[Mne_analysis] plotting topomap for SSP projection

Denis-Alexander Engemann denis.engemann at gmail.com
Wed Apr 23 07:14:50 EDT 2014
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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
> >>>
> >>> _______________________________________________
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