[Mne_analysis] Example on SPM Faces dataset - 2 questions
pascarel at dima.unige.it
pascarel at dima.unige.it
Fri Mar 25 16:45:47 EDT 2016
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
>>
>> _______________________________________________
>> 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
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