sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2ddeba80cfa60f906de1922768dc6dfb4d508cc129e7e8424e4fb709150fbf75 | MATLAB | 17,108 | 556 | function BCCT_showmap_subfun1(Parameter)
[Vbg Dbg] = Dynamic_read_dir_NIFTI(Parameter.BG);
[pth nam ext] = fileparts(Parameter.BG);
if strcmp(nam,'mni_icbm152_t1')
D_BG = reshape(Dbg,Vbg.dim);
D_BG(isnan(D_BG)) = 0;
D_BG(D_BG<30) = 30;
D_BG(D_BG>85) = 85;
D_BG = (D_BG-30)/55*0.99+0.005;
else
D_B... |
22fd4af2d7e2433714044b45b5ecfb58c3b36de38f289e57762c7d29369e9dda | MATLAB | 17,120 | 279 | function [] = waveform_plotting_local_v3(S)
% It plots waveform for multiple conditions (one group of participants).
% Typically used for plotting time series of MEG channel/source, locally.
% INPUTS:
% -S.data: Data that you want to plot
% ROIs (s... |
b31230d72e957fe356e8db4848f73dede0066c7d49bb711cacee58ff0e05fd6c | MATLAB | 17,235 | 636 | function [selected_file, selected_path] = rri_select_file(varargin)
%
% USAGE: [selected_file, selected_path] = ...
% rri_select_file(dir_name, fig_title)
%
% Allow user to select a file from a list of Matlab competible
% file format
%
% Example:
%
% [selected_file, selected_path] = ...
% ... |
49deee4167a256e679c5d1617ed8693fb4a324c47d563f97ad7b6760e150769e | MATLAB | 17,266 | 412 | function varargout = process_nst_extract_sensitivity_from_head_model( varargin )
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2013 Brainstorm by the University of Southe... |
74edf224af9ad4702df9838730043126099388ae2b8f165aa263b1a094642954 | MATLAB | 17,273 | 486 | %% =========================================================
% Partial Spearman correlations of ISPSDeg / Radius_z / Proj_impulse_z
% with each scale score (X)
% Controls: BDI, BAI (residual method)
% Data: F:\PIT\model\EEGmodelHC\OCD\OCD_M5b_Q.xlsx
% Output: F:\PIT\ISPSplot\relation (CSV + one 80x70 mm SVG per combin... |
11e758feb5343e781d869c77b716dff12b1b3e4db07749c556342e15f2816d22 | MATLAB | 17,332 | 552 | function BCCT_CaSCN_MAP_GUI
D.fig = figure('Name','Causal network of Structural Covaraince Connectivity(Seed to Whole Brain, volume-based)',...
'units','normalized',...
'menubar','none',...
'numbertitle','off',...
'color',[0.95 0.95 0.95],...
'position',[0.20 0.15 0.5... |
f58aa2c9c59fb5c4b420a3dcca26133a6b3347cfc4356cd27fff93637a595ddb | MATLAB | 17,369 | 501 | function [state, params, LL_complete]= saem(init, model, opt_params, Y_avg, Y, Y_mcmv, Ns, Np, P, dist_thr, gpu_flag, whiten_flag, mcmv_prior_flag)
%AUTHOR : NARAYAN SUBRAMANIYAM /AALTO/NBE/
% INPUTS
% 1) init : struct containing initial values for parameters and kalman
% mean/cov . init.A0, init.V_q0, init.q0, init.P0... |
d6a139c44a589e8b6df0e52f7f9fe6cb88eee6c48dd6ce5cafaa5c3d212de85b | MATLAB | 17,422 | 416 | % This script concatenates all the processed data contained in the
% allCTX and allCA1 mat files in Matlab arrays to make the plots of the
% network statistics of the events (Figs. 2 and 4 in the manuscript)
% --- Load data --------------------------------------------------------- %
load('Data\allCTX.mat')
load('D... |
6b45660319942ac6226012aed26fb669e4311f0e68cd4dbc3726ba756d29d4f9 | MATLAB | 17,454 | 435 | function data_analysis_software()
clear global;clear;clc;
%%
warning off
addpath(strcat(pwd,'\load_files'))
addpath(strcat(pwd,'\load_files\tiff'))
addpath(strcat(pwd,'\load_files\storm'))
addpath(strcat(pwd,'\load_files\tracks'))
addpath(strcat(pwd,'\load_files\image'))
addpath(strcat(pwd,'\loc_analysis'))
... |
87e3ea155e2ca54077055d2e8511ae83d9f699491b22e4145e287ce73e99ac26 | MATLAB | 17,475 | 534 | function BCCT_CON_Surf_GUI_freesurfer
D.fig = figure('Name','Brain Covaraince Connectivity(Seed to Whole Brain, Surfacce-based, (standard Freesurfer process))',...
'units','normalized',...
'menubar','none',...
'numbertitle','off',...
'color',[0.95 0.95 0.95],...
'posi... |
5893b56406cbbc23b956360a454150c1e6e843e4efd752ab6f31277fc822863a | MATLAB | 17,526 | 427 | % NOTE: This script is for regenerating figure_source_data.mat from the raw
% pipeline. It requires access to the lab network drive (S:\Roy) and raw
% .mat files from the imaging pipeline.
%
% For figure reproduction, this script is NOT needed. Instead, download
% figure_source_data.mat from Zenodo and place it in data... |
5b65a3ea23abd85dbbfd29fee9d8f2e77b367e527e0731f92559e04375751c1e | MATLAB | 17,594 | 440 | function [resels, reselspvert, edg] = SurfStatResels( slm, mask );
%Resels of surface or volume data inside a mask.
%
% Usage: [resels, reselspvert, edg] = SurfStatResels( slm [, mask] )
%
% slm.resl = e x k matrix of sum over observations of squares of
% differences of normalized residuals along eac... |
2d700899e38811ccc340f77c77c1d7b9385790969dd1be2f2d686f220bf5cfa8 | MATLAB | 17,692 | 406 | classdef NetworkAtlasFuncConn < nla.inputField.InputField
%NETWORKATLAS Network atlas, contains network + ROI details
properties (Constant)
name = 'net_atlas'
disp_name = 'Network atlas/Functional connectivity';
end
properties
net_atlas = false
func_conn = false
... |
18319abbcd3568537a680e414896bb7010fc6726f5ead9b6a6e96801f27167ca | MATLAB | 17,728 | 573 | function BCCT_ShowMap_GUI
D.fig = figure('Name','Showing TFRZP maps',...
'units','normalized',...
'menubar','none',...
'numbertitle','off',...
'color',[0.95 0.95 0.95],...
'position',[0.2 0.3 0.6 0.4]);
movegui(D.fig,'center');
dires = which('BCCT_ShowMap_GUI.... |
eec7e8fe6bc8b060b8b09ff6d8a54d8abec12626e7b2245add637606b5c355bf | MATLAB | 17,800 | 440 | function AS_MatrixShowFinalResPermVer(enhanind)
if nargin<1
enhanind = [];
end
[mpat,mnam,mext] = fileparts(which('AS_MatrixShowFinalResPermVer.m'));
load(fullfile(mpat,'gray.mat'))
colormapshow0 = AFNICOLORMAP(128);
% colormapshowO = AFNICOLORMAP(12);
colormapshow(1:64,:) = colormapshow0(1:64,:);
colormap... |
dcf4cf549c0332ea700e4b01b2f49b147be624acd95419ca1aa603380f55a23b | MATLAB | 17,821 | 440 | function AS_MatrixShowFinalResPermVer_bat(indir,outdir,enhanind)
if nargin<3
enhanind = [];
end
[mpat,mnam,mext] = fileparts(which('AS_MatrixShowFinalResPermVer.m'));
load(fullfile(mpat,'gray.mat'))
colormapshow0 = AFNICOLORMAP(128);
% colormapshowO = AFNICOLORMAP(12);
colormapshow(1:64,:) = colormapshow0(1... |
055230d1384c254ddb2897462d3b177ebf903159e675c28e10b6a137bc561e51 | MATLAB | 17,830 | 575 | function BCCT_showgcmap_subfun(Parameter)
[Vbg Dbg] = Dynamic_read_dir_NIFTI(Parameter.bgmap);
[pth nam ext] = fileparts(Parameter.bgmap);
if strcmp(nam,'mni_icbm152_t1')
D_BG = reshape(Dbg,Vbg.dim);
D_BG(isnan(D_BG)) = 0;
D_BG(D_BG<30) = 30;
D_BG(D_BG>85) = 85;
D_BG = (D_BG-30)/55*0.99+0.005;
else
... |
cb3e1cb8bcbed996e91e9b47affb8acc097127dd0494b5c01b16c06e38de6a82 | MATLAB | 17,857 | 577 | function BCCT_showgcmap_subfun2(Parameter)
[Vbg Dbg] = Dynamic_read_dir_NIFTI(Parameter.bgmap);
[pth nam ext] = fileparts(Parameter.bgmap);
if strcmp(nam,'mni_icbm152_t1')
D_BG = reshape(Dbg,Vbg.dim);
D_BG(isnan(D_BG)) = 0;
D_BG(D_BG<30) = 30;
D_BG(D_BG>85) = 85;
D_BG = (D_BG-30)/55*0.99+0.005;
else... |
7b8423bb707f1cb3dc8e1a3516bac800e10e8d9191670677feec0b01804e548e | MATLAB | 17,874 | 394 | function BCCT_CaSCN_computemain(Parameter)
pathfiles = which('BCCT.m');
[path nam ext] = fileparts(pathfiles);
Outputdir = Parameter.Outputdir;
RealCompPara.Outputdir = Outputdir;
Inputdir = Parameter.Inputdir;
RealCompPara.Inputdir = Inputdir;
SeedROItype = Parameter.SeedROItype;
RealCompPara.SeedROItype = See... |
fee6a334a7a5a9610ca863d9380459da241fc9365ed6405b977685c303cda32b | MATLAB | 17,918 | 429 | function [map,num,typ] = brewermap(N,scheme)
% The complete selection of ColorBrewer colorschemes (RGB colormaps).
%
% (c) 2015 Stephen Cobeldick
%
% Returns any RGB colormap from the ColorBrewer colorschemes, especially
% intended for mapping and plots with attractive, distinguishable colors.
%
% Syntax (basic... |
bc1b82362bedbd3db1f69cdda1178ab2a8b843c604b2ce6bb3b2e75a49a04819 | MATLAB | 17,944 | 388 | function [dPCAmodel, dPCAprojTrain, dPCAprojTest] = computedPCA(obj, dPCAOpt, processingOpt, trainOpt, testOpt, visOpt)
% COMPUTEDPCA Fit dPCA on training data and project train/test sets.
%
% -------------------------------------------------------------------------
% SYNTAX
% [dPCAmodel, dPCAprojTrain, dPCApro... |
22208942a78407dd168c4623e5da66c1dca845c6853fa1b6415bb58046baa998 | MATLAB | 17,967 | 414 | %% run_behavioral_association_analysis.m
% Association between parcel-wise/cluster-wise SF coupling metrics and
% developmental assessment scores while adjusting for family and maternal
% covariates.
%
% This script is a cleaned, public-release template for the analyses used to
% test associations between brain metrics... |
4fec8497adfa345cb9e23dab0f58bebe918dc6679d2500930407ef1a0a3894b7 | MATLAB | 17,983 | 424 | function varargout = process_nst_detect_bad( varargin )
% @=============================================================================
% This function is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2016 University of Southern California & McGill University
% This so... |
32ae088b3a54b5fa57406ab2ab482b7f460f7570a3b1c1eae622b8252206fd0a | MATLAB | 18,187 | 495 | function data = lvm_import(filename,verbose)
%LVM_IMPORT Imports data from a LabView LVM file
% DATA = LVM_IMPORT(FILENAME,VERBOSE) returns the data from a LVM (.lvm)
% ASCII text file created by LabView.
%
% FILENAME The name of the .lvm file, with or without ".lvm" extension
%
% VERBOSE How many messages to d... |
47dc6b6208de5b8cd211e93fd971426cb61adca43989de42793e5895dbe4500e | MATLAB | 18,215 | 421 | function loc_list_plot(data)
if isempty(data)~=1
fig = figure();
set(gcf,'name','Localizations List (2D)','NumberTitle','off','color',[0.1 0.1 0.1],'units','normalized','position',[0.3 0.15 0.4 0.7],'menubar','none','toolbar','figure');
defaultToolbar = findall(fig,'Type','uitoolbar');
a = ... |
1ad2928d191f9269a5bc2da0776cbec70b5e44dfa9de324df54cd91bbe5abff2 | MATLAB | 18,219 | 386 | function training_decoding(subject,settings)
%--------------------------------------------------------------------------
% Till Habersetzer, 27.01.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% Description:
% Performs subject-level training and evaluation of a neural decoding
... |
6e694edd52990309702b0644243c682b4742053ddcb990aafb6efdaf28b39fec | MATLAB | 18,229 | 564 | function BCCT_MOD_Surf_GUI_freesurfer
D.fig = figure('Name','Modulate effect of Covaraince Connectivity(Seed to Whole Brain, Surfacce-based, (standard Freesurfer process))',...
'units','normalized',...
'menubar','none',...
'numbertitle','off',...
'color',[0.95 0.95 0.95]... |
e163539252a67419db25a3f9de8d0c00108ec1fafbd3e7aa88c2e944a9b9f1fe | MATLAB | 18,230 | 399 | % ------------------------------------------------------------------------
% This script loads and processes EEG and respiration phase data from three
% sources: original, new, and simulated. It bins EEG amplitude according
% to Park et al. (2020) binning method, and generates permutation
% distributions. Normalized ve... |
a7285c7e888d5bee2240ddd051e3bac04b5b0c041752773a82e82953d3fdf163 | MATLAB | 18,543 | 615 | %% Convert SPM files to Fieldtrip raw
cd('D:\OPM - Pilot 2')
% Convert SPM data object to raw Fieldtrip format
data_orig = fDB.ftraw;
data_orig.grad = extractGradSelectedSensors(fDB);
data_orig_heart = fDH.ftraw;
data_orig_heart.grad = extractGradSelectedSensors(fDH);
%% Load required toolboxes incl. clean Fieldtri... |
ffea7d4087535c827e770d872e548c2da203c2f6449a8fda7c1f586bd1090663 | MATLAB | 18,626 | 520 | % internal function
% 'xform_nii.m' is an internal function called by "load_nii.m", so
% you do not need run this program by yourself. It does simplified
% NIfTI sform/qform affine transform, and supports some of the
% affine transforms, including translation, reflection, and
% orthogonal rotation (N*90 de... |
9111971fdd93a79059e601d02d092f9878fe7011be4c97295a49243c8f76a2b3 | MATLAB | 18,628 | 521 | % internal function
% 'xform_nii.m' is an internal function called by "load_nii.m", so
% you do not need run this program by yourself. It does simplified
% NIfTI sform/qform affine transform, and supports some of the
% affine transforms, including translation, reflection, and
% orthogonal rotation (N*90 ... |
4b8b3549a726b0f8e2f2a1b5c5fd44ddbc93e46d0d16381a3d897365fbfb4a34 | MATLAB | 18,974 | 585 | %% Overview
% The main goal of this pipeline is to simulate a source in the brain in
% presence of the cardiac field artefact (CFA), i.e. the electromagnetic
% signal from the heart. We validate whether the OP-MEG recordings can be
% corrected for the CFA and whether the brain source is retained. For this
% a dipole f... |
ff504eeb8733b42e2895842fe7fbc64a995f234cc6ab72d11797af445545cc88 | MATLAB | 19,096 | 523 | %%%% EXTERNAL FUNCTION
% function taken from the fastICA package
% complete software may be downloaded from http://research.ics.tkk.fi/ica/fastica/
function [Out1, Out2, Out3] = fastica(mixedsig, varargin)
%FASTICA - Fast Independent Component Analysis
%
% FastICA for Matlab 6.x
% Version 2.3, July 27 2004
% ... |
6670b3de15400e2cf0497901e9db0d6c28eb362efda5c62b1091a3c6608bbbbf | MATLAB | 19,194 | 542 | classdef parcellation
% Class-based representation of parcellations
%
% This class is designed to facilitate working with parcels and standard masks
% Key tasks are
%
% - Reading in a parcellation and matching it to a standard mask
% - Reshaping between volume and matrix representations of the parcellation
% -... |
ff4fef1f11d3c30a62eb107bf921ce37f2dcebdf3caee5d487e89b6818d37c16 | MATLAB | 19,297 | 413 | function [ H, P_binary, P_ROIs, MATF, cor_mat ] = static_FC_MEG_LBPD_D( S, data )
% It calculates static FC by computing Pearson's correlations of the
% envelope of the data given in input. It does that independently for each
% condition.
% Additionally, it can perform contrast between two conditions, plot the FC
% ma... |
0cf99419b9b5c8bde956ec172a0279eb33bc19e257e13a708ae4229308b00e78 | MATLAB | 19,316 | 397 | function EEG_regs_conv = c_eeg_power_regressors(parameters, delete_files)
%% EEG_regs_conv = e_eeg_power_regressors(mainpath, subject, delete_files)
%mainpath = '/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts/scriptTemplates/..';
tc_struct2ws('caller', parameters.main);
%% load parameters
tc_struct2ws('... |
1542dd948790988111127a8a9aedbde2aa9b843e6fd1d845bbb4e6a14e905d4c | MATLAB | 19,402 | 453 | function spt_layover_module_colocalization()
figure();
set(gcf,'name','Single Particle Tracks Colocalization','NumberTitle','off','color','w','units','normalized','position',[0.2 0.2 0.4 0.7],'menubar','none','toolbar','none','WindowButtonMotionFcn',@mouse_move,'WindowButtonDownFcn',@mouse_down,'windowkeypressfcn',@k... |
efafe197e65074d04e0a2caa0fbf6700ab652759dd4e600154ba87d25799f2e1 | MATLAB | 19,403 | 531 | function ShowResRadarSep_in(Outputdir)
% Outputdir = uigetdir(pwd,'Output Directory Selection');
OutputdirFig = [Outputdir,filesep,'ResRadarFigure'];
if isempty(dir(OutputdirFig))
mkdir(OutputdirFig)
end
% Outputdir = 'D:\testdata\AS_sub2cor1\testdata\';
LabedValmat = fullfile(Outputdir,'LabedVal.mat');
Rea... |
c4e23f741b45f791bb04124408a44074e7c3765aac41f7457103ec6528726a3e | MATLAB | 19,644 | 420 | %--------------------------------------------------------------------------
% Till Habersetzer, 24.06.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% Group Analysis and Visualization of Dipole Fits
%
% This script performs a group-level analysis of MEG dipole fitting
% results ... |
998b747537d748f8bb0f995ee4616125ccde4ab55544dff130ea6f419b1ec1d5 | MATLAB | 19,785 | 756 | function SurfStatWriteVol( d, Z, T );
%Writes volumetric image data in MINC, ANALYZE, NIFTI or AFNI format.
%
% Usage: fmris_write_image( d [, Z, T] ).
%
% d.file_name = file name with extension .mnc, .img, .nii or .brik as above
% Z = vector of slices.
% T = vector of times.
% If Z and T are o... |
c3a618162713f773d64dafe55d09c5393b7f876e56584b2f3662a932fa0ba493 | MATLAB | 19,815 | 615 | function BCCT_CaSCN_Surf_GUI_freesurfer
D.fig = figure('Name','Brain Covaraince Connectivity(Seed to Whole Brain, Surfacce-based, (standard Freesurfer process))',...
'units','normalized',...
'menubar','none',...
'numbertitle','off',...
'color',[0.95 0.95 0.95],...
'po... |
0a3ee430cd3a3aa548dea8299dd8c3f04ceeaae534658b1ba5180816349b176f | MATLAB | 20,263 | 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])
%
% ... |
b3db0b26ee491b9fb9a50abc5a3e740a77b582224a9f7c781f9cc331784134ae | MATLAB | 20,462 | 504 | function AS_MatrixShowFinalResPerm(enhanind)
if nargin<1
enhanind = [];
end
[mpat,mnam,mext] = fileparts(which('AS_MatrixShowFinalRes.m'));
load(fullfile(mpat,'gray.mat'))
colormapshow0 = AFNICOLORMAP(128);
% colormapshowO = AFNICOLORMAP(12);
colormapshow(1:64,:) = colormapshow0(1:64,:);
colormapshow(66:12... |
73aca5b0a7cadcecd33c626fa96efb3293865af96412ef8eec4d536afe1755f2 | MATLAB | 20,572 | 419 | %% Data Construction
% Load the data
[file,path] = uigetfile('*.mat','Select the file you want to load'); % Open a dialog so you can specify which file you want to load
selectedfile = fullfile(path,file); % Create the name for the file to load
load(selectedfile); % Load the file
% Clear up the work space
clear fi... |
261ea0d99af058b9e4523bb9eb5a495ec7d1fc5364ff88e68b284c6a578691c6 | MATLAB | 20,797 | 613 | %% HC
%% =========================
% A) Midfrontal–Lateral PFC [NO exclusion]
% Go = mean(contra, ipsi); NoGo = nogo
% width = 50 mm, Arial 9 pt (no bold), save as SVG
%% =========================
% If results_dir is not defined, use the current folder:
% results_dir = pwd;
% -------- 1) Organize data to plot: T... |
481e8137f0951085827aebb9e70f0b83997ef65a44eb042ae42ba8b110dcd58e | MATLAB | 21,012 | 653 | %% make grand average ERP
if ~exist('mainpath','var')
clearvars
% current working directory needs to be /path/to/scripts
mainpath = pwd;
else
clearvars -except mainpath
end
addpath([mainpath filesep 'toolboxes' filesep 'fieldtrip'])
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
addpath... |
e5ca64242ec5d66e7cb8374d54093272b42fd84ac7c1fb2f80bab569f2b234f8 | MATLAB | 21,034 | 466 | %%% READS EYE TRACKING DATA AND OUTPUTS OVER TRIAL HEATMAP %%%
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
diffFct=@(x,y) sqrt((y(:,1)-x(:,1)).^2+(y(:,2)-x(:,2)).^2);
subjDirOld=subjDir;
workingDirOld=workingDir;
%%
if computeForMultipleSubjects(1)~=0 % if multiple subjects are asked to be computed
... |
a8dfde0288449f0228a855c8ebbca0d6ecd03e7a0c554227b3cdcc7eedf6e507 | MATLAB | 21,257 | 616 | function [map1,act_x,act_y,act_t,quivers_X,quivers_Y,quivers_vx,quivers_vy,CVmap,v,vout,quivers_Xout,quivers_Yout, quivers_vxout,quivers_vyout,onedev,vari,SE]...
= cvmap(pix,framerate,images,mask,outs,velminin,velmaxin,velalgo,MINt,MAXt,winsize,before,wint,repolopt,repolap,tfilt,usespline,splineN)
% Function fo... |
630fbe88a20576de50381db6a2b94d6dc2ff72dd66806797e5ffbda1612d90df | MATLAB | 21,327 | 501 | %%
if ~(exist('mainpath','var') && exist('thisSubject','var'))
clearvars
% current working directory needs to be /path/to/scripts
mainpath = pwd;
thisSubject = 'S1';
else
clearvars -except mainpath thisSubject
end
addpath([mainpath filesep 'fmriRegAnalysis'])
addpath([mainpath filesep 'toolboxes' f... |
0b359dffc835486726a1d14080b2ccd851eb4364da9cc9a208a50b0675a39627 | MATLAB | 21,335 | 468 | classdef BstHelperTest < matlab.unittest.TestCase
properties
tmp_dir
end
methods(TestMethodSetup)
function setup(testCase)
tmpd = tempname;
mkdir(tmpd);
testCase.tmp_dir = tmpd;
utest_bst_setup();
end
end
methods(... |
06b3748bdaf7d087e88d24708e5104477268b04c6a55a8283825d3474330fcb8 | MATLAB | 21,582 | 586 | %%%%%%%%%
% This code contains various plot and analysis that we tried after GED
%%
addpath('/projects/MINDLAB2023_MEG-AuditMemDement/scripts/chiaramalvaso/GED_TSA2021');
addpath('/scratch7/MINDLAB2023_MEG-AuditMemDement/chiaramalvaso/GED_TSA2021');
%% *** START UP FUNCTIONS.. (LBPD_startup_D) ***
%starting up some f... |
2331be04947f81e59162e73c8bb5c1cce1ed8edbd5d1ad756403d41f538ee97e | MATLAB | 21,691 | 569 | % Stats and figures
% Other m-files required:
% EEGLAB toolbox: https://github.com/sccn/eeglab
% /private/doPermTest2.m
% /private/formatNBP.m
% /private/makefigure.m
% /private/subtightplot.m
% /private/figset.m
% Author: Cameron Hassall, Department of Psychology, MacEwan University
% email address: hass... |
1aad77ff48076cbfaafb4fe6e05a13e66dfd08774c17b0d6abd7e2ae1ed83c17 | MATLAB | 22,092 | 586 | function varargout = process_nst_cpt_fluences( varargin )
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2013 Brainstorm by the University of Southern California
% This sof... |
125438c55d22a9fb5a6f789c696e805e71c2e43ec95493ddb68549080c35aa77 | MATLAB | 22,146 | 677 |
function [Pool,Part,QV] = check_pooled_error(S);
% Pedagogical script to illustrate assumptions about error term(s) in
% repeated-measures multi-factorial ANOVAs performed on many observations
% (eg voxels in fMRI). Requires SPM8+ on path.
%
% Based on Henson & Penny (2003) Tech Report ("H&P03"):
% http://... |
fadef0bbddc98a6708c71c3873ca47082e0e9fbb775a723273928d8a3ea2821f | MATLAB | 22,264 | 444 | classdef TestPool < nla.DeepCopyable
%TESTPOOL Pool of edge and net tests to be run
properties
edge_test = false
net_tests = {}
data_queue = false
end
properties (Constant)
correlation_input_tests = ["kolmogorov_smirnov", "students_t", "welchs_t", "wilcoxon"]
en... |
ef5c942035a98877d746e75349f4d909c3c11af25cd62052c5518209d307cf9c | MATLAB | 22,357 | 379 | % current working directory needs to be /path/to/scripts
mainpath= pwd;
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
addpath([mainpath filesep 'fmriRegAnalysis'])
%%
hemis = {'lh', 'rh'};
if ~(exist('freqs','var'))
freqs = {'alpha', 'gamma'};
end
add_fname_freq = join(freqs, '_');
add_fname_fre... |
93607c3dcb32f932b0632d9b512369a9b0e945c7e71b4002425a8b1730edbf06 | MATLAB | 22,407 | 675 | function dimord = getdimord(data, field, varargin)
% GETDIMORD
%
% Use as
% dimord = getdimord(data, field)
%
% See also GETDIMSIZ, GETDATFIELD
% Please note that this function is called from many other FT functions. To avoid
% unwanted recursion, you should avoid (where possible) calling other FT functions
% insid... |
1711dd8bbf76ef372a976952e73921863098abe21d08f4262b0e9dff32911c14 | MATLAB | 22,423 | 396 | %% setup program
close all
clear
% current working directory needs to be /path/to/scripts
mainpath = pwd;
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
addpath([mainpath filesep 'fmriRegAnalysis'])
%%
% for binning = {'percentiles', 'binned'}
% clearvars -except binning
% binning = binning{1};... |
b50ed6f6c0487825e734a0593e501040563972f9c15c010de4016dbea514647d | MATLAB | 22,673 | 434 | function BCCT_CaSCN_stat_mainfunc(Parameter)
Outputdir = Parameter.Outputdir;
Inputdir1 = Parameter.Inputdir1;
Inputdir2 = Parameter.Inputdir2;
RealComp1 = load(fullfile(Inputdir1,'RealCompPara.mat'));
RealComp2 = load(fullfile(Inputdir2,'RealCompPara.mat'));
if ~strcmp(RealComp1.RealCompPara.mod,RealComp2.RealCompPar... |
ae44bd5b3b69a4b9c2f258321d54cc7f726b41a094dad8baecfed5344fe692f4 | MATLAB | 22,835 | 521 | function [cell,module,mc,trec,Forcec,xrefc,xsubc,cengc,ctheta,cellpos,polyrate,gactin,trac,aflow,modnum,sdist,mdist] =...
cms2Dv1_0(mpool,cpool,totact,maxpoly,kmod0,kcap,lcell,lmin,Kcell,nc,Fm,vu,kon,koff,Kc,Fb,Ksub,tint,durr,dynamicPlot,savedir,savename,runnum)
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
9d123429db3526e944937ac8fb6d48ad019fc1506de574b9922df29d401b48ca | MATLAB | 22,917 | 460 | classdef InstallSourceTest < matlab.unittest.TestCase
properties
tmp_dir
end
methods(TestMethodSetup)
function setup(testCase)
tmpd = tempname;
mkdir(tmpd);
testCase.tmp_dir = tmpd;
end
end
methods(TestMethodTeardown)
func... |
e388b2ffa2d93bb80efef7a4e7ef01116c7a3a942bd5ef7f193a565bcd279d27 | MATLAB | 22,985 | 505 | classdef Behavior < nla.inputField.InputField
properties (Constant)
name = 'behavior';
disp_name = 'Behavior';
end
properties
behavior_filename = false
behavior_full = false
behavior = false
behavior_idx = false
covariates = false
covariat... |
d6bca56fd6858151cf23ec709a4075fa26357ede639d0f87ddcd117f16de3f25 | MATLAB | 22,995 | 559 | function [ zmin, zmax] = ft_getminmax(cfg, data)
%function [cfg] = ft_singleplotTFR(cfg, data)
% FT_SINGLEPLOTTFR plots the time-frequency representation of power of a
% single channel or the average over multiple channels.
%
% Use as
% ft_singleplotTFR(cfg,data)
%
% The input freq structure should be a a time-frequ... |
94a7a8b782aadce35a7b82485f14b4d16dab80ab1c1b2b62c02c96179f7e0f0e | MATLAB | 23,103 | 577 | function AS_MatrixShowFinalResPermVer_bat_GUI(indir,outdir,enhanind,Coltype,PVALT,Pvalused,orders)
[mpat,mnam,mext] = fileparts(which('AS_MatrixShowFinalResPermVer_bat_GUI.m'));
load(fullfile(mpat,'MatColormap','mycolormap.mat'));
load(fullfile(mpat,'gray.mat'))
colormapshow0 = AFNICOLORMAP(128);
if Coltype==1
... |
2de840de7ceffd50b75b436c379cec9058bd0f8ba96b2d74410c72b7430ebf0e | MATLAB | 23,119 | 711 | % HYDRA SOLVER
% Version 1.0.0 --- January 2018
% Section of Biomedical Image Analysis
% Department of Radiology
% University of Pennsylvania
% Richard Building
% 3700 Hamilton Walk, 7th Floor
% Philadelphia, PA 19104
%
% Web: https://www.med.upenn.edu/sbia/
% Email: sbia-software at uphs.upenn.edu
%
% Cop... |
bf9197c2b1d6f39f007102b6b2441cfa4a50344f09f96c99b594478c84ca86af | MATLAB | 23,161 | 897 | function b = generative_model(A,D,m,modeltype,modelvar,params,epsilon)
% GENERATIVE_MODEL Run generative model code
%
% B = GENERATIVE_MODEL(A,D,m,modeltype,modelvar,params)
%
% Generates synthetic networks using the models described in the study by
% Betzel et al (2016) in Neuroimage.
%
% Inputs:
% ... |
28198911c796b3407115cd3e7a10da796bba9eef6d1000e26ce1f464db5f1df4 | MATLAB | 23,297 | 574 | function AS_MatrixShowFinalResPermVer_other_GUI(Pval,outdir,enhanind,Coltype,PVALT,Pvalused,orders)
[mpat,mnam,mext] = fileparts(which('AS_MatrixShowFinalResPermVer_bat_GUI.m'));
load(fullfile(mpat,'MatColormap','mycolormap.mat'));
load(fullfile(mpat,'gray.mat'))
colormapshow0 = AFNICOLORMAP(128);
if Coltype==1
... |
9813ee32d13bd610bd1d5ef66addf4256cccdc86ed3f89157a6deb6caf288bab | MATLAB | 23,429 | 600 | function varargout = panel_nst_fluences(varargin)
% panel_nst_fluences Edit ROI for fluences computation.
% USAGE: bstPanel = panel_nst_fluences('CreatePanel', OPTIONS) : Call from the interactive interface
% bstPanel = panel_nst_fluences('CreatePanel', sProcess, sFiles) : Call from the process ... |
5f861588ca8c20e945041068ea2cf4f55f4a17113b8af4c60960f7617cb63c45 | MATLAB | 23,572 | 554 | function DrawCombined_AllInOne2()
%% ==============================================================================
% All-in-one Figure (Width <= 190mm, Right margin = 4mm) [SVG]
% Row 1: HC -> WAIC + All Cues + Go Cues
% Middle: shared legend (behavior lines + M3c prediction shading)
% Row 2: OCD -> WAIC + Al... |
70a816ed91f5309c5a621ceb0277410d1cb0fe585bb35b7f965a764c334db9b3 | MATLAB | 23,746 | 719 | %% Overview
% The main goal of this pipeline is to simulate whether the proposed method
% for cardiac field artefact (CFA) correction is sensitive to simple
% mismatch in torso geometry used by the forward model.
%
% Starting from the original cardiac source misplacement simulation, this
% version evaluates whether cor... |
55d86bb04cc174e583f8c9dac2a1ff24b976c4f8c5c37cea5de88475eddb76d7 | MATLAB | 23,872 | 607 | %--------------------------------------------------------------------------
% Till Habersetzer, 01.07.2025
% Communication Acoustics, CvO University Oldenburg
% till.habersetzer@uol.de
%
% Description:
% This script performs a comprehensive analysis and visualization of MEG
% cross-correlation data. It focuses on... |
7ed31bebbcf541ddbf75c4a3a0601a1d5019c599f3fabcff14f32b7a984b1e79 | MATLAB | 23,923 | 635 | % HYDRA
% Version 1.0.0 --- January 2018
% Section of Biomedical Image Analysis
% Department of Radiology
% University of Pennsylvania
% Richard Building
% 3700 Hamilton Walk, 7th Floor
% Philadelphia, PA 19104
%
% Web: https://www.med.upenn.edu/sbia/
% Email: sbia-software at uphs.upenn.edu
%
% Copyright ... |
b4a80f13e5e87962fe16f9646718357ecce4ae15d74fd7cd9d3ae99910484fc1 | MATLAB | 24,128 | 490 | function BCCT_WTA_Stat_main_ver2(Parameter)
% Face a problem for the number of connects
% In later version, we would like to deal with it for the small ROM
% computer.
% Change this value to speed up when you have large ROM
Nslice = 1000;
%
Outdir = Parameter.Outdir;
Indir1 = Parameter.Input1;
Indir2 = Par... |
c57d860d84f9e1c276d8dd2642112d8b7fa6719d4c1248f27efc02e5da7ff80d | MATLAB | 24,305 | 631 | function varargout = process_nst_mbll( varargin )
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2013 Brainstorm by the University of Southern California
% This software i... |
9a1c81fd36014759282e8c579a4badd4b1c000e09fcb00ac611e3584f7922ec9 | MATLAB | 24,331 | 742 | %% Overview
% The main goal of this pipeline is to find to perform co-registration of
% the volume conduction model of the torso and the OP-MEG sensor locations
% (as tracked via retroflective markers).
% For this purpose, the 3D optical scan of the participant is aligned with
% volume conduction model, by selecting fi... |
5f477ca80c11b4f0acf103c0f4a1b75365b0f322c0fd101705a2712feb399ba2 | MATLAB | 24,625 | 680 | function varargout = process_nst_import_head_model( varargin )
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2013 Brainstorm by the University of Southern California
% Th... |
62a9d8b6a32368cd0584e6e0aa5d3c0bc28316fae81f703a48bf26413f4e58f6 | MATLAB | 24,630 | 533 |
clear variables
addpath(genpath('/Volumes/Samsung_T5/Milan_DA/OS_ephys_da/CorticoHippocampal'))
addpath ('/Volumes/Samsung_T5/Milan_DA/OS_ephys_da/ADRITOOLS')
cd('/Volumes/Samsung_T5/Milan_DA/RGS14_Ephys_da/Data_RGS14_Downsampled_First_Session')
% cd('/Volumes/Samsung_T5/Milan_DA/RGS14_Ephys_da/Data_RGS14_Downsampled'... |
d6ea6a36b11fc2b547d57061bdf1e8b088e245348ea40607e426bf1105936117 | MATLAB | 24,850 | 538 | classdef NLA_GUI < matlab.apps.AppBase
% Properties that correspond to app components
properties (Access = public)
NetworkLevelAnalysisUIFigure matlab.ui.Figure
FileMenu matlab.ui.container.Menu
OpenpreviousresultMenu matlab.ui.container.Menu
GridLay... |
dacce0129b4ec7357f4880a2352753afbeaafbcdf4975ef7f12c036382a92f20 | MATLAB | 25,123 | 672 | %%
% current working directory needs to be /path/to/scripts
mainpath = pwd;
addpath([mainpath filesep 'toolboxes' filesep 'fieldtrip'])
addpath([mainpath filesep 'toolboxes' filesep 'tc_functions'])
addpath([mainpath filesep 'scriptTemplates'])
ft_defaults
sigmoidFct=@(x,k) 1./(1+exp(-k.*x+k/2));
% puts all workspace... |
a5a10d8e4cd4f1a37b6ebbf75ff52485fad43eb7c73acdb6d98c11ab50b4fdfc | MATLAB | 25,703 | 717 | legend(app.UIAxes,'off')
nroi = size(app.dFC_project.dFC,1);
default_colors = transpose([(257-[1:256])/256; [1:128]/128,(129-[1:128])/128; [1:256]/256]);
default = [0 0.4470 0.7410;
0.900 0.150 0.0980;
0.9290 0.6940 0.1250;
0.4940 0.1840 0.5560;
0.2660 0.6740 0.4880;
0.3010 0.7450 0.9330;
0.6350 0.0780 0.1840;
0 0.44... |
434dfff0f37bdc1ba762314153aacab5ea55148f3c50e979fd8ff110444ee02c | MATLAB | 25,725 | 685 |
function [Zmat, Bmat, pZmat, pBmat, aY, X0r] = rsfMRI_GLM(S);
% [Zmat, Bmat, pZmat, pBmat, aY, X0r] = rsfMRI_GLM(S);
%
% Function (using SPM8 functions) for estimating linear regressions
% between fMRI timeseries in each pair of Nr ROIs, adjusting for bandpass
% filter, confounding timeseries (eg CSF) and (SVD of) ... |
fd1d745e9354763799497930ffd178cb7c8b01d5fbaa09ea81108f385db258cf | MATLAB | 26,186 | 841 | %% Overview
% The main goal of this pipeline is to simulate a cardiac field artefact
% (CFA), i.e. the electromagnetic signal from the heart and to illustrate
% how this manifests on OP-MEG channels on the scalp. Moreover, we validate
% whether the OP-MEG recordings can be corrected for the CFA. Specifically, a
% dipol... |
0e341b7004be9e42ed396020afd77f47e7a8d795a301558079e530783bc2adb6 | MATLAB | 26,666 | 503 | classdef ChordPlot < handle
%CHORDPLOT - Class to construct and display chord plots for network and edge tests
%
% obj = ChordPlot(network_atlas, axes, axis_width, plot_matrix, varargin)
% network_atlas - network atlas object used
% axes - the axis that the chord will be plotted in/on
% axis_width - the height ... |
a47e1e00e57fd5fac495202804e1308812452ca1ff4bfc92caf957b3eb8641be | MATLAB | 26,974 | 918 | function MAP4SL(cfg,filename,outputfolder)
% MAP4SL - Multiband Artefact Probe for Slice Leakage
%
% MAP4SL is a Matlab bases tool which is designed to identify the effect of
% an artefact in MRI data on other areas depending on the slice leakage in
% MR multiband EPI functional images.
%
% This tool calculates the... |
9694bf213d2524b89f0173da55a7fb3c6f0625a8df3267169116129293e5f0ba | MATLAB | 27,003 | 707 | function varargout = process_nst_glm_fit( varargin )
% process_compute_glm: compute the glm : find B such as Y = XB +e with X
%
% OlS_fit use an ordinary least square algorithm to find B : B= ( X^{T}X)^{-1} X^{T} Y
% AR-IRLS : Details about AR-IRLS algorithm can be found here :
% http://www.ncbi.nlm.nih.gov/pmc/art... |
a194973ee042a8aabd128ba660b2e8f960b9a20933de2246562737f33327da28 | MATLAB | 27,042 | 907 | %%%% EXTERNAL FUNCTION
% function taken from the fastICA package
% complete software may be downloaded from http://research.ics.tkk.fi/ica/fastica/
function [A, W] = fpica(X, whiteningMatrix, dewhiteningMatrix, approach, ...
numOfIC, g, finetune, a1, a2, myy, stabilization, ...
epsilon, maxNumIterations,... |
6af7bfa8891c9b3660aa8874818ac83678c93241c7941aacd50eafaf9b4d1833 | MATLAB | 27,133 | 723 | %% Overview
% The main goal of this pipeline is to simulate whether the proposed method
% for cardiac field artefact (CFA) correction is sensitive to mislocation
% of the dipole used to model the heart's electromagnetic field.
%
% Moreover, we test whether using two dipoles instead of one to model the
% heart, can corr... |
4aa765f7621b2307312ad482112f5541969e4f4a38e49359f5bd9403ade1b916 | MATLAB | 27,233 | 868 | %% cue
%% Two-condition plot: permutation results (Arial 9pt + 50 mm + no legend + 1000 dpi)
% Required variables (already available):
% TF1, TF2, MFchans, iFreq, freq.time, iTime, MFtime
% -----------------------------
% 0) Global font settings (recommended)
% -----------------------------
set(groot, 'defaultAxesFont... |
82dc8789d0a2bd5b0564f794e23a9434b7b89ee63cb057b07dbb9e15f9cfb469 | MATLAB | 27,286 | 769 | function [ peak_threshold, extent_threshold, ...
peak_threshold_1, extent_threshold_1, t, rho ] = ...
stat_threshold( search_volume, num_voxels, fwhm, df, p_val_peak, ...
cluster_threshold, p_val_extent, nconj, nvar, EC_file, expr, nprint );
%Thresholds and P-values of peaks and clusters of random field... |
d4c8b0f2c9d5aec4b850284895669b48364d07822d34c85ea1ed0c9b2650f478 | MATLAB | 27,360 | 546 | function BCCT_CaSCN_Surf_compute_freesurfer(Parameter)
mfilenam = which('BCCT.m');
[pat nam ext] = fileparts(mfilenam);
Outputdir = Parameter.Outdir;
Indir = Parameter.Indir;
marker = Parameter.markerdir;
Marker = {marker,['r',marker(2:end)]};
FSlab = Parameter.FSlabs;
if FSlab(1)
FStype = 'fsaverage';
... |
bda27673fcbfa07da98e10ce8b118aa2f728a8c2941229a315b51613f59e5713 | MATLAB | 27,525 | 718 | %%%%%%%%%%%%%%%%%%%%% Vectorize all trials at once %%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% =========================================================================
% Trial-level midfrontal theta POWER + Inter-channel Phase Co... |
717d9f2bd10466e1f86fb4ed9bb6cda74ffb41f492bcd6c7075bade8a489dbc9 | MATLAB | 28,188 | 746 | function varargout = process_nst_compare_montage( varargin )
% @=============================================================================
% This function is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2016 University of Southern California & McGill University
% Th... |
0b172febab5a5b40228a86cf0b0c4d49315e2c02d08a568fe5abc91ffa5b8f8f | MATLAB | 28,471 | 563 | classdef CSVImportTest < matlab.unittest.TestCase
properties
tmp_dir
end
methods(TestMethodSetup)
function setup(testCase)
tmpd = tempname;
mkdir(tmpd);
testCase.tmp_dir = tmpd;
utest_bst_setup();
end
end
methods(... |
d58be4a5f579d3ee227d07336a2a16c68fcff2149767906ba5ec205e17002d66 | MATLAB | 28,821 | 590 | function BCCT_SCN_stat_mainfunc(Parameter)
Outputdir = Parameter.Outputdir;
Inputdir1 = Parameter.Inputdir1;
Inputdir2 = Parameter.Inputdir2;
RealComp1 = load(fullfile(Inputdir1,'RealCompPara.mat'));
RealComp2 = load(fullfile(Inputdir2,'RealCompPara.mat'));
if ~strcmp(RealComp1.RealCompPara.mod,RealComp2.RealCo... |
463e2125979bf203a635ec582f994dcff9637ff30790d0f9c67a5efefb5fdd48 | MATLAB | 28,846 | 529 | classdef NetworkTestResult < matlab.mixin.Copyable
% Network level test results
% Class to store all relevant results for a network level test. Each test will create an instance of this to store results
%
% :param test_options: Options and inputs for tests to be run (also called input_struct)
% :par... |
12b464eeeb402ab488342c17252268cc7176998fe44ee110085ed750145405bc | MATLAB | 28,897 | 533 | classdef BrainPlot < handle
properties
plot_figure
edge_test_options
network_test_options
network_atlas
edge_test_result
network1
network2
test_name
upper_limit
lower_limit
color_map = cat(1, winter(1000), flip(autumn(1000)));
... |
427e18da7ea9da3efb355160706886df23488f7f84dfa6ecf8da8b35d978f935 | MATLAB | 29,208 | 702 | function [tensorOut, infoOut] = addVariable2Tensor(obj, tensorIn, opt)
%ADDVARIABLE2TENSOR Append a preprocessed variable as a new slice in the last dimension.
%
% [tensorOut, infoOut] = obj.addVariable2Tensor(tensorIn, opt)
%
% Designed to be called iteratively to build a regressor tensor. Each call
% appends ... |
f1edadef44db151356b2063b0d7e0810e9b9eb0de0798b484c8b60a81389f914 | MATLAB | 29,227 | 753 | function varargout = panel_nst_OM(varargin)
% panel_nst_OM Panel for the optimal montage
% USAGE: bstPanel = panel_nst_OM('CreatePanel', OPTIONS) : Call from the interactive interface
% bstPanel = panel_nst_OM('CreatePanel', sProcess, sFiles) : Call from the process editor
% s = panel... |
41ce1ad7e9d9b623dc40ee483359c5331a4d36b4deff836a23760addfc30092c | MATLAB | 29,231 | 754 |
addpath(genpath('S:/Roy/ryhattori-PatchWarp-1.3.3.0'));
% calculate trace means and stds
% TODO - report baseline trace means over each session, i.e. see if there is a drifting baseline in each session or for each roi
figGen=0;
fprintf('\n=== SWEEPING ALL ANIMALS IN MASTER PIPELINE ===\n');
for animal ... |
5da3320ed967d0ddffcd9d5ae53f17a3e9985323bd927f603689854ad8689f98 | MATLAB | 29,346 | 671 | function [neuralDecodingScores, neuralDecodingData, neuralDecodingModels] = neuralDecodingClassification(obj, processingOpt, trainOpt, testOpt, decoderOpt, visOpt)
% NEURALDECODINGCLASSIFICATION Decode task parameters from neural population activity.
%
% For each cross-validation fold the method trains one classi... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.