[Mne_analysis] Fwd: Example on SPM Faces dataset - 2 questions

Thu Mar 24 17:04:19 EDT 2016

Dear MNE users,

I came back with a problem using mne.gui.coregistration() with CTF data.

I loaded the spm sbj and the raw file  
SPM_CTF_MEG_example_faces1_3D_raw.fif and

1) I couldn't see Fiducial points
2) I couldn't see the MEG sensors

About point 1) the problem is that Christian Brodbeck wrote in the
email I attached.
If I change the 'kind' key of raw.info['dig'] to FIFF.FIFFV_POINT_CARDINAL
I'm able to see the fiducial points in the GUI, even if I think there  
is probably
a mistake in assignment the nasion, lpa and rpa.
I think the right assignment should be

raw.info['dig'][0]['ident'] = 2
raw.info['dig'][1]['ident'] = 1
raw.info['dig'][2]['ident'] = 3

Does it make sense?

About point 2) I thought the problem could be the 'coil_type' of  
raw.info['chs'] has
the value 201609. I tried to change this value but it didn't happen when
I import the data in the GUI.

I also tried to perform the co-registration in mne_analyze but when I  
import the
raw file I get the following error message
No suitable coordinate transformation found in  
SPM_CTF_MEG_example_faces1_3D_raw.fif

Thanks for any suggestions!

best regards
Annalisa

----- Messaggio inoltrato da Christian Brodbeck  
<christianbrodbeck at nyu.edu> -----
       Data: Mon, 5 Oct 2015 10:02:22 -0400
         Da: Christian Brodbeck <christianbrodbeck at nyu.edu>
Rispondi-A: Discussion and support forum for the users of MNE Software  
<mne_analysis at nmr.mgh.harvard.edu>
    Oggetto: Re: [Mne_analysis] Example on SPM Faces dataset - 2 questions
          A: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
         Cc: Discussion and support forum for the users of MNE  
Software <mne_analysis at nmr.mgh.harvard.edu>

Looking at the spm-faces raw info:

In [3]: raw.info['dig']
Out[3]:
[{'coord_frame': 4,
   'ident': 3,
   'kind': 2,
   'r': array([  4.30736691e-09,   9.82968360e-02,   0.00000000e+00],  
dtype=float32)},
  {'coord_frame': 4,
   'ident': 1,
   'kind': 2,
   'r': array([ -7.32455477e-02,  -3.20142135e-09,   0.00000000e+00],  
dtype=float32)},
  {'coord_frame': 4,
   'ident': 2,
   'kind': 2,
   'r': array([  7.07898811e-02,   2.96859071e-09,   0.00000000e+00],  
dtype=float32)}]

but in the GUI we are selecting fiducial points with

d['kind'] == FIFF.FIFFV_POINT_CARDINAL
and

In [8]: FIFF.FIFFV_POINT_CARDINAL
Out[8]: 1
In [12]: FIFF.FIFFV_POINT_HPI
Out[12]: 2

so, is there something wrong with the spm-faces file (Fiducials stored  
as HPI)? Or are fiducials sometimes identical with HPI and the GUI  
should use them as such?

The latter would actually cause a conflict with our KIT files, because  
HPI points and fiducials which are not identical have the same “ident”:

In [16]: [d for d in kraw.info['dig'] if d['kind'] < 3]
Out[16]:
[{'coord_frame': 4,
   'ident': 2,
   'kind': 1,
   'r': array([  0.00000000e+00,   1.07987508e-01,  -1.38777878e-17],  
dtype=float32)},
  {'coord_frame': 4,
   'ident': 1,
   'kind': 1,
   'r': array([ -7.57353827e-02,   1.04083409e-17,   1.38777878e-17],  
dtype=float32)},
  {'coord_frame': 4,
   'ident': 3,
   'kind': 1,
   'r': array([  6.99156001e-02,   0.00000000e+00,   1.38777878e-17],  
dtype=float32)},
  {'coord_frame': 4,
   'ident': 0,
   'kind': 2,
   'r': array([-0.07321275,  0.0070182 , -0.00094954], dtype=float32)},
  {'coord_frame': 4,
   'ident': 1,
   'kind': 2,
   'r': array([ 0.06706881,  0.01023183, -0.00318275], dtype=float32)},
  {'coord_frame': 4,
   'ident': 2,
   'kind': 2,
   'r': array([ 0.00344993,  0.11684198,  0.02777481], dtype=float32)},
  {'coord_frame': 4,
   'ident': 3,
   'kind': 2,
   'r': array([-0.03729108,  0.1059907 ,  0.03130391], dtype=float32)},
  {'coord_frame': 4,
   'ident': 4,
   'kind': 2,
   'r': array([ 0.0470689 ,  0.09996997,  0.03072358], dtype=float32)}]

Although a potential solution could use HPI only if no Cardinal points  
are present?

> On Oct 4, 2015, at 11:02 AM, Alexandre Gramfort  
> <alexandre.gramfort at telecom-paristech.fr> wrote:
>
> hi Annalisa,
>
>> I have two different questions about the example plot_spm_faces_dataset.py.
>>
>> 1) If I run the code and I try to plot the ICA components on time
>>
>>>>> show_picks = numpy.abs(eog_scores).argsort()[::-1][:5]
>>>>> fig1=ica.plot_sources(raw, show_picks, exclude=eog_inds)
>>
>>   I obtain the figure u find in attachment.
>>   My question is: why do I see the ref channels?
>>
>>   In the old mne-python version I had a different layout, as that
>>   shown in plot_ica_from_raw.py.
>>
>>   What's wrong?
>
> we improved the layout. But indeed there is no point is showing the
> meg reference channels.
>
> We'll fix it this week.
>
>> 2) I tried to co-register using mne.gui.coregistration()
>>
>>   I load the spm sbj and the raw file
>> SPM_CTF_MEG_example_faces1_3D_raw.fif.
>>   Does this file contain only the fiducial points?
>
> yes
>
>>   If yes, when I load the raw file I can't see the fiducials in the gui.
>
> maybe Christian knows. Do you see them with mne_analyze?
>
>>   Where I'm making a mistake?
>
> I don't think you do :)
>
> Best,
> Alex

----- Fine messaggio inoltrato. -----

-- 
Dott. Annalisa Pascarella
Istituto per le Applicazioni del Calcolo "M. Picone"
Consiglio Nazionale delle Ricerche
Via dei Taurini 19, 00185 Roma (Italy)
Ph.:+39-0649270946; Fax:+39-064404306
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