[Mne_analysis] Obtaining alignment points

[Eric Larson]

Hey Marmaduke,

I can't quite tell from your description what the integer values of the
'kind' field is for each point, but I assume it's 4 because you say that
they are all type FIFFV_POINT_EXTRA. I would have expected the 'kind' to
actually be FIFFV_POINT_CARDINAL (int value of 1), but in any case the
'ident' of each of those can be identified as FIFFV_POINT_LPA/NASION/RPA
(1/2/3).

Check out the sample dataset, for example:

>>> raw = mne.io.Raw(mne.datasets.sample.data_path() +
'/MEG/sample/sample_audvis_raw.fif')
>>> raw.info['dig'][0]
{'kind': 1, 'ident': 1, 'r': array([ -7.13766068e-02,   0.00000000e+00,
5.12227416e-09], dtype=float32), 'coord_frame': 4}
>>> raw.info['dig'][1]
{'kind': 1, 'ident': 2, 'r': array([  3.72529030e-09,   1.02605611e-01,
4.19095159e-09], dtype=float32), 'coord_frame': 4}
>>> raw.info['dig'][2]
{'kind': 1, 'ident': 3, 'r': array([  7.52676800e-02,   0.00000000e+00,
5.58793545e-09], dtype=float32), 'coord_frame': 4}

All three thus have type FIFFV_POINT_CARDINAL (1), with different 'ident'
1/2/3 to match which sub-type they are.

Are you reading in your data using one of the `read_raw_*` functions (I'm
not familiar with 4D data)? If so, it might be a bug that the type is
recorded as FIFFV_POINT_EXTRA instead of FIFFV_POINT_CARDINAL -- please
open an issue on the mne-python issue tracker so we can discuss further.

Cheers,
Eric



On Mon, Jun 16, 2014 at 1:02 AM, Denis A. Engemann <denis.engemann at gmail.com
> wrote:

>
>
> > On Jun 16, 2014, at 8:58 AM, Marmaduke Woodman <
> marmaduke.woodman at univ-amu.fr> wrote:
> >
> > Hi,
> >
> > In mne-python, I'd like to obtain the nasion, LPA & RPA points read from
> the head digitization. In my case using a 4D dataset, the raw.info['dig']
> field has exactly 3 points not of 'kind' FIFFV_POINT_EXTRA, and each of
> these three has 'kind' FIFFV_POINT_LPA, though their 'ident' field varies
> (1, 2, 3).
> >
> > I was expected one of each of FIFFV_POINT_{NASION, LPA, RPA}, but I must
> have missed something.
> >
> > Would someone be able to enlighten on this point?
> >
> >
> > Many thanks,
> > Marmaduke
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