[Mne_analysis] mne_do_inverse_operator
William W. Graves
william.graves at rutgers.edu
Fri May 2 14:44:48 EDT 2014
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
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