[Mne_analysis] Example on SPM Faces dataset - 2 questions
Alexandre Gramfort
alexandre.gramfort at telecom-paristech.fr
Fri Mar 25 16:50:29 EDT 2016
FYI
we provide in the spm dataset a trans file you can use. You can
rely on it and avoid the coregistration.
File is called:
MNE-spm-face/MEG/spm/SPM_CTF_MEG_example_faces1_3D_raw-trans.fif
HTH
Alex
On Fri, Mar 25, 2016 at 9:45 PM, <pascarel at dima.unige.it> wrote:
> hi Denis,
>
> yes, you are right!
> I can see only these 3 points since
> there are not other digitization points.
> Thus, I could perform the co-registration only using
> the fiducials.
>
> I waited to see also the helmet importing the raw data
> but I take this message error
> "No suitable coordinate transformation found in
> SPM_CTF_MEG_example_faces1_3D_raw.fif"
>
> Thanks for your answer!
>
> Best,
> Annalisa
>
>
>
> The green circles are identified
> dgw <dgwakeman at gmail.com> ha scritto:
>
>> Annalisa,
>>
>> The green circles represent the fiducials, so they are showing up
>> properly in mne_analyze.
>> What are you expecting to see?
>>
>> hth
>> d
>>
>> On Fri, Mar 25, 2016 at 3:19 PM, <pascarel at dima.unige.it> wrote:
>>> Dear Matti,
>>>
>>> thanks for your suggestion.
>>>
>>> I tried to do it but I see only three green circles.
>>>
>>> The file I used is SPM_CTF_MEG_example_faces1_3D_raw.fif
>>>
>>> What's wrong?
>>>
>>> Thanks for hep me
>>>
>>> Best regards,
>>> Annalisa
>>>
>>>
>>>
>>> Matti Hamalainen <msh at nmr.mgh.harvard.edu> ha scritto:
>>>
>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Mne_analysis mailing list
>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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>>>
>>>
>>> --
>>> 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
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> --
> 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
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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