[Mne_analysis] mne_do_inverse_operator
Alexandre Gramfort
alexandre.gramfort at telecom-paristech.fr
Fri May 2 16:21:53 EDT 2014
hi Will,
hope python will help.
ideally if matti has a bit of time you should share the files
so the bug can be reproduced and investigated.
Alex
On Fri, May 2, 2014 at 8:44 PM, William W. Graves
<william.graves at rutgers.edu> wrote:
> Hi Alex,
>
> Thanks for the reply. I ran "mne_show_fiff" on all the inputs (ave fiff
> files), and it nicely returned lots of fields and didn't complain. Since
> this only happened for one dataset but not the other 19, I tried
> specifically looking for tag 3522 that the error message complained about.
> When passing "--tag 3522" to mne_show_fiff, it just gave a blank line, in
> both the dataset with the error and one that had no error. So I guess next
> I'll try your Python suggestion.
>
> Thanks,
> Will
>
>> 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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>
>
> ---
> 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
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