[Mne_analysis] Example on SPM Faces dataset - 2 questions

[Christian Brodbeck]

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

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