[Mne_analysis] question about FIFF constants and CTF data

dgw dgwakeman at gmail.com
Fri Jun 27 09:20:39 EDT 2014
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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> 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> 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> wrote:
>> > Hi all,
>> >
>> > On Jun 26, 2014, at 11:29 PM, dgw <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['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>
>> 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['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['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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>> >
>> > --
>> > Gustavo Sudre
>> > _______________________________________________
>> > Mne_analysis mailing list
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>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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>> >
>> > 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
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>> > dispose of the e-mail.
>>
>>
>
>
> --
> Gustavo Sudre
>
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