[Mne_analysis] extracting sources from labels using mne_compute_raw_inverse

[Matt Panichello]

Hi Matti,

I see, thanks for clarifying.

Matt


On Fri, Aug 19, 2011 at 2:00 PM, Matti Hamalainen
<msh at nmr.mgh.harvard.edu>wrote:

>
> 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]
>>
>>
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>
>
>


-- 
Matthew Panichello
Research Coordinator, Cognitive Neuroscience Laboratory
Massachusetts General Hospital
Phone: 617-726-0308
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