sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ccd71e9d43b7312ffd4fa17a2ca78d0ce5ee9fd1817e1f9b8239431e66782c31 | MATLAB | 19,496 | 458 | function [tree, RootName, DOMnode] = xml_read(xmlfile, Pref)
%XML_READ reads xml files and converts them into Matlab's struct tree.
%
% DESCRIPTION
% tree = xml_read(xmlfile) reads 'xmlfile' into data structure 'tree'
%
% tree = xml_read(xmlfile, Pref) reads 'xmlfile' into data structure 'tree'
% according to yo... |
2315cd8516a75aadb937ce2cc62ba0021f39b0919dad02d4bfe364790dd513ef | MATLAB | 19,504 | 447 | function [label, tau] = CBIG_hMRF_find_and_fix_lost_parcels(label, avg_mesh, lh_mask, rh_mask,...
full_corr_mat, tau, params)
% [label, tau] = CBIG_hMRF_find_and_fix_lost_parcels(label, avg_mesh, lh_mask, rh_mask, full_corr_mat, tau, params)
%
% This function processes lost parcels given a set of parcellation labe... |
42669bf037d4fe0b267424bda760fff4bddce93c9b88d90029ceb92ece70ceed | MATLAB | 19,525 | 436 | function [dist_from_hyperplane, Y, svm_dist_pos_neg, svm_dist_pos_neg_matrix] = plugin_oofmridataobj_svm_contrasts_get_results_per_subject(DAT, svm_stats_results, DATA_OBJ)
% [dist_from_hyperplane, Y, svm_dist_pos_neg, svm_dist_pos_neg_matrix] = plugin_svm_contrasts_get_results_per_subject(DAT, svm_stats_results, DATA_... |
248a8a377aa31e875f2d70735c890d3423258f695cf06aa673009c0204d7f254 | MATLAB | 19,532 | 511 | function [map,num,typ,scheme] = brewermap(N,scheme) %#ok<*ISMAT>
% The complete selection of ColorBrewer colorschemes/palettes (RGB colormaps).
%
% (c) 2014-2022 Stephen Cobeldick
%
% Returns any RGB colormap from the ColorBrewer colorschemes, especially
% intended for mapping and plots with attractive, distinguishable... |
e401dc8874e9874f99273e6e5629d050df1e88e92e1e526b11a6da2fe8b3b9a7 | MATLAB | 19,538 | 373 | function in = LeG_intriangulation(vertices,faces,testp,heavytest)
% intriangulation: Test points in 3d wether inside or outside a (closed) triangulation
% usage: in = intriangulation(vertices,faces,testp,heavytest)
%
% arguments: (input)
% vertices - points in 3d as matrix with three columns
%
% faces -... |
7a5fa230d9123a42aed1f7e2cf3e30019f9fbeba91b9e082f0a6e16507dfba59 | MATLAB | 19,564 | 419 | %% prep_1b_prep_behavioral_data.m
%
%
% *USAGE*
%
% This optional script attaches behavioral/non-imaging data to the DAT
% structure defined by prep_1_set_conditions_contrasts_colors.m. It
%
% # calls a_set_up_paths_always_run_first, then loads DAT from
% image_names_and_setup.mat if not already in the workspace (fal... |
ae3ef76b8cc652f1da9e23f5840175ccbb0b7e8bb7a804a6eef0358282912fd5 | MATLAB | 19,572 | 552 | function ROI_table = plot_PLSDA_diagnostics_neuroimaging(results, XL, roiNames, atlasFile, varargin)
% plot_PLSDA_diagnostics_neuroimaging Plot and diagnose PLS-DA neuroimaging results (ROI/parcellation).
%
% This function provides generic visualization and diagnostics for PLS-DA
% results produced by PLSDA_neuroimagi... |
d2b44665e5e7bb8f1dc085cad157480a4907619b181241ca7659271a4b082fd4 | MATLAB | 19,574 | 411 | %% LaBGAScore_prep_s1_write_events_tsv.m
%
%
% *USAGE*
%
% This script reads logfiles, extracts the onsets, durations, and ratings for
% different conditions, and writes events.tsv files to the BIDS dir for
% each subject. It also contains an option to write a single phenotype file
% with trial-by-trial ratings for all... |
941b210a64784f6bc2a4c2030b1d81bc78c02b6a0cd1381f95b27dc84db02b11 | MATLAB | 19,600 | 632 | function outdata=specscope(indata)
% record and plot audio spectrogram
%
% Usage: outdata=specscope(indata)
%
% Input: indata (optional)
% Displays a recorded piece of data, if an argument is passed
% Otherwise displays audio data from an attached microphone
%
% Output: outdata (optional)
% If pres... |
fc06e402dbbdd8655aa44101d790fb2c024f89046ed3b0363baaf2d78b420e4b | MATLAB | 19,642 | 591 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
if ~contains(path, '/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
addpath(genpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab'));
end
%% ======================= compare... |
53e2e71398c68118616d2c52e98a439735fe57f92c838606fdff4081eaf9c809 | MATLAB | 19,648 | 395 | % std_erspplot() - plot STUDY cluster ERSPs. Displays either mean cluster ERSPs,
% or else all cluster component ERSPs plus the mean cluster
% ERSP in one figure per condition. The ERSPs can be plotted
% only if component ERSPs were computed and saved in the
% ... |
83e8fa5c52f33ef8966d6a9ef5d4dddbbd9ac25a3bb8d7ebda3c1cc5ddb85575 | MATLAB | 19,658 | 529 | function SANDIinput = setup_and_run_model_training_forGUI(SANDIinput, fig_ax)
% Main script to setup and train the Random
% Forest (RF) or multi-layers perceptron (MLP) regressors used to fit the
% SANDI model
%
% Author:
% Dr. Marco Palombo
% Cardiff University Brain Research Imaging Centre (CUBRIC)
% Cardiff Univers... |
b0d062034ed82ef2f527da9d8ed26a20078d47d414826b21935a64961604b8dd | MATLAB | 19,662 | 655 | function varargout = FTrack(varargin)
% FTRACK
% For all your fly-tracking needs! . See documentation for usage details.
% Last Modified by GUIDE v2.5 26-Nov-2007 18:07:29
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleto... |
521421faefed5a996d3b05c77c90efd460277245594593bd91a43148b54fb2ed | MATLAB | 19,677 | 664 | function outdata=specscopepp(indata)
global acq;
h=hamming(5);
mins=5e-008;
maxs=1e-004;
% record and plot audio spectrogram
%
% Usage: outdata=specscope(indata)
%
% Input: indata (optional)
% Displays a recorded piece of data, if an argument is passed
% Otherwise displays audio data from an attached micropho... |
a78ee8ad0ef6385affd5d04af9b7bcdc4d4983ac6fbd0bc52b0a7c5d3ce66386 | MATLAB | 19,683 | 580 | % Save back to the original image with a portion of slices that was
% loaded by "load_untouch_nii". You can process those slices matrix
% in any way, as long as their dimension is not altered.
%
% Usage: save_untouch_slice(slice, filename, ...
% slice_idx, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx])
%
% slice ... |
a23debefad7ed7144b8892cbedc7ff2980840ffc452dfb61a67fb3721bd641d2 | MATLAB | 19,757 | 566 | function myOISscr1(fname,saveid,p1,p2,p3,p4,p5,p6,p7,p8,p9,p10,p11,p12,p13,p14,p15,p16)
% Usage ... myOISscr1(fname,saveid,p1,a1,p2,a2,...)
%
% p#s = do_load, do_loadall, do_motc, do_maskreg, do_intc, do_motc_apply, do_intc_apply, do_keepalldata
% average_parms = [#off, #ims_per_trial, #trials]
%
% ex.
% myOISs... |
e6928cb105ab89161e168e20e1730e70712e94f7a872001f6e5f31ce71406bfa | MATLAB | 19,793 | 470 | classdef KTNSPOnline
% UEAMAPFILE -- Defines a class that contains information on a UEA
% electrode array using CMP files provided by Blackrock Microsystems.
%
% To load a CMP file type 'MapName = UEAMapFile' where MapName is the name
% of the variable that will be created and will contain the map class.
%
% E... |
823ff7fdbde6c944e49828f6f428eb5a0beabe1ff70375c197b2d2406190e98b | MATLAB | 19,797 | 635 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
if ~contains(path, '/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
addpath(genpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab'));
end
%% ======================= step 1 ... |
96eb04a0dae7e714738e6b612cfc58c64a058123fd95b1e58c0ee54e175b6cea | MATLAB | 19,813 | 444 | %% prep_3f_create_fmri_data_single_trial_object.m
%
%
% *USAGE*
%
% This script creates and saves an fmri_data_st object from the single-trial
% con images written to rootdir/firstlevel/model_x_yyy/sub-zz by
% LaBGAScore_firstlevel_s2_fit_model.m. It
%
% # loads DSGN/DAT if not already in the workspace, and excludes su... |
9d76672e004b3547ccc2c433a4c4f636d835af5b17c463ced4b684f850919cc5 | MATLAB | 19,877 | 467 | classdef GridFlex < uix.Grid & uix.mixin.Flex
%uix.GridFlex Flexible grid
%
% b = uix.GridFlex(p1,v1,p2,v2,...) constructs a flexible grid and
% sets parameter p1 to value v1, etc.
%
% A grid lays out contents from top to bottom and left to right.
% Users can resize contents by dragging... |
fc665dc1ede16e5caab0472854d92cc50a4cfc11f173ef9cbb6ea25d1ef24347 | MATLAB | 19,894 | 556 | %%% Supplementary Figure 5
% Structure:
% 1) Compute all data for Supplementary Figure 5A-C
% 2) Plot all panels
% 3) Save independent Zenodo MAT files for each final panel
%
% No local functions.
ccc;
%% Paths
% Supplementary Figure 5A-B: 400-ms ISI example, monkey C, nSTD = 9
SINGLEPATHs = dir("..\MAT Data\gr... |
d38dda3c9bd96cea59e1eb976ebdf64547f3bd1b69cf25cd1b8c90bd4750ba42 | MATLAB | 19,915 | 373 | function [refinedTrack, measurements, cntTrackOutput] = basicTransientTrackCrop(transDiffAnalysisRes, decompTrack)
%BASICTRANSIENTTRACKCROP splits decompTrack into tracklets/segments based on DC-MSS analysis & chop tracks in half if track duration is too long; and tally out tracks information/analysis in a matrix forma... |
e944f80441253c5c4123003a4b056550e8135bf5e70d6a792f5ce5718a6373ec | MATLAB | 19,926 | 631 | function [gridness, props] = Gridness(self, cel, varargin)
% Calculates the original gridness score of 'cel'. Continuizes all epochs.
%
% ARGUMENTS
%
% cel 1x2 vector indicating tetrode index and cell index
%
% RETURNS
%
% gridness a number indicating gridness score
% props struct of... |
4f83569cb27638d59219cd6e612dc0753d5f24b46413a9dd04ff65db03047c11 | MATLAB | 19,936 | 555 | function saveas(this,filename,format)
% Save GIfTI object in external file format
% FORMAT saveas(this,filename,format)
% this - GIfTI object
% filename - name of file to be created [Default: 'untitled.vtk']
% format - optional argument to specify encoding format, among
% VTK (.vtk,.vtp), Collada (... |
07ca4fea07addb59f5d9eb9673318a7ded2430fe3fdb505c11714621509fb009 | MATLAB | 19,952 | 464 | function newdata=jdatadecode(data,varargin)
%
% newdata=jdatadecode(data,opt,...)
%
% Convert all JData object (in the form of a struct array) into an array
% (accepts JData objects loaded from either loadjson/loadubjson or
% jsondecode for MATLAB R2016b or later)
%
% This function implements the JData Specification D... |
5aa60beaa992d29e7cb669fb936bad826d4423030b909b08535f45bfd3aa4acc | MATLAB | 19,956 | 471 | function ea_normalize_fibers(options)
% Normalize fiber to MNI space
vizz=1; % turn this value to 1 to visualize fiber normalization (option for debugging only, this will drastically slow down the process).
cleanse_fibers=0; % deletes everything outside the white matter of the template.
directory=[options.root,options... |
b5ff46c302aa95cabbd7f50b20abf4293021dcb1c93bb5efb4b39897b380be91 | MATLAB | 19,968 | 536 | % crossf() - Returns estimates and plot of event-related coherence (ERC) changes
% between data from two input channels. The lower panel gives the
% coherent phase difference between the processes. In this panel, for Ex.
% -90 degrees (blue) means xdata leads ydata by a quarter cycle... |
2c19aa4f31a067f193c7158308c8072aed3304149cb702d49f5a8b60a3420be1 | MATLAB | 19,972 | 532 | function SANDIinput = setup_and_run_model_training_with_dot_forGUI(SANDIinput, fig_ax)
% Main script to setup and train the Random
% Forest (RF) or multi-layers perceptron (MLP) regressors used to fit the
% SANDI model
%
% Author:
% Dr. Marco Palombo
% Cardiff University Brain Research Imaging Centre (CUBRIC)
% Cardif... |
9857494bef7584787071a19b787c9642acbfde8608d8b71ac5fed78c49d07695 | MATLAB | 19,986 | 611 | function dimord = getdimord(data, field, varargin)
% GETDIMORD
%
% Use as
% dimord = getdimord(data, field)
%
% See also GETDIMSIZ, GETDATFIELD
if ~isfield(data, field) && isfield(data, 'avg') && isfield(data.avg, field)
field = ['avg.' field];
elseif ~isfield(data, field) && isfield(data, 'trial') && isfield(dat... |
0d50d8eccc8016bc062223099c1e62ae3d71be28984dcc813e7c2271e558d05b | MATLAB | 19,997 | 474 | function [ likelihood, results] = CBIG_gwMRF_graph_cut_clustering_split_newkappa(x,prams,hemisphere)
% This function performs the actual clustering
%
% Input
% - x = input timeseries
% - prams = a struct containing various input parameters
% - hemisphere = a string indicating the hemisphe... |
825eb567122bfd553bd644ee651264c351f70a6bda61c4887d8f8a6352669d52 | MATLAB | 20,001 | 371 | % pop_dipfit_settings() - select global settings for dipole fitting through a pop up window
%
% Usage:
% >> OUTEEG = pop_dipfit_settings ( INEEG ); % pop up window
% >> OUTEEG = pop_dipfit_settings ( INEEG, 'key1', 'val1', 'key2', 'val2' ... )
%
% Inputs:
% INEEG input dataset
%
% Optional inputs:
% 'hdmfile' ... |
954e6f6b0ed2e290c1a610d20dc95b43808750fb22411c98526045468e104007 | MATLAB | 20,016 | 519 | function colocalMeasure = condColocGeneral(refInfo,tarInfo,condInfo,cellMask,...
distThreshToColocWithCond, colocDistThresh,numTarRefRand,numCondRand)
%CONDCOLOCGENERAL measure colocalization among three channels with segmented and/or detected objects
%
%SYNOPSIS colocalMeasure = condColocG... |
dc1b63de25212596b26d691ca0739226568807553a3337ea178a81344e55f1ae | MATLAB | 20,027 | 450 | function plottrials_flex(data, savepath, which_trials, dff_yaxis, dff_coloraxis, add2txt, print_flag, file_type)
% if which_trials is blank, plot all trials
% dff axes are 2 element vectors of lower and upper boundries (if empty: dff_yaxis = [-.1 .8], dff_coloraxis = [0 0.4];
% add2txt goes into title and filename (wit... |
62488f23d158863cb674a2f3d53bf2932dd74bff0d43c24dd0cb4d5f41782317 | MATLAB | 20,036 | 521 | function obj=redraw(obj,spacing,display)
% redraw Optimize location and size of axes in figure after resizing
%
% Syntax: gramm_object.redraw(spacing,display)
% spacing is an optional argument that indicates how far apart
% the elements should be. It is expressed in normalized units
% of the figure's smallest dimension... |
3c844ec8ff901ba0040c1c25dd559165be0a1bfbd0a8d754f6824ab02b6f8011 | MATLAB | 20,127 | 569 | % plotdata() - plot concatenated multichannel data epochs in two-column format
%
% Usage: >> plotdata(data)
% >> plotdata(data,frames)
% >> plotdata(data,frames,limits,title,channames,colors,rtitle,ydir)
%
% Necessary input:
% data = data consisting of consecutive epochs of (chans,frames)
... |
871d7f44110649aff093ce2e999260d214e02133a450c375a738e54f90fcd352 | MATLAB | 20,181 | 487 | % configure file for operations on streamline trackings results
%
% for BATCH EDITOR system (Volkmar Glauche)
%
% File created by Susanne Schnell
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ftrop = dti_cfg_ftrop
% --------------------------------------------------------------... |
66d72db0427735897fb999dcc1af138e083dfcefa984f247ef1b12b76101a34e | MATLAB | 20,184 | 643 | function [data, timestamps, info] = load_open_ephys_data(filename,varargin)
%
% [data, timestamps, info] = load_open_ephys_data(filename)
% [data, timestamps, info] = load_open_ephys_data(filename,'Indices',ind)
%
% Loads continuous, event, or spike data files into Matlab.
%
% Inputs:
%
% filename: path to file... |
36d89ea31d47799f7d1354bd91775ac316f4b576e7a817d5b97fcffe71777932 | MATLAB | 20,239 | 632 | function solve( prob )
global cvx___
p = prob.index_;
pr = cvx___.problems( p );
quiet = pr.quiet;
obj = pr.objective;
gobj = pr.geometric;
prec = pr.precision;
solv = pr.solver;
ndual = ~isempty( pr.duals );
shim = cvx___.solvers.list( solv.index );
if isempty(shim.eargs), eargs = {}; else eargs = shim.e... |
d60ee40f3628d04dac996c7b397f0e409614d1c90fd84c1ab6b9b50f61dafd87 | MATLAB | 20,271 | 546 | function [ results ] = plot_phase_precession( self, varargin )
%PLOT_PHASE_PRECESSION Makes the phase precession plot
%
% ARGUMENTS
%
% OPTIONAL ARGUMENTS
% cel 1 x 2 vector like [tetrode index, cell index]. If
% unassigned, uses self.cel.
% lfp Scalar integer that coresponds to which EEG... |
aa16385d9f9781bd25f6e03f8968381c115a9345317876ff2301a4ab01100960 | MATLAB | 20,276 | 531 | %% 3-D volume visualization
%% About volume visualisation
%
% Creating 3-D renderings of brain data and results can help localize brain
% activity and show patterns in a way that allows meaningful comparisons
% across studies.
%
% The CANlab object-oriented tools have methods built in for rendering
% volume data on br... |
4e106d99c4402fa901fd3ba1b3a1ffe54e246aee55a9d6408c3ea7c101446ea7 | MATLAB | 20,310 | 421 | % pop_importepoch() - Export epoch and/or epoch event information to the event
% structure array of an EEG dataset. If the dataset is
% the only input, a window pops up to ask for the relevant
% parameter values.
% Usage:
% >> EEGOUT = pop_importepoch( EE... |
4d4e5eabc5bf91d60251378c1f40d0ebcc0df8f2852e945b6b60540fc6683045 | MATLAB | 20,312 | 492 | %% Script for the analysis of MINFLUX signals from DNA-Paint labelled ALFA-tagged PIEZO1
% Dependencies: DBSCAN.m;
% SetALFAanalysisParameters.m, PlotRawData.m; PIEZO1Superparticle;
% PlotTrimerAnalysisResult.m; CalcTrimerAngle1.m
clear all;
close all;
Exclude = [];
%% %%%%%%%%%%... |
ae926529506d4946730ef1d88e9228cc41836500ae8f3a1934cd1d499ea0bc62 | MATLAB | 20,317 | 655 | function varargout = FTrack(varargin)
% FTRACK
% For all your fly-tracking needs! . See documentation for usage details.
% Last Modified by GUIDE v2.5 26-Nov-2007 18:07:29
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui... |
baf204d3b99e1b7df8305dc4275beffa6c3bd17f54fb69ddcbaef1f640ffce97 | MATLAB | 20,341 | 664 | function outdata=specscopepp(indata)
global acq;
h=hamming(5);
mins=5e-008;
maxs=1e-004;
% record and plot audio spectrogram
%
% Usage: outdata=specscope(indata)
%
% Input: indata (optional)
% Displays a recorded piece of data, if an argument is passed
% Otherwise displays audio data from an att... |
893254654953cd8e76556cafacdcafc361b963335fc425206a5cf407d0723a84 | MATLAB | 20,429 | 485 | %% DATA2STATES - converts raw data to states
% Converts raw data to states as pre-processing for information theoretic
% analyses as implemented in instinfo.
%
% Syntax: [StatesRaster,MethodResults] = data2states(DataRaster, MethodAssign)
%
% Input:
% DataRaster (cell array or double array) - trial data. If a double... |
494ad9700b25e2878a0c30877beb3314359fdb37d969dcac2729fdc553ed3461 | MATLAB | 20,442 | 615 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
if ~contains(path, '/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
addpath(genpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab'));
end
%% ======================= compare... |
371c04a41e6a9c20613e824d8aff1473629e55c8d54b0ac15e0b6e75fc472463 | MATLAB | 20,477 | 476 | %% Compares multiple sessions based on the contour maps of burst and tonic scatter maps
% Necessary to run the ApertureResponseTypes.m script for the respective
% stages first.
close all; clearvars; clc;
% Define areas to plot
area_names = {'BC','VPM','POm','ZIv'};
area_colors = {'#377eb8','#4daf4a','#984ea3','#ff7f00... |
36da3106a9506f23db66ba4cd37eaeacc18a25598a194dd0bf7bcc4af573acd3 | MATLAB | 20,505 | 409 | % teststat - EEGLAB statistical testing function
%
% Statistics are critical for inference testing in Science. It is thus
% primordial to make sure than all the statistics implemented are
% robust and at least bug free. Statistical function using complex
% formulas are inherently prone to bugs. EEGLAB functions are a... |
0834e4d03469d64d981c46bca382cbec2fc2d7c9b6593b2f75073dea7e706dfa | MATLAB | 20,515 | 501 | function varargout = ea_imageclassifier(varargin)
% EA_IMAGECLASSIFIER MATLAB code for ea_imageclassifier.fig
% EA_IMAGECLASSIFIER, by itself, creates a new EA_IMAGECLASSIFIER or raises the existing
% singleton*.
%
% H = EA_IMAGECLASSIFIER returns the handle to a new EA_IMAGECLASSIFIER or the handle to
%... |
eff2106537ae51d94b66eab21ba445724a2352c1b0637077506fdb023a1ee39a | MATLAB | 20,553 | 437 | % std_ersp() - Compute ERSP and/or ITC transforms for ICA components
% or data channels of a dataset. Save results into Matlab
% float files.
%
% Function description:
% The function computes the mean ERSP or ITC for the selected
% dataset ICA components or data c... |
a9c4ef6e55b0ae539395fe6e485fbf907e9b68f9a4c3131d6be0e71d2b73bb69 | MATLAB | 20,563 | 490 | function [XYZ_dest_mm, XYZ_dest_vx] = ea_map_coords(varargin)
% Coordinates mapping, support SPM, ANTs and FSL linear and non-linear
% transformation.
%
% Please use this function for any point transform within the Lead Suite
% environment. It should automatically detect whether to use ANTs, SPM or
% FSL based transfor... |
87aaecf901995369ce7bad190443f3fd45fc8eac96668e8c6cf00bba0ed69741 | MATLAB | 20,583 | 454 | function [sens] = ft_datatype_sens(sens, varargin)
% FT_DATATYPE_SENS describes the FieldTrip structure that represents
% an EEG, ECoG, or MEG sensor array. This structure is commonly called
% "elec" for EEG and "grad" for MEG, or more general "sens" for either
% one.
%
% The structure for MEG gradiometers and/or magn... |
e008b34628ce3f5451226a1c8d2579aafffb0ee7c1cfc1a5975d457474fccf03 | MATLAB | 20,721 | 353 | function ExtClustInfo_CWL(CWLclusterDir,C,j,Dmasked,OWLDir)
% save([OWLclus{i},filesep,'Piece',sprintf('%05d',iseg),'.mat'],...
% 'Pval_media_perm','Pval_mean_perm','Pval_std_perm','segind3','iseg','DATIND','V','Dmasked');
piecedir = [CWLclusterDir,filesep,'Group',sprintf('%03d',C(j,1)),'vsGroup',sprintf('%03d',C(j... |
773559e9b2fb793fbd30a625f1becdb6e72d10bb7101624d7b3606f929ea6607 | MATLAB | 20,825 | 497 | % bootstat() - accumulate surrogate data to assess significance by permutation of some
% measure of two input variables.
%
% If 'distfit','on', fits the psd with a 4th-order polynomial using the
% data kurtosis, as in Ramberg, J.S., Tadikamalla, P.R., Dudewicz E.J.,
% ... |
1a003515869c71ffb1b8ec68cc84435cc5276dad51509c950272c8290dee0f6a | MATLAB | 20,859 | 431 | %% Single Cell Reactivity
% Split cells into groups of aperture responding units
% Reponses can either be single-targeted ("wide" or "narrow"), "both" or
% "none"
% Define animal individuals to analyze
close all
clearvars
clc
spontWindow = [-0.6,-0.4]; % spontaneous window in sec (default: [-0.6,-0.4])
respWindow = ... |
889c83f7466d2cf894b9576baf13d059cdcd7a47dbf09a34a0389fbc49edd3ca | MATLAB | 20,908 | 601 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
if ~contains(path, '/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
addpath(genpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab'));
end
%% ======================= compare... |
f3f2351d509efc10314d69c63e082fc7b9a6f94ef40e3861f4bcaa356792d682 | MATLAB | 20,942 | 502 | function ea_autocoord(options)
% This function is the main function of LEAD-DBS. It will generate a
% vector of coordinates.
% Trajectory{1} will be the right trajectory, trajectory{2} the
% left one.
% For each hemisphere of the brain, this function will call the
% reconstruction routine ea_autocoord_side and lateron ... |
e39f52d876f5f623512c53f8347785dad7f053224f46c1b80d763b78373f2482 | MATLAB | 20,955 | 414 | % std_erpplot() - Command line function to plot STUDY cluster component ERPs. Either
% displays grand mean ERPs for all requested clusters in the same figure,
% with ERPs for different conditions (if any) plotted in different colors.
% Else, displays ERP for each speci... |
1180c70e489b9bdddaee2db6a1fe7045c431089ff0f96f303b76306b0f432b72 | MATLAB | 20,959 | 430 | %% c2h_run_multivariate_mediation.m
%
%
% *USAGE*
%
% Single-level multivariate mediation (PDM) on second-level CONTRAST images:
% does a multivariate brain pattern mediate the effect of a between-person
% treatment X on a between-person outcome Y?
%
% X group (one value per subject), from DAT.BETWEENPERSON.group
%... |
9f247108bda599017a869f02bd88fe4f46176ef72d2f7e59e520fcec3b07b50d | MATLAB | 20,974 | 663 | function [baseline, decline] = CBIG_hypoTest_4t(stats)
% [baseline, decline] = CBIG_hypoTest_4t(stats)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
beta = stats.Bhat;
betaCov = stats.CovBhat;
baseline = zeros(18, 3);
decline = zeros(18, 3);
%% ------------... |
874c037c02d5cb2fab6a126164579781b5aa478f9757735cdbeae14d99161597 | MATLAB | 20,993 | 542 | function [cuts,expslice,boundboxmm,allcontour]=ea_writeplanes(varargin)
% This function exports slice views of all electrode contacts reconstructed
% priorly. Images are written as .png image files. Bot transversal and
% coronal views are being exported. Additionally, overlays from atlas-data
% can be visualized via t... |
1914ed9ac0dfd636f62798fdaa79bf6bcd5ff40765510a0e16e0e431dafafd72 | MATLAB | 20,997 | 391 | classdef generalization_DS < handle
% This datasource object (DS) allows one to train a classifier on a specific
% set of labels, and then test the classifier on a different set of
% labels - which enables one to evaluate how similar neural representations
% are across different but related conditions (i.e.... |
b35103ffd0252a725af4d93ebf94b6f1df4263f6679bc4f53ca2301e6cfc7707 | MATLAB | 21,034 | 614 | %% PrL behavior-conditioned calcium AUC for Poking 1, Poking 2, and Others
% Uses the same denoise / normalization / real-neuron selection rule as
% calcium_data_PrL_SB_struct_clean.m, but DOES NOT delete the first 10 frames.
%
% Outputs:
% 1) Per-SB behavior-conditioned calcium AUC
% 2) Whole AUC across SB1-SB5 fo... |
96e95181f7b7fb3b7050ea4a9f1373ab6d47fdb4213ad97024c3cea16c75a430 | MATLAB | 21,059 | 307 | function HispeedTrials = getWhiskerContactsApertures(sessionDir)
configPath = 'C:\Users\Groh\DLC-Modules\Whiskertrack_Apertures-Heimburg-2021-11-11\config.yaml';
%% Grab the DLC (filtered) csv file with the bodyparts
videoDir = fullfile(sessionDir,'videos');
HispeedTrials = assignTrialsToVideos(videoDir);
try
py... |
e2a5a496f3a23dd6722ff56cc12d717e0c9c7cf85fcf059d3f33e573fc3ebaa4 | MATLAB | 21,074 | 529 | % supergui() - a comprehensive gui automatic builder. This function help
% to create GUI very fast without bothering about the
% positions of the elements. After creating a geometry,
% elements just place themselves into the predefined
% locations. It is especially... |
5e8c7436e43717954d02606419f7a86d36fccc7416b1bf55b971a424561d302c | MATLAB | 21,082 | 663 | function [baseline, decline] = CBIG_hypoTest_4t(stats)
% [baseline, decline] = CBIG_hypoTest_4t(stats)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
beta = stats.Bhat;
betaCov = stats.CovBhat;
baseline = zeros(18, 3);
decline = zeros(18, 3);
%% ------------... |
2f5a2749cd00555d111b4199008c6b9410eeb836756c0c93d4c3b079ba2e58d8 | MATLAB | 21,130 | 504 | %% Linear Mixed Model demo
%%
% This demonstration was prepared by Bogdan Petre and Tor Wager
%
% It includes code to perform a mixed-effects analysis on a dataset
% in both Matlab and R. The published version runs the Matlab code.
%
% To reproduce the analysis, you must have the dataset, which is in the
% |CANlab_h... |
db08ff8d30120f0b3abdcf1af704f50b940620b2fbf295ddfae628bfa588dc29 | MATLAB | 21,135 | 422 | function varargout = palm_help(varargin)
% Shows a help text. Call palm_help('logo') to show just the logo.
% _____________________________________
% Anderson M. Winkler
% FMRIB / Univ. of Oxford
% Mar/2014
% http://brainder.org
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% PALM -- Permut... |
cd89ac8337d2e74f69cf3ee036fd82a507d163be72506a8afd992c6d776fa1b4 | MATLAB | 21,153 | 478 |
% AnalysisBatchScript.m
% This scritp runs preliminary descriptive analysis to get a summary overview
% of the session. It is called by expPipeline and require output variables
% generated by that fucntion.
% List of analysis to perform
% 1. Spike-waveform, autocorrelogram and spatial position
% 2. Psth from ana... |
b899f86b4d6de15473f484e1701f22a4cf8fab8e0c90e1e06c017744d4d7531f | MATLAB | 21,201 | 584 | function ea_imshow3d(nii)
%
% This function displays a NifTi image.
%
% SYNTAX:
% imshow3d('anat_t1.nii')
% imshow3d('Users/user/Images/anat_t1.nii')
% imshow3d(anat_t1)
% imshow3d(anat_t1.img)
%
% Example1:
% nii = load_nii('t1.nii')
% imshow3d(nii)
%
% Example2:
% anat_t1 =... |
acd207ac78077f86314915672b24d05008dcab23ba4ec825f09d820a180d7009 | MATLAB | 21,279 | 546 | % ====================================
%% Help
% ====================================
%
% CBIG_supp_fig5_model_compare
%
% This script replicates Supplementary Figure 5: FC homogeneity and
% inhomogeneity of the NIH individual-specific networks as a function of
% the number of training subjects used to train MS-HBM (5,... |
38efd168607aa9ecc9b89c8ca5743563fe110f779f38cb3268813a4d56b2f033 | MATLAB | 21,303 | 425 | % pop_precomp() - precompute measures (spectrum, ERP, ERSP) for a collection of data
% channels. Calls std_precomp().
% Usage:
% >> [STUDY, ALLEEG] = pop_precomp(STUDY, ALLEEG); % pop up interactive window
% Inputs:
% STUDY - STUDY set structure containing (loaded) EEG datas... |
00eebed8c5bf1045fbf26b90799afabd6678d922818f2221bcdb32efef6992c6 | MATLAB | 21,312 | 673 | % topoimage() - plot concatenated multichannel time/frequency images
% in a topographic format
% Uses a channel location file with the same format as topoplot()
% or else plots data on a rectangular grid of axes.
% Click on individual images to examine separatel... |
60530f7d991b005aaf13e9d60b7900739fa90c8421206365b65ce264c03155e3 | MATLAB | 21,344 | 442 | function SessionMetadata = bz_SessionMetadataTextTemplate(basepath)
% This .m file is a generic template and will be copied to session
% folders/session folders and will be called basename_SessionMetadataText.m.
% It is represents code that will be used to
% create a basename.SessionMetadata.mat file. Edits here will ... |
d783685dc55b3687d3e4ba28871a0ea059223b6b47d0aaa23972e499ea280b92 | MATLAB | 21,347 | 516 | function [] = normCorreTifROIgui(moCorreImg)
%draw ROIs on concatenated motion corrected image data
sROI.img = moCorreImg;
sROI.nFrames = size(moCorreImg,3);
sROI.imgHeight = size(moCorreImg,1);
%this will be the main figure for drawing ROI
ui.roiGUI.fh = figure('Name','Choose frame and draw ROI','Visible','o... |
a1a1f8956aeef8ecb9dbf16b7819f1115f02f8d18c8470f9a4a13962db4c7ec4 | MATLAB | 21,503 | 430 | %% LaBGAScore_prep_parrec2bids.m
%
%
% *USAGE*
%
% This script converts Philips PARREC files to Nifti files and names and
% organizes them according to BIDS specification.
%
% Script should be run from the root directory of the superdataset, in this
% example case /data/proj_bitter-reward, and assumes that
% 1. the sou... |
ecb4bca8b9762a1849923536694f418b6cea9e6240959244e9ec629925d366f5 | MATLAB | 21,604 | 552 | function data = loadjson(fname,varargin)
%
% data=loadjson(fname,opt)
% or
% data=loadjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (q.fang <at> neu.edu)
% created on 2011/09/09, including previous works from
%
% Nedial... |
57b9a48e7a958479f01dbd6fe896e250581a0d6fd18e53b58b8601e4d6b8b0ba | MATLAB | 21,630 | 566 | %% modeltype3 - full Izhikevich network
% Generates data for the full Izhikevich neuron network. This network is
% precisely the 1000 neuron network described in Izhikevich 2003. In
% addition to the spontaneous activity produced by the network, square
% current pulses are supplied to subsets of excitatory neurons. The... |
9fc8db4efa85cd57bfded17806d7c517716d89845acd1f857a465774f24f4df0 | MATLAB | 21,769 | 691 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
if ~contains(path, '/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab')
addpath(genpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainSpace-latest/matlab'));
end
%% ======================= compare... |
79d4140ed1544bc932484335e350072b5d16a9c2f00b7a636d21994ab84ea08c | MATLAB | 21,788 | 441 | % std_makedesign() - create a new or edit an existing STUDY.design by
% selecting specific factors to include in subsequent
% 1x2 or 2x2 STUDY measures and statistical computations
% for this design. A STUDY may have many factors
% (task or... |
fe925c290a5240436ba1be48ecaf8f3b9402b50bce5d17cadce7d861a17c3d17 | MATLAB | 21,797 | 462 | %% LaBGAScore_firstlevel_s1_options_dsgn_struct.m
%
%
% *USAGE*
%
% This script sets the options and creates a CANlab-style DSGN structure
% variable, which are used by the subsequent script in the standard LaBGAS
% workflow, LaBGAScore_firstlevel_s2_fit_model, to fit first level models
% using CANlab and SPM functions... |
51164ec9369b0746a12c35ba746f9e5aab54552de591c1383547a7f78e9b8d3d | MATLAB | 21,813 | 548 | function [colocalMeasure, numOfObjects] = condColocPt2Pt2Blob(refCoords,tarCoords,condCoords,...
mask,distThreshToColocWithCond, colocDistThresh,numRandomizations, alpha)
%CONDCOLOCPT2PT2BLOB runs conditional colocalization for 2 channels of punctate objects with one channel non-punctate obj... |
91f652871226603d150f3c3d58a6da082f2a5b0a42c1a04120f5b4ca0a817558 | MATLAB | 21,834 | 430 | function go = LCN12_PET_preprocessing(dir_pet,infostring_tracer,infostring_PET,infostring_frames,dir_anat,name_logfile)
% assumptions:
% Data-organisation:
% Data are transformed to nifti format and organized according to BIDS.
% You have to specify a main directory where al the folders of the
% subje... |
27cbb34808ed256a54271cea08a17a422166abe6c43cbbc7ad91ad33f827efc2 | MATLAB | 21,849 | 426 | % pac() - compute phase-amplitude coupling (power of first input
% correlation with phase of second). There is no graphical output
% to this function.
%
% Usage:
% >> pac(x,y,srate);
% >> [coh,timesout,freqsout1,freqsout2,cohboot] ...
% = pac(x,y,srate,'key1', 'val1', 'key2', val... |
06e0d6682a6708d229d13a6f012b64804ca3db8764eb0088692a5f713a2cf5df | MATLAB | 21,851 | 444 | % pop_editeventfield() - Add/remove/rename/modify a field in the event structure
% of an EEG dataset. Can also be used to append new events to the end of the
% event structure or to delete all current events. If the dataset is
% the only input, a window pops up to ask for relev... |
6eda58300a0892bfc75838491c12354ae1bf6af308997212fc52671440ff9fec | MATLAB | 21,879 | 584 | function plotTracksTransDiffAnalysis2D(trackedFeatureInfo,transDiffAnalysisRes,timeRange,...
newFigure,image)
%PLOTTRACKSTRANSDIFFANALYSIS plots tracks in 2D highlighting the different diffusion segments within each track
%
%SYNOPSIS plotTracksTransDiffAnalysis2D(trackedFeatureInfo,transDiffAnalysisRes,timeRange,..... |
10d1cfcd08c0584338901462bf2842a7af52d6d2fe3213a316481bd4a3a7347a | MATLAB | 21,901 | 542 | function varargout = ea_anatomycontrol(varargin)
% EA_ANATOMYCONTROL MATLAB code for ea_anatomycontrol.fig
% EA_ANATOMYCONTROL, by itself, creates a new EA_ANATOMYCONTROL or raises the existing
% singleton*.
%
% H = EA_ANATOMYCONTROL returns the handle to a new EA_ANATOMYCONTROL or the handle to
% t... |
3ed3a3fa1d66bf4db6499b0d45ae8a6357f5257726715caa6e6e07df51717a7d | MATLAB | 21,926 | 587 | function plotTracksDiffAnalysis2D(trackedFeatureInfo,diffAnalysisRes,timeRange,...
newFigure,image,showConf,simplifyLin,offset,hideUnclass)
%PLOTTRACKSDIFFANALYSIS2D plots tracks in 2D highlighting the different diffusion types
%
%SYNOPSIS plotTracksDiffAnalysis2D(trackedFeatureInfo,diffAnalysisRes,timeRange,...
% ... |
93bf2ddbfc8ad9c6a662220dd42205ad9bd5ead878aa221f21b25fa641874f2e | MATLAB | 21,955 | 572 | function draggable(h,varargin)
% DRAGGABLE - Make it so that a graphics object can be dragged in a figure.
% This function makes an object interactive by allowing it to be dragged
% accross a set of axes, following or not certain constraints. This
% allows for intuitive control elements which are not buttons or o... |
63b023dfab9f2e7809922e184aeed4010d162c10d74a75971cdaf16e028a1bb1 | MATLAB | 21,985 | 530 | % Put all the mat files you want to analyze into one folder and navigate
% there.
matfiles = dir('*.mat');
% colnames = {'all','one','two','three','four','five','six','seven','eight','nine','ten','eleven','twelve'};
% colnames = {'left','right'};
colnames = {'left','right','three','four','five','six','seven','eigh... |
93cd15908870440c95eefedbfb9efaf4d008a2992bc1f3066e954692c023fee6 | MATLAB | 22,037 | 561 | %% Regression Walkthrough
%%
% This walkthrough works through multiple aspects of a basic 2nd-level (group)
% analysis. We are interested in activity related to emotion regulation
% for a contrast comparing reappraisal of negative images vs. looking at
% negative images without reappraisal, i.e., a [Reappraise Negativ... |
d761d4697c8e3a8cd12d0c4bb284187ee6a4de3d27d9313e076b4753d88befb3 | MATLAB | 22,037 | 433 | % DPRIME - Signal-detection theory sensitivity measure.
%
% d = dprime(pHit,pFA)
% [d,beta] = dprime(pHit,pFA)
%
% PHIT and PFA are numerical arrays of the same shape.
% PHIT is the proportion of "Hits": P(Yes|Signal)
% PFA is the proportion of "False Alarms": P(Yes|Noise)
% All numbers involved must be b... |
3f6d88580c9e362b2a46e0891b495bdc87582a1164247be35be46b786c15d249 | MATLAB | 22,055 | 617 | function [amplifier_channels, notes, aux_input_channels, spike_triggers,...
board_dig_in_channels, board_adc_channels, supply_voltage_channels, frequency_parameters ] =...
read_Intan_RHD2000_file(path,file)
% read_Intan_RHD2000_file
%
% Version 1.3, 10 December 2013
%
% Reads Intan Technologies RHD2000 data f... |
377671be1c760d0478ce87ff06ee31847bb18850b29065491d8922cb45811e8c | MATLAB | 22,064 | 475 | %% LaBGAScore_firstlevel_s1a_options_dsgn_multisess_multitask.m
%
%
% *USAGE*
%
% This script sets the options and creates a CANlab-style DSGN structure
% variable, which are used by the subsequent script in the standard LaBGAS
% workflow, LaBGAScore_firstlevel_s2_fit_model, to fit first level models
% using CANlab and... |
38743d13dc8f7f9691252ad1b63caa25b1c97c205b9e4ae63cbbea70aa999f98 | MATLAB | 22,093 | 614 | function ea_NBSrun(varargin)
%NBSrun Reads user inputs, performs basic error checking and then performs
%operations specified by user inputs.
%
% NBSrun(UI) operates on the user inputs in the structure UI.
%
% NBSrun(UI,S) attempts to write progress to the graphical user interface
% with handles S, otherw... |
1bf16430fe9696ec3a14915c0d148196bd7e63bf8b67525a05b95cf23b23fbf2 | MATLAB | 22,141 | 660 | function [counts,indices] = RadialMaze(data,baitedArms,varargin)
%RadialMaze - Compute simple statistics for the 8-arm radial maze task.
%
% Compute the number of reference and working memory errors, rewards found, etc.
%
% USAGE
%
% [counts,indices] = RadialMaze(data,baitedArms,<options>)
%
% data li... |
c8f3ec8143693441d4a3d531078df7b260f5ac9c6b5771075a4aced8dfd88d7b | MATLAB | 22,143 | 708 | function [res, errStr, oArg1]= dtdstruct_modify(varargin)
%
% function [res, errStr, oArg1]= dtdstruct_modify(dtdStruct, command, parm1[, parm2[, ...[, parmN]]])
%
% General method to manipulate a dtdStruct
%
% dtdStruct: should contain a valid dtdStruct
% command: spezifies the action and should contain a st... |
7f2816711bbbe231eb48285b9ee4037857da99eaa4e4a398dad13e3ca62de528 | MATLAB | 22,156 | 587 | function cs_fmri_conseed_pseed(dfold,cname,sfile,cmd,writeoutsinglefiles,outputfolder,outputmask)
tic
% if ~isdeployed
% addpath(genpath('/autofs/cluster/nimlab/connectomes/software/lead_dbs'));
% addpath('/autofs/cluster/nimlab/connectomes/software/spm12');
% end
if ~exist('writeoutsinglefiles','var')
w... |
8898272ca10de8aab45ed62d8edc72af67ac7bea0ffc865993110ec9f997381d | MATLAB | 22,237 | 541 | function atlases=ea_genatlastable(varargin)
% This function reads in atlases in the Lead-dbs/atlases directory and
% generates a table of all available atlas files.
% Atlastypes: 1 - RH
% 2 - LH
% 3 - both hemispheres (2 files present both in lhs and rhs
% folder
% ... |
4c9ebbc4252add71597482d8e7b46fdf26ebc9a1bbee64f71bdbce9ceb11fd23 | MATLAB | 22,260 | 722 | function M = run_measurement_prediction(mesh_mat, nirsmodel_file, roi_def, dmua_file, opts)
%RUN_MEASUREMENT_PREDICTION Predict noiseless channel-level responses from simulated ROI distributions.
%
% M = fnirspower.pipeline.run_measurement_prediction( ...
% mesh_mat, nirsmodel_file, roi_def, dmua_file, ...)
... |
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