mne.write_cov error

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1

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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2

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-R?mi

3

Hi Peng,

Do you have a traceback of why it failed with mne.write_cov? Did you try
Cov.save with your covariance matrix object?

Could you try those and see if that works?

4

???
???

??? iPad

? 2016?4?29??6:21?JR KING <jeanremi.king at gmail.com> ???

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:
Page Redirection
http://martinos.org/mne/dev/faq.html#how-should-i-regularize-the-covariance-matrix

Best,

Jean-R?mi

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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