[Mne_analysis] plotting topomap for SSP projection

Sat Apr 26 09:44:18 EDT 2014

hi Yuhan,

can you share a raw.fif file containing the measurement info you used
with mne.find_layout?

thanks
Alex

On Wed, Apr 23, 2014 at 3:32 PM, Denis-Alexander Engemann
<denis.engemann at gmail.com> wrote:
> Hi Yuhan,
>
> I just realized you in fact already tried find_layout. Sorry for the
> confusion.
> We'll meanwhile try to understand what's the exact issue and keep you
> posted.
>
> Best,
> Denis
>
>
> On Wed, Apr 23, 2014 at 1:14 PM, Denis-Alexander Engemann
> <denis.engemann at gmail.com> wrote:
>>
>> Yuhan,
>>
>> could your try using the mne.find_layout function?
>> It should recognize the correct layout and automatically corrects the
>> naming of the channels. Old Neuromag systems tends to have whitespaces in
>> the names which can lead to problems. It seems this is the case for your
>> system.
>>
>> Best,
>> Denis
>>
>>
>> On Wed, Apr 23, 2014 at 11:01 AM, Alexandre Gramfort
>> <alexandre.gramfort at telecom-paristech.fr> wrote:
>>>
>>> hi,
>>>
>>> I could reproduce the bug.
>>>
>>> I opened an issue.
>>>
>>> https://github.com/mne-tools/mne-python/issues/1235
>>>
>>> follow the issue to know when we fix it.
>>>
>>> thanks
>>>
>>> Best,
>>> Alex
>>>
>>>
>>> On Tue, Apr 22, 2014 at 10:23 PM, Chen, Yu-han <CHENY4 at email.chop.edu>
>>> wrote:
>>> > Hi Alex,
>>> >
>>> > Attached is the -proj.fif file. Thank you.
>>> >
>>> > Yuhan
>>> > ________________________________________
>>> > From: mne_analysis-bounces at nmr.mgh.harvard.edu
>>> > [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Alexandre Gramfort
>>> > [alexandre.gramfort at telecom-paristech.fr]
>>> > Sent: Tuesday, April 22, 2014 4:06 PM
>>> > To: Discussion and support forum for the users of MNE Software
>>> > Subject: Re: [Mne_analysis] plotting topomap for SSP projection
>>> >
>>> > so it should work...
>>> >
>>> > can you share the -proj.fif file that contains the projections to plot?
>>> >
>>> > A
>>> >
>>> >
>>> > On Tue, Apr 22, 2014 at 9:48 PM, Chen, Yu-han <CHENY4 at email.chop.edu>
>>> > wrote:
>>> >> The data was acquired on Elekta 306. Below are the channel names.
>>> >> Thanks.
>>> >>
>>> >> _______In [23]: print raw.ch_names
>>> >> ['MEG0113', 'MEG0112', 'MEG0111', 'MEG0122', 'MEG0123', 'MEG0121',
>>> >> 'MEG0132', 'MEG0133', 'MEG0131', 'MEG0143', 'MEG0142', 'MEG0141', 'MEG0213',
>>> >> 'MEG0212', 'MEG0211', 'MEG0222', 'MEG0223', 'MEG0221', 'MEG0232', 'MEG0233',
>>> >> 'MEG0231', 'MEG0243', 'MEG0242', 'MEG0241', 'MEG0313', 'MEG0312', 'MEG0311',
>>> >> 'MEG0322', 'MEG0323', 'MEG0321', 'MEG0333', 'MEG0332', 'MEG0331', 'MEG0343',
>>> >> 'MEG0342', 'MEG0341', 'MEG0413', 'MEG0412', 'MEG0411', 'MEG0422', 'MEG0423',
>>> >> 'MEG0421', 'MEG0432', 'MEG0433', 'MEG0431', 'MEG0443', 'MEG0442', 'MEG0441',
>>> >> 'MEG0513', 'MEG0512', 'MEG0511', 'MEG0523', 'MEG0522', 'MEG0521', 'MEG0532',
>>> >> 'MEG0533', 'MEG0531', 'MEG0542', 'MEG0543', 'MEG0541', 'MEG0613', 'MEG0612',
>>> >> 'MEG0611', 'MEG0622', 'MEG0623', 'MEG0621', 'MEG0633', 'MEG0632', 'MEG0631',
>>> >> 'MEG0642', 'MEG0643', 'MEG0641', 'MEG0713', 'MEG0712', 'MEG0711', 'MEG0723',
>>> >> 'MEG0722', 'MEG0721', 'MEG0733', 'MEG0732', 'MEG0731', 'MEG0743', 'MEG0742',
>>> >> 'MEG0741', 'MEG0813', 'MEG0812', 'MEG0811', 'MEG0822', 'MEG0823', 'MEG0821',
>>> >>   'MEG0913', 'MEG0912', 'MEG0911', 'MEG0923', 'MEG0922', 'MEG0921',
>>> >> 'MEG0932', 'MEG0933', 'MEG0931', 'MEG0942', 'MEG0943', 'MEG0941', 'MEG1013',
>>> >> 'MEG1012', 'MEG1011', 'MEG1023', 'MEG1022', 'MEG1021', 'MEG1032', 'MEG1033',
>>> >> 'MEG1031', 'MEG1043', 'MEG1042', 'MEG1041', 'MEG1112', 'MEG1113', 'MEG1111',
>>> >> 'MEG1123', 'MEG1122', 'MEG1121', 'MEG1133', 'MEG1132', 'MEG1131', 'MEG1142',
>>> >> 'MEG1143', 'MEG1141', 'MEG1213', 'MEG1212', 'MEG1211', 'MEG1223', 'MEG1222',
>>> >> 'MEG1221', 'MEG1232', 'MEG1233', 'MEG1231', 'MEG1243', 'MEG1242', 'MEG1241',
>>> >> 'MEG1312', 'MEG1313', 'MEG1311', 'MEG1323', 'MEG1322', 'MEG1321', 'MEG1333',
>>> >> 'MEG1332', 'MEG1331', 'MEG1342', 'MEG1343', 'MEG1341', 'MEG1412', 'MEG1413',
>>> >> 'MEG1411', 'MEG1423', 'MEG1422', 'MEG1421', 'MEG1433', 'MEG1432', 'MEG1431',
>>> >> 'MEG1442', 'MEG1443', 'MEG1441', 'MEG1512', 'MEG1513', 'MEG1511', 'MEG1522',
>>> >> 'MEG1523', 'MEG1521', 'MEG1533', 'MEG1532', 'MEG1531', 'MEG1543', 'MEG1542',
>>> >> 'MEG1541', 'MEG1613', 'MEG1612', 'MEG1611', 'MEG1622', 'MEG1623', 'MEG1621'
>>> >>  , 'MEG1632', 'MEG1633', 'MEG1631', 'MEG1643', 'MEG1642', 'ME!
>>> >>  G1641',
>>> >> 'MEG1713', 'MEG1712', 'MEG1711', 'MEG1722', 'MEG1723', 'MEG1721',
>>> >> 'MEG1732', 'MEG1733', 'MEG1731', 'MEG1743', 'MEG1742', 'MEG1741', 'MEG1813',
>>> >> 'MEG1812', 'MEG1811', 'MEG1822', 'MEG1823', 'MEG1821', 'MEG1832', 'MEG1833',
>>> >> 'MEG1831', 'MEG1843', 'MEG1842', 'MEG1841', 'MEG1912', 'MEG1913', 'MEG1911',
>>> >> 'MEG1923', 'MEG1922', 'MEG1921', 'MEG1932', 'MEG1933', 'MEG1931', 'MEG1943',
>>> >> 'MEG1942', 'MEG1941', 'MEG2013', 'MEG2012', 'MEG2011', 'MEG2023', 'MEG2022',
>>> >> 'MEG2021', 'MEG2032', 'MEG2033', 'MEG2031', 'MEG2042', 'MEG2043', 'MEG2041',
>>> >> 'MEG2113', 'MEG2112', 'MEG2111', 'MEG2122', 'MEG2123', 'MEG2121', 'MEG2133',
>>> >> 'MEG2132', 'MEG2131', 'MEG2143', 'MEG2142', 'MEG2141', 'MEG2212', 'MEG2213',
>>> >> 'MEG2211', 'MEG2223', 'MEG2222', 'MEG2221', 'MEG2233', 'MEG2232', 'MEG2231',
>>> >> 'MEG2242', 'MEG2243', 'MEG2241', 'MEG2312', 'MEG2313', 'MEG2311', 'MEG2323',
>>> >> 'MEG2322', 'MEG2321', 'MEG2332', 'MEG2333', 'MEG2331', 'MEG2343', 'MEG2342',
>>> >> 'MEG2341', 'MEG2412', 'MEG2413', 'MEG2411', 'MEG2423', 'MEG2422', 'MEG2421',
>>> >>  'MEG2433', 'MEG2432', 'MEG2431', 'MEG2442', 'MEG2443', 'MEG2441',
>>> >> 'MEG2512', 'MEG2513', 'MEG2511', 'MEG2522', 'MEG2523', 'MEG2521', 'MEG2533',
>>> >> 'MEG2532', 'MEG2531', 'MEG2543', 'MEG2542', 'MEG2541', 'MEG2612', 'MEG2613',
>>> >> 'MEG2611', 'MEG2623', 'MEG2622', 'MEG2621', 'MEG2633', 'MEG2632', 'MEG2631',
>>> >> 'MEG2642', 'MEG2643', 'MEG2641', 'EEG061', 'EEG062', 'STI101', 'STI201',
>>> >> 'STI301', 'MISC201', 'MISC202', 'MISC203', 'MISC204', 'MISC205', 'MISC206',
>>> >> 'MISC301', 'MISC302', 'MISC303', 'MISC304', 'MISC305', 'MISC306', 'CHPI001',
>>> >> 'CHPI002', 'CHPI003', 'CHPI004', 'CHPI005', 'CHPI006', 'CHPI007', 'CHPI008',
>>> >> 'CHPI009']
>>> >>
>>> >>
>>> >> _________________________________
>>> >> From: mne_analysis-bounces at nmr.mgh.harvard.edu
>>> >> [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Alexandre Gramfort
>>> >> [alexandre.gramfort at telecom-paristech.fr]
>>> >> Sent: Tuesday, April 22, 2014 3:34 PM
>>> >> To: Discussion and support forum for the users of MNE Software
>>> >> Subject: Re: [Mne_analysis] plotting topomap for SSP projection
>>> >>
>>> >> hi,
>>> >>
>>> >> can you paste the list of your channel names?
>>> >>
>>> >> print raw.ch_names
>>> >>
>>> >> on what system did you acquire your data?
>>> >>
>>> >> just a note Version 2.7.3 is unrelated to the MNE-Python version.
>>> >> Version 2.7.3 is for the unix commands.
>>> >>
>>> >> Alex
>>> >>
>>> >>
>>> >>> I'm trying to plot topoplot of EOG/ECG SSP projections but I got some
>>> >>> error
>>> >>> messages about the layout I used. Here is what I originally used:
>>> >>>
>>> >>> layout = mne.layouts.read_layout('Vectorview-all')
>>> >>> mne.viz.plot_projs_topomap(EOGprojs, layout=layout)
>>> >>>
>>> >>> The error message is:
>>> >>> RuntimeError: Cannot find a proper layout for projection
>>> >>> planar-998--0.200-0.500-PCA-01
>>> >>>
>>> >>> Then I tried something below and I still got the same error message:
>>> >>> raw_layout = mne.layouts.find_layout(raw.info, ch_type = 'mag')
>>> >>> mne.viz.plot_projs_topomap(EOGprojs, layout=raw_layout)
>>> >>>
>>> >>> I thought it was because the channel names in my data didn't have the
>>> >>> space
>>> >>> between MEG and the sensor number but I got the same error message
>>> >>> after I
>>> >>> change the layout channel name to be the same as my raw file. Is
>>> >>> there any
>>> >>> obvious mistake I made that causes this error message? My mne version
>>> >>> is
>>> >>> below:
>>> >>>
>>> >>> Version 2.7.3
>>> >>> SVN revision 3268
>>> >>> Build date is Thu Jan  6 02:23:43 EST 2011
>>> >>>
>>> >>>
>>> >>> Thanks!
>>> >>> Yuhan
>>> >>>
>>> >>> _______________________________________________
>>> >>> 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
>>> >>
>>> >> _______________________________________________
>>> >> 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
>>> >
>>> > _______________________________________________
>>> > 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
>>
>>
>
>
> _______________________________________________
> 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.
>