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Hello,</div>
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<br>
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I've been trying to put together all the pieces of code I needed for calculating whole brain functional connectivity from MEG recordings. The code is running and gives some results, but the connectivity matrix it produces seems to have some artefacts. Could
you advise what should I change to fix it?</div>
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I'm using data from the CamCAN project, and for now, I'm trying with a single subject.</div>
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Here is the script I'm using:<br>
<br>
<span style="font-family: "Courier New", monospace;">ft_defaults</span></div>
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meg_file = 'sub-CC110033_ses-rest_task-rest_proc-sss.fif';</div>
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mri_file = 'sub-CC110033_T1w.nii';</div>
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% from: https://natmeg.se/MEEG_course2018/preprocess_MRI_data2.html</div>
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%% HEAD MODEL %%</div>
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%% Reading files and determining coordinate system</div>
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mri = ft_read_mri(mri_file);</div>
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%% Reading Anatomical Landmark Coordinates from .jason file (MEG data folder)</div>
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fileName = 'sub-CC110033_ses-rest_task-rest_proc-sss_coordsystem.json'; % filename in JSON extension</div>
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fid = fopen(fileName); % Opening the file</div>
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raw = fread(fid,inf); % Reading the contents</div>
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str = char(raw'); % Transformation</div>
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fclose(fid); % Closing the file</div>
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coord_data = jsondecode(str); % Using the jsondecode function to parse JSON from string</div>
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<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
NAS = coord_data.AnatomicalLandmarkCoordinates.NAS;</div>
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LPA = coord_data.AnatomicalLandmarkCoordinates.LPA;</div>
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RPA = coord_data.AnatomicalLandmarkCoordinates.RPA;</div>
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%% Co-register MRI to Neuromag based on fiducials</div>
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cfg = [];</div>
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cfg.method = 'fiducial';</div>
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cfg.fiducial.nas = NAS;</div>
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cfg.fiducial.lpa = LPA;</div>
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cfg.fiducial.rpa = RPA;</div>
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cfg.coordsys = 'acpc'; % only with acpc coordinate system co-registration looks alright</div>
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mri_realigned_1 = ft_volumerealign(cfg, mri);</div>
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headshape = ft_read_headshape(meg_file); % Load head shape</div>
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grad = ft_read_sens(meg_file,'senstype','meg'); % Load MEG sensors</div>
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%% Automatic procedure called “iterative closest point” (icp) to fit fiducials and head points</div>
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cfg = [];</div>
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cfg.method = 'headshape';</div>
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cfg.headshape.headshape = headshape;</div>
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cfg.headshape.icp = 'yes';</div>
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cfg.coordsys = 'acpc';</div>
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cfg.headshape.interactive = 'no';</div>
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mri_realigned_2 = ft_volumerealign(cfg, mri_realigned_1);</div>
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% sensors do not fit the head shape at this point!</div>
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%% Checking co-registration</div>
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cfg = [];</div>
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cfg.method = 'headshape';</div>
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cfg.headshape.headshape = headshape;</div>
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cfg.coordsys = 'acpc';</div>
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cfg.headshape.icp = 'no';</div>
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cfg.headshape.interactive = 'no';</div>
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mri_realigned_3 = ft_volumerealign(cfg, mri_realigned_2);</div>
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% sensors fit the head shape now</div>
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%% Reslice MRI data and convert units</div>
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cfg = [];</div>
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cfg.resolution = 1;</div>
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mri_resliced_mm = ft_volumereslice(cfg, mri_realigned_3);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
mri_resliced_cm = ft_convert_units(mri_resliced_mm, 'cm');</div>
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%% Segment data into brain, skull, and scalp</div>
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cfg = [];</div>
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cfg.output = {'brain' 'skull' 'scalp'};</div>
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mri_segmented = ft_volumesegment(cfg, mri_resliced_cm);</div>
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%% Correct the segmentation</div>
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binary_brain = mri_segmented.brain;</div>
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binary_skull = mri_segmented.skull | binary_brain;</div>
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binary_scalp = mri_segmented.scalp | binary_brain | binary_skull;</div>
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binary_scalp = mri_segmented.scalp + binary_skull;</div>
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% use boolean logic together with IMERODE</div>
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binary_skull = binary_skull & imerode(binary_scalp, strel_bol(2)); % fully contained inside eroded scalp</div>
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binary_brain = binary_brain & imerode(binary_skull, strel_bol(2)); % fully contained inside eroded skull</div>
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%% Copy the segmented volume into a new structure</div>
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mri_segmented_2 = mri_segmented; % Copy stucture</div>
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mri_segmented_2.anatomy = mri_resliced_cm.anatomy; % Copy anatomical image</div>
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</div>
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% insert the updated binary volumes, taking out the center part for skull and scalp</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
mri_segmented_2.brain = binary_brain;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
mri_segmented_2.skull = binary_skull & ~binary_brain;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
mri_segmented_2.scalp = binary_scalp & ~binary_brain & ~binary_skull;</div>
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%% Construct mesh for brain segment</div>
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cfg = [];</div>
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cfg.method = 'projectmesh';</div>
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cfg.tissue = 'brain';</div>
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cfg.numvertices = 3000;</div>
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mesh_brain = ft_prepare_mesh(cfg, mri_segmented_2);</div>
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%% Construct head model for MEG</div>
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cfg = [];</div>
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cfg.method = 'singleshell';</div>
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headmodel = ft_prepare_headmodel(cfg, mesh_brain);</div>
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% from: https://natmeg.se/MEEG_course2018/preprocess_MRI_data2.html</div>
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% END of NatMEG tutorial</div>
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%% SOURCE MODEL %%</div>
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%% Load source model template</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
ftpath = 'fieldtrip-20220707\template\sourcemodel\standard_sourcemodel3d10mm.mat';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
load(ftpath);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
template_grid = sourcemodel;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
clear sourcemodel;</div>
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%% Prepare source model based on MNI template</div>
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cfg = [];</div>
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% cfg.warpmni = 'yes'; % Warning: please specify cfg.method='basedonmni' instead of cfg.warpmni='yes'</div>
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cfg.method = 'basedonmni';</div>
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cfg.nonlinear = 'yes';</div>
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cfg.unit = 'cm';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.resolution = 1;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.template = template_grid;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.headshape = headshape;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.headmodel = headmodel;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.mri = mri_resliced_cm;</div>
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<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
sourcemodel = ft_prepare_sourcemodel(cfg);</div>
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%% ########################################################################</div>
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%% SOURCE RECONSTRUCTION %%</div>
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<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
%% MEG preprocessing</div>
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cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.dataset = meg_file;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.continuous = 'yes';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.channel = {'MEG'};</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
data = ft_preprocessing(cfg);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.length = 2;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.overlap = 0.5;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
data = ft_redefinetrial(cfg, data);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.demean = 'yes';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
data = ft_preprocessing(cfg, data);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.resamplefs = 100;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.detrend = 'yes';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
meg_preprocessed = ft_resampledata(cfg, data);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
%% Compute the leadfield</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.grid = sourcemodel;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.headmodel = headmodel;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.channel = {'MEG'};</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
lf = ft_prepare_leadfield(cfg, meg_preprocessed);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
%% MEG frequency analysis [frequency band]</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
% compute sensors level Fourier spectra (for cross-spectral density computation)</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
% from: https://www.fieldtriptoolbox.org/tutorial/beamformer/</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
% https://github.com/fieldtrip/fieldtrip/blob/release/ft_freqanalysis.m</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.method = 'mtmfft';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.output = 'fourier';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.keeptrials = 'yes';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.tapsmofrq = 1;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.foilim = [8 13];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
freq_alpha = ft_freqanalysis(cfg, meg_preprocessed);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
%% Source reconstruction</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.frequency = [8 13];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.method = 'pcc';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.grid = lf;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.headmodel = headmodel;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.sourcemodel = sourcemodel;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.keeptrials = 'yes';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.pcc.lambda = '10%';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.pcc.projectnoise = 'yes';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.pcc.fixedori = 'yes';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
source = ft_sourceanalysis(cfg, freq_alpha);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
%% Compute connectivity</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
% from: https://www.fieldtriptoolbox.org/tutorial/networkanalysis/</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.method = 'coh';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.complex = 'absimag';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
source_conn = ft_connectivityanalysis(cfg, source);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
figure;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
imagesc(source_conn.cohspctrm);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
%% Read the atlas</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
atlas = ft_read_atlas('fieldtrip-20220707\template\atlas\aal\ROI_MNI_V4.nii');</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
%% Source interpolation</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.parameter = 'tissue';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.interpmethod = 'nearest';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
sourcemodel_interpolated = ft_sourceinterpolate(cfg, atlas, sourcemodel);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
%% Source parcelation</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
sourcemodel_interpolated.pos = source_conn.pos; % otherwise the parcellation won't work</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg = [];</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
% cfg.parcellation = 'parcellation'; % ft_sourceparcellate(cfg, source_conn, sourcemodel_interpolated) -> Error: Unrecognized field name "parcellation".</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
cfg.parameter = 'cohspctrm';</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
% parc_conn = ft_sourceparcellate(cfg, source_conn, atlas); % -> Error: the units of the source and parcellation structure are not consistent, please use FT_SOURCEINTERPOLATE</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
% parc_conn = ft_sourceparcellate(cfg, sourcemodel_interpolated, source_conn); % -> Error: This function requires parcellation data as input, see ft_datatype_parcellation.</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
parc_conn = ft_sourceparcellate(cfg, source_conn, sourcemodel_interpolated);</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
figure;</div>
<div style="font-family: "Courier New", monospace; font-size: 12pt; color: rgb(0, 0, 0);">
imagesc(parc_conn.cohspctrm);</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
Kind regards,</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Kinga</div>
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