[Mne_analysis] extracting sources from labels using mne_compute_raw_inverse

[Matti Hamalainen]

Hi,

With the labeldir option there will be only one summary waveform / label in the output file.

- Matti

On Aug 19, 2011, at 10:13 AM, Matt Panichello <panichem at nmr.mgh.harvard.edu> 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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