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

Mainak Jas mainakjas at gmail.com
Tue Jul 16 22:53:34 EDT 2019
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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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