[Mne_analysis] Example on SPM Faces dataset - 2 questions
pascarel at dima.unige.it
pascarel at dima.unige.it
Fri Mar 25 15:19:19 EDT 2016
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
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>> _______________________________________________
>> 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
More information about the Mne_analysis
mailing list