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Dear Alexander,
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<div class="">I am not sure whether I completely follow your diagnostic steps and your conclusions, but I would also check:</div>
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<div class="">- the alignment between the electrodes, volume conduction model, and source model.</div>
<div class="">- are the electrode positions expressed in the same coordinate system as the volume conductor/source model?</div>
<div class="">- are the leadfields well-behaved? For instance: if the dipole locations are too close to the innermost mesh, numerical problems may arise. </div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 12 Oct 2018, at 18:34, Nakhnikian, Alexander <<a href="mailto:Alexander_Nakhnikian@hms.harvard.edu" class="">Alexander_Nakhnikian@hms.harvard.edu</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear All,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Apologies for the long post, I've tried to be as succinct as possible while describing my problem is sufficient detail.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I've been trying to solve a problem with source modeling for sometime. I've found that distributed source estimates (MNE, sLORETA, eLORETA) are heavily biased towards the ventral temporal lobe. This
is the case with multiple data sets analyzed using both built-in field trip functions and imaging kernels generated by my own code. It occurs in within group grand averages and statistical contrasts between controls and patients. I've confirmed that sLORETA
and eLORETA are unbiased for noiseless data by filtering point sources through the resolution kernel. <font size="3" class="">I'm working on a Mac running OS 10.11.6 and the latest version of Field Trip. I'm using a standard 10/10 electrode layout (no individual
sensor locations) with 4 custom locations (PO9/PO10, M1/M2) and Field Trip's template BEM. The forward model is restricted to the </font>cortical mantle (I've had similar problems with whole brain forward models as well).</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I recently ran PCA at the source level to explore the issue. The data were collecting during quiet rest and bandpassed to isolate a peak that accounts for a significant difference between controls and
patients at the sensor level. The imaging kernel was applied to the sensor spectral matrix. To obtain the PCs, I analyzed the covariance of power among voxels. The rank of the voxel covariance matrix was 31 with the first 3 eigenvalues account for approximately
95% of the variance. Interestingly, the spatial distribution of the first three principal components exhibited the same bias as the sensor data. When I reconstructed the source data<span class="Apple-converted-space"> </span><i class="">omitting<span class="Apple-converted-space"> </span></i>the
first 3 components, the control-patient contrast localized to a collection of canonical DMN nodes. </div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">It seems extremely odd to me that removing so much of the information present in the original data returns a reasonable source-level contrast while the majority of variance is accounted for by what
is clearly bias. I cannot complete this analysis and submit the results unless I can isolate the problem and correct it so I can run the analysis without reducing the rank of the source data. If anyone can speculate on possible reasons for this problem and/or
potential solutions I would be grateful.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Thank you,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Alexander</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Alexander Nakhnikian, Ph.D.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Research Investigator</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 12pt;" class="">VA Boston Healthcare System</span><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Instructor in Psychiatry, Harvard Medical School</div>
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<span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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