sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
448a2e41481b6f82d4961f840b4819102ad856256d3319438b3ac1d79a20e452 | MATLAB | 22,268 | 535 | function colocMeasure = simulateCondColocGeneral(numRefObj,numTarObj,segmentation,...
cellMask,refColocWithCondFrac,tarColocWithCondFrac,...
tarColocWithRefAtCondFrac,tarColocWithRefNotAtCondFrac,varargin)
%SIMULATEPT2PT2BLOBCONDCOLOC simulate object positions to be used for general cond... |
6c0d099c50c78868075c91f7ff98527a274f523a6c22bd4b7edb0e23a5f94446 | MATLAB | 22,416 | 543 | function [] = minimalTifROIgui(tifFilePath)
IMGdata = justLoadTif(tifFilePath);
%draw ROIs on concatenated motion corrected image data
sROI.img = IMGdata;
sROI.nFrames = size(IMGdata,3);
sROI.imgHeight = size(IMGdata,1);
%this will be the main figure for drawing ROI
ui.roiGUI.fh = figure('Name','Choose fra... |
a6eb8a8fcdfc7c7c91597a2fd88e7eefaa04c0cbd033ab22ce1058711e640f67 | MATLAB | 22,434 | 774 | idx = cell(2,1);
idx{1} = 1:94+86;
idx{2} = 94+86+1:400;
%% Ketamine
within_ketamine = nan(12,2,2); % subj x BASE/PLOR x 4 matrices
filelist = dir('./KTM/Reordered_FCmat/');
for subj = 1:12
disp(subj)
load("./KTM/Reordered_FCmat/"+filelist(subj+2).name+"/BASE_noGSR_FCmat.mat"); FC_NG = FCmat;
... |
aba8c84d42fc6cf1c35903e9231de06ade7259257767810107568634ad328958 | MATLAB | 22,443 | 459 | function [methodsText, references, bibtexEntries] = generateMethodsText(param, varargin)
% bc.qm.generateMethodsText - Generate a methods section paragraph from BombCell parameters.
%
% Generates a ready-to-use methods section paragraph for scientific papers,
% with appropriate citations, based on the parameters used t... |
de711264c904c6239d709c2ab21bf30e8face91ec6bc7b5c4cecbcdeaae0fc62 | MATLAB | 22,466 | 667 | function preprocess_bids_minimal(bids_root, subj_list, keep_tasks, opts)
% preprocess_bids_minimal
%
% ONE-FILE, serial, lightweight SPM12 preprocessing for BIDS fMRI.
%
% Pipeline per selected run:
% 1) Segment T1 (deformation field only; once per sub+ses)
% 2) Realign: Estimate + Reslice mean only (no r*.nii time... |
69fe8ec4f3c11b0289f4a0cc3dbf4b130ca63ce08c05da5078da55a8c65634e1 | MATLAB | 22,506 | 461 | function IN = inpolyhedron(varargin)
%INPOLYHEDRON Tests if points are inside a 3D triangulated (faces/vertices) surface
%
% IN = INPOLYHEDRON(FV,QPTS) tests if the query points (QPTS) are inside
% the patch/surface/polyhedron defined by FV (a structure with fields
% 'vertices' and 'faces'). QPTS is an N-by-3 se... |
3e5c0bb64b112ec709b27b4bb65710352d382588ee7c608ce36241cd7f622963 | MATLAB | 22,615 | 660 | function varargout = ea_cortexselect(varargin)
% EA_CORTEXSELECT MATLAB code for ea_cortexselect.fig
% EA_CORTEXSELECT, by itself, creates a new EA_CORTEXSELECT or raises the existing
% singleton*.
%
% H = EA_CORTEXSELECT returns the handle to a new EA_CORTEXSELECT or the handle to
% the existing si... |
91369f73a180611fbea877dbb57054bd280667f2a98339433afaab24f8ba2e36 | MATLAB | 22,652 | 517 | % dipoledensity() - compute and optionally plot a measure of the 3-D spatial
% (in)homogeneity of a specified (large) set of 1- or 2-dipole
% component models, either as physical dipole density or as
% dipole-position entropy across subjects. In either case,
... |
5b012b0febd44aa79c7d82d24359238bdd09a8c896d45464b260598f0910bcb1 | MATLAB | 22,775 | 620 | % 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... |
4298b2173819b48b9d85b799616345158b0dd2a3cb8b38316cead5996c871e6b | MATLAB | 22,822 | 494 | function [rankStats] = bz_RankOrder(varargin)
% [rankStats] = RankOrder(varargin)
%
% Get rank order of spikes inside events from previously calculated
% bz_getRipSpikes structure. The 'corrEvents' output field structure shows
% rank correlation of each event with the selected 'templateType', and the
% 'pvalEve... |
e7f700afd915aae7d2713997e2610fd9d1cd5d50460de372721eec9c2e12a439 | MATLAB | 22,953 | 550 | function [ likelihood, results] = CBIG_gwMRF_graph_cut_clustering_split_newkappa_prod(x,prams,hemisphere)
% This function performs the actual clustering. This version is for the premulitiplied input data.
%
% Input
% - x = input data (premultiplied timeseries data)
% - prams = a struct containi... |
3d7b06fef091c5345639604176d78af36feb59916650eb2742eeb29b4283ef04 | MATLAB | 22,994 | 646 | 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... |
453b37fccf57dfdad52afe1d6bd8e13be561f4c7ca79e4d04accbf57cd33ad59 | MATLAB | 23,018 | 657 | function ea_mancor_updatescene(varargin)
hobj=varargin{1};
ev=varargin{2};
mcfig=varargin{3};
firstrun=getappdata(mcfig,'firstrun');
contrast=getappdata(mcfig,'contrast');
offset=getappdata(mcfig,'offset');
if isempty(contrast)
contrast=0.8;
end
if isempty(offset)
offset=0.3;
end
setappdata(mcfig,'offset',off... |
2928563a999ddb2454287c0273e36c6edcb28acca3707a2840743f61bfcee7bd | MATLAB | 23,057 | 608 | function [lh_labels, rh_labels] = CBIG_MSHBM_generate_individual_parcellation( ...
project_dir, mesh, num_sess, num_clusters, subid, w, c, subject_set)
% [lh_labels, rh_labels] = CBIG_MSHBM_generate_individual_parcellation(project_dir,mesh,num_sess,num_clusters,subid,w,c)
%
% This script will estimate the indi... |
069887694ac444fefc17dbf93385468f34e7e1d3d9b14763b45fd18cd096de45 | MATLAB | 23,084 | 608 | function [ EventDetectionReview ] = EventExplorer(basePath,events,varargin )
%EventExplorer is a GUI tool for exploring buzcode events and states files.
%
%INPUT
% events eventsName string (i.e. 'SlowWaves'),
% to load file: basePath/baseName.eventsName.events.mat
% -or-
% ... |
36992d5dc1f182abbc67ebbffa0c3c23b7432188e9b6945a668b22bc10656786 | MATLAB | 23,133 | 635 | function [Sxx, Syy, Sxy, xc, yc, um, vm] = compute_stress(x,y,tx,ty,K1,K2,h,BC)
%COMPUTE_STRESS.m COMPUTE MONOLAYER STRESSES FROM TRACTIONS
%
% [Sxx, Syy, Sxy, xc, yc, um, vm] = compute_stress(x,y,tx,ty,K1,K2,h,BC)
%
% Compute in-plane stress tensor components from a list of grid points
% (x,y) and nodal tractions (tx... |
b75e9dac75f6c28d9f158574e11cae1595fef7a7ec2fd764925f55367181079f | MATLAB | 23,139 | 376 | function ClincFreq_HeatNumStat(INDIR,OutHeatdir,SetUpPara,Para,AtlasTempU)
[V,D,namelist] = Dynamic_read_dir_NIFTI_sparse(INDIR);
D(isnan(D)) = 0;
D(isinf(D)) = 0;
D = D>0;
for i = 1:length(SetUpPara.ParaOut)
LabName = SetUpPara.ParaOut(i).LabName;
HeatDir{i} = [OutHeatdir,filesep,LabName,filesep];
% if onl... |
40fc1232860031ecc210d9a8b24905206af2b577b4d5515999770b67d78fa2b4 | MATLAB | 23,240 | 551 | function [lh_labels, rh_labels] = CBIG_ArealMSHBM_parcellation_single_subject(params)
% [lh_labels, rh_labels] = CBIG_ArealMSHBM_parcellation_single_subject(params)
%
% This function is a simplied wrapper to perform MSHBM individual areal-level
% parcellation for a single subject. This function prepare take simple inpu... |
c161f99b84bc6f40e11c734ddf5d2baeb6aaf3077a308d2a6c962b1ca2741a80 | MATLAB | 23,311 | 491 | %This script is designed to calculate coherence between pairs of channels
%using an adapted coherencyc function from chronux
%Saves a structure for each animal that contains a coherence matrix for
%each behavioral state (for this script: full recording, running time,
%running time within threshold, and non-runni... |
3a94774acd8fa4f865ad28038c20f1c889a85b7da5c28890e16fd06e1d5931e6 | MATLAB | 23,316 | 484 | function varargout = ea_genvat_butenko(varargin)
% Wrapper for OSS-DBS simulations.
% By Butenko and Li, konstantinmgtu@gmail.com
if nargin==2
S=varargin{1};
options=varargin{2};
elseif nargin==3
S=varargin{1};
options=varargin{2};
hFigure=varargin{3};
elseif nargin==1 && ischar(varargin... |
fd0e821e14692651dee7b9985288cee4e24ed5acbf650fdeef1e19ce983792fa | MATLAB | 23,316 | 486 | function [M_final,shifts_g,template,options,col_shift] = normcorre_batch(Y,options,template)
% online motion correction through DFT subpixel registration
% Based on the dftregistration.m function from Manuel Guizar and Jim Fienup
% INPUTS
% Y: Input data, can be already loaded in memory as a 3D
% ... |
eb0d8748eae6b5fc729a47369ed4c6231bf9c7617b00fb8af5f93871b74fb834 | MATLAB | 23,416 | 635 | function [amplifier_channels, notes, aux_input_channels, spike_triggers, board_dig_in_channels, supply_voltage_channels, frequency_parameters,board_adc_channels ]...
= read_Intan_RHD2000_file_bz
% read_Intan_RHD2000_file
%
% Version 2.01, 11 October 2017
%
% Reads Intan Technologies RHD2000 data file generated by... |
3669928a337920135f5a6c92bb95cffdf8db8bb87ed6d91b47ab3743183da51d | MATLAB | 23,457 | 497 | %This script is designed to calculate coherence between pairs of channels
%using an adapted coherencyc function from chronux
%ADDING STEPS TO LOOP THROUGH POSSIBLE SPEED RANGES - NOT DONE YET
%Saves a structure for each animal that contains a coherence matrix for
%each behavioral state (for this script: full r... |
f43681e5f359d7a15afa46ea3a497806ce3c0440f72b56339a3671aac50ac711 | MATLAB | 23,520 | 690 | function canlab_glm_subject_levels_old(dsgnarg, varargin)
% Performs lower level GLM analysis with SPM:
% 1. specifies model
% 2. estimates model
% 3. generates contrast images for model
% 4. creates directory with named links to spmT and con maps
% 5. publishes analyses with scn_spm_design_check
%
% :Usage:
... |
2cca7916919a905195ba093c1ff3b95f50e500321a0fc14255d56288ca565a11 | MATLAB | 23,647 | 537 | function spikes = bz_GetSpikes(varargin)
% bz_getSpikes - Get spike timestamps.
% if loading from clu/res/fet/spk files - must be formatted as:
% baseName.clu.shankNum
%
% USAGE
%
% spikes = bz_getSpikes(varargin)
%
% INPUTS
%
% spikeGroups -vector subset of shank IDs to load (Default: all)
% ... |
726b1c2202d814a9ef3bef3c04ce743bf20fbd99ff14b1084956f83388b93236 | MATLAB | 23,726 | 593 | % ====================================
%% Help
% ====================================
%
% CBIG_supp_fig4_lang_homo
%
% This script replicates Supplementary Figure 4: FC homogeneity and
% inhomogeneity restricted to the Language A and Language B networks.
% Four panels are produced:
% A - NIH test set resting-state ho... |
a67e65bfb52805f64ab2f3c897162b69d3794da7598ec6a54e928fe301c64fff | MATLAB | 23,728 | 378 | % pop_rejmenu() - Main menu for rejecting trials in an EEG dataset
%
% Usage: >> pop_rejmenu(INEEG, typerej);
%
% Inputs:
% INEEG - input dataset
% typerej - data to reject on (0 = component activations;
% 1 = raw electrode data). {Default: 1 = reject on raw data}
%
% Author: Arnaud Delorme,... |
786bdef557e25f17cabb51ac12991c889f2b2135c8cc00b27218b155c81862d8 | MATLAB | 23,756 | 691 | function make( varargin )
%
% Determine the base path
%
odir = pwd;
base = mfilename('fullpath');
base = fileparts( base );
%
% Check the force and runonly flags
%
args = varargin;
is_octave = exist( 'OCTAVE_VERSION', 'builtin' );
if is_octave,
force = true;
runonly = true;
indexonly = ... |
4e2e9713182b568309f4d2760f5a5cb6685952802aa137dd15d61b5e8db59622 | MATLAB | 23,769 | 479 | function [M_final,shifts_g,template,options,col_shift] = normcorre_batch(Y,options,template)
% online motion correction through DFT subpixel registration
% Based on the dftregistration.m function from Manuel Guizar and Jim Fienup
% INPUTS
% Y: Input data, can be already loaded in memory as a 3D
... |
cc784e586ef8dcca5e2792dc1f66756480904f3f7930f8cfa885235a21548000 | MATLAB | 23,783 | 583 | %% LaBGAScore_secondlevel_mvpa_beta_maps_conn.m
%
%
% *USAGE*
%
% This script runs MVPA regression analysis on a continuous outcome Y
% (default pcr, but can easily be adapted to pls or
% other machine learning algorithms) on an fmri_data
% object created from seed-based resting-state connectivity maps generated
% by t... |
b484f82949ab107008bf2253e3c56d396905c8b05e196515513003b68d3a49c6 | MATLAB | 23,800 | 547 | %% Step 4 Tiny Dancers: Group analyses for frequencies
clear all
clc
bigbin=5;
smallbin=3;
% load all frequency data
cd('D:\MUSICOM_EEG\PROC\Step3_frequencydata\3m');
FileNames_3m = {dir(['*_FREQ' '.mat']).name} ;
for k=1:1:length(FileNames_3m)
load(FileNames_3m{k})
avg_baseline_ssep_3m{k} = Tri... |
df75f3b0cfef09c5363b6155bbe9e1ff2df2c4ce8d52dee22c62bf62dcde922b | MATLAB | 23,836 | 632 | function read_Intan_RHD2000_file
% read_Intan_RHD2000_file
%
% Version 2.01, 11 October 2017
%
% Reads Intan Technologies RHD2000 data file generated by evaluation board
% GUI or Intan Recording Controller. Data are parsed and placed into
% variables that appear in the base MATLAB workspace. Therefore, it is... |
32d221db22ad6a0b6928b8d03f470648d66e46b03950d691424087c9dbf76c7a | MATLAB | 23,871 | 416 | function AnimalMetadata = bz_AnimalMetadataTextTemplate(basepath)
% This .m file is a generic template and will be copied to animal
% folders/session folders and will be called basename_AnimalMetadataText.m.
% It is represents code that will be used to
% create a basename.AnimalMetadata.mat file. Edits here will be re... |
39befecead83c4dc23f0734501b8ed849d37dae99e8b536fca83b1237ae4a9f1 | MATLAB | 23,976 | 634 | function read_Intan_RHD2000_file_noselect(file,path)
% read_Intan_RHD2000_file
%
% Version 2.01, 11 October 2017
%
% Reads Intan Technologies RHD2000 data file generated by evaluation board
% GUI or Intan Recording Controller. Data are parsed and placed into
% variables that appear in the base MATLAB workspac... |
5c776bd167daa64baeec06b982046d2b3d37a0ba8dd473850cf6593e0de6a3cb | MATLAB | 24,049 | 649 | function read_Intan_RHD2000_file(varargin)
% read_Intan_RHD2000_file
%
% Version 2.01, 11 October 2017
%
% Reads Intan Technologies RHD2000 data file generated by evaluation board
% GUI or Intan Recording Controller. Data are parsed and placed into
% variables that appear in the base MATLAB workspace. Therefore, it ... |
6e71f139b9662eb6e746f986dd2629696db0a065feaec64b6f80cc08d0fa2db1 | MATLAB | 24,057 | 863 | function [Results, Summary] = calcium_data_PrL_SB_struct_clean( ...
mouse_number, session_frame, matfilepath, corr_threshold, matfile, neuron_chosen_signal)
% Structured version of calcium_data_PrL_SB
%
% Inputs
% mouse_number : vector of mouse IDs
% session_frame : 6xN or 9xN session frame mat... |
cde80626c6eb6b6806728ba3d407d20f73824797d1d49e49d67fb984dd783c16 | MATLAB | 24,065 | 544 | % pop_comperp() - Compute the grand average ERP waveforms of multiple datasets
% currently loaded into EEGLAB, with optional ERP difference-wave
% plotting and t-tests. Creates a plotting figure.
% Usage:
% >> pop_comperp( ALLEEG, flag ); % pop-up window, interactive mode
% ... |
a41a399d1fa83a4ab7ffc00741bd30e708f8052713b315404465748686956413 | MATLAB | 24,066 | 468 |
classdef SSankey < handle
% Copyright (c) 2023-2024, Zhaoxu Liu / slandarer
% =========================================================================
% @author : slandarer
% 公众号 : slandarer随笔
% 知乎 : slandarer
% =========================================================================
% # update 2.0.0(2024-02-04)... |
230fa640bb078594eafc2bbc3823ba93e1dbef7bca8b0e52c1c263b3f2fdad3c | MATLAB | 24,196 | 598 | 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... |
215a0bcaa87c697c6079261b85631bdc2a5a847b1fa1831fbc8c6b188dca0a29 | MATLAB | 24,264 | 659 | function ROI_table = plot_ENet_diagnostics_neuroimaging(results, X, Y, roiNames, atlasFile, varargin)
% plot_ENet_diagnostics_neuroimaging Plotting and diagnostics for Elastic Net neuroimaging pipelines.
%
% This function visualizes and exports diagnostics from Elastic Net pipelines
% such as ENet_neuroimaging_pipelin... |
634befee34719465002dbb51c7f61db0fdfe15d8b8da75647547d2e87115e720 | MATLAB | 24,311 | 595 | function [RP, RESULTS]=rqa_legacy(DATA,TYPE,tau,dim,ZSCORE,NORM,SETPARA,SETVALUE,plotOption)
% [RP, RESULTS]=rqa_legacy(DATA,TYPE,EMB,DEL,ZSCORE,NORM,SETPARA,SETVALUE,plotOption)
% Inputs - DATA, a double-variable with each dimension of the
% to-be-analyzed signal as a row of numbers in a separate
% ... |
8a1763e8a41de5ea8405850cd533159df7f9e8e62c2581447731e62e939420f3 | MATLAB | 24,316 | 568 | %% Step 4 Tiny Dancers: Group analyses for ERP
% load all ERP data
clear all
clc
%% Load data
cd('D:\MUSICOM_EEG\PROC\Step3_ERPs\3m\');
FileNames = {dir(['*' '.mat']).name} ;
for k = 1:1:length(FileNames)
load(FileNames{k})
avg_baseline_3m{k} = ERP_baseline;
avg_control_3m{k} = ERP_co... |
157e243066fb92f1adcecfb79bb57e25450f8f8eede0b78dc99632f3bd34a2b9 | MATLAB | 24,375 | 699 | function varargout = auto_classify(varargin)
% AUTO_CLASSIFY M-file for auto_classify.fig
% AUTO_CLASSIFY, by itself, creates a new AUTO_CLASSIFY or raises the existing
% singleton*.
%
% H = AUTO_CLASSIFY returns the handle to a new AUTO_CLASSIFY or the handle to
% the existing singleton*.
%
% ... |
23a768ca3bf6bdc0ff2162909655a5f9f54eea23a3adfbf604de3f71ffc265bd | MATLAB | 24,396 | 646 | function saveNEV(NEV, varargin)
%%
% Save an .NEV file from an NEV structure (gained by using openNEV)
% Works with file spec 2.3
%
% Use saveNEV(NEV, filename, noreport)
% All input arguments are optional. Input arguments can be in any order.
%
% NEV: Name of the NEV structure to be saved.
% ... |
294420d5744696a4b1d74405fbefa1bf996b8e011d841b92ea448d5e2c66eace | MATLAB | 24,437 | 363 | % pop_statparams() - helper function for pop_erspparams, pop_erpparams, and
% pop_specparams.
%
% Usage:
% >> struct = pop_statparams(struct, 'default');
% >> struct = pop_statparams(struct, 'key', 'val', ...);
%
% Inputs:
% struct - parameter structure. When called with the 'default'
% ... |
5574c74c829b3cd069a3d98865ad1287e4a38307fbe4d70b3a3d48232c79a0cf | MATLAB | 24,471 | 495 | %% Basic script for decoding behavioral stimuli based on neural data
function [RastFig, DecodeFig, num_cv_splits, num_units] = runNeuralDecodingToolbox(raster_data_dir,area,condition,spikeType, ...
unitType,trialType,classifier_labels,classifierName,varargin)
options = inputParser;
checkArea = @(x) ischar(x) || is... |
7b78c60e971b17bb45b1068dd516314050bb258ac3beadb0a81495459491230a | MATLAB | 24,553 | 609 | function SANDIinput = setup_and_run_model_training(SANDIinput)
% 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 University, UK
% 4th A... |
175bca04c25c1d6879d2c072668c25692b04714bc5c6e70e73bc3fad5c601396 | MATLAB | 24,583 | 756 | function CFA_inout(H)
% function CFA_inout
movegui(H.fig,'west')
pathss = which('CFA_inout.m');
[pth nam ext] = fileparts(pathss);
IOsetupdir = [pth,filesep,'IOparameter',filesep];
if ~isempty(dir(IOsetupdir))
rmdir(IOsetupdir,'s')
mkdir(IOsetupdir);
else
mkdir(IOsetupdir);
end
load([pth,filesep,'colorforl... |
7cd11bcdae41a2d5aa0fb74cbca32ddb94281453a4fac141d97923aa29114ec2 | MATLAB | 24,608 | 569 | % pop_selectevent() - Find events in an EEG dataset. If the dataset
% is the only input, a window pops up to
% ask for the relevant parameter values.
%
% Usage: >> [EEGOUT,event_indices] = pop_selectevent( EEG, 'key1', value1, ...
% ... |
b6362cdc58cecd9c0657ae7aade582d5f9b1b4afb7c3a4f351924c8a07f0b59b | MATLAB | 24,628 | 688 | function varargout = ea_atlasselect(varargin)
% EA_ATLASSELECT MATLAB code for ea_atlasselect.fig
% EA_ATLASSELECT, by itself, creates a new EA_ATLASSELECT or raises the existing
% singleton*.
%
% H = EA_ATLASSELECT returns the handle to a new EA_ATLASSELECT or the handle to
% the existing singleton... |
d0ba93e0fa2f111c828902cee8c4cdb42ec6084a0cbe38b96b922ff3fe247b52 | MATLAB | 24,678 | 662 | %% demos - demonstrations of the analysis software
% Performs various information theoretic analyses using simple model data
% generated within. Each specific type of demo can be run individually.
%
% Other m-files required: whole software package
% Subfunctions: none
% MAT-files required: 2PIDMats.mat, 3PIDMats.mat, ... |
389ce78a147a387cc202a2a1e0f970a02bb2c78d23a77ec82d380c22af87c6e6 | MATLAB | 24,747 | 617 | function plotSaveConditionalColoc(PtOrBlob,plotting, saveRes,pathToSave, varargin)
%PLOTSAVECONDITIONALCOLOC plots and/or saves conditional colocalization results
%
% SYNOPSIS plotSaveConditionalColoc(PtOrBlob,plotting, saveRes, varargin)
%
%INPUT
% PtOrBlob: 1 for plotting Pt2Pt2Pt, 2 for Pt2Pt2Blob, or 3 for Gene... |
2a591043461bcf303676535406471634e36e287dbc958d8c1e1804386a9c41bb | MATLAB | 24,773 | 717 | function [SpikeLFPCoupling] = bz_GenSpikeLFPCoupling(spikes,LFP,varargin)
% SpikeLFPCoupling = GenSpikeLFPCoupling(spikes,LFP)
%
%INPUT
% spikes structure with fields (from bz_getSpikes)
% .times
% -or-
% {Ncells} cell array of spiketimes ... |
e64ca91bbc5dc4cf80b3256a7cea1f20cb8f2a6f4658282291bade8a2adc3df8 | MATLAB | 24,801 | 626 | %% LaBGAScore_cosmomvpa_searchlight_rsa.m
%
%
% *USAGE*
%
% This script uses functions of
% <https://www.cosmomvpa.org/index.html CoSMoMVPA> to
%
%
% # run first-level (i.e. within-subject) representational similarity
% analysis comparing behavioral and neural dissimilarity matrices
% for conditions of your choice ... |
c152f1412b6d52add3175c5c2ea8b58e67f03d3a4b9fcfbe7055cb1f54e36e0f | MATLAB | 24,855 | 505 | % pop_headplot() - plot one or more spherically-splined EEG field maps
% using a semi-realistic 3-D head model. Requires a
% spline file, which is created first if not found.
% This may take some time, but does not need to be
% done again for this ch... |
dc7aa31525c9070388c477dace5de8f3510eea12b3b3a61744799cd9067fa2a2 | MATLAB | 24,862 | 682 | function DEP = LaBGAScore_dep_map(target, varargin)
%
%
% *USAGE*
%
% Maps which dependency files a script or function actually reaches, by
% parsing it with mtree, resolving every called name against the index
% built by LaBGAScore_dep_build_index, and walking the result transitively.
%
% Two consumers:
%
% # LaBGASco... |
9f647ab70af698023f02532d2720a08bf85fde7fe2954ddfccfc459f620a5b70 | MATLAB | 24,879 | 555 | % statcond() - compare two or more data conditions statistically using
% standard parametric or nonparametric permutation-based ANOVA
% (1-way or 2-way) or t-test methods. Parametric testing uses
% fcdf() from the Matlab Statistical Toolbox.
% Usage:
% >> [stats, d... |
58724d80a44abd91fc7169c84bdd737bfba9b63094ef90f12f850b4d3ea8157c | MATLAB | 24,900 | 499 | function results = ea_discfibers_ui_enablerules(app,flag)
app.isbusy(1);
if ~isfield(app.tractset.results,ea_conn2connid(app.tractset.connectome))
val='off';
else
val=ea_bool2onoff(isfield(app.tractset.results.(ea_conn2connid(app.tractset.connectome)),... |
969a8da34e006dfe29ee30b947f11937f39f65c701ea48c0b179bd971dd3614e | MATLAB | 24,916 | 647 | function results = PLSDA_neuroimaging_pipeline(X,Y,opts)
% PLSDA_neuroimaging_pipeline Robust PLS-DA pipeline for neuroimaging feature matrices.
%
% This function implements Partial Least Squares Discriminant Analysis (PLS-DA)
% for binary classification with repeated nested k-fold cross-validation.
% It is designed ... |
26f3ab3314b5eb5a81f5a8a03623e776fa279017714265659c4662a68831cf73 | MATLAB | 24,992 | 624 | function [lh_labels, rh_labels] = CBIG_ArealMSHBM_dMSHBM_generate_individual_parcellation(project_dir, ...
mesh, num_sess, num_clusters, subid, w, c, subject_set)
% [lh_labels, rh_labels] = CBIG_ArealMSHBM_dMSHBM_generate_individual_parcellation ...
% (project_dir, mesh, num_sess, num_clusters, subid, w, c, subjec... |
8fc01ba01877994510c5c30efa8bf5d6c1e7d594a3154bf8a129e1150e79c5ff | MATLAB | 25,074 | 699 | function varargout = auto_classify(varargin)
% AUTO_CLASSIFY M-file for auto_classify.fig
% AUTO_CLASSIFY, by itself, creates a new AUTO_CLASSIFY or raises the existing
% singleton*.
%
% H = AUTO_CLASSIFY returns the handle to a new AUTO_CLASSIFY or the handle to
% the existing singleton*.
%
... |
6bdeb7fa5e689f09641ac1a217d20c0f9b634c208e760b31c58daf7778183625 | MATLAB | 25,155 | 727 | 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... |
49484da7e6bd78401db2826712a0467290a5c50b4420f6e08aaf9714bf35b9ad | MATLAB | 25,184 | 641 | %% Tutorial for xml_io_tools Package
% *By Jarek Tuszynski*
%
% Package xml_io_tools can read XML files into MATLAB struct and writes
% MATLAB data types to XML files with help of simple interface to
% MATLAB's xmlwrite and xmlread functions.
%
% Two function to simplify reading and writing XML files from MAT... |
ac31203677d3c8cf8201424965bbd3d9889ee52e903e16e5fc5ed86df950c7ac | MATLAB | 25,199 | 749 | function cs_fmri_conseed_seed_tc(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')
... |
b3f7c07f09e78e47501efe16d41cb8cec21b9444313436f4649477c60ee355d9 | MATLAB | 25,380 | 538 | % pop_runica() - Run an ICA decomposition of an EEG dataset using runica(),
% binica(), or another ICA or other linear decomposition.
% Usage:
% >> OUT_EEG = pop_runica( EEG ); % pops-up a data entry window
% >> OUT_EEG = pop_runica( EEG, 'key', 'val' ); % no pop_up
%
% Graphic interface:
% "ICA ... |
79699fccf894fe8df6b6cd7f55094f4fcb2f381aec992cfcafe6f20c68e60e0e | MATLAB | 25,394 | 609 | % corrimage() - compute correlation image between an event and amplitude
% and phase in the time-frequency domain.
%
% Usage:
% corrimage(data, sortvar, times);
% [times, freqs, alpha, sigout, limits ] = corrimage(data, sortvar, ...
% times, 'key1', val1, 'key2'... |
388a3b5e668dca9fe18cb3d93f5194af9cd71deda2ea45e347d406b39c1e0cba | MATLAB | 25,498 | 418 | function ClincFreq_HeatNumStat(INDIR,OutHeatdir,SetUpPara,Para,AtlasTempU,dbmask)
[V,D,namelist] = Dynamic_read_dir_NIFTI_sparse(INDIR);
D(isnan(D)) = 0;
D(isinf(D)) = 0;
D = D>0;
outind = find(dbmask==0);
D(outind,:) = 0;
Dvol = sum(D)';
Dvole = sum(D,2);
IgV = Para.IgP;
indexs = find(Dvole>=(size(D,2)*IgV/100));
Dma... |
23863c56d0b3645ab541445b70f0da59b494ba663fad17c39ce7b0217d2db1a9 | MATLAB | 25,562 | 605 | classdef ea_trajectory < handle
% Trajectory class to handle trajectories in lead dbs resultfig / 3D Matlab figures
% A. Horn
properties (SetObservable)
elstruct % reconstruction of electrodes as handled by ea_elvis
plan2elstruct % reconstruction (pseudo) of stereotactical plan
plan... |
3f864dc9bf62adfdeaeeda63d239954b4fa376fd073e402da5845a82c30d1874 | MATLAB | 25,662 | 665 | % tftopo() - Generate a figure showing a selected or representative image (e.g.,
% an ERSP, ITC or ERP-image) from a supplied set of images, one for each
% scalp channel. Then, plot topoplot() scalp maps of value distributions
% at specified (time, frequency) image points. Else, ... |
c828ce62ba4493d23a4c9f697a5b2df8a246aca2062488bd2e6020691912eddc | MATLAB | 25,681 | 678 | %% Figure 5A-C
% Prediction-error GC during active task engagement.
% Structure:
% 1) Compute all data required for Figure 5A-C
% 2) Draw Figure 5A, Figure 5B, and Figure 5C
% 3) Save one independent MAT file for each final panel
%
% Notes:
% - No local functions.
% - No mixed upload MAT files.
% - Suppleme... |
2f71c0f2d6a36be16a7a6aeaa71af61f8fa3774584484f9078645476d279d638 | MATLAB | 25,717 | 669 | function results = PLSR_neuroimaging_pipeline(X,Y,opts)
% PLSR_neuroimaging_pipeline Robust PLS regression pipeline for neuroimaging feature matrices.
%
% This function implements Partial Least Squares Regression (PLSR)
% for continuous outcomes with repeated nested k-fold cross-validation.
% It is designed for neuro... |
bb12137b47827e9b34bf2661fad85f591f2e1dc4e8a2cefbf306440f61dc1d24 | MATLAB | 25,793 | 656 | % pop_editeventvals() - Edit events contained in an EEG dataset structure.
% If the dataset is the only input, a window pops up
% allowing the user to insert the relevant parameter values.
%
% Usage: >> EEGOUT = pop_editeventvals( EEG, 'key1', value1, ...
% ... |
aa4814b1f1b43fae577a57dfe2a4106e1e34adafa6d535458b466bb7c3b629d6 | MATLAB | 25,961 | 669 | function Params = CBIG_MSHBM_estimate_group_priors(project_dir,mesh,num_sub,num_sess,num_clusters,varargin)
% Params = CBIG_MSHBM_estimate_group_priors(project_dir,mesh,num_sub,num_sess,num_clusters,varargin)
%
% This script will estimate group priors for individual-level parcellation
% generation. The estimated group... |
b05db17b332d055eb29d08823136f3c0e6473c9c9736ae2347e8e24040428679 | MATLAB | 25,962 | 645 | classdef ScrollingPanel < uix.Container & uix.mixin.Panel
%uix.ScrollingPanel Scrolling panel
%
% p = uix.ScrollingPanel(p1,v1,p2,v2,...) constructs a scrolling panel
% and sets parameter p1 to value v1, etc.
%
% A scrolling panel is a standard container (uicontainer) that shows
% one i... |
948f06391ee6fa80231b20d6a6d8b91978b71e70a9449ac4cd0176ac5c7c18ae | MATLAB | 26,003 | 741 | function ea_imshowpair(Img, options, title, callingfunction, helptext)
% this function is based on IMSHOW3DFULL by Maysam Shahedi and supports
% truecolor images. Windowed view is adapted from MAGNIFY by Rick Hindman.
%
% Todd Herrington, 2016-03-16
if ~exist('callingfunction','var')
callingfunction='normalization... |
90533b30d742a48308789e6e1c544465df93fc37a4abb1a4ad44fa2e0f9b098d | MATLAB | 26,077 | 535 | classdef (CaseInsensitiveProperties = true) functionalSpreadPlot < ...
iosr.statistics.functionalPlot
%FUNCTIONALSPREADPLOT Draw a functional plot showing data spread
%
% Use this class to plot the spread of data against a continuous
% variable. The class calculates point-wise statistics for each set of
% ... |
dbf600a672807f69ef13da27db067481b53d36559ad9c785bb1dd92c865cc2f5 | MATLAB | 26,243 | 647 | function plotSaveConditionalColocDiffMarker(PtOrBlob,plotting, saveRes,pathToSave, varargin)
%PLOTSAVECONDITIONALCOLOC plots and/or saves conditional colocalization results
%
% SYNOPSIS plotSaveConditionalColoc(PtOrBlob,plotting, saveRes, varargin)
%
%INPUT
% PtOrBlob: 1 for plotting Pt2Pt2Pt, 2 for Pt2Pt2Blob, or ... |
8434fa3a2f46db263b382bb27e82deef2c6ac929e170aa37553aff14d9fd2093 | MATLAB | 26,255 | 718 | % miro :: Measured Impulse Response Object
%
% miro Class Definition
%
% 2012 by Benjamin Bernschütz (bBrn)
% Cologne University of Applied Sciences
% Institute of Communication Systems
% mail benjamin.bernschuetz@fh-koeln.de
% GSM +49 171 4176069
% Phone +49 221 8275 ... |
ceb59e9022a6dc2dc2cfa0287eddc7d83190910b486ac6ba05bda35ce3b1a225 | MATLAB | 26,261 | 788 | function CFA_inout(H)
% function CFA_inout
movegui(H.fig,'west')
pathss = which('CFA_inout.m');
[pth nam ext] = fileparts(pathss);
IOsetupdir = [pth,filesep,'IOparameter',filesep];
if ~isempty(dir(IOsetupdir))
rmdir(IOsetupdir,'s')
mkdir(IOsetupdir);
else
mkdir(IOsetupdir);
end
load([pth,filesep,'colorforl... |
1253ffc85615e01782a09a24c950e554e8e8c4ff7f36b8f740159fc0f5eebb41 | MATLAB | 26,311 | 411 | function [Ihat,Ihat_train_global,val_struct] = ea_compute_unified_model(numTestIt, obj, fibsval, Ihat, Ihat_train_global, patientsel, training, test, Iperm,vals,usedidx)
% this needs to be edited when external model is brought back
% if obj.useExternalModel == true
% S = load(obj.ExternalModelFile);
% ... |
efb90bd349c6747d06fbbc6839f45cdb691fa9a2cb4020412a7064cb6c0c235e | MATLAB | 26,512 | 439 | function h = copyUIAxes(varargin)
% The use of Matlab's copyobj() is not supported with UI axes.
% use COPYUIAXES to copy the content of a UI axis to a new figure.
% COPYUIAXES receives the handle to a UI axes and copies all of its
% children and most of its properties to a new axis. If the UI axis
% has a legend... |
0d9415004ad50f33c4244992a09e3de0cea48fd4349e287d8ee4c3606a72e5f1 | MATLAB | 26,647 | 821 | function icatb_defaults
% All the GIFT toolbox defaults are stored in this file
if (isdeployed)
gicaInstallDir = getenv('GICA_INSTALL_DIR');
defsFile = fullfile(gicaInstallDir, 'icatb_defaults.m');
if (~isempty(dir(defsFile)))
icatb_eval_script(defsFile);
return;
en... |
ffd50aa9a1a34b27815c7b75d924a42111783ac7a3f2dd8c74aa972c49434633 | MATLAB | 26,685 | 561 | function [status] = ft_hastoolbox(toolbox, autoadd, silent)
% FT_HASTOOLBOX tests whether an external toolbox is installed. Optionally
% it will try to determine the path to the toolbox and install it
% automatically.
%
% Use as
% [status] = ft_hastoolbox(toolbox, autoadd, silent)
%
% autoadd = 0 means that it will ... |
8288e66c14d5939d259d6ce630df82950f105b1692851a3b81e5983b77c8878f | MATLAB | 26,717 | 536 | function [M_final,shifts,template,options,col_shift] = normcorre(Y,options,template)
% online motion correction through DFT subpixel registration
% Based on the dftregistration.m function from Manuel Guizar and Jim Fienup
% INPUTS
% Y: Input data, can be already loaded in memory as a 3D
% ... |
a846124d5d8b20de1b652801be73a83cdad96d00a907f504074b6e480a98de48 | MATLAB | 26,905 | 998 | function [Results, Summary] = calcium_data_PrL_SB_struct_clean_WTdownsample60( ...
mouse_number, session_frame, matfilepath, corr_threshold, matfile, ...
neuron_chosen_signal, group_label, nRepeats, frac_keep, useParallel)
% Structured version of calcium_data_PrL_SB with repeated WT downsampling
%
% Main change... |
88b19176bdd93b056e4438418efce6f9349bcdcff67443aaf3e49405e5a18b64 | MATLAB | 26,930 | 555 | %% Visualize individual responses upon stimulus presentation
% Choose a stage and plot the stage progression
close all; clearvars; clc;
% Make the user pick the two "ResponsePattern" mat files to compare
scriptFullPath = matlab.desktop.editor.getActiveFilename();
try load(regexprep(scriptFullPath, 'Scripts.*', 'Scripts... |
eeb1a49b1240d40b58f94664d385eea27b1d75b54ffc29293cd987b04855c9ab | MATLAB | 26,943 | 720 | function [norm] = electroderealign(cfg);
% ELECTRODEREALIGN rotates and translates electrode positions to
% template electrode positions or towards the head surface. It can
% either perform a rigid body transformation, in which only the
% coordinate system is changed, or it can apply additional deformations
% to the i... |
b6c9abdeb01e27a1f9dfd4cbabc4691d66123d7449785050139b4e1b09b529cb | MATLAB | 27,008 | 503 | % std_preclust() - select measures to be included in computation of a preclustering array.
% This array is used by pop_clust() to find component clusters from a
% specified parent cluster.
% Selected measures (dipole location, ERPs, spectra, scalp maps, ERSPs,
% ... |
50f7b20f4363546d66f3614a48f077c7f5ac4c8daa3886b77b71465784dc20b4 | MATLAB | 27,014 | 531 | function [M_final,shifts,template,options,col_shift] = normcorre(Y,options,template)
% online motion correction through DFT subpixel registration
% Based on the dftregistration.m function from Manuel Guizar and Jim Fienup
% INPUTS
% Y: Input data, can be already loaded in memory as a 3D
% ... |
1aa598af099adf7f787b669d2f3059e9c07054a8586cce7bbdfe9cde59429a17 | MATLAB | 27,050 | 570 | % pop_newset() - Edit/save EEG dataset structure information.
%
% Usage:
% >> [ALLEEG EEG CURRENTSET] = pop_newset( ALLEEG, EEG, CURRENTSET,...
% 'key', val,...);
% Inputs and outputs:
% ALLEEG - array of EEG dataset structures
% EEG - current dataset structur... |
4e1b60b9d87834a108029026814fac94ef0d980c2926c83182f641349645cfc1 | MATLAB | 27,105 | 818 | function varargout = ea_cat_run(job)
% Segment a bunch of images
% ______________________________________________________________________
%
% FORMAT cat_run(job)
%
% job.channel(n).vols{m}
% job.channel(n).biasreg
% job.channel(n).biasfwhm
% job.channel(n).write
% job.tissue(k).tpm
% job.tissue(k).ngaus
%... |
a2594804643d2a127bceab77ee6929619330d938709780a7edbffb0d711d3b7d | MATLAB | 27,155 | 582 | % std_dipplot() - Commandline function to plot cluster component dipoles. Dipoles for each
% named cluster is displayed in a separate figure. To view all the clustered
% components in the STUDY on the same figure (in a separate subplot), all
% STUDY clusters must be req... |
ee4c9415053eba4d637bd37d46b65beeaa3c724df5d4c660c4c2ba48c0eb71b2 | MATLAB | 27,200 | 832 | %lets start easy - just get all the responsive ones and plot the average
%directional response
load('/Volumes/Samsung_T5 1/2-photon imaging/vt062617/incides.mat')
load('/Volumes/Samsung_T5/2-photon imaging/vt062617/incides.mat')
cd ../../../../../../../Volumes/'Samsung_T5 1'/'2-photon imaging'/vt062617
cd ../../../../.... |
cdefe70bc37a88a187643a635c555416bc11046e0687b6877c0ec4b60b364b49 | MATLAB | 27,340 | 546 | % std_readersp() - load ERSP measures for data channels or for all
% components of a specified cluster. This function is
% also being used to read ITC and ERPimage data.
% Usage:
% >> [STUDY, erspdata, times, freqs, erspbase] = ...
% std_readersp(STUDY, ALLEEG, v... |
c006ec3e944891b85a2b9d43dbed494b80668e2e7a7d33485c95a5904088caf3 | MATLAB | 27,487 | 720 | % ====================================
%% Help
% ====================================
%
% CBIG_test_MSHBM_esfmri_homo
%
% This script tests the MS-HBM model on the electrostimulation fMRI
% (esfMRI) dataset using leave-one-run-out cross-validation. Two
% independent homogeneity tests are performed:
%
% (1) Pre-op res... |
bd00c4d807c26499bfb28ab15ef3de44fc21668df7517f96745cc0c6d882ed5c | MATLAB | 27,501 | 556 | %% TestElectrodes - Class representing a Ben's Gun configuration of Test Electrodes (up to rotation!)
% note that the precise rotation depends on the kinematics of the
% sterotactic frame/the micro drive device
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Lux... |
7a86396216ddca750dadfc2545c8bc7f667d3e2418538df0d17d2b298f6ba9fb | MATLAB | 27,521 | 754 | function varargout = FAnalyze(varargin)
% FANALYZE
% For all your trajectory analysis needs! . See documentation for usage details.
%Written by Dan Valente
%November 2007
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton... |
3d832fc3998aa827a9643f5a41f974717f98cf5776fa0e62c43fbac87cf9a1e1 | MATLAB | 27,582 | 509 | % pop_chanplot() - graphic user interface (GUI)-based function with plotting
% options for visualizing. Only channel measures (e.g., spectra,
% ERPs, ERSPs, ITCs) that have been computed and saved in the study EEG
% datasets can be visualized. These can be computed using ... |
e058a4d68aeb62b9ec9451ce386004f7a6e1aee3a6f4d0012220d82d028dd954 | MATLAB | 27,634 | 651 | % eeg_context() - returns (in output 'delays') a matrix giving, for each event of specified
% ("target") type(s), the latency (in ms) to the Nth preceding and/or following
% urevents (if any) of specified ("neighbor") type(s). Return the target event
% and urevent numbe... |
e7dbb70c09cd2b4056f08407b6be5f3f3a16c7a852d8089b4b9f438639b20574 | MATLAB | 27,719 | 880 | %% Cosine dissimilarity + BOLD dissimilarity vs stimulus position
clear; clc;
loadparam;
% Create ensemble of 200 stimulus positions
num_samples = 200;
% Set seed
rng(1, "twister");
stim_array = topology.L * rand(2, num_samples);
% tolerance for bold calculation
tol = 1e-5;
% Record total length used and times to ... |
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