[Mne_analysis] mne_do_inverse_operator
Alexandre Gramfort
alexandre.gramfort at telecom-paristech.fr
Thu May 1 16:42:28 EDT 2014
hi Will,
can you run mne_show_fiff on all the input fif files to see if one is corrupted?
you could also try to compute the forward with Python to see if it passes.
At least the error message should be more informative. Cf.
http://martinos.org/mne/dev/auto_examples/plot_make_forward.html
HTH
Alex
On Thu, May 1, 2014 at 6:18 PM, William Graves
<wgraves at psychology.rutgers.edu> wrote:
> Hi Dan,
>
> I have 368 GB available, so I imagine that's not the problem.
>
> Maybe this is a clue: When I try to open the corresponding *ave.fif file in
> mne_analyze, I can view it just fine. But if I also pick the *inv.fif that
> was generated from it (using the command I pasted previously), I get this
> error:
>
> Desired tag (unknown [3522]) not found
>
> Any ideas?
>
> Thanks,
> Will
>
> Hi,
>
> How much free disk space is there?
>
> df -h $megdir/$rundir/
>
> HTH
> D
>
> On Thu, May 1, 2014 at 11:37 AM, William W. Graves
> <william.graves at rutgers.edu> wrote:
>
> Dear MNE Experts,
>
>
> I suspect this is a question for Matti, but of course I'll be happy to get
>
> help from anyone. When I launch mne_do_inverse_operator, it goes through
>
> the whole process, then at the very end it gives a "Segmentation fault".
>
> Oddly, I have a group of 20 participants, all analyzed the same way, but
>
> it only does this for one of them. I'd appreciate any help/insight you can
>
> give. Here's the full screen output, in case it helps:
>
>
> wgraves at argus:~/data/ld_fmri/data/4803/freesurf/4803/MEG/run03_lexdec01>
>
> mne_do_inverse_operator --fwd $megdir/$rundir/${meas}-ico-4-fwd.fif
>
> --fixed --depth --megreg 0.1 --noisecov $megdir/$rundir/$cov
>
>
> mne_inverse_operator version 2.33 compiled at Aug 14 2013 04:19:05
>
>
> Compute the MNE inverse operator decomposition
>
>
> Forward solution :
>
> /home/wgraves/data/ld_fmri/data/4803/freesurf/4803/MEG/run03_lexdec01/run03_xtraClean_0.1_40Hz_word_nonword_ave-ico-4-fwd.fif
>
> Noise covariance matrix :
>
> /home/wgraves/data/ld_fmri/data/4803/freesurf/4803/MEG/run03_lexdec01/run03_xtraClean_0.1_40Hz_word_nonword-cov.fif
>
> Source covariance matrix : identity matrix
>
> Destination for the inverse operator data :
>
> /home/wgraves/data/ld_fmri/data/4803/freesurf/4803/MEG/run03_lexdec01/run03_xtraClean_0.1_40Hz_word_nonword_ave-ico-4-meg-fixed-inv.fif
>
> Include MEG data.
>
> Noise-covariance regularization (mag) : 0.10
>
> Noise-covariance regularization (grad) : 0.10
>
> Employ depth weighting.
>
> limit = 10.00
>
> exponent = 0.80
>
>
> Reading the forward solution....
>
> Read data for 306 MEG channels and 5112 sources
>
> Free source orientations.
>
> The forward computation was performed in head coordinates.
>
> Read 2 source spaces with a total of 5112 source locations
>
> Source spaces are now in head coordinates.
>
> Channel description list matched with the composite forward
>
> solution matrix.
>
> Local surface coordinate system forward matrix will be employed.
>
>
> Loaded projection from
>
> /home/wgraves/data/ld_fmri/data/4803/freesurf/4803/MEG/run03_lexdec01/run03_xtraClean_0.1_40Hz_word_nonword-cov.fif:
>
> # 1 : planar-999--0.080-0.080-PCA-01 : 1 vecs : 204 chs MEG active
>
> # 2 : axial-999--0.080-0.080-PCA-01 : 1 vecs : 102 chs MEG active
>
> # 3 : planar-801--0.200-0.200-PCA-01 : 1 vecs : 204 chs MEG active
>
> # 4 : axial-801--0.200-0.200-PCA-01 : 1 vecs : 102 chs MEG active
>
>
> Read a full noise covariance matrix from
>
> /home/wgraves/data/ld_fmri/data/4803/freesurf/4803/MEG/run03_lexdec01/run03_xtraClean_0.1_40Hz_word_nonword-cov.fif
>
> Picked appropriate channels from the sensor noise covariance matrix.
>
> MEG/EEG correlations omitted.
>
> Average noise-covariance matrix diagonals:
>
> Magnetometers : 170.14 fT reg = 0.10
>
> Planar gradiometers : 38.99 fT/cm reg = 0.10
>
> Noise-covariance regularized as requested.
>
> Projection applied to the covariance matrix.
>
> Decomposing the noise covariance...
>
> Estimated covariance matrix rank = 302 (0.00206112)
>
> 302 MEG and 0 EEG-like channels remain in the whitened data
>
> done.
>
>
> Creating the depth weighting matrix...
>
> 204 planar channels
>
> limit = 3613/5112 = 10.000623
>
> scale = 2.06846e-07 exp = 0.8
>
> Picked elements from a free-orientation depth-weighting prior into
>
> the fixed-orientation one.
>
> Converted the forward solution into the fixed-orientation mode.
>
> Creating the source covariance matrix:
>
> Depth-weighting applied.
>
> done
>
>
> Applying linear projection to the forward solution...done
>
> Whitening the forward solution...done
>
> Scaling the source covariance...done
>
> Decomposing...
>
> Applying a priori source weighting to the forward solution...done
>
> Transpose...done
>
> SVD...done
>
> largest singular value = 0.171679
>
> scaling factor to adjust the trace = 25.2724 (nchan = 306 nzero = 4)
>
> done
>
>
> Writing the solution to
>
> /home/wgraves/data/ld_fmri/data/4803/freesurf/4803/MEG/run03_lexdec01/run03_xtraClean_0.1_40Hz_word_nonword_ave-ico-4-meg-fixed-inv.fif...Segmentation
>
> fault
>
> Inverse operator decomposition failed (see above)
>
>
> Thanks in advance,
>
> Will
>
>
> ---
>
> William W. Graves, Ph.D.
>
> Assistant Professor, Department of Psychology
>
> Rutgers, The State University of New Jersey
>
> Smith Hall, Room 337
>
> 101 Warren Street, Newark, NJ 07102
>
> Voice: 973-353-3947
>
> Fax: 973-353-1171
>
> http://lbbil.rutgers.edu
>
>
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>
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>
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>
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>
>
>
> ---
> William W. Graves, Ph.D.
> Assistant Professor, Department of Psychology
> Rutgers, The State University of New Jersey
> Smith Hall, Room 337
> 101 Warren Street, Newark, NJ 07102
> Voice: 973-353-3947
> Fax: 973-353-1171
> http://lbbil.rutgers.edu
>
>
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