[Mne_analysis] Conforming to Montage Deprecations
Eric Larson
larson.eric.d at gmail.com
Sat Dec 28 16:33:38 EST 2019
External Email - Use Caution
The channel positions might differ a bit because of a slightly different
`head_size` parameter of make_standard_montage, or because we now properly
transform the channel positions to head coordinates (defined by LPA,
Nasion, and RPA).
Eric
On Fri, Dec 27, 2019 at 10:20 PM Bianca Islas <biancaisla1 at gmail.com> wrote:
> External Email - Use Caution
>
> When I input `print(raw.ch_names)` before I would get the right channels
> regardless of capitalization, oddly enough. Although further on in the
> script it now makes sense that when I would try to do averaging it was
> telling me that it did not recognize ‘FP1’ as a channel. So, thank you
> very much Eric, for pointing this difference out. After migrating the code
> to the suggested commands the montage went from this:
>
>
>
> To this:
>
>
>
> The channel count is accurate now, and the raw.plot output looks exactly
> as it did before. As for the specifics, when I print(raw.info[‘chs’]) to
> troubleshoot location it is still off but only by thousandths for the
> y-axis and hundredths in the y and z axes. Is this a by-product of the
> aforementioned “shrinking” mentioned before?
>
> *From: *Eric Larson <larson.eric.d at gmail.com>
> *Sent: *Friday, December 27, 2019 7:38 PM
> *Subject: *Re: [Mne_analysis] Conforming to Montage Deprecations
>
>
>
> * External Email - Use Caution *
>
> It looks like our standard_1020 names follow a different capitalization
> pattern:
>
>
>
>
> https://github.com/mne-tools/mne-python/blob/master/mne/channels/data/montages/standard_1020.elc#L107
>
>
>
> So if you do something like:
>
>
>
> raw.rename_channels(lambda x: x.lower().capitalize())
>
>
>
> Or go the direct dictionary route:
>
>
>
> raw.rename_channels(dict(FP1='Fp1', OZ='Oz', FZ='Fz', FP2='Fp2', PZ='Pz',
> CZ='Cz', FPZ='Fpz'))
>
>
>
> Some variant like this should allow not having the warning without needing
> to pass `raise_if_subset=False`. And if you have channels that are actually
> not EEG, make sure to do raw.set_channel_types
> <https://mne.tools/dev/generated/mne.io.Raw.html#mne.io.Raw.set_channel_types>
> to set them to the correct channel types.
>
>
>
> As for the channel count mismatch, what extra channels are in raw.ch_names
> that you don't expect to be there? Does raw.plot() look reasonable?
>
>
>
> Eric
>
>
>
>
>
> On Fri, Dec 27, 2019 at 12:58 AM Bianca Islas <biancaisla1 at gmail.com>
> wrote:
>
> * External Email - Use Caution *
>
> When I implement the changes this way, I get a ValueError that reads:
>
> “DigMontage is a only a subset of info. There are 7 channel positions not
> present it the DigMontage. The required channels are: {'FP1', 'OZ', 'FZ',
> 'FP2', 'PZ', 'CZ', 'FPZ'}. You can use `raise_if_subset=False` in
> `set_montage` to avoid this ValueError and get a DeprecationWarning
> instead.”
>
>
>
> If I do as suggested above I do not get an error I get an output of what
> which channels will be ignored and a warning that reads:
>
> “Reading 0 ... 2552079 = 0.000 ... 1276.040 secs...
>
>
>
>
>
> <ipython-input-12-e47b0d549095>:8: RuntimeWarning: Could not parse meas
> date from the header. Setting to None.
>
> data_format='int32', date_format='mm/dd/yy', preload=True,
> verbose='debug')
>
>
>
>
>
> DigMontage is a superset of info. 78 in DigMontage will be ignored. The
> ignored channels are: {'T5', 'Oz', 'C5', 'PO9', 'AF1', 'PO3', 'AF4', 'F1',
> 'FC4', 'CP3', 'AF6', 'FC6', 'Fz', 'Cz', 'CP5', 'TP7', 'FC3', 'AF8', 'T10',
> 'P10', 'FT7', 'P6', 'T3', 'TP10', 'PO1', 'AF5', 'P5', 'Iz', 'FC5', 'TP9',
> 'POz', 'FC2', 'PO8', 'AF3', 'AF10', 'CP2', 'T9', 'PO4', 'PO2', 'FT10',
> 'P2', 'T6', 'AF7', 'AF9', 'C6', 'A2', 'PO5', 'PO6', 'F6', 'A1', 'P1',
> 'F10', 'Fp2', 'C2', 'FT8', 'F5', 'AF2', 'P9', 'FCz', 'O9', 'CP4', 'Fp1',
> 'PO7', 'PO10', 'C1', 'F9', 'CP1', 'O10', 'FT9', 'CP6', 'TP8', 'F2', 'T4',
> 'CPz', 'Pz', 'AFz', 'Fpz', 'FC1'}
>
>
>
>
>
> <ipython-input-12-e47b0d549095>:13: RuntimeWarning: DigMontage is a only a
> subset of info. Did not set 7 channel positions:
>
> FP1, OZ, FZ, FP2, PZ, CZ, FPZ
>
> raw.set_montage(montage, raise_if_subset=False)
>
>
>
> Out[12]:
>
> <RawCNT | st003_PAMR_s1079_20080319.cnt, n_channels x n_times : 38 x
> 2552080 (1276.0 sec), ~740.0 MB, data loaded>”
>
>
>
> This is very problematic as I am only supposed to have 23 EEG, 5 EMG, 2
> EOG, 1ECG, 2 MISC (skin conductance), and 1 Stim channel.
>
>
>
> - Bianca
>
>
>
>
>
> *From: *Alexandre Gramfort <alexandre.gramfort at inria.fr>
> *Sent: *Thursday, December 26, 2019 11:35 PM
> *To: *Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> *Subject: *Re: [Mne_analysis] Conforming to Montage Deprecations
>
>
>
> External Email - Use Caution
>
>
>
> hi Bianca,
>
>
>
> are you doing:
>
>
>
> raw = mne.io.read_raw_cnt(fname)
>
> montage = mne.channels.make_standard_montage(kind=’standard_1020)
>
> raw.set_montage(montage)
>
>
>
> ?
>
>
>
> this should set the chs and the dig.
>
>
>
> the reason we have changed this is that we want to make sure that the
> channel
>
> locations are can considered to be in head coordinate system so you can
> relate
>
> them to fsaverage for example. Is the shrinking problematic for you?
>
>
>
> Alex
>
>
>
> On Fri, Dec 27, 2019 at 4:43 AM Bianca Islas <biancaisla1 at gmail.com>
> wrote:
>
> >
>
> > External Email - Use Caution
>
> >
>
> > Happy Holidays MNE Team,
>
> >
>
> >
>
> >
>
> > I am trying to conform to the new deprecation that has occurred in
> developer version 0.19 concerning the montage. My input file is a
> Neuroscan (.cnt) file extension type and thus my script previously read
> `mne.io.read_raw_cnt(fname, montage=’standard_1020’, etc …)`. However, I
> have migrated this to a separate command
> `mne.channels.make_standard_montage(kind=’standard_1020)`. When doing this
> it skews my X,Y,Z locations. For example, when I pass `print(raw.info[‘chs’])`
> my FP1 EEG electrode location is skewed from
>
> >
>
> >
>
> >
>
> > `’loc’: array([-0.0294367, 0.0839171, -0.00699, 0. ,
> 0. , 0. , 0. , 0. , 0. ,
> 0. , 0. , 0. ])`
>
> >
>
> >
>
> >
>
> > to
>
> >
>
> >
>
> >
>
> > `’loc’: array([-0.20257819, 0.21764863, 0.95477283, nan,
> nan,
>
> >
>
> > nan, nan, nan, nan, nan,
>
> >
>
> > nan, nan]).
>
> >
>
> >
>
> >
>
> > Furthermore, when I input `print(raw.info)` the previous code output
> under `dig : list | 26 items (3 cardinal, 23 EEG)` while the latter code
> displays NoneType in the `dig`. While this seems like it would be a
> straight-forward change, it is definitely not as easy in practice. Is
> there any reason that it is not reading my montage as a standard_1020
> anymore?
>
> >
>
> >
>
> >
>
> > Thank you for any assistance provided,
>
> >
>
> > Bianca Islas
>
> >
>
> > _______________________________________________
>
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>
> > Mne_analysis at nmr.mgh.harvard.edu
>
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>
>
>
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