[Mne_analysis] mne.write_cov error

JR KING jeanremi.king at gmail.com
Thu Apr 28 18:21:14 EDT 2016
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Dear Peng,

You shouldn't save your covariance in a text file. Covariance object
contains headers/metadata

You should do:

import mne
epochs = mne.read_epochs(epochs_path)

# compute covariance
cov = mne.compute_covariance(epochs, tmax=0.)

# save covariance object
cov.save('my_file-cov.fif')

# read covariance object
cov = mne.read_cov(fname_cov)


Try following the website tutorials first:
http://martinos.org/mne/dev/auto_examples/io/plot_read_noise_covariance_matrix.html#sphx-glr-auto-examples-io-plot-read-noise-covariance-matrix-py
http://martinos.org/mne/dev/faq.html#how-should-i-regularize-the-covariance-matrix

Best,

Jean-Rémi




On 28 April 2016 at 17:17, Peng Zan <zanpeng.pz at gmail.com> wrote:

> Dear mne expert,
>
> I wanted to write a covariance matrix into a *-cov.fif file using python
> command 'mne.write_cov' but failed. I saved the covariance matrix into a
> txt file 'R2262.txt' and then read it via python to cov_matrix. The error
> occurred in the step of 'write_cov'. In tutorial, only file name and the
> matrix are needed. Everything should be correct but it said 'str' had no
> attribute 'save'. The detail is as follows.
>
> >>> cov =
> open('/Users/Peng/Documents/MNE/MNE_analysis/MNE_TRFs/MEG/R2262_S0807/R2262cov.txt');
> cov_matrix = cov.read()
>
> >>>
> mne.write_cov('/Users/Peng/Documents/MNE/MNE_analysis/MNE_TRFs/MEG/R2262_S0807/R2262_trf-cp-cov.fif',cov_matrix)
>
> Traceback (most recent call last):
>
>   File "<stdin>", line 1, in <module>
>
>   File
> "/Users/Peng/Library/Python/2.7/lib/python/site-packages/mne-0.12.dev0-py2.7.egg/mne/cov.py",
> line 1181, in write_cov
>
>     cov.save(fname)
>
> AttributeError: 'str' object has no attribute 'save'
>
>
> Do you have any idea how should this work?
>
> Thank you very much!
>
> Sincerely,
>
> Peng
>
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