[Mne_analysis] extracting sources from labels using mne_compute_raw_inverse

[Matti Hamalainen]

Hi again,

On Aug 19, 2011, at 1:27 PM, Matt Panichello wrote:

> 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?

The about 11000 is the total number of sources which is ok. Nothing to worry about there.

- Matti

 
> 
> 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/f4951c4c/attachment.html