[Mne_analysis] question about FIFF constants and CTF data

dgw dgwakeman at gmail.com
Fri Jun 27 10:02:32 EDT 2014
Search archives: 
The only one I am aware of is EGI's photogrammetry system, but I think you
need to be using EGI equipment to use it (you could contact them and ask.
They are very helpful.)

D


On Fri, Jun 27, 2014 at 9:37 AM, Ghuman, Avniel <ghumana at upmc.edu> wrote:

> Hi Dan (or anyone else),
>
> Do you know where I can get more information about automated
> coregistration based on photos? I believe you generally need a 3-d camera.
> I have been trying to find a reference and/or someone who can help us test
> something like that out here...
>
> Best wishes,
> Avniel
>
> ________________________________
> From: mne_analysis-bounces at nmr.mgh.harvard.edu [
> mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of dgw [
> dgwakeman at gmail.com]
> Sent: Friday, June 27, 2014 9:20 AM
> Cc: Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] question about FIFF constants and CTF data
>
> Hi Gustavo,
>
> I guess to answer your original question it sounds like everything was
> done correctly in the file conversion. In MNE vocab we would call those HPI
> coils (which can produce either continuous or one shot head position
> measurements). From the photos, you can try to generate your MRI-MEG
> transform by eye (or there are some software packages, which if you have a
> sufficient number of photos and sufficient geometric information about
> where the photos were taken from, there are automated techniques, but I
> believe these require you to acquire the photos in a particular manner). If
> you don't have any points except for those three you can use mne-python (or
> most MEG software packages) to get a transformation matrix, but as I said
> with only three points getting a reliable data fit can be difficult (for
> future studies I would recommend using a polhemus etc. to get additional
> points).
>
> HTH,
> D
>
>
> On Fri, Jun 27, 2014 at 9:03 AM, Gustavo Sudre <gsudre at gmail.com<mailto:
> gsudre at gmail.com>> wrote:
> Anyone that knows the CTF system better, please feel free to correct me.
>
> AFAIK, they're closer to cHPI coils, but called CHL (Continuous Head
> Localization). They were not digitized (i.e. no Polhemus or laser scanner),
> but photos of the coil locations were taken for each subject, and some
> subjects did have their MRIs with vitamin E locators. But the coils are
> normally placed along the 3 standard fiducial locations, and plugged to the
> machine at specific ports (e.g. nasion coil into nasion port, etc). I'm
> assuming the ds to fiff conversion takes that into consideration when
> converting those coils into the dig struct, but I could be wrong, and
> that's where the first question about point coordinates and identity came
> from. Also, when continuous head localization is used, the information in
> these 3 coils is saved as 3 special channels in the ds file.
>
> Best,
>
> Gus
>
>
> On Thu, Jun 26, 2014 at 8:20 PM, dgw <dgwakeman at gmail.com<mailto:
> dgwakeman at gmail.com>> wrote:
> Hi Gustavo,
>
> On Jun 26, 2014, at 6:15 PM, Gustavo Sudre wrote:
>
> > The question is really 2-fold:
> >
> > 1) Looking at the value of ident and kind keys of the output I sent in
> my first e-mail, and comparing them to FIFF constants, it tells me
> something about those points (regardless of their order in the dict). Based
> on the coordinates, shouldn't that first point in the output be nasion
> (according to the manual, ident=2)? To answer Dan's question about
> digitization, I don't know about this specific dataset, but I see a similar
> pattern on the ones I have. In those cases, there was no digitization
> per-se (i.e. not like what I used to do with a Polhemus and the Elekta
> machine), but there are 3 electrodes placed near the fiducial points that
> are plugged to the machine accordingly to their positions on the head. So,
> maybe that's how they would get assigned to particular points.
> >
> Are these electrodes or Head Position Indicator Coils (or whatever the CTF
> name is). An electrode is used for measuring EEG data, while an HPI coil
> produces a magnetic field that is used to determine the head position. Is
> there no digitization at all (not with photos or a laser scanner)?
>
> > 2) Does this matter at all? In other words, say the identity of the
> points is indeed mislabeled (but again, that's what I'm wondering in the
> first question). Does it matter going forward, when using the MRI-MEG
> transformation matrix, creating fwd solutions, etc? I can see how it would
> matter, but maybe the transformations are performed in ways that they don't.
> >
> If you haven't digitized any of the positions in any way, it will be very
> difficult to get an accurate MRI-MEG transformation matrix. If that matrix
> is inaccurate it will introduce error into your forward solution. From your
> description it sounds like there would only be three points to fit (which I
> suspect are HPI coils).
>
> HTH,
> D
>
> > Let me know if I made it more confusing than before :)
> >
> > Thanks,
> >
> > G
> >
> >
> > On Thu, Jun 26, 2014 at 5:52 PM, Denis A. Engemann <
> denis.engemann at gmail.com<mailto:denis.engemann at gmail.com>> wrote:
> > Hi all,
> >
> > On Jun 26, 2014, at 11:29 PM, dgw <dgwakeman at gmail.com<mailto:
> dgwakeman at gmail.com>> wrote:
> >
> >> Hi Gustavo,
> >>
> >> I'm not entirely sure what your question is, but I can tell you this. I
> don't think lists are ordered in python (and raw.info<http://raw.info>['dig']
> is a list).
> >
> > Lists are ordered, dictionaries aren't.
> >
> >> It seems that in the case of the file you are talking about, you get
> three HPI locations and 2 EEG locations.
> >>
> >
> > IIRC you normally get 3 fiducials followed by 2 hpi coils
> >
> >> Are you asking why aren't there fiducial points? If so can you tell us
> more about the data, were these points digitized?
> >
> > good idea :-)
> >
> >>
> >> Thanks,
> >> D
> >>
> >>
> >>
> >> On Thu, Jun 26, 2014 at 4:00 PM, Gustavo Sudre <gsudre at gmail.com
> <mailto:gsudre at gmail.com>> wrote:
> >> hey all
> >>
> >> I'm working with CTF data after converting them to FIFF. I used a
> simple mne_ctf2fiff call, and my data has no digitized points nor EEG.
> After looking at raw.info<http://raw.info>['dig'] I was a bit unsure
> about the location of the 3 electrodes that were used (LPA, RPA, nasion),
> so I decided to check a sample dataset just to verify it wasn't something
> weird with my data.
> >>
> >> So, I converted Brainstorm's sample raw .ds to FIFF (sorry, I didn't
> find a sample .ds by the MNE-python gang ;) ), and looked at the dig
> structure. Here's what I see:
> >>
> >> In [8]: raw.info<http://raw.info>['dig']
> >> Out[8]:
> >> [{'coord_frame': 4,
> >>   'ident': 3,
> >>   'kind': 2,
> >>   'r': array([  7.45058060e-09,   8.64083171e-02,   0.00000000e+00],
> dtype=float32)},
> >>  {'coord_frame': 4,
> >>   'ident': 1,
> >>   'kind': 2,
> >>   'r': array([ -6.84481487e-02,  -5.76255843e-09,   0.00000000e+00],
> dtype=float32)},
> >>  {'coord_frame': 4,
> >>   'ident': 2,
> >>   'kind': 2,
> >>   'r': array([  7.05333501e-02,   5.87897375e-09,   0.00000000e+00],
> dtype=float32)},
> >>  {'coord_frame': 4,
> >>   'ident': 1,
> >>   'kind': 3,
> >>   'r': array([-0.02922045, -0.09704589,  0.0735818 ], dtype=float32)},
> >>  {'coord_frame': 4,
> >>   'ident': 2,
> >>   'kind': 3,
> >>   'r': array([ 0.03363838, -0.09628744,  0.0735818 ], dtype=float32)}]
> >>
> >> The two last points are not present in my actual data, but the output
> above can be used to illustrate my question. Based on the coordinates in
> head space, shouldn't the first point be nasion (FIFFV_POINT_NASION,
> ident=2)?
> >>
> >> Maybe I'm misreading something in the manual, but it's something that
> has been bugging me for a while, and I was wondering if you guys could
> quickly point out my mistake!
> >>
> >> Thanks,
> >>
> >> G
> >>
> >>
> >> --
> >> Gustavo Sudre
> >>
> >> _______________________________________________
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> Mne_analysis at nmr.mgh.harvard.edu>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
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> it is
> >> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> >> contains patient information, please contact the Partners Compliance
> HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> >> but does not contain patient information, please contact the sender and
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> >> dispose of the e-mail.
> >>
> >>
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> Mne_analysis at nmr.mgh.harvard.edu>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
> >> The information in this e-mail is intended only for the person to whom
> it is
> >> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> >> contains patient information, please contact the Partners Compliance
> HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> >> but does not contain patient information, please contact the sender and
> properly
> >> dispose of the e-mail.
> >
> >
> >
> > --
> > Gustavo Sudre
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu<mailto:Mne_analysis at nmr.mgh.harvard.edu
> >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> > contains patient information, please contact the Partners Compliance
> HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
>
>
>
>
> --
> Gustavo Sudre
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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