[Mne_analysis] Example on SPM Faces dataset - 2 questions

Fri Mar 25 13:25:22 EDT 2016

Hi Annalisa,

In mne_analyze, you 

1) Load the FreeSurfer surfaces (Load surface…)
2) Load the digitization data from the file rather than try to open the raw file (Load digitizer data…)

The rest of the alignment steps are described in Section 12.11 of the MNE manual.

Best,
Matti

> On Mar 24, 2016, at 5:04 PM, 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
> 
> From: Christian Brodbeck <christianbrodbeck at nyu.edu>
> Subject: Re: [Mne_analysis] Example on SPM Faces dataset - 2 questions
> Date: October 5, 2015 at 10:02:22 AM EDT
> 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>
> Reply-To: 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 <http://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 <http://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 <mailto: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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