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

[Marijn van Vliet]

        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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