tutorial

PURPOSE

SYNOPSIS

DESCRIPTION

% Preparation

CROSS-REFERENCE INFORMATION

• apply_ica_eeg Apply ICA to EEG data
• apply_ica_meg Apply ICA to MEG data
• calculate_connectivity Calculate connectivity matrix from the result of fiber tracking
• calculate_fodf Calculate fiber orientation density function (fodf)
• calculate_roi_current Calculate ROI-current
• check_denoised_meg Check denoised MEG data
• check_imported_fmri Check imported fMRI result
• check_removing_eog_from_eeg Check the result of removing EOG components from EEG data
• check_removing_eog_from_meg Check the result of removing EOG components from MEG data
• classify_ic_eeg Aucomatically classify ICs into brain activites and noise
• classify_ic_meg Aucomatically classify ICs into brain activites and noise
• combine_trial_eeg Combine trials across runs
• combine_trial_meg Combine trials across runs
• common_average_eeg Take common average
• construct_brain_model Construct brain model
• construct_cortical_surface_model Construct cortical surface model from T1 image using FreeSurfer
• coregister_images Coregister T1 and cortical surface models to FA images
• correct_baseline_eeg Correct baseline of EEG data
• correct_baseline_meg Correct baseline of MEG data
• correct_bias_in_T1 Correct bias in T1 image.
• correct_classify_ic_eeg Manually correct classification of ICs
• correct_classify_ic_meg Manually correct classification of ICs
• correct_motion_in_dmri Correct motion in dMRI
• create_fa_from_dmri Create Fractional Anisotropy (FA) image from dMRI
• create_mask_for_fiber_tracking Create mask for fiber tracking
• create_movie Create movie showing signal flows
• create_project Set paths and parameters for all the processes
• detect_blink_from_eog Detect trials in which blinks occurred for visual task
• estimate_dynamics_model Estimate linear dynaics model constrained by anatomical connectivity
• estimate_source_current_eeg Estimate source currents from EEG data
• estimate_source_current_meeg Estimate source currents from MEG data
• estimate_source_current_meg Estimate source currents from MEG data
• extract_brain_from_T1 Extract brain from T1 image
• extract_brain_from_dmri Make mask to extract brain from dMRI
• fiber_tracking Execute fiber tracking
• fiber_tracking_for_movie Execute fiber tracking for creating movie
• filter_eeg Filter EEG data
• filter_meg Filter MEG data
• import_T1 convert T1 DICOM files to NIfTI(.nii)
• import_blink_from_eeg Import blink information from EEG data to MEG data
• import_dmri Import dMRI
• import_eeg Construct brain model
• import_fmri Import fMRI result
• import_meg Import MEG data
• make_trial_eeg Make trial data
• make_trial_meg Make trial data
• parcel_cortical_surface Parcel cortical surface
• parcel_fa_volume Parcel FA volume based on parcelled cortical surface
• prepare_input_for_movie Prepare the following variables for creating movie
• prepare_leadfield_eeg Prepare leadfield matrix
• prepare_leadfield_meg Prepare leadfield matrix
• regress_out_eog_from_eeg Regress out EOG components from EEG data
• regress_out_eog_from_meg Regress out EOG components from MEG data
• reject_channel_eeg Reject noisy EEG channels
• reject_channel_meg Reject noisy MEG channels
• reject_trial_eeg Reject trials in which blinks occurred
• reject_trial_meg Reject trials in which blinks occurred
• remove_env_noise_meg Remove environmental noise from MEG data using reference sonsor data by temporal PCA
• remove_noise_ic_eeg Remove noise ICs from EEG data
• remove_noise_ic_meg Remove noise ICs from MEG data
• remove_noise_in_fa Remove ambient noise in FA image by using brain mask extracted from T1
• segment_T1 Segment T1 image.
• separate_eeg Separate trials into auditory, somatosensory, and visual tasks
• separate_meg Separate trials into auditory, somatosensory, and visual tasks
• show_connectivity Show connectivity
• show_ic_eeg Show ICs
• show_ic_meg Show ICs
• show_source_current_eeg Show source current estimated from EEG data
• show_source_current_meeg Show source current estimated from EEG-MEG data
• show_source_current_meg Show source current estimated from MEG data
• show_trial_average_eeg Show trial-averaged EEG data
• show_trial_average_meg Show trial-averaged MEG data
• apply_ica_eeg Apply ICA to EEG data
• check_removing_eog_from_eeg Check the result of removing EOG components from EEG data
• classify_ic_eeg Aucomatically classify ICs into brain activites and noise
• common_average_eeg Take common average
• correct_baseline_eeg Correct baseline of EEG data
• correct_classify_ic_eeg Manually correct classification of ICs
• detect_blink_from_eog Detect trials in which blinks occurred for visual task
• estimate_source_current_eeg Estimate source currents from EEG data
• filter_eeg Filter EEG data
• import_blink_from_eeg Import blink information from EEG data to MEG data
• import_eeg Construct brain model
• make_trial_eeg Make trial data
• prepare_leadfield_eeg Prepare leadfield matrix
• regress_out_eog_from_eeg Regress out EOG components from EEG data
• reject_channel_eeg Reject noisy EEG channels
• reject_trial_eeg Reject trials in which blinks occurred
• remove_noise_ic_eeg Remove noise ICs from EEG data
• show_ic_eeg Show ICs
• show_source_current_eeg Show source current estimated from EEG data
• show_trial_average_eeg Show trial-averaged EEG data
• vbmeg This function is an environmental configuration file of VBMEG.

SOURCE CODE

0001 %% Preparation
0002 
0003 % Download and unzip tutorial.zip
0004 % Copy and paste all the files to $your_dir
0005 % Start MATLAB (This tutorial was developed using MATLAB 2013b)
0006 % Change current direcotry to $your_dir/program
0007 
0008 %% Starting a project
0009 
0010 % Addting paths to necessary toolboxes
0011 addpath(path_of_VBMEG);% VBMEG
0012 vbmeg
0013 addpath(path_of_SPM8);% SPM8
0014 
0015 % Creating a project
0016 sub='s006';% s006 or s043
0017 p=create_project(sub);% Set paths and parameters for all the processes
0018 
0019 %% Brain modeling
0020 import_T1(p);% Convert T1 DICOM files to NIfTI
0021 correct_bias_in_T1(p);
0022 segment_T1(p);
0023 construct_cortical_surface_model(p);% Apply Freesurfer
0024 construct_brain_model(p);% Define current sources
0025 
0026 %% Import fMRI information
0027 import_fmri(p);
0028 check_imported_fmri(p);% Show .act file
0029 
0030 %% EEG preprocessing
0031 close all
0032 import_eeg(p);% Convert BrainAmp file to MAT
0033 filter_eeg(p);
0034 make_trial_eeg(p);
0035 detect_blink_from_eog(p);
0036 regress_out_eog_from_eeg(p);% Prefix : r_
0037 check_removing_eog_from_eeg(p);
0038 correct_baseline_eeg(p);% Prefix : br_
0039 combine_trial_eeg(p);
0040 apply_ica_eeg(p);
0041 classify_ic_eeg(p);
0042 correct_classify_ic_eeg(p);% Need inputs
0043 show_ic_eeg(p);
0044 remove_noise_ic_eeg(p);% Prefix : i_
0045 reject_channel_eeg(p);% Prefix : ri_
0046 reject_trial_eeg(p);% Prefix : rri_
0047 common_average_eeg(p);% Prefix : crri_
0048 separate_eeg(p);% Prefix : crri_
0049 show_trial_average_eeg(p);
0050 
0051 %% Source imaging from EEG data
0052 close all
0053 prepare_leadfield_eeg(p);
0054 estimate_source_current_eeg(p);
0055 show_source_current_eeg(p);
0056 
0057 %% MEG preprocessing
0058 close all
0059 import_meg(p);
0060 remove_env_noise_meg(p);
0061 check_denoised_meg(p);
0062 filter_meg(p);
0063 make_trial_meg(p);
0064 import_blink_from_eeg(p);
0065 regress_out_eog_from_meg(p);% Prefix : r_
0066 check_removing_eog_from_meg(p);
0067 correct_baseline_meg(p);% Prefix : br_
0068 combine_trial_meg(p);
0069 apply_ica_meg(p);
0070 classify_ic_meg(p);
0071 correct_classify_ic_meg(p);% Need inputs
0072 show_ic_meg(p);
0073 remove_noise_ic_meg(p);% Prefix : i_
0074 reject_channel_meg(p);% Prefix : ri_
0075 reject_trial_meg(p);% Prefix : rri_
0076 separate_meg(p);% Prefix : rri_
0077 show_trial_average_meg(p);
0078 
0079 %% Source imaging from MEG data
0080 close all
0081 prepare_leadfield_meg(p);
0082 estimate_source_current_meg(p);
0083 show_source_current_meg(p);
0084 
0085 %% Source imaging from EEG-MEG data
0086 close all
0087 estimate_source_current_meeg(p);
0088 show_source_current_meeg(p);
0089 
0090 %% dMRI processing
0091 close all
0092 extract_brain_from_T1(p);
0093 import_dmri(p);
0094 correct_motion_in_dmri(p);% 30 min
0095 extract_brain_from_dmri(p);
0096 create_fa_from_dmri(p);
0097 coregister_images(p);% 1 hour
0098 remove_noise_in_fa(p);
0099 parcel_cortical_surface(p);
0100 parcel_fa_volume(p);
0101 create_mask_for_fiber_tracking(p);
0102 calculate_fodf(p);
0103 fiber_tracking(p);% 3 hours
0104 calculate_connectivity(p);
0105 show_connectivity(p);
0106 
0107 %% Dynamics modeling
0108 close all
0109 calculate_roi_current(p);
0110 estimate_dynamics_model(p);
0111 
0112 %% Creating movie showing signal flows
0113 prepare_input_for_movie(p);
0114 fiber_tracking_for_movie(p);
0115 create_movie(p);
0116 
0117 
0118