[Mne_analysis] extracting sources from labels using mne_compute_raw_inverse

[Matt Panichello]

Matti and Hari, thanks for explaining the summary waveform option. I removed
the labeldir flag and can extract ~100 sources for each V1 ROI.

Dan, thanks also for your insight. Do you think that a highly decimated
surface will undermine an analysis in any way? What is a more typical number
of vertices for the entire brain?

Thanks again!

Matt



On Fri, Aug 19, 2011 at 12:21 PM, Matti Hamalainen
<msh at nmr.mgh.harvard.edu>wrote:

> 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]
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20110819/65f0a578/attachment.html