[Mne_analysis] Example on SPM Faces dataset - 2 questions
dgw
dgwakeman at gmail.com
Fri Mar 25 15:25:29 EDT 2016
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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