[Mne_analysis] Strange errors with calculating source estimates in a frequency band
Silfverberg Sebastian
sebastian.silfverberg at aalto.fi
Thu Jul 31 02:14:38 EDT 2014
Hi everyone!
I have been trying to code a program that would enable to plot user selectable time windows of averaged source estimates in a certain frequency band in real time with FieldTrip Buffer. I'm now trying to simulate that in offline mode with looping through the epochs.get_data() and then building an Epoch from a single epoch with EpochsArray (because that's the way the real time sytem works). I end up with a couple of odd errors using compute_source_psd_epochs depending on how long my time window is. If my time window is shorter than 10 seconds, my error is this:
/usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in execfile(fname, *where)
173 else:
174 filename = fname
--> 175 __builtin__.execfile(filename, *where)
/home/silfves1/mne-python/examples/omatfunktiot/jatk_off.py in <module>()
380
381
--> 382 stc = compute_source_psd_epochs(epochs=ep, inverse_operator=inverse_operator, lambda2=lambda2, method=method, fmin=15.0, fmax=25.0, pick_ori=None, pca=True, bandwidth=bandwidth, n_jobs=10, return_generator=False)
383
384
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc in compute_source_psd_epochs(epochs, inverse_operator, lambda2, method, fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive, low_bias, return_generator, n_jobs, verbose, pick_normal)
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/utils.pyc in verbose(function, *args, **kwargs)
549 return ret
550 else:
--> 551 ret = function(*args, **kwargs)
552 return ret
553
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc in compute_source_psd_epochs(epochs, inverse_operator, lambda2, method, fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive, low_bias, return_generator, n_jobs, verbose, pick_normal)
669 # return a list
670 stcs = list()
--> 671 for stc in stcs_gen:
672 stcs.append(stc)
673
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc in _compute_source_psd_epochs(epochs, inverse_operator, lambda2, method, fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive, low_bias, n_jobs, verbose)
519
520 dpss, eigvals = dpss_windows(n_times, half_nbw, n_tapers_max,
--> 521 low_bias=low_bias)
522 n_tapers = len(dpss)
523
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/time_frequency/multitaper.pyc in dpss_windows(N, half_nbw, Kmax, low_bias, interp_from, interp_kind)
202 # only calculate the highest Kmax eigenvalues
203 w = linalg.eigvals_banded(ab, select='i',
--> 204 select_range=(N - Kmax, N - 1))
205 w = w[::-1]
206
/usr/lib/python2.7/dist-packages/scipy/linalg/decomp.pyc in eigvals_banded(a_band, lower, overwrite_a_band, select, select_range)
698 return eig_banded(a_band, lower=lower, eigvals_only=1,
699 overwrite_a_band=overwrite_a_band, select=select,
--> 700 select_range=select_range)
701
702 _double_precision = ['i','l','d']
/usr/lib/python2.7/dist-packages/scipy/linalg/decomp.pyc in eig_banded(a_band, lower, eigvals_only, overwrite_a_band, select, select_range, max_ev)
490 vl, vu, il, iu = 0.0, 0.0, min(select_range), max(select_range)
491 if min(il, iu) < 0 or max(il, iu) >= a1.shape[1]:
--> 492 raise ValueError('select_range out of bounds')
493 max_ev = iu - il + 1
494 else: # 1, 'v', 'value'
ValueError: select_range out of bounds
However, if my time window is 10 seconds, here's the error then:
error Traceback (most recent call last)
/usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in execfile(fname, *where)
173 else:
174 filename = fname
--> 175 __builtin__.execfile(filename, *where)
/home/silfves1/mne-python/examples/omatfunktiot/jatk_off.py in <module>()
380
381
--> 382 stc = compute_source_psd_epochs(epochs=ep, inverse_operator=inverse_operator, lambda2=lambda2, method=method, fmin=15.0, fmax=25.0, pick_ori=None, pca=True, bandwidth=bandwidth, n_jobs=10, return_generator=False)
383
384
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc in compute_source_psd_epochs(epochs, inverse_operator, lambda2, method, fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive, low_bias, return_generator, n_jobs, verbose, pick_normal)
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/utils.pyc in verbose(function, *args, **kwargs)
549 return ret
550 else:
--> 551 ret = function(*args, **kwargs)
552 return ret
553
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc in compute_source_psd_epochs(epochs, inverse_operator, lambda2, method, fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive, low_bias, return_generator, n_jobs, verbose, pick_normal)
669 # return a list
670 stcs = list()
--> 671 for stc in stcs_gen:
672 stcs.append(stc)
673
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc in _compute_source_psd_epochs(epochs, inverse_operator, lambda2, method, fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive, low_bias, n_jobs, verbose)
545
546 # compute tapered spectra in sensor space
--> 547 x_mt, freqs = _mt_spectra(data, dpss, sfreq)
548
549 if k == 0:
/home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/time_frequency/multitaper.pyc in _mt_spectra(x, dpss, sfreq, n_fft)
439 # remove mean (do not use in-place subtraction as it may modify input x)
440 x = x - np.mean(x, axis=-1)[:, np.newaxis]
--> 441 x_mt = fftpack.fft(x[:, np.newaxis, :] * dpss, n=n_fft)
442
443 # only keep positive frequencies
/usr/lib/python2.7/dist-packages/scipy/fftpack/basic.pyc in fft(x, n, axis, overwrite_x)
213
214 if axis == -1 or axis == len(tmp.shape) - 1:
--> 215 return work_function(tmp,n,1,0,overwrite_x)
216
217 tmp = swapaxes(tmp, axis, -1)
error: failed in converting 1st argument `x' of _fftpack.zrfft to C/Fortran array
I don't know, why these error come up. Do some of you have any ideas to help? Thank you so much!
Best regards
Sebastian
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140731/55d6286b/attachment.html
More information about the Mne_analysis
mailing list