[Mne_analysis] mne_do_inverse_operator

[William Graves]

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
>> 
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> 

---
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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