[FieldTrip] Motor beta activity - DICS solution more noisy than sensor data?
Eelke Spaak
eelke.spaak at donders.ru.nl
Fri Nov 22 12:59:34 CET 2013
As confirmed by Robert, there is indeed a bug in the handling of
distance units in ft_prepare_leadfield. This function will now (FTP
release as of tonight) throw an error if units are not in agreement.
Discussion of this bug will continue at
http://bugzilla.fcdonders.nl/show_bug.cgi?id=2387 or at one of the
related bugs.
Cheers,
Eelke
On 22 November 2013 11:51, Eelke Spaak <eelke.spaak at donders.ru.nl> wrote:
> Following this up: Jan-Mathijs' suggestion did the trick (as usual,
> thanks), at least for the tutorial code. It turns out that it is now
> required to explicitly convert the geometric objects to 'm' before
> doing source analysis.
>
> I am certain that this was not required in the past, as I taught
> workshops with the beamforming-extended tutorial where we did not do
> the unit conversion and results looked fine. So now we will
> investigate what exactly changed and make sure that either the
> conversion is done automatically or the user is informed of
> non-matching units.
>
> Best,
> Eelke
>
>
> On 22 November 2013 09:11, jan-mathijs schoffelen
> <jan.schoffelen at donders.ru.nl> wrote:
>> To all,
>>
>> This reply should have gone to Eelke and not to the whole list. Apologies
>> for that. For those who understand Dutch: doe er je voordeel mee.
>>
>> Groeten,
>> Jan-Mathijs
>>
>>
>>
>> On Nov 22, 2013, at 9:03 AM, jan-mathijs schoffelen wrote:
>>
>> Hoi Eelke,
>>
>> Ik zou in eerste instantie handmatig alle geometrische objecten (headmodel,
>> sourcemodel, grad) naar 'm' ft_convert_units'en. Dit is de conventie die de
>> forward module verwacht. Ik gok dat de high-level functies dit niet
>> afdwingen, waardoor de leadfields er bekaaid van af komen.
>>
>> Gr,
>> JM
>>
>> On Nov 22, 2013, at 8:41 AM, Eelke Spaak wrote:
>>
>> Hi everyone,
>>
>> Thanks very much for your great input so far! Actually, as Jörn
>> suggested, I did the very straightforward check (thanks for the tip :)
>> ) of running one of our tutorial test scripts
>> (test_beamforming_extended), and it turns out this one does not
>> produce the same results as depicted here:
>> http://fieldtrip.fcdonders.nl/tutorial/beamformingextended . So, most
>> likely somewhere a bug has been introduced...
>>
>> Hopefully I can find out what it is today and fix it. Will keep you posted!
>>
>> Best,
>> Eelke
>>
>> On 22 November 2013 08:06, "Jörn M. Horschig" <jm.horschig at donders.ru.nl>
>> wrote:
>>
>> Hi Eelke,
>>
>>
>> since everyone jumped on the train, here my 2 cents:
>>
>> To verify whether this is a newly introduced bug, maybe run a tutorial test
>>
>> script that includes beamforming. If they look alright, it gets more likely
>>
>> that it is you or your data and not fieldtrip :) It's not definite evidence
>>
>> of course though. SinceVitoria also experiences strange things, it might be
>>
>> something worthwhile to investigate.
>>
>>
>> My initial guess from the plots is that there is something wrong with the
>>
>> forward model. All unit problems should have been resolved, but just to be
>>
>> sure you could check whether all objects are in the same unit (make it 'cm'
>>
>> as the grads are).
>>
>>
>> Best,
>>
>> Jörn
>>
>>
>> Charidimos Tzagarakis wrote:
>>
>>
>> Eelke,
>>
>> Thinking again about my second suggestion (regarding individual
>>
>> variability) I actually can't think of a case where this could realistically
>>
>> produce what you get. On the other hand, looking at TF maps per subject and
>>
>> channel (on the "helmet" layout), normalised with a "rest" epoch, may help
>>
>> spot something unusual.
>>
>> Best,
>>
>> Haris
>>
>>
>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>>
>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>
>>
>>
>>
>> On 21 November 2013 18:09, Charidimos Tzagarakis <haristz at gmail.com
>>
>> <mailto:haristz at gmail.com>> wrote:
>>
>>
>> Hi Eelke,
>>
>> Provided there is no major recent revision of the DICS code, I
>>
>> would have expected motor desynchronisation to show up pretty
>>
>> well. Are the maps shown at source and channel level straight
>>
>> differences of L and Right hand conditions at the beta band (I
>>
>> hope I am correctly interpreting your paradigm) ? If so it might
>>
>> be helpful in pinpointing the problem/as a sanity check to see
>>
>> what happens when you use beta desynchonisation (ie change
>>
>> relative to the baseline) instead for each condition, and see
>>
>> source/channel maps of that separately for L and R and then when
>>
>> you take the difference. I suppose the main element this checks
>>
>> for is whether L and R conditions have the same baseline.
>>
>> This doesn't immediately explain why source and channel results
>>
>> are different but in the absence of any other clues it may be a
>>
>> way to 2ble check the whole process.
>>
>>
>>
>> Another point to consider is that, although beta changes should
>>
>> appear in all subjects, it is possibly true that there are
>>
>> individual differences in the actual beta range and frequency bin
>>
>> of maximum effect. If you are using the same settings for all
>>
>> subjects when you beamform with DICS you may be missing some of
>>
>> the effect (true, this is also the case for channel data but there
>>
>> may be subtle differences that add up - there are many voxels and
>>
>> few channels). I believe it may be useful to see what happens when
>>
>> you run the beamformer tailored to each subject's particular beta
>>
>> characteristics (ie change the "foi" for each subject, keep the
>>
>> tapsmofrq the same - possibly smaller) and then combine everything
>>
>> (you'll need of course to come up with a relative metric such as
>>
>> perc. change when you combine all subjects to account for the
>>
>> slightly different frequencies you used )
>>
>>
>> Best,
>>
>> Haris
>>
>>
>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>>
>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>
>>
>>
>>
>> On 21 November 2013 10:36, Eelke Spaak <eelke.spaak at donders.ru.nl
>>
>> <mailto:eelke.spaak at donders.ru.nl>> wrote:
>>
>>
>> Fellow FieldTrippers,
>>
>>
>> Currently I am looking at a contrast for left- versus
>>
>> right-hand index
>>
>> finger button presses. As expected, on sensor level (combined
>>
>> planar
>>
>> gradient, grand average) I see a clear lateralisation in beta band
>>
>> power starting at least 0.5s before the button press (see
>>
>> https://db.tt/Rtch3Qjy). Both 'blobs' are significant; there is
>>
>> clearly more beta power ipsilateral to the response hand. I would
>>
>> prefer to do further analyses on source level, so I attempt to
>>
>> reconstruct the sources for this effect using DICS beamformer
>>
>> (common
>>
>> filter, applied to both conditions separately; fixedori and
>>
>> realfilter
>>
>> = 'yes'). The grand average results for this (again contrast
>>
>> left vs
>>
>> right response hand) are shown at https://db.tt/IBQZG0d8 .
>>
>> (Ignore the
>>
>> R/L-flip, this is radiological convention.)
>>
>>
>> As you can see, the source level solution is much more blurry
>>
>> than on
>>
>> sensor level. This picture is without using any regularisation
>>
>> (lambda
>>
>> parameter), the results are even worse when I use lambda =
>>
>> '5%'. The
>>
>> negative blob (right hand higher power than left) becomes
>>
>> 'marginally
>>
>> significant' on source level (p ~ 0.06) where it was p < 0.001 on
>>
>> sensor level. The positive blob is nowhere near significant.
>>
>> Also, the
>>
>> individual results are much less topographically consistent on
>>
>> source
>>
>> than on sensor level (explaining the worse statistics).
>>
>>
>> I have checked the segmentation of my MRIs, the 'gray' seems to be
>>
>> nicely within the head all the time. Also, I have manually
>>
>> verified
>>
>> the alignment of headmodel, sourcemodel, and gradiometer
>>
>> information
>>
>> for all subjects.
>>
>>
>> As a final note, the above sensor-level plot was taken from a
>>
>> 'slice'
>>
>> out of a planar-gradient time-frequency analysis (mtmconvol). The
>>
>> ingredient for the beamformer was an mtmfft fourier spectrum
>>
>> on the
>>
>> axial gradiometer data, obtained for just the time-frequency
>>
>> range of
>>
>> interest (subselect toilim [-0.5 0], mtmfft foi = 23,
>>
>> tapsmofrq = 7).
>>
>> When I compute condition-averaged power based on these fourier
>>
>> spectra
>>
>> and look at the contrast, the results are again as expected:
>>
>> https://db.tt/n2P3UKcQ (of course less localised because of axial
>>
>> gradient vs planar). The freq structures underlying this
>>
>> contrast are
>>
>> exactly the same as those going into ft_sourceanalysis, so the
>>
>> problem
>>
>> must be in the source analysis step (and/or in the preparation
>>
>> of the
>>
>> geometric information, although these seem fine by visual
>>
>> inspection).
>>
>>
>> Does anyone have any idea that might explain these seemingly
>>
>> contradictory results? I would have expected demixing to improve
>>
>> signal-to-noise ratio, rather than worsen it.
>>
>>
>> Thanks!
>>
>> Best,
>>
>> Eelke
>>
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>>
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>>
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>>
>>
>>
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>>
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>> _______________________________________________
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>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> Jan-Mathijs Schoffelen, MD PhD
>>
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>> http://www.hettaligebrein.nl
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> Jan-Mathijs Schoffelen, MD PhD
>>
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>> http://www.hettaligebrein.nl
>>
>>
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