[Mne_analysis] mne_do_inverse_operator

[dgw]

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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