[Mne_analysis] Maxfilter and PCA-mag-v# projections

[Samu Taulu]

        External Email - Use Caution        

Hi Marijn,

Empty room PCA vectors and the external SSS vectors that are based on a
physical model (vector spherical harmonics converging at the origin of the
coordinate system) typically span a very similar signal subspace.
Therefore, it sounds strange if your MaxFilter-processed data look very bad
while SSP-processed data with just three empty room vectors are good, and
potential bad channels have been excluded in the operations. I would like
to understand what's going on. You could try MaxFilter with a lower
external expansion order by setting -out 1 and then MaxFilter and SSP
should be even more compatible in your case. But I doubt that this solves
the problem. I would be happy to take a look at your problematic file, if
possible?

Best,
Samu


On Wed, Jul 17, 2019 at 12:08 AM Marijn van Vliet <w.m.vanvliet at gmail.com>
wrote:

>         External Email - Use Caution
>
> Thanks, Mainak! I managed to find the files based on this. Sadly, using
> the fine calibration files did not make the filter much better. So I'm
> going with Denis' advice: drop the SSS for this particular subject.
>
> On Wed, Jul 17, 2019 at 5:54 AM Mainak Jas <mainakjas at gmail.com> wrote:
>
>>         External Email - Use Caution
>>
>> Hi Marijn,
>>
>> Regarding your first, question:
>>
>> > can anyone enlighten me a little about the three 'default' projections
>> PCA-mag-v1, PCA-mag-v2 and PCA-mag-v3. Where do they come from
>>
>> They are coming from the empty room recording.
>>
>> Also,
>> > However, I don’t have access to a crosstalk file or a fine calibration
>> file
>>
>> According to Maxfilter manual, you can find them at:
>>
>> $(NEUROMAG_ROOT)/databases/ctc/ct_sparse.fif
>> $(NEUROMAG_ROOT)/databases/sss/sss_cal.dat
>>
>> Best,
>> Mainak
>>
>> Best,
>> Mainak
>>
>> On Tue, Jul 16, 2019 at 12:32 PM Denis A. Engemann <
>> denis-alexander.engemann at inria.fr> wrote:
>>
>>>         External Email - Use Caution
>>>
>>> I’d say if your data is clean enough to do without maxfilter then don’t
>>> bother with it. The proj approach is less invasive and more conservative.
>>>
>>> > On 16 Jul 2019, at 18:26, Marijn van Vliet <w.m.vanvliet at gmail.com>
>>> wrote:
>>> >
>>> >        External Email - Use Caution
>>> >
>>> > Hi Denis,
>>> >
>>> > thanks for confirming that the PCA projections are indeed dropped.
>>> > Q1: I’m careful to take bad channels into account. However, I don’t
>>> have access to a crosstalk file or a fine calibration file. Maybe these
>>> will make all the difference.
>>> > W2: I guess you are right in that I don’t *need* maxfilter, since the
>>> data is pretty clean to begin with. I was just wondering about the
>>> interplay between the PCA projections and maxfilter, since the projections
>>> seem superior in this case.
>>> >
>>> > best,
>>> > Marijn.
>>> >
>>> >> On 16 Jul 2019, at 18:52, Denis-Alexander Engemann <
>>> denis.engemann at gmail.com> wrote:
>>> >>
>>> >>        External Email - Use Caution
>>> >>
>>> >>
>>> >> First they are discarded as you project to the low rank coordinate
>>> system of maxfilter. After this the SSPs are not valid any longer. Question
>>> : do you take into account bad channels before computing maxfilter? It
>>> sounds as if something is not right with its computation.
>>> >> Question 2: if your data looks good, do you need maxfilter then in
>>> the first place?
>>> >>
>>> >> Denis
>>> >>
>>> >> On Tue 16 Jul 2019 at 15:32, Marijn van Vliet <
>>> marijn.vanvliet at aalto.fi> wrote:
>>> >>        External Email - Use Caution
>>> >>
>>> >> Dear MNE users,
>>> >>
>>> >> can anyone enlighten me a little about the three 'default'
>>> projections
>>> >> PCA-mag-v1, PCA-mag-v2 and PCA-mag-v3. Where do they come from and
>>> why are they
>>> >> "discaded" by the maxfiltering process? My mags look pretty clean
>>> with them
>>> >> applied, but after maxfiltering, they look much worse, similar to not
>>> applying
>>> >> the PCA projections.
>>> >>
>>> >> best,
>>> >> Marijn.
>>> >>
>>> >>
>>> >> --
>>> >> Marijn van Vliet
>>> >> Postdoctoral Researcher
>>> >> Department of Neuroscience and Biomedical Engineering
>>> >> Aalto University, Finland
>>> >>
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>
>
> --
> Marijn van Vliet
> w.m.vanvliet at gmail.com
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