1aSEM_micronsC=[];
all_rr1a_percentC=[];
all_rr1aSEM_percentC=[];
all_rr2a_micronsC=[];
all_rr2aSEM_micronsC=[];
all_rr2a_percentC=[];
all... |
054d51f0af5f0516695f5c36bd9a551fb5018e4215974469ae910b8fa17a1756 | MATLAB | 3,622 | 100 | % 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... |
82698a33abf3fd989880e9826a79afd7ff0aee28bceb0dfa95ac433097fbb1c5 | MATLAB | 3,622 | 113 | function [srcProj, detProj, link] = placeAndProjectOptodes(head, probeInfo, opts)
%PLACEANDPROJECTOPTODES Adjust probe coords and project to scalp nodes.
%
% [srcProj, detProj, link] = fnirspower.fwdcomp.placeAndProjectOptodes(head, probeInfo, opts)
%
% Inputs
% ------
% head : struct with fields
% ... |
dd34127b87d206eae1ac410678670dc837ff13baa969a896254a0c67b348a3a3 | MATLAB | 3,622 | 125 | function [ IDX,timestamps ] = bz_INTtoIDX(INT,varargin)
%[IDX] = bz_INTtoIDX(INT) Converts state on/offsets to vector of indices
%
%INPUT
% INT: {nstates} cell array of [nintervals x 2] start and end times.
% (optional) can be TSObject intervalSet
% -or-
% structure with f... |
0ad68899af4f90f3c32d4eb288f5b67a79606d8f457df59e04a181f75d994213 | MATLAB | 3,623 | 106 | function [passTrackLogic, numPassTrack, statPassTrack, lftPassTrack] = selTrackChecker(decompTrack, checkFr, minLft)
%PASSTRACKCHECKER checks for decompound tracks that pass through pre-defined frame and satisfy minimum lifetime
%
%SYNOPSIS: [passTrack, passTrackId] = selTrackChecker(decompTrack, frameCheck, minLft)
%
... |
7917c4e6017aaff44d503f94670283f11acab44ff22ee48ca524fc239d4dd83e | MATLAB | 3,623 | 88 | function [maskDens, maskDensMat, maskDensMatCov] = plotSpkMaskDensity(actinPropPerTimeStructArr, subgroupArr, pixelSize)
%PLOTSPKMASKDENSITY collect and plot speckle Mask Density
%
%SYNOPSIS: [maskDens, maskDensMat, maskDensMatCov] = plotSpkMaskDensity(actinPropPerTimeStructArr, subgroupArr, pixelSize)
%
%INPUT: actinP... |
7ded6f376442b9dff995eaee369a9f83d2ef9b20f14c3dee4080aabe81d5ddbf | MATLAB | 3,623 | 67 | function Obj=SOFAconvertFHK2SOFA(miroObj)
% OBJ=SOFAconvertFHK2SOFA(miroObj) converts the HRTFs described in miroObj
% to SOFA. miroObj is the miro object saved at the Fach-Hochschule Köln
% provided by Benjamin Bernschütz.
% Reference to the source format: http://www.audiogroup.web.fh-koeln.de/ku100hrir.html
% Re... |
84451255ff6f73b4e68794dc967b8317682d61e433111329762d9898267eccd8 | MATLAB | 3,623 | 85 | function [imgRGB, imgMask, xBounds, yBounds, smoothGrid, cmap] = makeMetricMap(metricVals, valPositions, gridRes, xLimits, yLimits, cmapInfo, sd)
% [imgRGB, imgMask, xBounds, yBounds, smoothGrid, cmap] =
% makeMetricMap(metricVals, valPositions, gridRes, xLimits, yLimits, cmapInfo, sd)
%
% Creates a gridded color im... |
f460c687dca18e7e1c7f47e5a3347fab451651a34f1d67b582808abe4ecbf84f | MATLAB | 3,623 | 118 | function [L_l,R_l] = lindemannInh(L,R,fs,c_inh,dim)
%LINDEMANNINH Signal pre-processing for Lindemann's cross-correlation
%
% [L_L,R_L] = IOSR.AUDITORY.LINDEMANNINH(L,R,FS) pre-processes left L and
% right R signals for the cross-correlation function based on Lindemann's
% precedence model [1,2]. A crucial param... |
99d1bc1374b970c5dbe67e2b1cb17d86e3dc06840c0db490422ba258e708f073 | MATLAB | 3,626 | 99 | % ====================================
%% Help
% ====================================
%
% CBIG_supp_fig1_fc_similarity
%
% This script replicates Supplementary Figure 1: the vertex-wise Pearson
% correlation between the NIH-34 and HCP-40 group-average whole-brain
% functional connectivity (FC) fingerprint maps. For eac... |
53bc777179e1c464555bf09c87b29be0561b2b55a3b5f2443cc4e484c8d19eac | MATLAB | 3,627 | 103 | %
% Copyright 2017-2023 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with
% Sandia Corporation, the U.S. Government retains certain rights in this software.
%
% See LICENSE for full license details
%
% Basic example of how to use the CrossSim matrix interface directly from Matlab
% This uses the C... |
f6d0e2d9ac625d6f2cf18bee7f522fabea2aebc27a2b68724bacfecc82b45941 | MATLAB | 3,631 | 89 | function X = gursoy_atun_layout(A,varargin)
% GURSOY_ATUN_LAYOUT Layout a graph by uniformly distributing vertices
%
% Instead of trying to optimize an objective function of forces or springs
% in the layout, the Gursoy-Atun layout distributes vertices uniformly
% within a topology subject to keeping vertices nearby t... |
1558d0243ab81b5c6e4fc635115f553553900d7bcc776f84f988a6af9f2bb85c | MATLAB | 3,633 | 105 | function [H, pValue, KSstatistic] = kstest_2s_2d(x1, x2, alpha)
% kstest_2s_2d - FUNCTION Two-sample Two-dimensional Kolmogorov-Smirnov Test
%
% Usage:[H, pValue, KSstatistic] = kstest_2s_2d(x1, x2 <, alpha>)
%
% The paired-sample Kolmogorov-Smirnov test is a statistical test used to
% determine whether two sets of dat... |
7c1d9be2d9dc0db1c8ff347f5fd107f28d51f90463740bf57a9f90fbf041de15 | MATLAB | 3,633 | 73 | %% Ordered probability matrix (Pairwise temporal ordering)
% This section computes the ordered probability matrix
% from spike trains across trials.
% x2_nMat : number of times neuron i fires AFTER neuron j
% x2_n0Mat : total comparable spike pairs (excluding ties)
x2_nMat = zeros(n_ne);
x2_n0Mat = zeros(n_ne);
... |
0a3b933327f93b86ff66e8189144446d39ac2f4f78210328f5daad8a99bede0c | MATLAB | 3,634 | 94 | % dipfit_erpeeg - fit multiple component dipoles using DIPFIT
%
% Usage:
% >> [ dipole model EEG] = dipfit_erpeeg(data, chanlocs, 'key', 'val', ...);
%
% Inputs:
% data - input data [channel x point]. One dipole per point is
% returned.
% chanlocs - channel location structure (returned by ... |
04a105c7ffb981ce322544c7dfa48c15ca9710fcc9586982b9a0ce164df5d5a3 | MATLAB | 3,637 | 94 | function varargout = add(tree,uid,type,parameter)
% XMLTREE/ADD Method (add childs to elements of an XML Tree)
% FORMAT vararout = add(tree,uid,type,parameter)
%
% tree - XMLTree object
% uid - array of uid's
% type - 'element', 'chardata', 'cdata', 'pi' or 'comment'
% parameter - property name (a char... |
4da613c669ca8fefdefcb40a320ab8b06cff0c52b309460c7b14f5c93604fc70 | MATLAB | 3,637 | 123 | classdef HBoxFlex < uix.HBoxFlex
%uiextras.HBoxFlex A dynamically resizable horizontal layout
%
% obj = uiextras.HBoxFlex() creates a new dynamically resizable
% horizontal box layout with all parameters set to defaults. The
% output is a new layout object that can be used as the parent for
... |
e9add03d73e226f970c938f589c1c7b1b19d54baabe8a4d34447c00a43c2e131 | MATLAB | 3,637 | 123 | classdef VBoxFlex < uix.VBoxFlex
%uiextras.VBoxFlex A dynamically resizable vertical layout
%
% obj = uiextras.VBoxFlex() creates a new dynamically resizable
% vertical box layout with all parameters set to defaults. The output
% is a new layout object that can be used as the parent for other... |
fa159e4589e528772078292f0e599e31177a1876f75b377441d7e6dabd049423 | MATLAB | 3,638 | 93 | function series = fgn_sim(n, H)
% Generate Fractional Gaussian Noise (FGN) time series
% inputs:
% n (integer): Desired length of the series
% H (real number): Hurst exponent for the output series (0 < H < 1)
%
% outputs:
% series: Real-valued time series of length n with Hurst ... |
2639073f623f657b9e0e91364ee1df8bbc375928c1a5246a3a05f16fbf9945de | MATLAB | 3,641 | 113 | % entropy_rej() - calculation of entropy of a 1D, 2D or 3D array and
% rejection of odd last dimension values of the input data array
% using the discrete entropy of the values in that dimension
% (and using the probability distribution of all columns).
%
% Usage:
% >> [entropy... |
902ac59b8a8552fca548d7769c8ad95e32a137fefa2ca03c04bed71bf21f7795 | MATLAB | 3,641 | 113 | function [cY,mY,ng] = motion_metrics(Y,bnd,batch_size,var_name)
% computes several metrics for the quantitative assessment of the registration
% INPUTS
% Y: registered time series in a loaded or memory mapped array
% bnd: number of pixels to be exluded to avoid NaN effects
% [x_... |
ac77fd51e094f0a2a1222204f104847c7dca4792f0b21cf689d1e37704fa1c05 | MATLAB | 3,642 | 111 | % % simple flow from genotype to RC/non-RC
% figure('Name','sankey demo1','Units','normalized','Position',[.05,.2,.5,.56])
% links={'WT','RC',29;'Mutant','RC',2;'WT','Non-RC', 78;'Mutant','Non-RC',30};
% SK=SSankey(links(:,1),links(:,2),links(:,3));
% SK.ColorList=[0.0, 0.7, 0.0;
% 0.8, 0.0, 0.0;
% 0.0, 0.0, 1.... |
f767dd600c79d94de2ee3a94d7d7415e9e60cead345fa068ce9cf6e0c8b713b2 | MATLAB | 3,642 | 119 | function [y,yi,subim1loc,im1loc]=positionMask2d(mainParms,subParms,mainIm,subIm)
% Usage ... y=positionMask2d(mainParms,subParms,mainIm,subIm)
%
% mainParms=[xSize,ySize,xFOV,yFOV,x0loc,y0loc]
% subParms=[xSize,ySize,xFOV,yFOV,x0loc,y0loc]
%
% Ex. positionMask2d([],[],im1)
if length(mainParms)<6,
if length(mainParms... |
c2fb7fe2ab6465ac5a97fe4d7409c1061650636d82b91ec5664ef7e2abfc21ba | MATLAB | 3,643 | 123 | function plywrite(filename,faces,verts,varargin)
% plywrite(filename,faces,verts)
% Will write a face vertex mesh data in ply format.
% faces -> polygonal descriptions in terms of vertex indices
% verts -> list of vertex coordinate triplets
% faces and verts can be obtained by using the MATLAB isosurface function.... |
a228035f68c1fe7ef530a3c4a328479b6bde8be97aaf7b92423611f1de682b36 | MATLAB | 3,644 | 117 | % interface program for batch program
%
% Author: Marco Reisert
% PC 2010
function out = dti_tracking_global_ui(P)
h = findobj(0,'tag','fiberGT_main');
if ~isempty(h)
delete(h);
end;
if isfield(P,'temp') %% GT accum
fiberGT_tool('loadFTR',P.filenameFTR{1});
ftr = fiberGT_tool('createEFTR',P.numi... |
63cce6265b9fe0c8ae3d8eff433dfc7ed76ba3a14f25a1fc4e7f190fa90c4142 | MATLAB | 3,645 | 148 | function [tuning_curve theta ang_hd mr u2] = PolarMap(self,variableName,root,varargin)
% [tuning_curve theta ang_hd mr] = PolarMap(self,root,'x')
%
% Tuning of the user defined variable as a function of a polar variable.
%
% Inputs:
% root - The CMBObject that we lie within (CMBHOME.Session)
%
% variableName - Whic... |
d3d586d9b9507bef318c048b94c906f000c4eec74ff1c11948eb93629278b4a6 | MATLAB | 3,645 | 87 | function ea_get_probab_axon_state_for_multisource(results_folder,damaged_as_activated)
% Estimate probability of axon activation based on a sweep of parameters
% special case for multisource probabilistic PAM
% (e.g. fiber diameters).
% By Butenko and Li, konstantinmgtu@gmail.com
arguments
results_folder ... |
109a491cc6d6acc16b75ebf16d2c03daed2c6200428e6050bc73fb9e07fcffe2 | MATLAB | 3,648 | 142 | % Script that carries out cross-correlation analyses shown in Figure 5:
% NB apical area vs NC transcription levels and
% NC apical area vs NC transcription levels
close all
clear all
%% load data
load("combined_data_for_correlationsNEW.mat")
maxLagMinutes = 23;
analysis_number = 3;
% 1 is NB area vs SC Intensity
... |
e99349e7b4eb5466d9f21fcacd616b6dde62f823d58a4f6ce19c3bc36fbbbb35 | MATLAB | 3,649 | 95 | %% params
nChTopo = eval(['nCh', topoArea]);
coherencespctrm = eval(['coherencespctrm_topo', topoArea]);
if strcmp(topoArea, 'AC')
posIndex = 1;
else
posIndex = 2;
end
%% time-frequency
figure;
plotSize = mu.autoplotsize(nChTopo);
for cIndex = 1:nChTopo
mu.subplot(plotSize(1), plotSize(2), cIndex, "paddin... |
82e90080beefd19259bfba68f0d984079a8ed58736aebee513725bb66db5612e | MATLAB | 3,650 | 100 | function ResampleBinary(inputName,outputName,nChannels,up,down)
%ResampleBinary - Resample binary data file.
%
% Resample binary data file, e.g. create LFP file from raw data file.
%
% USAGE
%
% ResampleBinary(inputName,outputName,nChannels,up,down)
%
% inputName binary input file
% outputName binar... |
da2163c0a865a799155eaf0844dadb67aa7943014181b14d21ad8c39e97cafc8 | MATLAB | 3,650 | 154 | function h=ellipse(ra,rb,ang,x0,y0,C,Nb)
% Ellipse adds ellipses to the current plot
%
% ELLIPSE(ra,rb,ang,x0,y0) adds an ellipse with semimajor axis of ra,
% a semiminor axis of radius rb, and an orientation of the semimajor
% axis with an angle of ang (in radians) rotated counter-clockwise
% from the x-axis. The el... |
7a9331992cc2f4160bd6c2034ecdaf632e240a1a37040330b166d19e45dfe36d | MATLAB | 3,651 | 69 | function [S,f,R,Serr]=mtspectrumtrigpt(data,E,win,params,fscorr)
% Multi-taper time-frequency spectrum - point process times
%
% Usage:
%
% [S,f,R,Serr]=mtspectrumtrigpt(data,E,win,params,fscorr)
% Input:
% data (structure array of one channel of spike times;
% also accepts 1d column ve... |
018bcd5a3bc9cc11f7614092dd39b0599357d288bf6bd624ab3fada7fb54bece | MATLAB | 3,653 | 99 | function ccfs = clustering_coefficients(A,varargin)
% CLUSTERING_COEFFICIENTS Compute the clustering coefficients for vertices.
%
% ccfs = clustering_coefficients(A) returns the clustering coefficients for
% all vertices in A. The clustering coefficient is the ratio of the number
% of edges between a vertex's neighbor... |
40d66efd09b5c90dd0cde2e8be02395a93938dc9b0a6ebf74d11e8f09041e36d | MATLAB | 3,653 | 112 | function clustered = CBIG_IndCBM_generate_MSHBM_params(lh_profile, rh_profile, lh_labels, rh_labels)
% clustered = CBIG_IndCBM_generate_MSHBM_params(lh_profile, rh_profile, lh_labels, rh_labels)
%
% This function can generate parameters used in MSHBM algorithm for a given
% group-level parcellation with average profil... |
7da3581d63906effebc93b00c26b8e891c7be95e3d8a1479e071d016bae2dca9 | MATLAB | 3,653 | 94 | function [trace_stamp, trace_num, ttlabel, tracetype] = pooltrace(handles)
trace_stamp = []; trace_num = 0; tracetype = [];
ttlabel = [];
if handles.plotRawdff == 1
if ~isempty(handles.cfeature_dff)
trace_stamp = cat(2, trace_stamp, handles.cfeature_dff);
for i = 1:size(handles.cfeature_df... |
e8905064f0c60766dba4542db96a2e430d3ce6b5537b37962efab9ad72396c10 | MATLAB | 3,654 | 104 | function [chosenfluor,chosenROIs,chosentemps,chosenFrameRate,chosenIndex]=compare_tuning_old(headpath,savemode)
%give the headpath (genotype) go to the extracted folder
%bring up the different ROIs for each
%let the user select which ROI they want to use as the one to compare for
%THAT fly
%take the dff for those - an... |
94a340b317b1511171447f47a525439e96fb77c4a2c7d1bf68e77303462348ad | MATLAB | 3,659 | 21 | %% createColorImage (RGB) from colormap and indexed image
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dept. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2009 - 2017
% mail@andreashusch.de, husch.andreas@chl.lu
function image = createColorImage(rawImageData, myCol... |
bbaba9439e27d315890bc65d62a9b47de5760e2e0082a2e1e3d29444d62a0718 | MATLAB | 3,659 | 123 |
%%
clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
% set parameters
% input parameters
% subjs = {'S01' 'S02' 'S03' 'S04' 'S05' 'S06' 'S07' 'S08' 'S09' 'S13' 'S15' 'S16' 'S17' 'S18' 'S19' 'S20' 'S21' 'S22' 'S32' 'S36' 'S37' 'S38' 'S39' 'S40' 'S41' 'S42' 'S43' 'S44' 'S45' 'S... |
e25563b493e029204344f2880fde10e8a5a4493c0d8f246d4795e68f979b3e70 | MATLAB | 3,659 | 81 | % std_renamestudyfiles() - rename files for design 1 if necessary. In design
% 1, for backward compatibility, files could have
% legacy names. For consistency these files now
% need to be renamed. Note that the STUDY is
% ... |
a3bf9cd34a8e492dcd91ac84ce9ca719525adfe1dcef4c297956cf8e0bdcdbd9 | MATLAB | 3,660 | 73 | function [dS,f]=mtdspectrumc(data,phi,params)
% Multi-taper frequency derivative of the spectrum - continuous process
%
% Usage:
%
% [dS,f]=mtdspectrumc(data,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, win, t have to be i... |
139ff0a1ae1010b027cd9d58448176dea8293f9852b7ab6ed623235f3106c505 | MATLAB | 3,662 | 95 | % Copyright(c) 2011 - 2018 Thermo Fisher Scientific - LSMS
%
% Permission is hereby granted, free of charge, to any person obtaining a copy
% of this software and associated documentation files (the "Software"), to deal
% in the Software without restriction, including without limitation the rights
% to use, copy, modi... |
226bc9837fe95caffcdeb554878ae2aa01a34f1ac8d06dce770cd0771a363297 | MATLAB | 3,662 | 93 | function FV2=ea_smoothpatch(FV,mode,itt,lambda,sigma)
% This function PATCHSMOOTH smooths a triangulated Mesh, with accurate
% curvature flow smoothing, or laplacian smoothing with inverse vertice
% distance based umbrella weights.
%
% FV2=smoothpatch(FV,mode,itt,lambda,sigma);
%
% Inputs,
% FV : A struct con... |
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