[Mne_analysis] Example on SPM Faces dataset - 2 questions
pascarel at dima.unige.it
pascarel at dima.unige.it
Fri Mar 25 17:00:43 EDT 2016
Hi Alex,
yes, I have seen this file, but I asked you since
I need to perform the co-registration for other
CTF files that I converted in .fif and thus I
wanted to understand the correct procedure.
So, since mne.gui.coregistration doens't work correctly
I'll use mne_analyze with only the 3 fiducial points.
Thanks!
best,
Annalisa
Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> ha scritto:
> 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
>>>>>>
>>>>>> _______________________________________________
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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
>>>>
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>>>> 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
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> 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
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