Problem with mne.pick_types

Mailing List Archive (read-only)
1

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria
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2

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

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is
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3

I have one bad channel but it is not included in selection. Can it however
cause problems?

-Maria

Here are the outputs:
evoked.info['bads']
Out[54]: [u'MEG 2511']

but

In [53]: selection
Out[53]:
['MEG 0133',
'MEG 0212',
'MEG 0223',
'MEG 1313',
'MEG 1322',
'MEG 1443',
'MEG 0132',
'MEG 0213',
'MEG 0222',
'MEG 1312',
'MEG 1323',
'MEG 1442',
'MEG 1513',
'MEG 0242',
'MEG 0233',
'MEG 1343',
'MEG 1332',
'MEG 2613',
'MEG 1512',
'MEG 0243',
'MEG 0232',
'MEG 1343',
'MEG 1333',
'MEG 2612',
'MEG 1523',
'MEG 1612',
'MEG 1623',
'MEG 2413',
'MEG 2422',
'MEG 2643',
'MEG 1522',
'MEG 1613',
'MEG 1622',
'MEG 2412',
'MEG 2423',
'MEG 2642']

2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

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Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

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is
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
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4

I manged to solve this already.

-Maria

2014-08-27 13:11 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

I have one bad channel but it is not included in selection. Can it however
cause problems?

-Maria

Here are the outputs:
evoked.info['bads']
Out[54]: [u'MEG 2511']

but

In [53]: selection
Out[53]:
['MEG 0133',
'MEG 0212',
'MEG 0223',
'MEG 1313',
'MEG 1322',
'MEG 1443',
'MEG 0132',
'MEG 0213',
'MEG 0222',
'MEG 1312',
'MEG 1323',
'MEG 1442',
'MEG 1513',
'MEG 0242',
'MEG 0233',
'MEG 1343',
'MEG 1332',
'MEG 2613',
'MEG 1512',
'MEG 0243',
'MEG 0232',
'MEG 1343',
'MEG 1333',
'MEG 2612',
'MEG 1523',
'MEG 1612',
'MEG 1623',
'MEG 2413',
'MEG 2422',
'MEG 2643',
'MEG 1522',
'MEG 1613',
'MEG 1622',
'MEG 2412',
'MEG 2423',
'MEG 2642']

2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

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
MyComplianceReport.com: Compliance and Ethics Reporting . 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.

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is
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5

Hi,

2014-08-27 14:02 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

I manged to solve this already.

now I'm curious, what was the problem?

-Denis

-Maria

2014-08-27 13:11 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

I have one bad channel but it is not included in selection. Can it however

cause problems?

-Maria

Here are the outputs:
evoked.info['bads']
Out[54]: [u'MEG 2511']

but

In [53]: selection
Out[53]:
['MEG 0133',
'MEG 0212',
'MEG 0223',
'MEG 1313',
'MEG 1322',
'MEG 1443',
'MEG 0132',
'MEG 0213',
'MEG 0222',
'MEG 1312',
'MEG 1323',
'MEG 1442',
'MEG 1513',
'MEG 0242',
'MEG 0233',
'MEG 1343',
'MEG 1332',
'MEG 2613',
'MEG 1512',
'MEG 0243',
'MEG 0232',
'MEG 1343',
'MEG 1333',
'MEG 2612',
'MEG 1523',
'MEG 1612',
'MEG 1623',
'MEG 2413',
'MEG 2422',
'MEG 2643',
'MEG 1522',
'MEG 1613',
'MEG 1622',
'MEG 2412',
'MEG 2423',
'MEG 2642']

2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

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
MyComplianceReport.com: Compliance and Ethics Reporting . 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.

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Mne_analysis Info Page

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
MyComplianceReport.com: Compliance and Ethics Reporting . 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.

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6

There was one channel two times in selection...

However, it seems to cause a problem if some of the channels in selection
is bad.
I would like to plot a subset of channels from each data file in a loop as
follows:

picks = mne.pick_types(evoked.info,selection=selection)

                idx = 0
                for ax_row in axes:
                        for ax in ax_row:
                                ax.plot(evoked_raw.times,
evoked_raw.data[picks[idx]])
                                idx += 1

Is it somehow possible to, for example, plot a blank plot if there is a bad
channel in selection?

-Maria

2014-08-27 15:05 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi,

2014-08-27 14:02 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

I manged to solve this already.

now I'm curious, what was the problem?

-Denis

-Maria

2014-08-27 13:11 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

I have one bad channel but it is not included in selection. Can it

however cause problems?

-Maria

Here are the outputs:
evoked.info['bads']
Out[54]: [u'MEG 2511']

but

In [53]: selection
Out[53]:
['MEG 0133',
'MEG 0212',
'MEG 0223',
'MEG 1313',
'MEG 1322',
'MEG 1443',
'MEG 0132',
'MEG 0213',
'MEG 0222',
'MEG 1312',
'MEG 1323',
'MEG 1442',
'MEG 1513',
'MEG 0242',
'MEG 0233',
'MEG 1343',
'MEG 1332',
'MEG 2613',
'MEG 1512',
'MEG 0243',
'MEG 0232',
'MEG 1343',
'MEG 1333',
'MEG 2612',
'MEG 1523',
'MEG 1612',
'MEG 1623',
'MEG 2413',
'MEG 2422',
'MEG 2643',
'MEG 1522',
'MEG 1613',
'MEG 1622',
'MEG 2412',
'MEG 2423',
'MEG 2642']

2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

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
MyComplianceReport.com: Compliance and Ethics Reporting . 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.

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it is
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contains patient information, please contact the Partners Compliance
HelpLine at
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7

Or could it alternatively be possible to plot also the bad channels?

I have:

picks = mne.pick_types(evoked_raw.info,selection=selection)

I think that this shouldn't exclude bads because I have not exclude='bads'.

However, picks doesn't include the channels in selection that are marked as
bad.

In the reference of mne.picks_type it is said:

exclude : list of string | str

List of channels to exclude. If empty do not exclude any (default). If
?bads?, exclude channels in info[?bads?]

-Maria

2014-08-27 19:02 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

There was one channel two times in selection...

However, it seems to cause a problem if some of the channels in selection
is bad.
I would like to plot a subset of channels from each data file in a loop as
follows:

picks = mne.pick_types(evoked.info,selection=selection)

                idx = 0
                for ax_row in axes:
                        for ax in ax_row:
                                ax.plot(evoked_raw.times,
evoked_raw.data[picks[idx]])
                                idx += 1

Is it somehow possible to, for example, plot a blank plot if there is a
bad channel in selection?

-Maria

2014-08-27 15:05 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi,

2014-08-27 14:02 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

I manged to solve this already.

now I'm curious, what was the problem?

-Denis

-Maria

2014-08-27 13:11 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

I have one bad channel but it is not included in selection. Can it

however cause problems?

-Maria

Here are the outputs:
evoked.info['bads']
Out[54]: [u'MEG 2511']

but

In [53]: selection
Out[53]:
['MEG 0133',
'MEG 0212',
'MEG 0223',
'MEG 1313',
'MEG 1322',
'MEG 1443',
'MEG 0132',
'MEG 0213',
'MEG 0222',
'MEG 1312',
'MEG 1323',
'MEG 1442',
'MEG 1513',
'MEG 0242',
'MEG 0233',
'MEG 1343',
'MEG 1332',
'MEG 2613',
'MEG 1512',
'MEG 0243',
'MEG 0232',
'MEG 1343',
'MEG 1333',
'MEG 2612',
'MEG 1523',
'MEG 1612',
'MEG 1623',
'MEG 2413',
'MEG 2422',
'MEG 2643',
'MEG 1522',
'MEG 1613',
'MEG 1622',
'MEG 2412',
'MEG 2423',
'MEG 2642']

2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

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
MyComplianceReport.com: Compliance and Ethics Reporting . 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.

_______________________________________________
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Mne_analysis at nmr.mgh.harvard.edu
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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
MyComplianceReport.com: Compliance and Ethics Reporting . 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.

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8

Hi Maria,

it seems you found a 'bug' in the documentation. If you hit
'mne.pick_types? in and IPython terminal you can see that 'exclude'
defaults to bads.
I guess that would explain your problem?

-Denis

2014-08-27 18:46 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Or could it alternatively be possible to plot also the bad channels?

I have:

picks = mne.pick_types(evoked_raw.info,selection=selection)

I think that this shouldn't exclude bads because I have not exclude='bads'.

However, picks doesn't include the channels in selection that are marked
as bad.

In the reference of mne.picks_type it is said:

exclude : list of string | str

List of channels to exclude. If empty do not exclude any (default). If
?bads?, exclude channels in info[?bads?]

-Maria

2014-08-27 19:02 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

There was one channel two times in selection...

However, it seems to cause a problem if some of the channels in selection
is bad.
I would like to plot a subset of channels from each data file in a loop
as follows:

picks = mne.pick_types(evoked.info,selection=selection)

                idx = 0
                for ax_row in axes:
                        for ax in ax_row:
                                ax.plot(evoked_raw.times,
evoked_raw.data[picks[idx]])
                                idx += 1

Is it somehow possible to, for example, plot a blank plot if there is a
bad channel in selection?

-Maria

2014-08-27 15:05 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi,

2014-08-27 14:02 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

I manged to solve this already.

now I'm curious, what was the problem?

-Denis

-Maria

2014-08-27 13:11 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

I have one bad channel but it is not included in selection. Can it

however cause problems?

-Maria

Here are the outputs:
evoked.info['bads']
Out[54]: [u'MEG 2511']

but

In [53]: selection
Out[53]:
['MEG 0133',
'MEG 0212',
'MEG 0223',
'MEG 1313',
'MEG 1322',
'MEG 1443',
'MEG 0132',
'MEG 0213',
'MEG 0222',
'MEG 1312',
'MEG 1323',
'MEG 1442',
'MEG 1513',
'MEG 0242',
'MEG 0233',
'MEG 1343',
'MEG 1332',
'MEG 2613',
'MEG 1512',
'MEG 0243',
'MEG 0232',
'MEG 1343',
'MEG 1333',
'MEG 2612',
'MEG 1523',
'MEG 1612',
'MEG 1623',
'MEG 2413',
'MEG 2422',
'MEG 2643',
'MEG 1522',
'MEG 1613',
'MEG 1622',
'MEG 2412',
'MEG 2423',
'MEG 2642']

2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

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
MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
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9

Is it somehow possible to include the bads if they are in selection?

-Maria

2014-08-27 19:51 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

it seems you found a 'bug' in the documentation. If you hit
'mne.pick_types? in and IPython terminal you can see that 'exclude'
defaults to bads.
I guess that would explain your problem?

-Denis

2014-08-27 18:46 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Or could it alternatively be possible to plot also the bad channels?

I have:

picks = mne.pick_types(evoked_raw.info,selection=selection)

I think that this shouldn't exclude bads because I have not
exclude='bads'.

However, picks doesn't include the channels in selection that are marked
as bad.

In the reference of mne.picks_type it is said:

exclude : list of string | str

List of channels to exclude. If empty do not exclude any (default). If
?bads?, exclude channels in info[?bads?]

-Maria

2014-08-27 19:02 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

There was one channel two times in selection...

However, it seems to cause a problem if some of the channels in
selection is bad.
I would like to plot a subset of channels from each data file in a loop
as follows:

picks = mne.pick_types(evoked.info,selection=selection)

                idx = 0
                for ax_row in axes:
                        for ax in ax_row:
                                ax.plot(evoked_raw.times,
evoked_raw.data[picks[idx]])
                                idx += 1

Is it somehow possible to, for example, plot a blank plot if there is a
bad channel in selection?

-Maria

2014-08-27 15:05 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi,

2014-08-27 14:02 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

I manged to solve this already.

now I'm curious, what was the problem?

-Denis

-Maria

2014-08-27 13:11 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

I have one bad channel but it is not included in selection. Can it

however cause problems?

-Maria

Here are the outputs:
evoked.info['bads']
Out[54]: [u'MEG 2511']

but

In [53]: selection
Out[53]:
['MEG 0133',
'MEG 0212',
'MEG 0223',
'MEG 1313',
'MEG 1322',
'MEG 1443',
'MEG 0132',
'MEG 0213',
'MEG 0222',
'MEG 1312',
'MEG 1323',
'MEG 1442',
'MEG 1513',
'MEG 0242',
'MEG 0233',
'MEG 1343',
'MEG 1332',
'MEG 2613',
'MEG 1512',
'MEG 0243',
'MEG 0232',
'MEG 1343',
'MEG 1333',
'MEG 2612',
'MEG 1523',
'MEG 1612',
'MEG 1623',
'MEG 2413',
'MEG 2422',
'MEG 2643',
'MEG 1522',
'MEG 1613',
'MEG 1622',
'MEG 2412',
'MEG 2423',
'MEG 2642']

2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

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10

Have you tried to to pass exclude= when invoking mne.pick_types?

-Denis

2014-08-27 19:09 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Is it somehow possible to include the bads if they are in selection?

-Maria

2014-08-27 19:51 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

it seems you found a 'bug' in the documentation. If you hit
'mne.pick_types? in and IPython terminal you can see that 'exclude'
defaults to bads.
I guess that would explain your problem?

-Denis

2014-08-27 18:46 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Or could it alternatively be possible to plot also the bad channels?

I have:

picks = mne.pick_types(evoked_raw.info,selection=selection)

I think that this shouldn't exclude bads because I have not
exclude='bads'.

However, picks doesn't include the channels in selection that are marked
as bad.

In the reference of mne.picks_type it is said:

exclude : list of string | str

List of channels to exclude. If empty do not exclude any (default). If
?bads?, exclude channels in info[?bads?]

-Maria

2014-08-27 19:02 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

There was one channel two times in selection...

However, it seems to cause a problem if some of the channels in
selection is bad.
I would like to plot a subset of channels from each data file in a loop
as follows:

picks = mne.pick_types(evoked.info,selection=selection)

                idx = 0
                for ax_row in axes:
                        for ax in ax_row:
                                ax.plot(evoked_raw.times,
evoked_raw.data[picks[idx]])
                                idx += 1

Is it somehow possible to, for example, plot a blank plot if there is a
bad channel in selection?

-Maria

2014-08-27 15:05 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi,

2014-08-27 14:02 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

I manged to solve this already.

now I'm curious, what was the problem?

-Denis

-Maria

2014-08-27 13:11 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

I have one bad channel but it is not included in selection. Can it

however cause problems?

-Maria

Here are the outputs:
evoked.info['bads']
Out[54]: [u'MEG 2511']

but

In [53]: selection
Out[53]:
['MEG 0133',
'MEG 0212',
'MEG 0223',
'MEG 1313',
'MEG 1322',
'MEG 1443',
'MEG 0132',
'MEG 0213',
'MEG 0222',
'MEG 1312',
'MEG 1323',
'MEG 1442',
'MEG 1513',
'MEG 0242',
'MEG 0233',
'MEG 1343',
'MEG 1332',
'MEG 2613',
'MEG 1512',
'MEG 0243',
'MEG 0232',
'MEG 1343',
'MEG 1333',
'MEG 2612',
'MEG 1523',
'MEG 1612',
'MEG 1623',
'MEG 2413',
'MEG 2422',
'MEG 2643',
'MEG 1522',
'MEG 1613',
'MEG 1622',
'MEG 2412',
'MEG 2423',
'MEG 2642']

2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

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11

Unfortunately, that didn't solve the problem.

-Maria

2014-08-27 20:16 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Have you tried to to pass exclude= when invoking mne.pick_types?

-Denis

2014-08-27 19:09 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Is it somehow possible to include the bads if they are in selection?

-Maria

2014-08-27 19:51 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

it seems you found a 'bug' in the documentation. If you hit
'mne.pick_types? in and IPython terminal you can see that 'exclude'
defaults to bads.
I guess that would explain your problem?

-Denis

2014-08-27 18:46 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

Or could it alternatively be possible to plot also the bad channels?

I have:

picks = mne.pick_types(evoked_raw.info,selection=selection)

I think that this shouldn't exclude bads because I have not
exclude='bads'.

However, picks doesn't include the channels in selection that are
marked as bad.

In the reference of mne.picks_type it is said:

exclude : list of string | str

List of channels to exclude. If empty do not exclude any (default). If
?bads?, exclude channels in info[?bads?]

-Maria

2014-08-27 19:02 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

There was one channel two times in selection...

However, it seems to cause a problem if some of the channels in
selection is bad.
I would like to plot a subset of channels from each data file in a
loop as follows:

picks = mne.pick_types(evoked.info,selection=selection)

                idx = 0
                for ax_row in axes:
                        for ax in ax_row:
                                ax.plot(evoked_raw.times,
evoked_raw.data[picks[idx]])
                                idx += 1

Is it somehow possible to, for example, plot a blank plot if there is
a bad channel in selection?

-Maria

2014-08-27 15:05 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi,

2014-08-27 14:02 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:

I manged to solve this already.

now I'm curious, what was the problem?

-Denis

-Maria

2014-08-27 13:11 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:

I have one bad channel but it is not included in selection. Can it

however cause problems?

-Maria

Here are the outputs:
evoked.info['bads']
Out[54]: [u'MEG 2511']

but

In [53]: selection
Out[53]:
['MEG 0133',
'MEG 0212',
'MEG 0223',
'MEG 1313',
'MEG 1322',
'MEG 1443',
'MEG 0132',
'MEG 0213',
'MEG 0222',
'MEG 1312',
'MEG 1323',
'MEG 1442',
'MEG 1513',
'MEG 0242',
'MEG 0233',
'MEG 1343',
'MEG 1332',
'MEG 2613',
'MEG 1512',
'MEG 0243',
'MEG 0232',
'MEG 1343',
'MEG 1333',
'MEG 2612',
'MEG 1523',
'MEG 1612',
'MEG 1623',
'MEG 2413',
'MEG 2422',
'MEG 2643',
'MEG 1522',
'MEG 1613',
'MEG 1622',
'MEG 2412',
'MEG 2423',
'MEG 2642']

2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

Hi Maria,

Do you have one bad channel? Take a look at evoked.info['bads']
pick types automatically excludes those.

-Denis

2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>
:

Hi all,

I have used mne.pick_types as follows:

picks = mne.pick_types(evoked.info,selection=selection)

where selection includes 36 channel names.
However, picks is an array with only 35 elements.
I wonder what could be wrong there?

Regards,
Maria

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12

Hi all,

I took a look at Maria's script. It turns out that the bad channels were
not picked in Raw, which is why they couldn't be picked downstream in the
Epochs and Evoked objects. Picking 'bads' in Raw solved the problem.

Mainak