[Mne_analysis] Conforming to Montage Deprecations

[Bianca Islas]

        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
Sent: Thursday, December 26, 2019 11:35 PM
To: Discussion and support forum for the users of MNE Software
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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