[Mne_analysis] Fwd: Example on SPM Faces dataset - 2 questions
Jaakko Leppäkangas
jaeilepp at student.jyu.fi
Fri Mar 25 04:30:35 EDT 2016
Hi Annalisa,
the landmarks are transformed to RAS coordinate system when the data is
converted to fif format. As the constant definitions map to nasion = 2, lpa
=1 and rpa = 3 ('ident' in chs) they seem correct to me.
The second point seems like a bug to me. I've opened an issue here
https://github.com/mne-tools/mne-python/issues/3071
-Jaakko
On 24 March 2016 at 22:04, <pascarel at dima.unige.it> wrote:
> 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
>
>
> ---------- Forwarded message ----------
> From: Christian Brodbeck <christianbrodbeck at nyu.edu>
> To: 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>
> Date: Mon, 5 Oct 2015 10:02:22 -0400
> Subject: Re: [Mne_analysis] Example on SPM Faces dataset - 2 questions
> 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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