sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c05e8143bfe3944b89ef166a6e3118e0bf5f5aacd21a9ffcc58cb9df468b08c5 | MATLAB | 7,608 | 223 | function [decodinginfo,errorpos_all] = decoding_position_PFC_novelfamiliar_trial(animalprefix,day,ep,eprun,timerange,cellthresh)
%---------------------------------------------------------------%
% This is the function for PFC decoding of spatial locations %
% using the rate maps from one epoch to decode position in... |
61c9df2d2ab1c39d51c12d62f5fbc5a09ea26cf007f3a6d002648c76a2bdaa20 | MATLAB | 7,613 | 223 | function [decodinginfo,errorpos_all] = decoding_position_CA1_novelfamiliar_trial(animalprefix,day,ep,eprun,timerange,cellthresh)
%---------------------------------------------------------------%
% This is the function for CA1 decoding of spatial locations %
% using the rate maps from one epoch to decode position in... |
8fbf21a2808297ee125b9a8120b4b662c4a90f09b4391676c3b6ccb86c153f3f | MATLAB | 7,619 | 222 | function [app,behavDIO,soundinfo]=nextStateAction(app) %MDPState,RATState
%Maciej's MDP - PHASE 3-4
s = app.MDPState;
r = app.RATState;
nAreas = 6;
behavDIO.action=0;
soundinfo.toplay=0;
soundinfo.line = [];
s.soundIsPlaying=soundIsPlaying(app);
s.behavior = categorical({'no'});
s.rewsize = 0;
% s.area = r.area.num;
% ... |
f81ece8f01976e6e550a09bd45826558457f108b656abd3679c4398fd432612b | MATLAB | 7,650 | 222 | function [snr_times, deuteron_tables, expdata] = ...
prepare_one_session_folder(expdata, i, S)
row = expdata.rat_table(i, :);
out_folder_rat = expdata.folders.out_folder_rat;
fname = sprintf('%02d_%s', row.SessionID, row.SessionType{1});
out_folder_session = fullfile(out_folder_rat, fname);
if ~isfolder(out_fold... |
8973b864bb2f439b0a1e32721f18358ed8edc9af4c2d92848b14c994f0995c31 | MATLAB | 7,679 | 201 | function [T, paramF] = createSSAblock(Told,paramFold,bf,ssa_att)
% 2000<=bf<=35000 !!!!!!!
df=2^(1/6);
% params-------------------------------------------------------------------
type = cell(500, 1);
type(:) = {'freq'};
speaker = ones(500,1)*3;
samp_rate = ones(500,1)*192000;
trial_dur = ones(500,1)*300;
stime = ones(5... |
c90ce04e4cdcfa72b4c59579a42b82b9fb2a48fe52db8a9a886cdf4c3dd2511f | MATLAB | 7,679 | 216 | function flatten_single_experiment(input_folder)
% JN 2021-02-12
sampling_rate = 32000;
half_window_silence_sec = 0.005; % 5 ms, this is hard-coded in `flatten_noise_areas.m`
% Function flatten_single_experiment() creates a flattened DB for a single RIFF processed experiment.
% The function operates on the outputs of... |
28bf48da52945007360b08d605d8f7a1aa800986d9db95f20149146284372cb0 | MATLAB | 7,680 | 176 | function filename=preprocess_functional_filsigreg(subjectdir, filename, fil, gsr, wmcsfr)
% starts functional brain preprocessing
% realgin all functional scans
% This section is using FSL's MCFLIRT tool to conduct
% motion correction and then plotting out and saving the motion
% parameters as a separate JPEG f... |
c7d37045150d4639999cd8f8fd5a46e670c748f93334ef939855cdd249f5d8c9 | MATLAB | 7,690 | 253 |
%This code implements multi-region graph cut image segmentation according
%to the kernel-mapping formulation in M. Ben Salah, A. Mitiche, and
%I. Ben Ayed, Multiregion Image Segmentation by Parametric Kernel Graph
%Cuts, IEEE Transactions on Image Processing, 20(2): 545-557 (2011).
%The code uses Veksler, Boykov... |
1cd52d8aecf4ce21c89613642cbc1b8a895e34430b98387db399e23a7e8bf26d | MATLAB | 7,738 | 125 | % ClinicalASL toolbox 2025, JCWSiero
%%%%%%%%%%%%%%%%%%%%% ASL Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% written by Jeroen Siero 25-05-2023 for the MOYAMOYA study
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL analysis, CBF, map smoo... |
6f9ef4fd6c2c643c5a6b3ff5b83faf4d00d189e05fe14765c64e7e4d17f0406c | MATLAB | 7,780 | 218 | classdef TrialState < ExperimentState
%TRIALSTATE ExperimentState when the subject is on the platform.
% This is the only state during which trials will be played and advanced.
% Author: Lasse Osterhagen
properties
% Reinsert an 'early jump' stimulus at the end of the
% trialGenerator
reinsert = false;
... |
f12ec029163e6aec1063c949d115247fbd02b7a9110dd60f6c6dc5c048ffe010 | MATLAB | 7,831 | 257 | % [kcMax,A0,kcGM,d0,d] = getDcorrSect(im,r,Ng,Na,figID)
% ---------------------------------------
%
% Estimate the image sectorial cut-off frequency based on decorrelation analysis
%
% Inputs:
% im 2D image to be analyzed
% r Fourier space sampling of the analysis (default: r = linspace(0,1,50)
% ... |
098195482711de54c3389df07cd36f2b9e8a07a62203f3f60ed40f1d901f6c96 | MATLAB | 7,879 | 188 | function TD_plots_mean(U,r_components,left,group_ind,groups,saveDir,fs)
%Generate a figure for each CPD component contains. Plotting channels activations on the left and
%right hemisphere. Taking group indeces to use in bar plots
% Plotting the mean of the signatures of each group of subjects
noSamp... |
1ff68c519a2ac1c5ff2a883e84155b9d3f9ec011791105499be27a9711d38bea | MATLAB | 7,913 | 241 | function [L,N] = superpixels(varargin)
%SUPERPIXELS 2-D superpixel over-segmentation of images
%
% [L,NumLabels] = superpixels(A,N) computes superpixels of image A using
% N as the requested number of superpixels. A must either be a 2-D
% grayscale image or a 2-D RGB image. The first output argument, L, is a
% ... |
0bc2b25522d10d2aef01224f8fd5aa72b1d585d973a5a32f2a728d569d156cf8 | MATLAB | 7,923 | 182 | %---------------------------------------------------------------%
% This is the main script for UMAP transformation of neuronal %
% population activity. The UMAP MATLAB toolbox (V4.1) is %
% needed (https://www.mathworks.com/matlabcentral/fileexchange/%
% 71902-uniform-manifold-approximation-and-projection-u... |
b8b05cb54588242a4884b9b4a3ad854b48b7da1f7ac2f3b5d9d365464977b189 | MATLAB | 7,963 | 231 | % Authors : Tatjana Schmitt & Simon Wadle 2019-2022
%function reads tiff stacks and scales pixels down to end size
function resized_image = tiff_stack_import_block_process(tiff_fullpath, end_size)
if iscell(tiff_fullpath)
nr_tiffs = size(tiff_fullpath,2);
nr_frames = zeros(1,nr_tiffs);
%calcu... |
1a1dfb243273f8c9275872c760656303d57bfe7d5a7129eeb18736ab361f82df | MATLAB | 8,009 | 127 | %% LaBGAS_get_firstlvl_dsgn_obj
%
% This script contains a function that defines a number of fields of
% the CANlab style first level DSGN structure array
% for Maaike's emosymp study on IAPS picture-induced bodily symptoms.
% This function is used in LaBGAS_1_spm_fit_firstlvl_models.m to
% run first level analysis us... |
747736a7c4df6a8e5ae6e97ed031f079c1d3d20802b15c72aab0e62b985af4a0 | MATLAB | 8,071 | 149 | function shearletSystem = SLgetShearletSystem2D(useGPU, rows, cols, nScales, shearLevels, full, directionalFilter, quadratureMirrorFilter)
%SLgetShearletSystem2D Compute a 2D shearlet system.
%
%Usage:
%
% shearletSystem = SLgetShearletSystem2D(useGPU, rows, cols, nScales)
% shearletSystem = SLgetShearletSystem2D(useGP... |
cff5206533e2890e400202237aece0796500a5aef3df407a13786a3e91ad06fe | MATLAB | 8,076 | 220 | function coord = Coordinator(varargin)
% Coordinator class constructor.
% COORD = COORDINATOR(MAIN_SIGNAL) constructs a Coordinator
% for the given Main_signal.
% COORD = COORDINATOR(BASIC_LINE) constructs a Coordinator
% for the given BASIC_LINE.
% Coordinator is the base class of all Coordinators.
% Th... |
23a07b2ac4c407cc9fbde109c09d31f78ada6840bd1dfd43f0de0cedaed3088c | MATLAB | 8,091 | 314 | %% Add paths
clear; clc;
% TDR path
tdrDir = '/Users/jeongjunpark/Desktop/Joonyeol/Mante';
addpath(fullfile(tdrDir,'TDR'));
addpath(fullfile(tdrDir,'TDR','nansuite'));
addpath(fullfile(tdrDir,'TDR','tools'));
%% Load data
% firing rate
% time = 101:20:621 (300 = stimulus onset)
% time window = 20ms(0~19ms) from time... |
b8472f49dd942e6acab0f10fbf99fb831a1d237c0e7ab0863467e57c36ce49c0 | MATLAB | 8,129 | 194 | %% Parameters
ROIs_for_Dom = {'HGPM','HGAL','PT','PP','STGP','STGM','STGA','InsP','STSL','MTGP','MTGM','MTGA','SMG','AGA','IFGop','IFGtr','IFGor','MFG','OG',...
'dPreCG','vPreCG','vPostCG','PMC','PHG','FG','ITGP','ITGM','ITGA','TP','InsA','GR','Amyg','Hipp'};
measure = 'envCorrDBTorth_gamma';
threshold = 1/... |
6316f2eb9dbfe421912f63ddb2c1c084738f534e26af0bf6f07089e1edf3b6a4 | MATLAB | 8,218 | 205 | classdef GapTrainingGUI < DetectionGUI
%GAPTRAININGGUI GUI for gap detection training.
% Allows to change properties of a GapTrainingStimuliGenerator to change
% gap properties. Furthermore, allows to change the maximum reaction time
% after stimulus offset, that will lead to a reward.
% Author: Lasse Osterhagen... |
f80963a0ee8ca2c2b296952ad3fd9f74430acf77c850f39728b4297b5312f6e9 | MATLAB | 8,233 | 214 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <trAlign: aligns an input signal with a reference signal >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Softw... |
5605c673d925222f9988079a1fe8b18ae7b96e1d92473a329a3b2302c35f6c5e | MATLAB | 8,246 | 132 | function SUBJECT = ASLConvertDICOMtoNIFTI(SUBJECT, imager, vTR_only)
% ClinicalASL toolbox 2023, JCWSiero
SUBJECTdir = SUBJECT.SUBJECTdir;
DICOMinputdir = SUBJECT.DICOMdir;
NIFTIoutputdir = SUBJECT.NIFTIdir;
% check operating system: unix vs windows
if isunix % unix
if nargin == 2
if strcmp(image... |
bb9f753d7ed8e6fb040c5948b538da34ed7d3be5251900f412918ab9f213b54f | MATLAB | 8,249 | 296 | % This code is a modified version of the original code from Mante et al 2013.
% V. Mante, D. Sussillo, K. V. Shenoy, W. T. Newsome, Context-dependent computation by recurrent dynamics in prefrontal cortex. Nature. 503, 78–84 (2013).
%% Add paths
clear; clc;
% TDR path
tdrDir = ''; % put your code directory
addpath(f... |
a6fcbb29de5bda110ed0dea263902d443baeb6369eb1b720cd1709347ff3ac85 | MATLAB | 8,328 | 143 | clear
close all
clc
% settings
filename_exe = 'behavioral_data_exe'; % these are duration data of all valid trials of the sessions in which mirror neurons were recorded (177 MN)
filename_obs = 'behavioral_data_obs';
% load data
load (filename_exe)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
f726037f3f22672a9388d8b1cd222102a6d69b7b2ec5e4f4216d796c5358f81b | MATLAB | 8,367 | 323 | %%%This program is written by Zhenzhou Wang, for more information please
%%%contact: zzwangsia@yahoo.com or wangzhenzhou@sia.cn
%%%This program is free for academic use only.
%%%Please reference and acknowledge the following paper:
%%%%%%[1]Z.Z. Wang, "A new approach for Segmentation and Quantification of Cells or ... |
785984c495b758b68eade2704ff98d64b224b4a202b6fdb0c902b1c021123685 | MATLAB | 8,386 | 245 | %% Constant decleration and loading
%clear
% close all
constants
options = odeset('RelTol',1e-4,'AbsTol',1e-4);
%% Choice of stimulation parameters
start_stim = 1.015; % [s] When to start the current stimulation
end_stim = 60; % [s] When to end it
f_stim = 1; % [Hz] At what frequency do you want ... |
69301fb42840b3e5214f39a28089d064b38458e91a1fd334c20c43dd228a65be | MATLAB | 8,406 | 298 | %% Add paths
clear; clc;
% TDR path
tdrDir = '/Users/jeongjunpark/Desktop/Joonyeol/Mante';
addpath(fullfile(tdrDir,'TDR'));
addpath(fullfile(tdrDir,'TDR','nansuite'));
addpath(fullfile(tdrDir,'TDR','tools'));
%% Load data
% firing rate
% time = 101:20:621 (300 = stimulus onset)
% time window = 20ms(0~19ms) from time... |
5f0b80fb4be1bcee9bf49441a761094ca6430da002b2c22cf033b237d9dda7b6 | MATLAB | 8,448 | 310 | %% Add paths
clear; clc;
% TDR path
tdrDir = '/Users/jeongjunpark/Desktop/Joonyeol/Mante';
addpath(fullfile(tdrDir,'TDR'));
addpath(fullfile(tdrDir,'TDR','nansuite'));
addpath(fullfile(tdrDir,'TDR','tools'));
%% Load data
% firing rate
% time = 101:20:621 (300 = stimulus onset)
% time window = 20ms(0~19ms) from time... |
39ee30b25fb2ad2c1cfb282cda564fa8379d8a8c2592dac36dcd56d3578f1305 | MATLAB | 8,476 | 331 | %%%This program is written by Zhenzhou Wang, for more information please
%%%contact: zzwangsia@yahoo.com or wangzhenzhou@sia.cn
%%%This program is free for academic use only.
%%%Please reference and acknowledge the following paper:
%%%%%%[1]Z.Z. Wang, "A new approach for Segmentation and Quantification of Cells or ... |
afec77f851936a99a500c6d0746c008d89019eac09fdd3a555a7913c9091dfab | MATLAB | 8,534 | 201 | function TD_plots(U,r_components,left,condition_ind,conditions,saveDir,fs)
%plots time, channel, and subj components
% Plotting channels activations on the left and
%right hemisphere. Taking condition indeces to use in bar plots
noSamples_time=length(U{1});
xbase=1;ybase=1; activations=zeros(4... |
ff1bd2d28fc5bae49bde3963ffda920d49c14734fb822948585bde666a679519 | MATLAB | 8,570 | 217 | % It is sample MATLAB codes for the manuscript entitled
% "A magnetoencephalography dataset during three-dimensional reaching movements for brain-computer interfaces".
% A "topoplot" function and related sub-functions in the EEGLAB toolbox are needed to plot a topography.
% The EEGLAB software is available at htt... |
085ed0681dd006f41c22dc4398b8bce65f929311c8885313871a764493d2bc7b | MATLAB | 8,586 | 264 | function [ stat_out ] = cs_nmri_statistics( all_subjects, opt, params )
%[ all_subjects ] = nmri_statistics( all_subjects, opt, params )
% Will do generate a tabulated overview of metrics (all that are readable)
% via nmri_load_metrics for any number of subject
%
% all_subjects = cell array of subjects (see nm... |
3ffb9b77ce85922fe82ea883ace7c2ae9a0de27919bc7756b55e37dc9238261e | MATLAB | 8,615 | 265 | function [ stat_out ] = cs_nf_ft_statistics( all_subjects, opt, params )
%[ all_subjects ] = nf_ft_statistics( all_subjects, opt, params )
% Will do generate a tabulated overview of metrics (all that are readable)
% via nf_ft_load_metrics for any number of subject
% %s_
% all_subjects = cell array of subjects ... |
830a7f1bd8071f66b7ce0f1ace2917540659a0519e71a99fa056101a58776379 | MATLAB | 8,616 | 221 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <fitHRF: Generates a series of HRFs and performs a best-fit GLM to input data >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as publ... |
07d2443fc2b4dfac539c4de7e24615b6f43f9d8926c8baa14ab8570f007dd3df | MATLAB | 8,645 | 137 | %% LaBGAS_get_single_trial_dsgn_obj
%
% This script contains a function that defines a number of fields of
% the CANlab style first level DSGN structure array
% for Maaike's emosymp study on IAPS picture-induced bodily symptoms.
% This function is used in LaBGAS_1_spm_fit_firstlvl_models.m to
% run first level analysi... |
5831e2e0fcd3293463217446ca6b8bb92981864489f544dc301f251b2b47c12e | MATLAB | 8,660 | 227 | % HEADER:
% This script allows you to test model-, rat- and human-driven classification
% of epileptic brain states (interictal, preonset, onset and ictal)
% using prototype comparison. It looks at 'individualized' and 'generalized'
% classification performance, where 'individualized' means the performance in
% ... |
9ff21e73b4db83ffac435a0dc6412fbb4cf03598df2b5dc45e13eb7ea2de4b55 | MATLAB | 8,668 | 126 | % Do PALM on IGE - controls (ImCoh/Power ~ group)
analysis_dir = '/home/uni10/nmri/projects/cstier/aging_analysis/export/all_subjects';
export_func = '/home/uni10/nmri/projects/cstier/aging_analysis/export/all_subjects/yeo/';
export_th = '/home/uni10/nmri/projects/cstier/aging_analysis/export/all_subjects/ld10_sm/yeo/... |
70ce5343d7bbda72eb50cd41c55a03ff44ff912682c958a767e9c180ce750b7f | MATLAB | 8,693 | 309 | function [x,fval,exitflag,output] = fminsearchbnd(fun,x0,LB,UB,options,varargin)
% FMINSEARCHBND: FMINSEARCH, but with bound constraints by transformation
% usage: x=FMINSEARCHBND(fun,x0)
% usage: x=FMINSEARCHBND(fun,x0,LB)
% usage: x=FMINSEARCHBND(fun,x0,LB,UB)
% usage: x=FMINSEARCHBND(fun,x0,LB,UB,options)
% usage: x... |
51669491642e470cec7db1e4be7784dad6b089335c51830a741581b12698bdb7 | MATLAB | 8,696 | 303 | function output=new_data_plotter(DATAFILE,SAVEFILE)
%GUI for choosing a cluster for ephys_cluster.m
%
% load the information collected by outloop
load(DATAFILE,'variableCellArray','peakLocation','property_names')
% load the scores, their locations, the file number, and
% the peak locations for subsequent saving
syl... |
eeb165cf08778bd82f1f15c5387078e8d9678056f23ba87f812a643a3d4953ad | MATLAB | 8,754 | 210 | %% Direction Tuning
% align preferred direction to 0 degree to combine data
% include only when there are tuning data of both two prior block
% Fig 4.
clear; clc; close all;
load('Tuning.mat');
%% fit tuning curve to each monkey's data
% choose a monkey
monkey = 'B'; % A for Monkey A, B for Monkey B
if strcmp(monkey,... |
95d63d4f54b4a99323a285c5e88accdc0ccd31fdcc248f90b68bd2c9325677c9 | MATLAB | 8,812 | 225 | % fdr_bh() - Executes the Benjamini & Hochberg (1995) and the Benjamini &
% Yekutieli (2001) procedure for controlling the false discovery
% rate (FDR) of a family of hypothesis tests. FDR is the expected
% proportion of rejected hypotheses that are mistakenly rejected
% (i... |
be313a892e3a743f80d23706dff3251c322ec135ed1406669388a6965399dad2 | MATLAB | 8,831 | 143 | function MRI_DIAMOX_UMCU_ClinicalASL_SSVB_CVR_IMAGER(inputdir, outputdir)
% ClinicalASL toolbox 2025, JCWSiero
% for MRI DIAMOX scans, via IMAGER
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL analysis, CBF, map smoothing, CVR registration, cal... |
f16e610777b4b08ed230f92983532f2c67a01a6fe88562b2c185d43a7a045496 | MATLAB | 8,846 | 240 | %analyze_results
%--------------------------------------------------------------------------
% Analysis file for the data from manuscript "Causal evidence for frontal
% cortex organization related to perceptual decision-making"
%
% The file runs all TMS analyses reported in the paper.
%
% Written by: Doby Rah... |
273e8bdad14b1db9e6a2bac114905ca691db65f5848940713fe9f30e4becf2ea | MATLAB | 8,923 | 234 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <fitHRF2: Generates a series of HRFs and performs a best-fit GLM to input data >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as pub... |
36d34f06db95ea64ffc2ef7d88eb03abad7f0898c85ad9e480bc9f892a60e39b | MATLAB | 8,933 | 225 | %---------------------------------------------------------------%
% This is the main script for getting all dichotomies after %
% UMAP transformation. UMAP MATLAB toolbox (V4.1) is needed %
% (https://www.mathworks.com/matlabcentral/fileexchange/ %
% 71902-uniform-manifold-approximation-and-projection-u... |
8221dfa2ee1c12dfb647ebaec6552b34f224516d75a8b0d3cce24d6d9840f04b | MATLAB | 8,937 | 319 | %% Add paths
clear; clc;
% TDR path
tdrDir = '/Users/jeongjunpark/Desktop/Joonyeol/Mante';
addpath(fullfile(tdrDir,'TDR'));
addpath(fullfile(tdrDir,'TDR','nansuite'));
addpath(fullfile(tdrDir,'TDR','tools'));
%% Load data
% firing rate
% time = 101:20:621 (300 = stimulus onset)
% time window = 20ms(0~19ms) from time... |
cad04743aa61545b29c6eae6b9de2655b99b02797c5fe647a7d7794af6c63a84 | MATLAB | 8,985 | 343 | %% mean dir std
clear; clc;
%%%%%%%%% Monkey A %%%%%%%%%
load('direction_day_A.mat');
ah_std = mean(sb1c100std-sb2c100std,1);
al_std = mean(sb1c008std-sb2c008std,1);
a1 = sb1c100std-sb2c100std;
a2 = sb1c008std-sb2c008std;
t = 1:20:981;
t = t-400;
fig_a = figure;
subplot(1,2,1)
errorbar(t,mean(sb1c100std,1),std(sb1c1... |
60c01a92631d6a12b8ebf4a07c4c07c3f9dce3a1db2c872100214bae429f778a | MATLAB | 8,986 | 194 | % Modify to specify image file subdirectories, wildcards to locate images, condition names
%
%% Set up conditions
% ------------------------------------------------------------------------
% conditions = {'C1' 'C2' 'C3' 'etc'};
% structural_wildcard = {'c1*nii' 'c2*nii' 'c3*nii' 'etc*nii'};
% functional_wildcard = {'... |
90a5f98470a23e9b807e00bb9b6607060c2b2b405de05cb4d6bbe7d026f58c73 | MATLAB | 9,029 | 216 | %---------------------------------------------------------------%
% This is the main script for calculating the distance of %
% neural states of the same spatial location vs. the same %
% trajectory phase in the original state space. %
% -- Wenbo Tang (Jan 07, 2023) ... |
b930dc7e202195dfc8ef6330418c9b64d9ab36bc4fca9386df9e1c3a0d9393f0 | MATLAB | 9,029 | 288 | function [Y,ndx,dbg] = natsortfiles(X,rgx,varargin)
% Natural-order / alphanumeric sort of filenames or foldernames.
%
% (c) 2014-2021 Stephen Cobeldick
%
% Sorts text by character code and by number value. File/folder names, file
% extensions, and path directories (if supplied) are sorted separately to
% ensure... |
136dfc915ec322442988d138a30df6ee050b8c9b3c02df2364abad80750fb6bf | MATLAB | 9,103 | 135 | % ClinicalASL toolbox 2023, JCWSiero
%%%%%%%%%%%%%%%%%%%%% ASL Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% written by Jeroen Siero 25-05-2023 for the APRICOT study
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL analysis, CBF, map smoot... |
578874b96355370e94e6ee0163fb72d3016ae2be88827d0bfc60b718bcd50f21 | MATLAB | 9,130 | 238 | % This script runs single-level mediation models for proj-emosymp
% (Van den Houte, Bogaerts, et al, in prep), in patients only,
% with the following variables
% X: CTQ
% M: different options
% 1. NPS response (including subregions) for each contrast
% 2. voxel-wise brain mediator
% 3. Principal Directions of Mediati... |
86f8ed8dcffc5876b47f92df5608ac185a741095cb18f209adfa0e961c9a4ee3 | MATLAB | 9,153 | 240 | %% Parameters
ROIs_for_RS = {'HGPM','HGAL','PT','PP','STGP','STGM','STGA','InsP','STSU','STSL','MTGP','MTGM','MTGA','SMG','AGA','AGP','IFGop','IFGtr','IFGor','MFG','SFG','ACC','OG','TFG','dPreCG','dPostCG','vPreCG','vPostCG','PMC','CingM','PCCpreCun','PHG','FG','ITGP','ITGM','ITGA','TP','InsA','fOperc','GR','SPL','L... |
9dfadd318cf5d0ce6b0d10d5e788c392794c227f0f390412bae78f0c6125432e | MATLAB | 9,362 | 255 | function gramm_2x2laminar_subline(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM(1:560);
clear... |
33696822479af63bfb5ca2ad61ad63ff000c3a4dbfeb502422ee0be733b8d9ff | MATLAB | 9,363 | 251 | %---------------------------------------------------------------%
% This is the main script for calculating population vector %
% (PV) similarity -- Wenbo Tang (Jan 05, 2023) %
%---------------------------------------------------------------%
clc
close all
clear all;
%%
% set directory
famnov_dir =... |
b537b472afe1970c8739c28137565af837fcad553198baa76e0967a5f2c9306d | MATLAB | 9,371 | 269 | % This script runs a 5-fold cross-validated lasso-PCR model to predict
% somatic symptom ratings from brain responses to positive, negative, and
% neutral IAPS pictures (3 condition images from classic GLM per subject)
% for proj-emosymp (Van den Houte, Bogaerts, et al, in prep).
%
% It requires all study-specific and ... |
7e5b97cd8942b63fd1c109a73823f5e7ab9de5093bb215d285cd04fc39c1bf78 | MATLAB | 9,672 | 362 | function [ subject, data ] = nmri_autodetect_artifacts( subject, data, params )
%[ subject, data ] = nmri_autodetect_artifacts( subject, data, params )
% This function will do automated trials and channel artifact selection
% similar to the vft_rejectvisual
%
% subject = subject structure, see nmri_read_subject
... |
99cb4c119f37571acf0e1bd22ed428dcc61dcc59073244ace9c990d475f25389 | MATLAB | 9,687 | 368 | %% Correlation between FR ratio and difference of the directions(preferrred-target)
% Fig. 2, d-i
clear; clc; close all;
%load spike data
load('spikes.mat');
%load preferred and target directions
load('pf_tar_dirs.mat');
% Responses to prior direction
% Monkey A
targetHighWide_A = mSpikes_A_b1c100; % wide-prior, h... |
4fc374984005d7827ac51cefd606ce8632d9c601c290c8a78d53d68e2e96b79c | MATLAB | 9,693 | 211 | clear all;close all;clc;
preproc_dir='E:\mouse_development';
template_dir = 'E:\mouse_development\md_brain_atlas';
ROIs = {'Somatosensory_Cortex' 'SCR' 'VIS1R'};
option_cohr = 1;
%Load HRF
load('E:\code\HRF\hrf.mat'); %hrf
hrf2 = [zeros(1,5) hrf]; %Should delay a little
cd(preproc_dir)
age_list = dir('mous... |
f86921907ac2f846a556b60c3890e294cea0dd03a9b4ef1bab779ab0e6a4811c | MATLAB | 9,696 | 142 | % ClinicalASL toolbox 2023, JCWSiero
%%%%%%%%%%%%%%%%%%%%% ASL Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% written by Jeroen Siero 30-04-2025 for the APRICOT/MOYAMOYA/PXE/STROKE study
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL anal... |
5573e49735abff20ffb1f9039c98f33819c7d8e08081a0f366f16d0863e07b65 | MATLAB | 9,718 | 307 | function IDX = singleSessionIDX(penetration,sdfwin,X);
%% load session data
global STIMDIR
cd(STIMDIR)
load(penetration,'STIM')
matobj = matfile(penetration);
%% Set up variables for electrode loop
% Balance conditions
if ~any(contains(STIM.paradigm,'brfs'))
warning('no brfs on day...')
disp(penetration)
e... |
82e15310c4c46a9b13f4dfa684d4aee84543d344fba425bf77e396f6804c7081 | MATLAB | 9,755 | 227 | %% Function to do the anchoring analysis based on vessels
% 2021/11/12-
% Yunhao Bai & Bokai Zhu
% Features:
%'_cellRatio': instead of simple cell number encountered, use the cell overlap pixel ratio to reflect the cell distribution
% use additional filter to solve the overlapping issue when adjacent tumo... |
92c87dc56a1d5e4397364cf589023e3c5cc4e0cf397c50c3e9fa1f3c2737dace | MATLAB | 9,755 | 151 | function MRI_DIAMOX_UMCU_ClinicalASL_CVR_IMAGER(inputdir, outputdir)
% ClinicalASL toolbox 2025, JCWSiero
% for MRI DIAMOX scans, via IMAGER
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL analysis, CBF, map smoothing, CVR registration, calculat... |
9b4e8fc77ce7b542951b7ea10d3ccc3830f012dbe4e1a19e733d6bdeace07b4e | MATLAB | 9,766 | 227 | %---------------------------------------------------------------%
% This is the main script for calculating the distance of %
% neural states of the same spatial location vs. the same %
% trajectory phase on UMAP neural manifolds. The UMAP MATLAB %
% toolbox (V4.1) is needed (https://www.mathworks.com/ ... |
34b7d110fce6979a164896fea41e4fdb86e45e5e21ed4af36403d8406e36658d | MATLAB | 9,768 | 233 | function [behav_distrib_feat,gmm_grp,cluster_seeds] = generate_behavior_clusters(DLC_data,subsampling,...
N_run_tsne,N_run_gmm,min_nb_frames_per_cluster)
% This function performs multiple iterations of tSNE dim reduction followed
% by GMM clustering to behavioral clu... |
7b8e402bf4bfe5c5def010a43f341c0d7276d066e9be4e4cfc312a087372deb1 | MATLAB | 9,778 | 154 | function [y_hat_wi] = MIRO_Fast_Wiener_Video(z, y_hat, sigma,sampling)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This algorithm is adapted from the article:
%
% [1] K. Dabov, A. Foi, and K. Egiazarian, "Video denoising by sparse 3D
% transform-domain collaborative filtering," Eur... |
4a4e3cd0aab0bdf2ed48857057342a2d50a4ec947c86e27c7ae4fe804982f436 | MATLAB | 9,878 | 286 | %BONE2 Black-blue-white colormap
%
% Examples:
% map = bone2;
% map = bone2(len);
% B = bone2(A);
% B = bone2(A, lims);
%
% Similar to MATLAB's bone function, this colormap has been designed to
% achieve perceptual uniformity.
%
% The function can additionally be used to convert a real-valued array ... |
b04140fed5a674c03344ac81a3a169d8fd1efb23b9393813f64f5821ee516688 | MATLAB | 9,914 | 286 | %THERMAL Black-purple-red-yellow-white colormap
%
% Examples:
% map = thermal;
% map = thermal(len);
% B = thermal(A);
% B = thermal(A, lims);
%
% A colormap designed to replicate the tones of thermal images, as well as
% achieve perceptual uniformity.
%
% The function can additionally be used to co... |
9118bace581a8ca249657b9e1f18f0f0f80524d8835c993c3500df15c41ead66 | MATLAB | 9,925 | 286 | %SEPIA Black-brown-white colormap
%
% Examples:
% map = sepia;
% map = sepia(len);
% B = sepia(A);
% B = sepia(A, lims);
%
% A colormap designed to replicate the sepia tones of old photographs, as
% well as achieve perceptual uniformity.
%
% The function can additionally be used to convert a real-va... |
2df586b5b3f9ca04b3591cb6f5deb6e7a256acb937dadf7e504d91a0db76f0b1 | MATLAB | 9,929 | 303 | function [ stat_out ] = cs_create_global_files( all_subjects, opt, params )
% This script makes files with global statistics for selected metrics for
% frequency-specific statistical analyses
%
% Written by NF and modified by Christina Stier, 2020/22
% Will do generate a tabulated overview of metrics (all that are rea... |
015d20f2d6399730e41096e8aa3b70498927f025e6d8697b7db66bfce8bfcad6 | MATLAB | 9,933 | 239 |
clear all
% Defining network model parameters
% PC In TC TI TRN
W = xlsread('./FLNe.xlsx','Sheet2');
vth = [10,4,10,4,4];
tau_v = [40,10,200,20,40];
Tsig= [12,10,12,10,10];
%beta_ad = [0,4.5,0,4.5,4.5];
alpha_ad =[0, -2,0,-2,-2];
p=[ 10, 4, 10, 4, 4;... |
45c2a0e957e5bd3e70ac32618cc95ad58178332391d991bc1946d441ba269d46 | MATLAB | 9,933 | 386 | function IDX = IDX_iScienceSubmission_findTimingOffsets
%% load session data
global STIMDIR
cd(STIMDIR)
didir = strcat(STIMDIR,'\');
saveName = 'IDX_iScienceSubmission_highContrast.mat'; % THIS IS CONTRAST LEVELS OF .41-.75 INCLUSIVE
anaType = '_AUTO.mat';
flag_saveIDX = true;
kls = 0;
list = dir([didir '*' ... |
102a3d540c827548f235c5745e2276d7490365423d0f5575e2f3dd531be93ec1 | MATLAB | 9,940 | 323 | %% Population Vector Decoder / Maximum Likelihood Estimate
% Fig. 3, e-f
clear; clc; close all;
% load experimental data
load('Monkeys_cir.mat');
Monkeys = Data;
% gamma parameters of prefer and null response distribution
% high, prefer
hp = Monkeys(1).Tuning_pfnull(1,:);
nanidx = find(isnan(hp));
hp(nanidx) = [];
p... |
1810dcf387a191c097af74953d9a3714b1a3dafda37fbc9fbf6e1b0b3a7efca9 | MATLAB | 9,940 | 346 | function fit = fit_meta_d_MLE(nR_S1, nR_S2, s, fncdf, fninv)
% fit = fit_meta_d_MLE(nR_S1, nR_S2, s, fncdf, fninv)
%
% Given data from an experiment where an observer discriminates between two
% stimulus alternatives on every trial and provides confidence ratings,
% provides a type 2 SDT analysis of the data.
%... |
a033dbcaee0c47940ed240d8b96fb9289607d119805abbfb4c21d6590454d1ea | MATLAB | 9,950 | 287 | %COPPER2 Black-copper-white colormap
%
% Examples:
% map = copper2;
% map = copper2(len);
% B = copper2(A);
% B = copper2(A, lims);
%
% A brighter variation of MATLAB's copper colormap, which also continues on
% to white. This colormap has been designed to achieve perceptual
% uniformity.
%
% The f... |
a297267a51afec0157b82cadaf2fb51f62654c4924fc8f574fb0b941dbfd3fe0 | MATLAB | 9,986 | 287 | %DAWN Black-purple-blue-green-yellow-white colormap
%
% Examples:
% map = dawn;
% map = dawn(len);
% B = dawn(A);
% B = dawn(A, lims);
%
% A black to white colormap with several distinct pastel shades reminiscent
% of colors at dawn. This colormap has been designed to achieve perceptual
% uniformity.... |
b7329260fec738d26f9dcdc1247a4fd49fad0bcb4b5115aa3ba384526b6c07e7 | MATLAB | 9,996 | 287 | %DUSK Black-purple-blue-green-red-yellow-white colormap
%
% Examples:
% map = dusk;
% map = dusk(len);
% B = dusk(A);
% B = dusk(A, lims);
%
% A black to white colormap with several distinct pastel shades reminiscent
% of colors at dusk. This colormap has been designed to achieve perceptual
% uniform... |
9dde78d63d8fb62292eb258c09f4801e8465bc338237d28d4c71b221538f0de8 | MATLAB | 10,002 | 320 | function [hF1,hF2,hB] = imoverlay2(B,F,climF1,climF2,climB,cmap1,cmap2,alpha,haxes)
%Other than the function of image overlaying same as the 'imoverlay'function
%This function is specifically used for showing two sets of data with two different colormaps,
%and showing two colorbars. In the current situation, data wa... |
42b71c501bacb14c4e5e11a8626311c38d9f90f9392a49794e0732f23f3c4ff8 | MATLAB | 10,020 | 243 | function [varargout]=errorbarxy(varargin)
% ERRORBARXY is a function to generate errorbars on both x and y axes
% with specified errors modified from codes written by Nils Sjöberg
% (http://www.mathworks.com/matlabcentral/fileexchange/5444-xyerrorbar)
%
% errorbarxy(x, y, lerrx, uerrx, lerry, uerry) pl... |
dd0019a8714215ad4dea640d2c2b647897fd78f528703a5a49261897a67be968 | MATLAB | 10,100 | 324 | % Make sure tm goes out to .9 (in time for the second stimuli) Hopefully I
% can crop the extra .1 later if needed. But this should at least show me
% the second peak as a sanity check.
clear
tic
didir = 'T:\diSTIM - adaptdcos&CRF\STIM\';
saveName = 'diIDX_AUTO_halfTM_MedMedC'; % THIS IS CONTRAST LEVELS OF .41-.75 I... |
865e6fa72eba7eb4fd40b7e2b552e10a4183336345c169b250c49c0d0dde935c | MATLAB | 10,132 | 114 | function SUBJECT = ASLSaveResultsCBFAATCVR_FAST(SUBJECT)
% ClinicalASL toolbox 2025, JCWSiero
% Registration postACZ to preACZ
if strcmp(SUBJECT.RegistrationMethod,'elastix')
% use Elastix: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, "elastix: a toolbox for intensity based medical image reg... |
db79c79bef9badbd18af71aeea703e506563554763a7510cee7be1dbf4539477 | MATLAB | 10,134 | 222 | % Neuromag layout of planar gradiometer
% This function returns the positions of 204 MEG channels
% Copyright by Hong Gi Yeom
% You can use this code for academic purposes
function [position]=neuromag_layout_planar()
p=[
1 -48.186871 26.886379 6.000000 3.500000 0113
2 -48.186871 31.886379 6.000000 3.500000 0112
4 -39... |
8fd27fffbc110e46e73df45e94573a243f904827825cabba1e22fe0b12d86e03 | MATLAB | 10,135 | 215 | function file_format_data=get_file_format(stimlist)
str={};
global BF;
global BFTHR;
global NBTHR;
nb=BF;
str{1}=['BF=',num2str(nb),';'];
bft=BFTHR;
str{2}=['BFTHR=',num2str(bft),';'];
nbt=NBTHR;
str{3}=['NBTHR=',num2str(nbt),';'];
% run_mode=get(meta,'Run_mode');
% str{4}=['META_RUN_MODE=''',run_mode,''';'];
% nu... |
9182102e7d4f5fb5c8dd3c019486ed402ed2971ce89b33e21638f90b244cd67d | MATLAB | 10,143 | 214 | function file_format_data=get_file_format(stimlist)
str={};
global BF;
global BFTHR;
global NBTHR;
nb=BF;
str{1}=['BF=',num2str(nb),';'];
bft=BFTHR;
str{2}=['BFTHR=',num2str(bft),';'];
nbt=NBTHR;
str{3}=['NBTHR=',num2str(nbt),';'];
% run_mode=get(meta,'Run_mode');
% str{4}=['META_RUN_MODE=''',run_mode,''';'];
% nu... |
6a22372bc2165d1ae980126586e2b156967a338e50255adc0e304355c3b0c12f | MATLAB | 10,152 | 320 | function dirTuningInfo = dirTuningEst(directions, resp, Wgt);
rMax = max(resp);
maxIndex = find(resp == rMax);
if length(maxIndex) > 1
maxIndex = maxIndex(1);
end
startDir = directions(maxIndex)*pi/180.0;
startDirPre = directions(maxIndex)-60;
if startDirPre < 0
startDirPre = startDirPre+360.0;
... |
75a964ef28fbd279532d2e9dc4f452c64991e2bf8957e0313f1a6836b7764ba0 | MATLAB | 10,153 | 259 | % This script runs single-level mediation models for proj-emosymp
% (Van den Houte, Bogaerts, et al, in prep), with the following variables
% X: group (patients versus controls)
% M: different options
% 1. NPS response (including subregions) for each contrast
% 2. voxel-wise brain mediator
% 3. Principal Directions of... |
ad6f904246f9d33147d78cd7a2d0395af891c3dd91fe6044613a5849977467fa | MATLAB | 10,189 | 283 | function f = MakeONFilter(Type,Par)
% MakeONFilter -- Generate Orthonormal QMF Filter for Wavelet Transform
% Usage
% qmf = MakeONFilter(Type,Par)
% Inputs
% Type string, 'Haar', 'Beylkin', 'Coiflet', 'Daubechies',
% 'Symmlet', 'Vaidyanathan','Battle'
% Par integer, it is a parameter related t... |
0fe2b8fa0f3729d1562b8887abf45a06600c888298baa6a89eab8f7ca3ffcb94 | MATLAB | 10,284 | 422 | %%%This program is written by Zhenzhou Wang, for more information please
%%%contact: zzwangsia@yahoo.com or wangzhenzhou@sia.cn
%%%This program is free for academic use only.
%%%Please reference and acknowledge the following paper:
%%%%%%[1]Z.Z. Wang, "A new approach for Segmentation and Quantification of Cells or ... |
34541537f684e6760b2bf71495947c65bf92d472a23dd4bec734d1852ded3de6 | MATLAB | 10,311 | 270 | function GLM_getOnsets()
% intended for OBIWAN hedonic reactivity task
% get onsets
% Simplified model on ONSETs 7 (STARTTRIAL, 2*TASTE, 3*questions 1 RINSE)
% last modified on MARCH 2021
dbstop if error
clear all
ana_name = 'GLM_GUSTO';
session = {'second'};
%% DEFINE PATH
cd ~
home = pwd;
homedir = [home '/OB... |
b0dcb143a10ae4aa79c0967ca7c94d30900483e1f740052e4ed5eac853e4863b | MATLAB | 10,353 | 314 |
%Load the individual deltaF signals for each trial and the concatenated deltaF signal for all trials
%Load all of the behav files and make sure the names are changed to the
%corresponding trial. For example, for trial 2, name it behav_2 for trial
%3, name it behav_3 and so on.
%% Calculate the Z-score for the deltaF ... |
cddee5756894c2fed5ee37163b7a1ccaf158e276c94dc7eb9a661413ce46e12c | MATLAB | 10,453 | 154 |
% ClinicalASL toolbox 2023, JCWSiero
%%%%%%%%%%%%%%%%%%%%% ASL Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% written by Jeroen Siero 25-05-2023 for the MOYAMOYA study
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL analysis, CBF, map smo... |
1de9c235f294eaa5897988ee2cfffdfd056ac12d9b638a430037850655ed272b | MATLAB | 10,509 | 250 | %---------------------------------------------------------------%
% This is the main script for CCGP of different environments %
% using linear SVMs; Libsvm MATLAB toolbox (V3.22) is needed %
% (https://www.csie.ntu.edu.tw/~cjlin/libsvm/). %
% -- Wenbo Tang (Jan 07, 2023) ... |
50265aac44245386305af90f2d53d4a2cd55cd86906639c47292671992e07498 | MATLAB | 10,513 | 292 | function [synaptic_weight, list_pot, list_dep, ca3_peak_locations] = Sim_CA3CA1_Romani(velocity, inductions, init_weight, L, n_ca3, param)
% get the basic setup parameter as length of track, number of CA3, peak
% positions, time step, duration of the plateau
if nargin < 4
L = 187;
end
... |
f3cd23e924e4376c6cd90faf0631e612ccb103859618af302ea7316b6e974f7f | MATLAB | 10,553 | 258 | classdef ToneTrainingGUI < DetectionGUI
%TONETRAININGGUI is a GUI for tone in noise detection training.
% Allows to change properties of a ToneTrainingStimuliGenerator to change
% tone properties. Furthermore, allows to change the maximum reaction time
% after stimulus offset, that will lead to a reward.
% Autho... |
f4ceb117612c16664b4fa22e305c95f9f563af145077c5c4914b18dedd5fef9c | MATLAB | 10,579 | 304 | function decodinginfo = decoding_position_PFC_novelfamiliar_cross(animalprefix,day,ep,linfields,decoded_trajtime)
%---------------------------------------------------------------%
% This is the function for PFC decoding of spatial locations %
% during the test trial (cross-validation procedure) %
% -- We... |
5f16ef97ea0d4ed119dfda1718bffcc98d115dd199bc48cba9665fba48ee1517 | MATLAB | 10,619 | 255 | % This code performs eye-tracking data processing and analysis. It extracts
% fixation events from eye-tracking data files and calculates the mean
% deviation of the fixations in the x and y axes. It then saves the mean
% deviation values for each participant and task in a structure called
% meanDeviationData.
%
%... |
486929514b59b48a59fade3ec1696c235e4e3dd7d7377decfe1bc65a8a694ee1 | MATLAB | 10,674 | 288 |
%Load the individual deltaF signals for each trial and the concatenated deltaF signal for all trials
%Load all of the behav files and make sure the names are changed to the
%corresponding trial. For example, for trial 2, name it behav_2 for trial
%3, name it behav_3 and so on.
%% Calculate the Z-score for the deltaF ... |
dbcf05f93c89c24a7384fa60e090c561c084f0ccaf2fb55c7f816d02364d4b86 | MATLAB | 10,722 | 152 | % ClinicalASL toolbox 2023, JCWSiero
%%%%%%%%%%%%%%%%%%%% ASL Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% written by Jeroen Siero 25-05-2023 for the MOYAMOYA study
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL analysis, CBF, map smoot... |
5adf9a34e4f5ace24514b9202300a21d09e2d1345e4fc915051472bbe9877773 | MATLAB | 10,733 | 305 | function decodinginfo = decoding_position_CA1_novelfamiliar_cross(animalprefix,day,ep,linfields,decoded_trajtime)
%---------------------------------------------------------------%
% This is the function for CA1 decoding of spatial locations %
% during the test trial (cross-validation procedure) %
% -- We... |
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