[Mne_analysis] extracting sources from labels using mne_compute_raw_inverse

[Hari Bharadwaj]

Hi Matt,
   Did you load the outname_raw.fif in mne_browse_raw to take a look? I
haven't used this command much but I think this command only saves
summary waveforms for each label i.e the average over the labels.. i.e
one time course per label (for fixed orientation inverse) in the
directory.. Not sure why it saved 2 for the V1 label and 3 for the
fusiform label...

If the directory has 2 V1 labels (lh and rh for instance), I'd expect to
get 2 timecourses in the outfile + possibly stim channels..

Regards,
Hari

On Fri, August 19, 2011 10:13 am, Matt Panichello wrote:
> Hi all,
>
> I am trying to extract the sources from labels using
> mne_compute_raw_inverse. The command finishes without error, but extracts
> extremely few sources for each label: 2 for a V1 label, and 3 for a rather
> large fusiform label. Both labels are based on the freesurfer parcellation
> of the surface and look fine in tksurfer. The exact command I am dropping
> looks like this:
>
> mne_compute_raw_invers  --in (raw fif file)   --inv (inverse solution)
> --labeldir (label directory)   --picknormalcomp   --align_z    --snr 3
> --out (outname)
>
> and my output is below. Any help would be appreciated!
>
> Thank you,
>
> Matt
>
>
> mne_compute_raw_inverse version 1.15 compiled at Aug 19 2011 04:09:29
>
> input  file            : S011/PM01_clean_raw.fif
> inverse operator file  : S011/ROI_freq/PM01_raw-5-meg-inv.fif
> SNR                    : 3.000000
> Additional channels    : 'STI 014'
> All label files in S011/ROI_freq/ will be processed.
> Source locations will be listed in head coordinates.
>
> Reading the inverse operator...
>         Read 2 source spaces from S011/ROI_freq/PM01_raw-5-meg-inv.fif
> with
> a total of 11402 source locations
>         Read the sensor covariance matrix (full)
>         Read the source covariance matrix (diagonal)
>         Measurement file id not found (omit matching).
>         Solution is based on MEG.
>         Inverse operator information was stored in head coordinates.
>         Source orientation prior information read.
>         Depth-weighting prior information read.
>         Source orientations read.
>         Singular values read.
>         Eigenvectors read.
>         Number of channels = 305
>         Number of sources  = 11402
>         Free source orientations
>         Location information in head coordinates
>         Projection in effect:
>                 # 1 : axial-PCA-01 : 1 vecs : 102 chs MEG active
>                 # 2 : axial-PCA-02 : 1 vecs : 102 chs MEG active
>                 # 3 : axial-PCA-03 : 1 vecs : 102 chs MEG active
>                 # 4 : axial-PCA-04 : 1 vecs : 102 chs MEG active
>
> Adding derived data to the inverse operator (nave = 1)...
>         Projection applied to the covariance matrix.
>         Decomposing the sensor noise covariance matrix...
>         Eigenvalue decomposition had been precomputed.
>         Eigenleads multiplied with Cholesky decomposition of the source
> covariance matrix.
>         nave change: 1 -> 1
>
> Raw data file S011/PM01_clean_raw.fif:
>
> Processing label directory S011/ROI_freq/...
> 2 left-hemisphere labels in S011/ROI_freq/
> 1 right-hemisphere labels in S011/ROI_freq/
> Processing left-hemisphere labels...[done]
> Processing right-hemisphere labels...[done]
>
> Saving raw estimates...
>         Data will be split into <= 1907.3 MByte pieces
>         Processing raw data [2000 samples in each buffer] .........[1000
> samples in each buffer] [done]
>         393000 samples (including skips) saved to
> S011/ROI_freq/rh.V1.PM01.normal-mne_raw.fif ... closing...[done]
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-- 
Hari Bharadwaj