[Mne_analysis] plotting topomap for SSP projection

Denis-Alexander Engemann denis.engemann at gmail.com
Wed Apr 23 09:32:22 EDT 2014
Search archives: 
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
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