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Hi Kirandeep,
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<div class="">Is there a relationship between whether or not the job crashes, and the exact length of the data (I assume a ‘resting state’) recording? If so, you might be suffering from an out-of-memory problem, which for some reason is not well handled (by
means of an informative error) by matlab. If it is indeed a memory problem, a cheap answer would be: run your jobs on a computer that has a larger RAM. </div>
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<div class="">Alternatively (and more constructively), you may consider to specify cfg.projectmom = ’no’; prior to ft_sourceanalysis. I would assume that - given that you also specify cfg.kurtosis = ‘yes’ - the source projected sensor data are not really needed
in memory for downstream processing. The fact that you specified projectmom to be yes, will lead to the creation of a lot of data, i.e. 500 Hz * 720 seconds * 15000 dipoles * 8 bytes per sample = 4.32e10 bytes ~ 40 GB, which is quite a lot.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<blockquote type="cite" class="">
<div class="">On 28 Jul 2022, at 16:25, Kirandeep Kaur via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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<div dir="ltr" class="">Dear all, this is a query regarding implementation of LCMV beamformer.
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<div class="">I am using ft_sourceanalysis to compute the beamformer virtual channels and kurtosis for data collected from Elekta Neuromag 306 channels MEG scanner. However, while scanning the grid (typically ranging from 12,000 - 15,000 points), my MATLAB
(R2021a) simply shuts down without any error. This also typically happens after the function has scanned >11,000 grid points. </div>
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<div class="">This problem is occurring for roughly 40% of my subjects. The sampling rate is downsampled to 500Hz, and the duration of continuous MEG record for which I am computing the beamformer is typically 10-12 minutes. I am using the reconstructed MRI
from Freesurfer (orig.magz) for constructing the head model. A snapshot of the code I am using is given here : </div>
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<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
%% compute leadfield<span class="gmail-Apple-converted-space"> </span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg = [];</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.channel = <span class="gmail-s1" style="color:rgb(170,4,249)">'MEG'</span>;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.headmodel = headmodel;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.sourcemodel = sourcemodel;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
<span class="gmail-s2" style="">cfg.normalize = </span><span class="gmail-s1" style="color:rgb(170,4,249)">'yes'</span><span class="gmail-s2" style="">;
</span>% normalisation avoids power bias towards centre of head</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.reducerank = 2;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
leadfield = ft_prepare_leadfield(cfg, cov_matrix);</div>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px">
<span class="gmail-Apple-converted-space"> </span><br class="webkit-block-placeholder">
</p>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(170, 4, 249);" class="">
<span class="gmail-s2" style="">save (</span>'leadfield'<span class="gmail-s2" style="">);<span class="gmail-Apple-converted-space"> </span></span></div>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px">
<span class="gmail-Apple-converted-space"> </span><br class="webkit-block-placeholder">
</p>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
%% %plot svd of covariance matrix<span class="gmail-Apple-converted-space"> </span></div>
<p class="gmail-p5" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(2,128,9);min-height:12px">
<span class="gmail-Apple-converted-space"> </span><br class="webkit-block-placeholder">
</p>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
[u,s,v] = svd(cov_matrix.cov);</div>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px">
<span class="gmail-Apple-converted-space"> </span><br class="webkit-block-placeholder">
</p>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
figure;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
semilogy(diag(s),<span class="gmail-s1" style="color:rgb(170,4,249)">'o-'</span>);</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(170, 4, 249);" class="">
<span class="gmail-s2" style="">savefig (gcf, </span>'svd_covariance.fig'<span class="gmail-s2" style="">,
</span>'compact'<span class="gmail-s2" style="">); <span class="gmail-Apple-converted-space">
</span></span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
close <span class="gmail-s1" style="color:rgb(170,4,249)">all</span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
%% compute the LCMV beamformer<span class="gmail-Apple-converted-space"> </span></div>
<p class="gmail-p5" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(2,128,9);min-height:12px">
<span class="gmail-Apple-converted-space"> </span><br class="webkit-block-placeholder">
</p>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg = [];</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.method = <span class="gmail-s1" style="color:rgb(170,4,249)">'lcmv'</span>;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.sourcemodel = leadfield;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.headmodel = headmodel;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.lcmv.keepfilter = <span class="gmail-s1" style="color:rgb(170,4,249)">'yes'</span>;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
<span class="gmail-s2" style="">cfg.lcmv.fixedori = </span><span class="gmail-s1" style="color:rgb(170,4,249)">'yes'</span><span class="gmail-s2" style="">;
</span>% project on axis of max variance using SVD</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.lcmv.lambda = <span class="gmail-s1" style="color:rgb(170,4,249)">'5%'</span>;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.lcmv.kappa = 69;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
<span class="gmail-s2" style="">cfg.lcmv.projectmom = </span><span class="gmail-s1" style="color:rgb(170,4,249)">'yes'</span><span class="gmail-s2" style="">;
</span>% project dipole time series in direction of maximal power<span class="gmail-Apple-converted-space"> </span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.lcmv.kurtosis = <span class="gmail-s1" style="color:rgb(170,4,249)">'yes'</span>;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.lcmv.keepmom = <span class="gmail-s1" style="color:rgb(170,4,249)">'yes'</span>;</div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
source = ft_sourceanalysis(cfg, cov_matrix);</div>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px">
<span class="gmail-Apple-converted-space"> </span><br class="webkit-block-placeholder">
</p>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
save (<span class="gmail-s1" style="color:rgb(170,4,249)">'source'</span>);<span class="gmail-Apple-converted-space"> </span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
<span class="gmail-Apple-converted-space"><br class="">
</span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
<span class="gmail-Apple-converted-space">-------------------------------------------------------</span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
<span class="gmail-Apple-converted-space"><br class="">
</span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
<span class="gmail-Apple-converted-space"><br class="">
</span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal; font-family: Courier;" class="">
<span class="gmail-Apple-converted-space" style=""><br class="">
</span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class="">
<span class="gmail-Apple-converted-space" style=""><font face="arial, sans-serif" style="" class="">Any help regarding this would be very useful since I am not able to find a solution to this problem. </font></span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class="">
<span class="gmail-Apple-converted-space" style=""><font face="arial, sans-serif" style="" class=""><br class="">
</font></span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class="">
<span class="gmail-Apple-converted-space" style=""><font face="arial, sans-serif" style="" class="">Kind regards, </font></span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class="">
<span class="gmail-Apple-converted-space" style=""><font face="arial, sans-serif" style="" class=""><br class="">
</font></span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class="">
<span class="gmail-Apple-converted-space" style=""><font face="arial, sans-serif" style="" class="">Kirandeep Kaur, </font></span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class="">
<span class="gmail-Apple-converted-space" style=""><font face="arial, sans-serif" style="" class="">Research Fellow, Aston University, </font></span></div>
<div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class="">
<span class="gmail-Apple-converted-space" style=""><font face="arial, sans-serif" style="" class="">Birmingham, UK</font></span></div>
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