sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d64674a60a2f88038830cd26f2fadf71b7896525bb02523100b52b5fe0449589 | MATLAB | 6,382 | 172 | function frequency = Frequency(timestamps,varargin)
%Frequency - Compute instantaneous frequency for a point process (e.g. a spike train).
%
% Compute instantaneous frequency either by smoothing the point process using a fixed
% or adaptive Gaussian kernel, or by simply taking the inverse of the interevent intervals.
... |
7a345f4e59aee09948c04447bbfee12a2d7dfb83c4b0746623ef1e06a47fee73 | MATLAB | 6,383 | 137 | function [MRSCont] = osp_saveJMRUI(MRSCont)
%% [MRSCont] = osp_saveJMRUI(MRSCont)
% This function writes all MRS data loaded by OspreyLoad to separate
% jMRUI-readable .TXT files.
%
% One .TXT file is produced for unedited MRS data
% (PRESS, sLASER, etc.), four .TXT files are produced for MEGA-edited
% dat... |
1a3ed5551d30478103361406ceb11b5103790fad92f9c948ba529dff155d3350 | MATLAB | 6,392 | 165 | function M = smc_oopsi_backward(S,V,P)
% this function iterates backward one step computing P[H_t | H_{t+1},O_{0:T}]
% Input---
% Sim: simulation metadata
% S: particle positions and weights
% P: parameters
% Z: a bunch of stuff initialized for speed
% t: current time step
%
% Output is a single structure ... |
1225d105c3ef2238a7b10ac73fb1f8d46fdd81333b89e10f212c0c2dbf32e47b | MATLAB | 6,393 | 185 | % Main script for analyzing laminar depth profiles of SANDI intra-soma signal fraction
% across von Economo atlas
%
% Reference:
% Lee H, ..., Huang S, Communications Biology, 2026
%
% Requirements:
% - FreeSurfer installed and configured
% - FreeSurfer fsaverage surface and annotation files available
% - Economo-Koski... |
3db9368b71852eab84b09abd96b28e084d92c6e349a9fe94e205be1fe61936c2 | MATLAB | 6,393 | 178 | function [niiSOS, niiSENSE, noise_array] = osp_cpx2nii(cpxFile, sinFile, niiSOSFile, niiSENSEFile, launchViewer)
%%[niiSOS, niiSENSE] = osp_cpx2nii(cpxFile, sinFile, niiSOSFile, niiSENSEFile, launchViewer)
% Reads complex Philips data (*.cpx) and geometry (.sin) files and
% converts the image to NIfTI (*.nii) form... |
a12528c7958ee5445b9b897ac1898e51901e44f2ff9ecfadbdd206764e092902 | MATLAB | 6,393 | 264 | function OUT = db_cluster_table(clusters,DB,varargin)
% function OUT = db_cluster_table(clusters,DB,varargin)
%
% tor wager
% counts studies and contrasts in each cluster
%
% clusters is a struct in which XYZmm field has list of points
% --should be output of database2clusters, which contains all fields
% DB is databas... |
1e4a7a26c5c010410981e9d63b3e04ff4feb9c2ebbfdcdc8269c98565ef7c897 | MATLAB | 6,394 | 189 | function [net, info] = fast_rcnn_train(varargin)
%FAST_RCNN_TRAIN Demonstrates training a Fast-RCNN detector
% Copyright (C) 2016 Hakan Bilen.
% All rights reserved.
%
% This file is part of the VLFeat library and is made available under
% the terms of the BSD license (see the COPYING file).
run(fullfile(fileparts(m... |
e8ce2652bba4a4f4ac1105637dbf832619a90bfb97ccc953ecfbcfdab92d197f | MATLAB | 6,396 | 215 | function [merged unused] = tapas_uniqc_propval(propvals, defaults, varargin)
% Create a structure combining property-value pairs with default values.
%
% [MERGED UNUSED] = TAPAS_UNIQC_PROPVAL(PROPVALS, DEFAULTS, ...)
%
% Given a cell array or structure of property-value pairs
% (i.e. from VARARGIN or a structure of pa... |
4029a63f77adc9d68f8ae3e2dc5f281de6a33a1ffd118385e984ff241b88a25c | MATLAB | 6,397 | 176 | % POP_FUSECHANREJ - Make sure the same subject and session have the same
% removed. If not remove channel not in common.
% Usage:
% >> ALLEEG = pop_fusechanrej(ALLEEG);
%
% see also: pop_clean_rawdata
% Copyright (C) 2022 Arnaud Delorme, UCSD
%
% This file is part of EEGLAB, see http://www.eegl... |
24bcd54c91f12d94e8332ef8a1bf2affe94858cbc0d0b90f99caf9a262067f91 | MATLAB | 6,398 | 143 | % std_topomovie - make movie in the frequency domain
%
% Usage:
% >> [STUDY] = std_movie(STUDY, ALLEEG, key1, val1, key2, val2, ...);
%
% Inputs:
% STUDY - STUDY structure comprising some or all of the EEG datasets in ALLEEG.
% ALLEEG - vector of EEG dataset structures for the dataset(s) in the STUD... |
6c86573353ba7747ef806426813d8daeb5df706d060a367422c735bab93be3f5 | MATLAB | 6,399 | 168 | function info = step1RunSearchlight(opt)
% Step 1 : running searchlight (SL)
% get the smoothing parameter for 4D map
funcFWHM = opt.funcFWHM;
% set output folder/name
savefileMat = fullfile(opt.pathOutput, ...
[opt.taskName, ...
'_SL_VisDirSel',...
... |
c8ce88aab778c3163365c9f440bd2fc4bca0126bda3747be9bbc229bdf8b6f44 | MATLAB | 6,399 | 189 | function [net, info] = fast_rcnn_train(varargin)
%FAST_RCNN_TRAIN Demonstrates training a Fast-RCNN detector
% Copyright (C) 2016 Hakan Bilen.
% All rights reserved.
%
% This file is part of the VLFeat library and is made available under
% the terms of the BSD license (see the COPYING file).
run(fullfile(fileparts(m... |
a38543c7cf1818c069564cb569297b484250e0bf1fbdf18bd39ecf24d75bb84a | MATLAB | 6,401 | 212 | %% Add path
addpath('H:\Kaizhen\Anxiety_behavior_phenotyping_analysis\Ethological_Behavior\Markov_Chain_Analysis')
%% Define file names for 16 mice
fileNames = {...
'C1_behavior_states_timestamps.xlsx', ...
'C2_behavior_states_timestamps.xlsx', ...
'C3_behavior_states_timestamps.xlsx', ...
'C4_... |
1fdafe68f4b375ab68e17fc9c2a4ecef483501000d937c0858a8b2ed6007f59b | MATLAB | 6,402 | 114 | % This function loads a single file and gathers all of the needed
% information. fOutID should be the output file handle from
% main_diagnostics. singleSetFile should reflect its name.
function single_diagnostic(fOutID, singleSetFile)
% Storing what's going to be written to the csv in a variable to act as
% a b... |
8151993c03cc812e353a6d2c9507ee6daf52730a65fb2355d9ab46f19eda4d1f | MATLAB | 6,403 | 154 | function [cov_signal_epoched, cov_noise_epoched, artifact_threshold_out,Treshold1] = clean_SENSAI(artifact_threshold_in, refCOV, Eval, Evec, cov_total, signal_type)
% This GEDAI function estimates signal and noise covariances analytically
%% Creative Commons License
%
% Copyright: Tomas Ros & Abele Michela
% ... |
b82d47a4d3f05f5a4864cf5be64e388f8c68d710cf9830cf223e88fcbbad8167 | MATLAB | 6,403 | 148 | clear; close;
%specify ages to include in analysis
ages = {'05', '08', '12', '18', '24'};
%specify other info about data
tasks = {'hand', 'social'};
cohorts = {'gm', 'uk'};
% create empty table
columnNames = {'ID', 'Cohort', 'Task', 'Age', 'Channel', 'Homer_Pruned_Total', 'Average_SCI', 'Average_PSP', 'Percentage_Mo... |
a156011d50a9a115f5c0698bbafcded0659d063b77f6cdb66aa0d73673265afc | MATLAB | 6,404 | 170 | function varargout = pdftops(cmd)
%PDFTOPS Calls a local pdftops executable with the input command
%
% Example:
% [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for future refere... |
df2627db1d86fec5db1128f1ef8b19a6fadc06fd20dcf211ecfda69c6b9e4853 | MATLAB | 6,408 | 223 | function [MI_td,shuffmean,shuffstd,shuffsig,Hs]...
= MutualInformation(fname,ops)
%calculates mutual information between a stimulus or behavior of
%interest, and the firing rate, based on the underlying GLM
%
%%Inputs:
% fname: glm fit file
% ops: main structure with following info
% masktype: 'test' ... |
6d859f274fffad14de29934afd3e16e0f7122c99aecff6c7bc2679328d490e32 | MATLAB | 6,409 | 187 | function setpos(h,fmt,href)
% SETPOS Set graphics object position in a flexible way.
% SETPOS(H,FMT) sets the position property of graphics object
% with handle H, according to FMT that can be expressed using different
% units. H must have a "Position' property.
%
% FMT is a char array containing 4 strin... |
dfde73e2b71166dffa89906f0df8978970f5254903bdd62ffe124bd9252a5d04 | MATLAB | 6,409 | 126 | function chGroups = getChannelGroups(params, groupSpecification)
% returns channel groups (cell array) based on group specification
% (c) Jiri, Apr16
chGroups = [];
%% load 'H' & selCh
name_selCh = ['selCh_H_' params.thisData];
load(params.storage.cacheFile, 'H', name_selCh);
selCh_H = eval(name_selCh);
selCh_raw = ... |
200cbaeaf39ba17d74ba479c58feabbf9749593deadd41367f39288589dbd084 | MATLAB | 6,413 | 168 | function out = SY_SpreadRandomLocal(y, l, numSegs, randomSeed)
% SY_SpreadRandomLocal Bootstrap-based stationarity measure.
%
% numSegs time-series segments of length l are selected at random from the time
% series and in each segment some statistic is calculated: mean, standard
% deviation, skewness, kurtosis, PermEn... |
a16d7ca9dac33dd8180e8d30d1dba11b79e061711fab79b3aacbac09b6a5ec85 | MATLAB | 6,414 | 136 | %% TestQSMMatrixPhantom - Tier 2 synthetic-phantom QSM method regression matrix
%
% Runs the one-stop SEPIA pipeline on a small, deterministically-generated
% synthetic phantom (test/phantom/generate_synthetic_phantom.m) once per
% QSM dipole-inversion method in methodQSMName (sepia_universal_variables.m)
% AND per mat... |
44436a2dd029dd5f5e64f9b74f67870e0108aaa9eadd62907858b72d2f3c3b1c | MATLAB | 6,418 | 188 | % PLOTPROJ - plot projections of one or more ICA components along with
% the original data (returns the data plotted)
%
% Usage:
% >> [projdata] = plotproj(data,weights,compnums);
% >> [projdata] = plotproj(data,weights,compnums, ...
% title,limits,chanlist,channames,co... |
c09e8a653e78a4e1c1f135e0b65708c1966a3afc24e8058cd05297cd9910d9ec | MATLAB | 6,421 | 167 | function [MRSCont] = OspreyAddImages(MRSCont)
%% [MRSCont] = OspreyAddImages(MRSCont)
% This function allows adds the three plane images into the container to
% make it transferable
%
% USAGE:
% MRSCont = OspreyAddIamges(MRSCont);
%
% INPUTS:
% MRSCont = Osprey MRS data container.
%
% OUTPUTS:... |
ead44a75259ac1d63391e4922678f24419b6bfbb6e05befaf3e6f57f5fea0bee | MATLAB | 6,421 | 153 | function out = IN_MultivariateAMI(y, tauMethod, estMethod, extraParam)
% IN_MultivariateAMI Multivariate automutual information, I(x_t; x_{t-tau}, x_{t-2tau})
%
% Measures how much information the past two points (spaced tau apart, with tau
% estimated from the series' own autocorrelation structure) jointly carry abo... |
096c06dec6182e1c38d008d66602357fb7bbdedc303cdf20ed118e88e31bae02 | MATLAB | 6,422 | 210 | function info = plotTCA_ephysFig(K, drawLines, varargin)
%VIZ_KTENSOR Visualize a ktensor
%
% Xticks = cell array (one per mode)
% Xticklabels = cell array (one per mode)
% Xlims = cell array (one per mode)
% Ylims = cell array (one per mode)
% Hrelspace = Relative Horizontal Space Between Plots (.1)
% HspaceLeft = Abs... |
75e23e9a8d0e4a6131e04fd30ab31c039350cc585d7abdac04681f84cc0469bf | MATLAB | 6,422 | 183 | function [c, r, t, cpulse, acq_codes] = tapas_physio_read_physlogfiles_brainproducts(log_files, ...
cardiac_modality, verbose)
% reads out physiological time series (ECG, PMU, resp belt) and timing vector for BrainProducts .eeg file
%
% [cpulse, rpulse, t, c, acq_codes] = tapas_physio_read_physlogfiles_brainprodu... |
3d8932c63cf8aeb7ffc69b590de6a7acfdf221f60a8007a9ab543f9750d04c4b | MATLAB | 6,424 | 164 | function out = NL_nlpe(y, de, tau, maxN, theilerWin)
% NL_nlpe Normalized drop-one-out constant interpolation nonlinear prediction error.
%
% Computes the nlpe for a time-delay embedded time series using Michael Small's
% code, nlpe (renamed MS_nlpe here):
%
% ---INPUTS:
% y, the input time series
% de, the embedding... |
c1a41d00580513054794cd0cb65b9f49819067c0a61a712833d7898c3e86d32c | MATLAB | 6,426 | 192 | function [handle,pltchans,epos,Zi] = topoplotIndie(Values,chanlocs,varargin)
headrad = 0.5;
GRID_SCALE = 64;
CIRCGRID = 201;
HEADCOLOR = [0 0 0];
HLINEWIDTH = 1.7;
BLANKINGRINGWIDTH = .035;
HEADRINGWIDTH = .007;
plotrad = .6;
Values = double(Values);
SHADING = 'int... |
0d4b8ad8d315c073de90b341afd70826d1666ebeafc77d76e8d9c76db0355e6d | MATLAB | 6,427 | 178 | %%Figure S3A
%PCA analysis and visualization of 32 molecular descriptors for the 690
%odorants from the DoOr database (gray dots), and the 35 odorants in
%our panel (red dots)
%% clear workspace
clear all; clc
%% read data
%define and load the .xlsx file
filename = 'eDragon Descriptors for Panel of 35 Odorants';
%... |
3c1f9962ce141de6629f05c10b9fda4f1b28dbc4d2f8896bf131cbaeecc4deda | MATLAB | 6,428 | 212 | % createfigure Create figures for generic decoding results
%
% Author: Tomoyasu Horikawa <horikawa-t@atr.jp>, Shuntaro C. Aoki <aoki@atr.jp>
%
clear all;
%% Data settings
resultsDir = './results/';
resultsFileFeatPred = fullfile(resultsDir, 'FeaturePrediction.mat');
resultsFileCatIdent = fullfile(resultsDir, 'Cate... |
86ce4969a1cb4562c14c971d486d62a21062b4a850c5b29e8d132324220490b4 | MATLAB | 6,429 | 168 | function PCs = pca(this, cutoff, pcDimension)
% Computes principal component analysis (PCA) of image time series
%
% Y = MrImage()
% PCs = pca(this, cutoff, pcDimension)
%
% This is a method of class MrImage.
%
% Spatial PCA (default):
% The principal component analysis report representative spatial
% distributions... |
44783d5aced14af1b1aba154f08e2619a8f386cf09976b2f19309b2676526483 | MATLAB | 6,432 | 178 | function [obj] = ft_determine_units(obj)
% FT_DETERMINE_UNITS tries to determine the units of a geometrical object by
% looking at its size and by relating this to the approximate size of the
% human head according to the following table:
% from 0.050 to 0.500 -> meter
% from 0.500 to 5.000 -> decimeter
% ... |
20be288aba81d2d76620e02c0f46cf257c4cafcb6a9e85392faf844ef8a033fb | MATLAB | 6,433 | 227 | function images = get_stimulusimages(username, accessKey)
% get_stimulusimages Get stimulus images from ImageNet
%
% Note:
%
% This script is for downloading all 1200 training and 50 test images of
% experimental stimulus used in Horikawa and Kamitani 2017
% "Generic decoding of seen and imagined objects using hier... |
ef67cf1619560d8698a0062f94edf7751a70e156a648404ae335afad29b39071 | MATLAB | 6,433 | 174 | % EEG_EVENTTABLE - returns all events contained in the EEG structure (and
% optionally exports them to a CSV file)
%
% Usage:
% >> events = eeg_eventtable(EEG);
%
% Inputs:
% EEG - EEG structure
%
% Optional inputs:
% 'unit' - Unit of events containing time samples, can be either... |
b467e1f493d2cc09814a2d6b79bb5d59f9821b1c95f9475645681bd9cb2d6fde | MATLAB | 6,434 | 221 | clc;
clear;
close all;
%
subj_files = dir("*_eeg.mat");
similarity_over_coherences = struct("subj_n",{},"coh_sig",{});
similarity_over_conditions = struct("subj_n",{},"cond_sig",{});
MY_rdmSets = struct("subj_n",{},"rdmSet",{});
%load delay files
directory = 'D:\Program Files\MATLAB\Joint_Perception_P... |
f1258ef6140be684460d25497995708b29fe1daf0af36e1b4a9b052f2b8e8f14 | MATLAB | 6,442 | 221 | function [output]=pieceWiseUnmixing(signal, reference, Fs, varargin)
% for now, only work with vectors for both inputs
% first scale is always correspond to 4 slices.
% alternatively, use 1sec window with overlap (from 0% to 90% ovlp)
% Output strucutre:
% output.residual
% output.coefficient
% Variable Input Ar... |
b6d52a470bc5325eab15a4bec3fd912546eecdffe2c2a1a046c6d5bee73f7e10 | MATLAB | 6,443 | 152 | function data = speedcells(data)
% function data = speedcells(data,vbins,ngaussigma,maxlag)
% setting some inital parameters (user input)
vbins = 0.02:0.01:0.2; % m/s
ngaussigma = 2; % sigma of the Gaussian filter (in number of datapoints, i.e. [ngaussigma/framerate] sec). Put ngaussigma=0 if not using Gaussian f... |
4837534fbcfb395b0e5e6031ad553e9cddbbfcf616cd4305da4ceb1805244190 | MATLAB | 6,446 | 230 | function sx = gen_input_spikes(fr, T, varargin)
% GENERATE_INPUT_SPIKES - Generate spike trains from firing rates
%
% H1 Line: Create Poisson spike trains with optional noise modulation
%
% Syntax:
% sx = generate_input_spikes(fr, T)
% sx = generate_input_spikes(fr, T, F, NI, sigma_n, tau_n)
% sx = generate_input... |
f6911b4fb430f5c72c2c2e4ada88f45acb18953cb36ee8157d238b0964396e0e | MATLAB | 6,447 | 153 | function [cov_signal_epoched, cov_noise_epoched, artifact_threshold_out,Treshold1] = clean_SENSAI(artifact_threshold_in, refCOV, Eval, Evec, cov_total, varargin)
% This GEDAI function estimates signal and noise covariances analytically
%% Creative Commons License
%
% Copyright: Tomas Ros & Abele Michela
% ... |
32a7f4743f9f0a4ef01cc4b93e802f15c2d030e9b104a6e084669244a15c2e88 | MATLAB | 6,449 | 152 | % EEG_IMPORT - Import data files in a variety of supported format
%
% Usage:
% >> EEG = eeg_import(fileIn);
% >> EEG = eeg_import(fileIn, 'key', 'val', ...);
%
% Inputs:
% fileIn - [string] input file name. The function used to import the file is
% based on the file extension.
% '.set' - POP_LOADS... |
2e7ef24f2b0e1e24bbac7735cfe4f92b6f81afbac68a70a7d5171be569a9b31a | MATLAB | 6,451 | 141 | function out = BF_CumSumBridgeStats(p)
% BF_CumSumBridgeStats CUSUM/bridge stationarity statistics on a cumulative sum.
%
% Given a series p_t whose mean is being tested for stationarity, forms
% cumsum(p) and computes: linear-fit statistics on the cumsum (cf. SY_Trend),
% a CUSUM 'bridge' relative to the endpoint-to-... |
807e7f9da1558165795a583ba6fc895e75a8d76655547cc9df4dd38ec6bbedfe | MATLAB | 6,452 | 166 | %% [chi] = Wrapper_QSM_MEDI(localField,mask,matrixSize,voxelSize,algorParam, headerAndExtraData)
%
% Input
% --------------
% localField : local field map (tissue fields), in Hz
% mask : signal mask
% matrixSize : size of the input image
% voxelSize : spatial resolution of each dimension of the data,... |
3d8e9aa364e96c57b0e07301987920f7762e6401d589d93a73937542d0eca07c | MATLAB | 6,454 | 179 | function [dataPlot, displayRange, resolution_mm] = extract_plot_data(this, varargin)
% Extracts (and manipulates) data for plotting with arguments from MrImage.plot
%
% Y = MrImage()
% Y.extract_plot_data('ParameterName', 'ParameterValue' ...)
%
% This is a method of class MrImage.
%
% IN
% varargin 'Parameter... |
0c4aea1f39704442cf4453f236d2cdea2c67803dd0ae8201ef613ab113dfabf1 | MATLAB | 6,455 | 176 | function [rvt, timeRpulseMax, timeRpulseMin, verbose] = ...
tapas_physio_rvt_peaks(fr, t, sample_points, verbose)
% computes respiratory volume per time from filtered time series
%
% [rvt, rpulseMax, rpulseMin] = tapas_physio_rvt_peaks(fr, t)
%
%
% NEW:
% The respiratory volume/time is computed by interpolating ... |
cca8b3357449ff891ce4cbae2010977a8bdfed790ee5a2dedf66a58d10c76447 | MATLAB | 6,456 | 186 | function [ suma ] = nf_read_suma( suma_dir, ld, surf_class)
%[ suma ] = nf_read_suma( suma_dir, ld, surf_class)
% Will read in the SUMA surface of a specific ld from the specified dir
% will return a strcut with
% .pos = vertices
% .tri = faces
% .curv = curvature
% .annot = annotations
% .annot_key = annotations k... |
0e5d5f2984f71ca5c1e1f2ed98534c242f54f92a98e123847c85a1cfabccd9c0 | MATLAB | 6,458 | 152 | % POP_TIMTOPO - call the TIMTOPO function for epoched EEG datasets.
% Plots the epoch mean for each channel on a single axis,
% plus scalp maps of the data at specified latencies.
% Usage:
% >> pop_timtopo( EEG, timerange, topotimes, title, 'key', 'val', ...);
%
% Inputs:
% EEG ... |
b6a0792dfc84c0d5982a0d58d48a491dd1b4c121ec9eec3a31e07c2770339b73 | MATLAB | 6,459 | 169 | function info = step1RunSearchlight_noMask(opt)
% Step 1 : running searchlight (SL)
% get the smoothing parameter for 4D map
funcFWHM = opt.funcFWHM;
% set output folder/name
savefileMat = fullfile(opt.pathOutput, ...
[opt.taskName, ...
'_SL_VisDirSel_n... |
acae30cb618c3d5582b14bbea9e50946c0dd9b4d306ad77bbee69ebcc22a519b | MATLAB | 6,461 | 201 | function varargout=getLFPpowerSpec(lfpFile,nCh,targetCh,saveFile,varargin)
% [spec,t,f]=getLFPpowerSpec(lfpFile,nCh,targetCh,saveFile,...)
%
% spec is power spectrum density in uV^2/Hz
% (as long as I understood mtcsglong() correctly)
%
% options and defaults
% whitening=true;
% nFFT=2^11;
% samplingRate=1250; %1/... |
21937d5144c3d857b7a04aefa0f7a54ce50352c838fd9470a6e4edbaa980040f | MATLAB | 6,462 | 157 | function [VOLLOCS, LOCS, verbose] = tapas_physio_create_scan_timing_from_end_marker_philips(log_files, thresh, sqpar, verbose)
%extracts slice and volume scan events from gradients timecourse of Philips
% SCANPHYSLOG file
%
% [VOLLOCS, LOCS] = tapas_physio_create_scan_timing_from_gradients_philips(logfile,
% thresh... |
663537581b5b6622a48c94d738bab94620629e937b3943661fdf0d86b5bb36d4 | MATLAB | 6,463 | 174 | function [freq] = ft_datatype_freq(freq, varargin)
% FT_DATATYPE_FREQ describes the FieldTrip MATLAB structure for freq data
%
% The freq data structure represents frequency or time-frequency decomposed
% channel-level data. This data structure is usually generated with the
% FT_FREQANALYSIS function.
%
% An example o... |
edad5d11423bc6ae19be50e5011d9e7b370f970e91ef34225b5ca7078ef5dcb7 | MATLAB | 6,468 | 207 | function visualMotionLocalizer(cfg)
%
% (C) Copyright 2018 Mohamed Rezk
% (C) Copyright 2020 CPP visual motion localizer developers
if nargin < 1
cfg.design.localizer = 'MT';
end
getOnlyPress = 1;
% Clear all the previous stuff
clc;
if ~ismac
close all;
cle... |
29a6a00be7384e6fd68a0237545a920425298c3bced61e654087208a6a3b7b0c | MATLAB | 6,469 | 160 | function PlotExtendedData10(datadir, codedir)
%PlotExtendedData10 - Plots Extended Data 4.
% INPUTS:
% datadir - Local directory where ProcessData_ExtendedData10.mat was saved after running ProcessData_ExtendedData10
% codedir - Local directory where code (e.g., published/EstrousRPE/) was saved
%% Set up paths
s ... |
86275eb7df44cb809aa3d11c996c8f9b5ed1d1c8fadc45e0c968ef4615d6af54 | MATLAB | 6,469 | 188 | function run_permucorr_examples
%RUN_PERMUCORR_EXAMPLES Run permutation correlation examples.
% Generates random multivariate data for 2 "dependent" samples X and Y.
% Each sample has 20 variables, each pair with a correlation of 0, except
% for the first 5 variables which have a weak positive correlation, and
%... |
8385219649e7116c6250fd54d0bc6cbc25a8c8e33ff12905ea063eb372a88c51 | MATLAB | 6,472 | 155 | function fig = plotSingleSensor(parentFIG,UOI,coordinates)
%Plots a figure with 3 axes
% (1) The signal of all direct neighboor of a UOI within a neighborhood
% specified by the user
% (2) The signal of the UOI itself in large
% (3) STA Video corresponding to that unit of the entire chip
%
% INPUT:
... |
8f5dcc21b49013969195fd95a1c315d47db47484f6e6876a9bec4de43ef970ea | MATLAB | 6,474 | 172 | % examine burst dynamics in mice
% user must select files they wish to analyze from the list below (lines
% 38-60). The code will automatically run with the sample data in the
% Github. If the user would like to analyze any of the other data, they
% must add it to the current folder from FigShare. Be sure to have t... |
eb137c713d399f4c8f1c450fe4119aaa7ac9c31c2e0ce2a4faf7515a3095a571 | MATLAB | 6,474 | 164 | function shuffle_icaReacCCG_chamberCondDur(basename)
[~,ratName,~]=fileparts(basename);
[rootPath,sesName,~]=fileparts(basename);
fprintf('%s load files for %s\n',datestr(now),sesName);
load(fullfile(rootPath,'data',[sesName '-icaReac.mat']))
load(fullfile(rootPath,'data',[sesName '.sleepstate.states.mat']))
load(ful... |
0fee8bdd69c44e5ef435b0100e06b53c4a639c9d9e439df5c97c2c2f0b7f67ac | MATLAB | 6,480 | 142 | function triggers = getTriggers_locExtrema(params)
% triggers on local extrema of predictor variable, defined in:
% params.locExtrema = struct(...
% 'predictor', params.response, ...
% 'minOrMax', 'both', ... % options: min, max, both
% 'deadPeriod', 1, ... % in [... |
0486b55c3f5c73ecc5fc2fc83e08ab2a75180199e367e00cad4548f6c089b198 | MATLAB | 6,483 | 146 | function this = subsasgn(this, subs, A)
% Subscript assignment for GIfTI objects
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: subsasgn.m 6513 2015-08-05 17:52:13Z guillaume $
switch subs(1).ty... |
4000a4ed15ee671135a16efdc573008f9aae79a3392833bc32aa63d27013ae5c | MATLAB | 6,483 | 241 | function [avgSpk] = Vol_all_cells(all_SU,goods,all_S,all_index,win,varargin)
%plot heatmats aligned to reward volume for all cells
%plots the average psth for reward volume at each task event.
%plots a hmat
% input:
% all_SU - the data of all cells
% goods - cells you want to include
% all_S - data of all cells
% all... |
777127fac94a6af09565fcf10a4a9fd346d3736e13c119a489926b55fd1001b7 | MATLAB | 6,486 | 121 | function [PC_norm,PC_residual,PC,between_mod_k] = participation_coef_norm(W,Ci,n_iter,par_comp)
%PARTICIPATION_COEF_NORM
%
% [PC_norm,PC_residual,PC,between_mod_k] = participation_coef_norm(W,Ci,n_iter,par_comp);
%
% Participation Coefficient (Guimera and Amaral 2005,Nature,433:895-900) is a measure
% of di... |
39beb4aa73c8033d724b12198f7df778a65254d2d168b9e0abe9e081bd72c7fc | MATLAB | 6,488 | 128 | function plot_task_performance
close all
clear all
clc
% Plot task performance.
% Select a folder containing data.
folder_name = uigetdir;
cd(folder_name)
% Control.
load('behavior_control.mat')
behavior = behavior_control;
clear behavior_control
% Initialize.
correct_rate_animal_session = [];
for animal_num = 1:n... |
95d680fdd8e2813e02fac950cc86052454eca9e04ea8df086c6697697d7177af | MATLAB | 6,495 | 128 | % DEMO1_RSA_ROI_sim is a script. It is a sample recipe file which will
% simulate some fMRI data and then run through an "RoI-based" RSA pipeline for
% the simulated data
%
% Cai Wingfield 5-2010, 6-2010, 7-2010
%__________________________________________________________________________
% Copyright (C) 2010 Medical Re... |
faaaf99d382c719f64815ce2ff8ff9e671d32a8939fe7b4e04222845fea549cf | MATLAB | 6,496 | 204 | classdef nnconv < nntest
properties (TestParameter)
bias = {false true}
fw = {0 1 3 5}
fh = {0 1 2 3}
stridex = {1 2 3}
stridey = {1 2 3}
emptyw = {false true}
pad = {0 1 2}
stride = {1 2 3 4}
padx1 = {0 1 2}
padx2 = {0 1 2}
pady1 = {0 1 2}
pady2 = {0 1 2}
dilatex =... |
8b63f2ba0bd43d5b2e596b7e335816bab01b3d247510bd030be1ec830ec3c3d7 | MATLAB | 6,498 | 204 | classdef nnconv < nntest
properties (TestParameter)
bias = {false true}
fw = {0 1 3 5}
fh = {0 1 2 3}
stridex = {1 2 3}
stridey = {1 2 3}
emptyw = {false true}
pad = {0 1 2}
stride = {1 2 3 4}
padx1 = {0 1 2}
padx2 = {0 1 2}
pady1 = {0 1 2}
pady2 = {0 1 2}
dilatex =... |
b2e0479abc0a58f5a06f80fb0aa44498b247ae358ab6eee4d277b9c846132fa6 | MATLAB | 6,501 | 224 | function [hdr, nameFlag] = read_buffer_offline_header(headerfile)
% function [hdr, nameFlag] = read_buffer_offline_header(headerfile)
%
% This function reads a FCDC buffer header from a binary file or text file
%
% On return, nameFlag has one of the following values:
% 0 = No labels were generated (fMRI etc.)
% 1 ... |
6fb7a2cf4e8dc8ed9df6134a823a3979bf8829bd2b431937a3af83de4e8b1943 | MATLAB | 6,504 | 205 | function M = realphasefactory(n, z0, zmax)
% Returns a manifold struct to optimize over phases of fft's of real signals
%
% function M = realphasefactory(n)
% function M = realphasefactory(n, z0)
% function M = realphasefactory(n, z0, zmax)
%
% If x is a real vector of length n, then y = fft(x) is a complex vector
% wh... |
5cf74500b7652b5f9a6ec0981a0de4795c62fc309419f416fde55ce17aa5e542 | MATLAB | 6,507 | 237 | % load original network
NT = NetworkObj('../networks/circlenuchexresv_N20.net',struct('dim',2))
%%
NT.plotNetwork()
hold all
%% set up and mesh single flat perinuclear sheet
% pick out reservoir nodes
resvnodes = [];
for nc = 1:NT.nnode
if (~isempty(NT.nodelabels{nc}))
if (NT.nodelabels{nc}(1)=='R')
... |
c54f71d07d7a88219229792e627cf18cea5a0343bdc7fd276f47f9cf94205eb1 | MATLAB | 6,512 | 173 | function [ci_lo, ci_up, p] = bootConfint(x, B, alternative, user_opts)
% bootConfint
% Compute confidence intervals based on bootstrap distribution using
% various methods and use them to derive p-values for hypothesis testing.
%
% [ci_lo, ci_up, p] = bootConfint(x, B, alternative, user_opts)
%
% Currently tw... |
5c60f9fd90877a188e384c801e3cd50835c2c75b888fd33c07450cef3174c0b8 | MATLAB | 6,517 | 129 | function MRSCont = osp_scale_yaxis(MRSCont,Module)
switch Module
case 'OspreyLoad'
ppmmax = 4.5;
ppmmin = 0.2;
Range = zeros(2,MRSCont.nDatasets(1),MRSCont.nDatasets(2));
for kk = 1 : MRSCont.nDatasets(1)
for ll = 1: 1:MRSCont.nDatasets(2)
... |
435926733d2e2f51d9ebc75c6995056c8738712acd344e8d4dd7ff8935b00902 | MATLAB | 6,523 | 163 | function spectra = spectra_hilb_sessions(params, trials)
% computes spectra for each trial using band-pass filtering + Hilbert
% transform + amplitude envevelope
% extracta trials
% trials =
% data: [3073x125x500 double]
% time: [3073x1 double]
% sessTime: [3073x500 double]
% labels: ... |
5683b53c44b48baece7fd291b1627ae7ad0a031502d10f67adb4097044ed18d9 | MATLAB | 6,523 | 207 | % (C) Copyright 2018 Mohamed Rezk
% (C) Copyright 2020 CPP visual motion localizer developpers
% Adapted by Iqra for repeated targets task
% Direction 0 dots move right
% Direction 180 dots move left
% Direction 90-up, 270-down
%% Visual motion localizer
getOnlyPress = 1;
more off;
% Clear all the previous stuff
c... |
408d17343e3bbf818af4accddbc0dee14a9689f50e7833df29bbd30b8f6b05e6 | MATLAB | 6,527 | 196 | % MATCORR - Find matching rows in two matrices and their corrs.
% Uses the Hungarian (default), VAM, or maxcorr assignment methods.
% (Follow with MATPERM to permute and sign x -> y).
%
% Usage: >> [corr,indx,indy,corrs] = matcorr(x,y,rmmean,method,weighting);
%
% Inputs:
% x = first input... |
2dfe51ebfc473517a2e62a4c28e8f477994f0bd92efabfa0640548685df8fe66 | MATLAB | 6,529 | 146 | % Main script for computing depth-averaged group-mean fsaverage surface maps of
% laminar SANDI metrics
%
% Reference:
% Lee H, ..., Huang S, Communications Biology, 2026
%
% Requirements:
% - FreeSurfer installed and configured
% - FreeSurfer recon-all completed for each subject
% - Depth-resolved Group-mean SANDI su... |
b16267749518b7f8d1836b99ecae055fec53e0122dbdc31d152c74f2fcc3df2a | MATLAB | 6,529 | 221 |
% the commands to make the preprocess data
usetorch = false;
savedir = '~/projects/dynamics/data/maggie/';
%% reward epoch
disp('reward epochs')
epoch = 'reward';
decodertype = 'psth';
usemlb = true;
if usemlb
savename = strcat(savedir,'preprocess_mlb_shuffle_',epoch,'_',decodertype,'.mat');
else
savename = ... |
8f706604a98374aa81a4a24ad9768cbe90d3496b6ecb981cf43241eca0518fbd | MATLAB | 6,530 | 266 | function x = tapas_uniqc_resizeNd(x,newsiz)
%RESIZE Resize any arrays and images.
% Y = TAPAS_UNIQC_RESIZEND(X,NEWSIZE) resizes input array X using a DCT (discrete
% cosine transform) method. X can be any array of any size. Output Y is
% of size NEWSIZE.
%
% Input and output formats: Y has the same class as... |
979160972031ff8cf2d8b596e3ca48825bae87d601893e78b50de87323fcb09d | MATLAB | 6,530 | 201 | %% This script compares the overlap between ROIs drawn by hand and freesurfer projected ROIs from the adult average brain
clear all; clc;
subj = {
'bb02_mri0_mask', 'bb11_mri0_mask', 'bb56_mri0_mask', 'bb22_mri0_mask',...
'bb62_mri0_mask', 'bb07_mri0_mask', 'bb67_mri0_mask', 'bb28_mri0_mask',...
'bb14_mr... |
ae21148e9d0647bd54eb1ecd1e977fa5d8b40c7fb15894623041afe9e9e5a96e | MATLAB | 6,533 | 161 | function [A, R] = generalized_procrustes(A_measure)
% Rotationally align clouds of points (generalized Procrustes problem)
%
% function X = generalized_procrustes(A_measure)
%
% The input is a 3D matrix A_measure of size nxmxN. Each of the N slices
% A_measure(:, :, i) is a cloud of m points in R^n. These clouds are
% ... |
afce9050b7b18247000d5876e1bdd52d52968a05a7fea65d7fd25619c3004a27 | MATLAB | 6,533 | 158 | function TOL_fig_young1967(config,params,dat)
% TOL_fig_young1967, figure of Young et al.'s (1948) apparatus and design
% Figure S5 for: Duvelle and Grieves (2026) Tolman's Sunburst Maze 80
% years on: A meta-analysis reveals poor replicability and little evidence for
% shortcutting. European Journal of Neuroscience.... |
e3a852a795e6c6e9cc6d6d8110df881d4676042ffc7e23bee106eb80502365e2 | MATLAB | 6,536 | 228 | function str = hlp_tostring(v)
% Get an human-readable string representation of a data structure.
% String = hlp_tostring(Data)
%
% The resulting string representations are usually executable, but there are corner cases (e.g.,
% certain anonymous function handles and large data sets), which are not supported. For
% gen... |
11163765399381dfdf9f48bcaa5a173be4c1c2aa7698ed94d3da0ef359d15c25 | MATLAB | 6,537 | 211 | function M = fixedrankfactory_2factors_subspace_projection(m, n, k)
% Manifold of m-by-n matrices of rank k with two factor quotient geometry.
%
% function M = fixedrankfactory_2factors_subspace_projection(m, n, k)
%
% A point X on the manifold is represented as a structure with two
% fields: L and R. The matrix L (mxk... |
7f52412a874241096b54edf66602acfba12a2850c041f924f4546f53403bac4c | MATLAB | 6,537 | 139 | classdef McsCmosSpikeSorterSource < handle
% Holds the contents of a SpikeSorter source in a CMOS-MEA file
%
% Important fields:
% UnitEntities - (cell array) List of McsCmosSpikeSorterUnit
% objects, one for each sorted unit in the data
% source. Hol... |
26c74eea7e98bd91b4e10c493b84528977871c00db7f58b18607db7020f29465 | MATLAB | 6,541 | 156 | %% single trials: brain + DMN or DAN + selCh
% plots 3D brain with highlighted NN + selCh
% (c) Jiri, Feb24
%% settings
sel_AA = {
'Default';
'Dorsal Attention';
};
sel_viewAngles = {
% 'sagittal L', [-90, 0]; % sagittal R = 100,10 (90, 0)
% 'axial', [0, 90]; % axial = 0,90 ... |
fe658afce0356e1199177af59de1a0a2c225413a25c8474f0dd15d69ef3b91e5 | MATLAB | 6,541 | 206 | function [f,p,ci,stats,tbl,dist] = permuanova1(x,group,varargin)
%PERMUANOVA1 Permutation-based one-way ANOVA and Kruskal-Wallis test.
% F = PERMUANOVA1(X) performs a permutation-based one-way analysis of
% variance (ANOVA) for comparing the means of two or more groups of data
% in matrix X, and returns the test... |
6eb9e9f66d2c1f6dce36b1c58d37a9346fe82f0158796716ad2b84d552482053 | MATLAB | 6,543 | 176 | % surrogdistrib - Build surrogate distribution
%
% surrog = surrogdistrib(data, varargin);
%
% Inputs:
% data - [cell] data arrays for which to compute a surrogate
% distribution.
%
% Optional inputs:
% 'method' - ['bootstrap'|'perm'] use either 'bootstrap' or 'permutation'
% method. Bootstr... |
9f6f30dc18338cf933d7dee1f101e8a14b88ac5fc629c8753b7c5c7793583dbb | MATLAB | 6,547 | 146 | %% paths = generate_synthetic_phantom(outputDir, matrixSize)
%
% Description: deterministically builds a small multi-echo GRE-like
% synthetic phantom (magnitude + phase NIfTI, a brain mask NIfTI, and a
% sepia_header.mat) under outputDir, for use as Tier-1 regression-test
% input. Fully self-contained: no external too... |
ec98d850d0116d5729a027395281b9dde69d8cc614e817dd448e1adcba6f7003 | MATLAB | 6,549 | 219 | function B = medfilt3_nan(A,siz,padopt,CHUNKFACTOR)
%MEDFILT3 1-D, 2-D and 3-D median filtering.
% B = MEDFILT3(A,[M N P]) performs median filtering of the 3-D array A.
% Each output pixel contains the median value in the M-by-N-by-P
% neighborhood around the corresponding pixel in the input array.
%
% ... |
8d47e4d571aeb1bc569261c14451530d67e3ddd47eee6db0d54ba200b0a6f700 | MATLAB | 6,550 | 223 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%
% res = fitDispersion(Dpara_in,Dpara_ex,Dorth,vf,vf_csf,snr,noisedeg, proto,Smeas,dirs256,disptypes,fod)
%
% fits dispersion depending on ratios of SH coeffs
% Dpara_in,Dpara_ex,Dorth,vf,vf_csf - parameters of the micromodel
% snr,noisedeg ... |
56f75f78a83b5e43a232d9d34e034eeca31e764fd01a8f9a59faa2c1a57320dd | MATLAB | 6,553 | 202 | function [MC_Setup,activation_proportions,icon] = meta_prob_activation(DB,Xi,contrasts,connames,Xinms)
% [MC_Setup,activation_proportions,icon] = meta_prob_activation(DB,[X indicator mtx],[contrasts],[con. names],[Xinms])
%
% This function writes 'Activation_proportion.img'
% --a weighted map of the proportion of indep... |
9d745e85936136282e8db3f579315fa87e9b14dbb7d91eb0192c1700d4d21c8b | MATLAB | 6,553 | 208 | function writeFileNifti(ni)
% Write a VISTASOFT nifti structure into a file compatible with the NIFTI-1
% standard.
%
% writeFileNifti(ni)
%
% INPUTS:
% ni - a nifti file structure (.nii or .nii.gz)
%
% OUTPUTS:
% none.
%
% Web Resources:
% mrvBrowseSVN('writeFileNifti')
%
% Example:
% ni = ... |
1ea1f282194b4594f8527b0505b25f0f0f670d07444679c9a07cc4571d0da040 | MATLAB | 6,554 | 142 | function [evaltermin,TermCondDataAdd] = EvalTermCond
% Function determines whether prespecified set of termination conditions
% have been satisfied.
% Termination conditions (case 1):
% (1) The algorithm must have progressed at least 2 generations following
% the implementation of memory structure-de... |
52532cba7acadbcdf93ddcfe4502b1652570cccf306a0798a7ee54ffb093256a | MATLAB | 6,556 | 186 | function [z,p,ci,stats,dist] = permuztest(x,m,sigma,varargin)
%PERMUZTEST One-sample permutation-based Z-test.
% Z = PERMUZTEST(X,M,SIGMA) performs a one-sample permutation test based
% on the Z-statistic of the null hypothesis that the data in X come from
% a distribution with mean M, and returns the test stati... |
a769e9ed87b29ad49e080b0a526c6ac3fa5df3b20f3b2c7c37f1f2ea0c630c85 | MATLAB | 6,557 | 172 | function out = WL_DetailCoeffs(y, wname, maxlevel)
% WL_DetailCoeffs Detail coefficients of a wavelet decomposition.
%
% Compares the detail coefficients obtained at each level of the wavelet
% decomposition from 1 to the maximum possible level for the wavelet given the
% length of the input time series (computed usi... |
f2b08a99de708836be9959e92d1f36b3c4d31245f4e1b5bf96ff14eb2aa0ae07 | MATLAB | 6,558 | 175 | function NetMet = plotNodeCartography(adjMs, Params, NetMet, Info, originalCoords, ...
originalChannels, HomeDir, fileNameFolder, oneFigureHandle)
% Plot individual node cartography plots per recording.
% Part of Step 4A of MEANAP.
% Parameters
% ----------
% adjMs : struct
% structure where each field contai... |
3c64c45907630dcfffe4cdae64dabc871d85445e3e437de1910c0b17f11bc6bf | MATLAB | 6,559 | 185 | %% ----------------------------------------------------
% Load data
% -----------------------------------------------------
load('FeaturesSelect_forPub.mat')
%% ----------------------------------------------------
% Experiment parameters
% -----------------------------------------------------
numIter = 100;... |
4c07832a5d66f1479457bc6e0f2f8937a78bb188b2812c898f9f12aca09c1349 | MATLAB | 6,559 | 189 | %% ASCII
clearvars
% Load data
folder = 'Q:\EYELINK_data';
files = dir([folder, '\*.asc']);
% Get trial info
trials = cell(size(files,1),1);
for i=1:size(files,1)
fprintf(1,'#%d\n',i); %print file nr
% load data
data = read_eyelink_asc([folder,'\',files(i).name]);
% define trials
trial... |
1cafabf5b4a9ced5fc9c6f4e33990f93be07b08576c8800aedb1c97af52e2eaa | MATLAB | 6,565 | 197 | function check_dump(path)
% This is used to explore Cytosim's linear system in matlab
% - load the matrices and vector from Cytosim's dump
% - plot convergence pattern of BICGstab, with and without preconditionning
%
% F. Nedelec, 16.10.2014, 03.2018, 06.2018, 26.01.2019, 30.06.2019
if nargin < 1
path = '.';
end
... |
7e004b71616028648f5c84df3ae3d13c3f89020106bac466acd99588e2b009fd | MATLAB | 6,565 | 174 | function volumes = sero_pulseq_recon2DEPI_siemens_per_bval(fn_data, fn_seq, xps_fn, rec_delay)
% volumes = pulseq_recon2DEPI_siemens_per_bval(fn_data, fn_seq, xps_fn, rec_delay)
% Reads Siemens raw data and performs ghost correction per unique b-value.
% Based on pulseq_recon2DEPI_siemens.
% All processing downstream (... |
c0126f90087d828998352550edc4f94257d87b4acb2dd3c738a89a49b506bdaa | MATLAB | 6,566 | 148 | function [coeff,score,explained]=SpinalCompCor(basedir,spinemask,fMRIpath,prefix,options)
% SpinalCompCor performs PCA in spinal cord fMRI noise ROI and outputs
% components
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% ****************************** IMPORTANT! ***************************... |
5ae9e727dd0297a1d48843b27605e643daf2b4579494257b11379f67ab1d2696 | MATLAB | 6,568 | 147 | function out = DN_SimpleFit(x, dmodel, numBins)
% DN_SimpleFit Fit a simple model to the distribution of time-series values.
%
% Uses the 'fit' function from Matlab's Curve Fitting Toolbox to fit a simple
% parametric model to an estimate of the distribution of values in the time
% series, ignoring their temporal orde... |
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