[Mne_analysis] create_ecg_epochs with mne-12
Elena Orekhova
orekhova.elena.v at gmail.com
Thu May 12 08:34:13 EDT 2016
Dear Jean-Remi,
Below is information you asked for.
MEG channels are 0 to 305.
Elena
######################
raw._data.shape
(336, 247500)
reject
{'grad': 2.5e-10, 'mag': 6e-12}
picks
array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,
65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,
78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,
91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103,
104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,
117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129,
130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155,
156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168,
169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181,
182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194,
195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220,
221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233,
234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246,
247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259,
260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272,
273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285,
286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298,
299, 300, 301, 302, 303, 304, 305])
raw.ch_names
Out[94]:
[u'MEG0113',
u'MEG0112',
u'MEG0111',
u'MEG0122',
u'MEG0123',
u'MEG0121',
u'MEG0132',
u'MEG0133',
u'MEG0131',
u'MEG0143',
u'MEG0142',
u'MEG0141',
u'MEG0213',
u'MEG0212',
u'MEG0211',
u'MEG0222',
u'MEG0223',
u'MEG0221',
u'MEG0232',
u'MEG0233',
u'MEG0231',
u'MEG0243',
u'MEG0242',
u'MEG0241',
u'MEG0313',
u'MEG0312',
u'MEG0311',
u'MEG0322',
u'MEG0323',
u'MEG0321',
u'MEG0333',
u'MEG0332',
u'MEG0331',
u'MEG0343',
u'MEG0342',
u'MEG0341',
u'MEG0413',
u'MEG0412',
u'MEG0411',
u'MEG0422',
u'MEG0423',
u'MEG0421',
u'MEG0432',
u'MEG0433',
u'MEG0431',
u'MEG0443',
u'MEG0442',
u'MEG0441',
u'MEG0513',
u'MEG0512',
u'MEG0511',
u'MEG0523',
u'MEG0522',
u'MEG0521',
u'MEG0532',
u'MEG0533',
u'MEG0531',
u'MEG0542',
u'MEG0543',
u'MEG0541',
u'MEG0613',
u'MEG0612',
u'MEG0611',
u'MEG0622',
u'MEG0623',
u'MEG0621',
u'MEG0633',
u'MEG0632',
u'MEG0631',
u'MEG0642',
u'MEG0643',
u'MEG0641',
u'MEG0713',
u'MEG0712',
u'MEG0711',
u'MEG0723',
u'MEG0722',
u'MEG0721',
u'MEG0733',
u'MEG0732',
u'MEG0731',
u'MEG0743',
u'MEG0742',
u'MEG0741',
u'MEG0813',
u'MEG0812',
u'MEG0811',
u'MEG0822',
u'MEG0823',
u'MEG0821',
u'MEG0913',
u'MEG0912',
u'MEG0911',
u'MEG0923',
u'MEG0922',
u'MEG0921',
u'MEG0932',
u'MEG0933',
u'MEG0931',
u'MEG0942',
u'MEG0943',
u'MEG0941',
u'MEG1013',
u'MEG1012',
u'MEG1011',
u'MEG1023',
u'MEG1022',
u'MEG1021',
u'MEG1032',
u'MEG1033',
u'MEG1031',
u'MEG1043',
u'MEG1042',
u'MEG1041',
u'MEG1112',
u'MEG1113',
u'MEG1111',
u'MEG1123',
u'MEG1122',
u'MEG1121',
u'MEG1133',
u'MEG1132',
u'MEG1131',
u'MEG1142',
u'MEG1143',
u'MEG1141',
u'MEG1213',
u'MEG1212',
u'MEG1211',
u'MEG1223',
u'MEG1222',
u'MEG1221',
u'MEG1232',
u'MEG1233',
u'MEG1231',
u'MEG1243',
u'MEG1242',
u'MEG1241',
u'MEG1312',
u'MEG1313',
u'MEG1311',
u'MEG1323',
u'MEG1322',
u'MEG1321',
u'MEG1333',
u'MEG1332',
u'MEG1331',
u'MEG1342',
u'MEG1343',
u'MEG1341',
u'MEG1412',
u'MEG1413',
u'MEG1411',
u'MEG1423',
u'MEG1422',
u'MEG1421',
u'MEG1433',
u'MEG1432',
u'MEG1431',
u'MEG1442',
u'MEG1443',
u'MEG1441',
u'MEG1512',
u'MEG1513',
u'MEG1511',
u'MEG1522',
u'MEG1523',
u'MEG1521',
u'MEG1533',
u'MEG1532',
u'MEG1531',
u'MEG1543',
u'MEG1542',
u'MEG1541',
u'MEG1613',
u'MEG1612',
u'MEG1611',
u'MEG1622',
u'MEG1623',
u'MEG1621',
u'MEG1632',
u'MEG1633',
u'MEG1631',
u'MEG1643',
u'MEG1642',
u'MEG1641',
u'MEG1713',
u'MEG1712',
u'MEG1711',
u'MEG1722',
u'MEG1723',
u'MEG1721',
u'MEG1732',
u'MEG1733',
u'MEG1731',
u'MEG1743',
u'MEG1742',
u'MEG1741',
u'MEG1813',
u'MEG1812',
u'MEG1811',
u'MEG1822',
u'MEG1823',
u'MEG1821',
u'MEG1832',
u'MEG1833',
u'MEG1831',
u'MEG1843',
u'MEG1842',
u'MEG1841',
u'MEG1912',
u'MEG1913',
u'MEG1911',
u'MEG1923',
u'MEG1922',
u'MEG1921',
u'MEG1932',
u'MEG1933',
u'MEG1931',
u'MEG1943',
u'MEG1942',
u'MEG1941',
u'MEG2013',
u'MEG2012',
u'MEG2011',
u'MEG2023',
u'MEG2022',
u'MEG2021',
u'MEG2032',
u'MEG2033',
u'MEG2031',
u'MEG2042',
u'MEG2043',
u'MEG2041',
u'MEG2113',
u'MEG2112',
u'MEG2111',
u'MEG2122',
u'MEG2123',
u'MEG2121',
u'MEG2133',
u'MEG2132',
u'MEG2131',
u'MEG2143',
u'MEG2142',
u'MEG2141',
u'MEG2212',
u'MEG2213',
u'MEG2211',
u'MEG2223',
u'MEG2222',
u'MEG2221',
u'MEG2233',
u'MEG2232',
u'MEG2231',
u'MEG2242',
u'MEG2243',
u'MEG2241',
u'MEG2312',
u'MEG2313',
u'MEG2311',
u'MEG2323',
u'MEG2322',
u'MEG2321',
u'MEG2332',
u'MEG2333',
u'MEG2331',
u'MEG2343',
u'MEG2342',
u'MEG2341',
u'MEG2412',
u'MEG2413',
u'MEG2411',
u'MEG2423',
u'MEG2422',
u'MEG2421',
u'MEG2433',
u'MEG2432',
u'MEG2431',
u'MEG2442',
u'MEG2443',
u'MEG2441',
u'MEG2512',
u'MEG2513',
u'MEG2511',
u'MEG2522',
u'MEG2523',
u'MEG2521',
u'MEG2533',
u'MEG2532',
u'MEG2531',
u'MEG2543',
u'MEG2542',
u'MEG2541',
u'MEG2612',
u'MEG2613',
u'MEG2611',
u'MEG2623',
u'MEG2622',
u'MEG2621',
u'MEG2633',
u'MEG2632',
u'MEG2631',
u'MEG2642',
u'MEG2643',
u'MEG2641',
u'STI001',
u'STI002',
u'STI003',
u'STI004',
u'STI005',
u'STI006',
u'STI007',
u'STI008',
u'EEG030',
u'EEG048',
u'EEG057',
u'EEG058',
u'EEG059',
u'EOG061',
u'EOG062',
u'ECG063',
u'EMG064',
u'MISC001',
u'STI101',
u'STI201',
u'STI301',
u'CHPI001',
u'CHPI002',
u'CHPI003',
u'CHPI004',
u'CHPI005',
u'CHPI006',
u'CHPI007',
u'CHPI008',
u'CHPI009']
On 12 May 2016 at 12:18, JR KING <jeanremi.king at gmail.com> wrote:
> Dear Elena,
>
> This may be due to this bug fix:
>
> https://github.com/mne-tools/mne-python/pull/3055/files
>
> Previously, a synthetic ecg channel was incorrectly created even when the
> ecg channel was set by the user.
>
> To check that the `create_ecg_epochs` function works on your computer,
> try:
>
> ```
> from mne.io import Raw
> from mne.preprocessing import create_ecg_epochs
> from mne.datasets import sample
>
> data_path = sample.data_path()
> fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
> raw = Raw(fname, preload=True)
>
> ecg_epochs = create_ecg_epochs(raw, tmin=-.15, tmax=.4,
> l_freq=1.0, h_freq=20.0,
> reject=dict(grad=4000e-13),
> ch_name=None, picks=None)
> ```
>
> I haven't been able to reproduce your error, so I suspect that there is
> something wrong with your raw. Can you report us
>
> ```
> raw._data.shape
> raw.ch_names
> reject
> picks
> ```
>
> Best,
>
> Jean-Rémi
>
> On 12 May 2016 at 04:52, Elena Orekhova <orekhova.elena.v at gmail.com>
> wrote:
>
>> Hello mne developers,
>>
>> I upgraded to mne-12 by
>> % pip install --upgrade --user mne
>>
>> (although the output indicates that in this way I installed mne-0.11.0
>> ...? See below )
>> #################
>> Collecting mne
>> Using cached mne-0.12.0.tar.gz
>> Installing collected packages: mne
>> Running setup.py install for mne ... done
>> Successfully installed mne-0.11.0
>> ################
>>
>> After the upgrade running this line (that previously worked OK)
>> ecg_epochs = create_ecg_epochs(RAW, reject=reject, tmin=-.15, tmax=.4,
>> ch_name=ECG_ch, l_freq=1.0, h_freq=20.0, picks=picks)
>> gives me an error:
>> Data must be a 2D array of shape (n_channels, n_samples
>>
>> The full error output is below.
>> I believe that this relates to the upgrade.
>>
>> Regards,
>> Elena
>>
>>
>>
>>
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