[Mne_analysis] picking timecourses out of vertex points
Alex Clarke
alex at csl.psychol.cam.ac.uk
Mon Jan 26 15:22:33 EST 2009
Hello,
In the mne_epochs2mat command if you use the option --mat <name>, then
it should produce an output file, that can be read into matlab.
I've also been trying to perform TF analysis from ROI data and have been
having problems with the mne_compute_raw_inverse step.
Although the command runs and ends without producing an error message,
all the values at each vertex are zero. I have been using the commmand
as follows:
mne_compute_raw_inverse
--in mb_041_raw_ssst.fif
--inv mb_041_raw-5-meg-inv.fif
--nave 1
--snr 3
--spm
--picknormalcomp
--align_z
--label Orb-lh.label
--labelselout
(have also tried adding --set 1 but can't see why would need it as it's
raw data).
This produces a new fif file as expected, but when I checked the data to
see if it had worked properly all values were zero. I checked using
matlab utilities:
data = fiff_setup_read_raw('Orb-lh-spm_raw.fif');
[data2,times] = fiff_read_raw_segment(data,400000,403000);
Which shows all data points are zero.
Any help or suggestions whould be appreciated,
Alex
Command line output from mne_compute_raw:
mne_compute_raw_inverse version 1.4 compiled at Apr 5 2007 15:59:00
input file :
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/mb_041_raw_ssst.fif
baseline : 0.00 ... 1000.00 ms
inverse operator file :
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/basic_041_moss_450-5-meg-inv.fif
SNR : 3.000000
Do dSPM
Label files to process :
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/Orb-lh.label
Source locations will be listed in head coordinates.
Reading the inverse operator...
Read 2 source spaces from
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/basic_041_moss_450-5-meg-inv.fif
with a total of 12850 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 = 193
Number of sources = 12850
Free source orientations
Location information in head coordinates
Adding derived data to the inverse operator (nave = 1)...
Decomposing the sensor noise covariance matrix...
Eigenvalue decomposition had been precomputed.
SSS was applied to the data. Effective number of channels = 64
129 small eigenvalues detected
Eigenleads multiplied with Cholesky decomposition of the source
covariance matrix.
nave change: 1 -> 1
Raw data file
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/mb_041_raw_ssst.fif:
sfreq = 1000.000000 Hz
nchan = 341
Processing label
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/Orb-lh.label...
2653 points in label
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/Orb-lh.label
115 sources within label
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/Orb-lh.label
Selective inverse operator ready.
Wrote selected to
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/Orb-sel-lh.label
Reading data 1000 shorts in buffer
........................................................................................................
........................................................................................................
........................................................................................................
........................................................................................................
.......................................
/work/imaging3/MEG/AC_MEG_object_processing/Moss/MEG/subjects/meg08_0041/basic/epoch/Orb-lh-spm_raw.fif
[done]
Keller, Corey J. wrote:
> Hi,
>
>
>
> Okay so I am almost there. I am using mne_compute_raw_inverse to pull
> the raw data from my labels and then input the output file from
> mne_compute_raw_inverse into mne_epochs2mat to pull the epochs into
> matlab. Here are my two commands:
>
>
>
> mne_compute_raw_inverse --in
> /space/multnomah/3/users/gow/VP16/MEG/subj_VP16001/raw_data/VP16001_block1_raw.fif
> --bmin -200 --bmax 1000 --set 7 --inv
> /space/multnomah/3/users/gow/VP16/MEG/subj_VP16001/averages_covariances/VP16001_runs1234_LP50_avg-7-meg-eeg-inv.fif
> --label
> /space/multnomah/3/users/gow/VP16/MEG/ck_analysis/3_Reference_Labels/PROZ06006/lPSTG-lh.label
>
>
>
> mne_epochs2mat --raw
> /space/multnomah/3/users/gow/ck_analysis/3_Reference_Labels/PROZ06006/lPSTG-lh-mne_raw.fif--mat
> VP16001_block1_trig3 --event 3 --tmin -200 --tmax 1000 --inv
> /space/multnomah/3/users/gow/VP16/subj_VP16001/averages_covariances/VP16001_runs1234_LP50_avg-7-meg-eeg-inv.fif
> --sel sm_meg_eog.sel
>
>
>
> It tells me no output file specified yet in the manual there is no
> option for an output file. Is this the right syntax for these commands?
> Thanks again.
>
>
>
> Best,
>
> Corey
>
>
>
>
>
> *From:* Matti Hamalainen [mailto:msh at nmr.mgh.harvard.edu]
> *Sent:* Saturday, January 24, 2009 11:30 AM
> *To:* Keller, Corey J.
> *Cc:* Asaf Bachrach; mne_analysis at nmr.mgh.harvard.edu
> *Subject:* Re: [Mne_analysis] picking timecourses out of vertex points
>
>
>
> There is also a program called mne_epochs2mat which does exactly this
> and takes a raw data file containing the source space signals as input.
>
>
>
> - Matti
>
> On Jan 24, 2009, at 9:32 AM, "Keller, Corey J." <CJKELLER at PARTNERS.ORG
> <mailto:CJKELLER at PARTNERS.ORG>> wrote:
>
> Hi Asaf,
>
>
>
> Thanks for the info. But will that be epoched data? Sorry I do not
> use the mne stream much. I’m trying to pull the epoched data from a
> given label, not the raw data. Thanks.
>
>
>
> -Corey
>
>
>
>
>
> *From:* Asaf Bachrach [mailto:asaf at MIT.EDU]
> *Sent:* Saturday, January 24, 2009 5:17 AM
> *To:* Keller, Corey J.
> *Cc:* mne_analysis at nmr.mgh.harvard.edu
> <mailto:mne_analysis at nmr.mgh.harvard.edu>
> *Subject:* Re: [Mne_analysis] picking timecourses out of vertex points
>
>
>
> Hi,
>
> the relevant command it mne_compute_raw_inverse. It will allow you
> to extract the raw time course from a specific label.
>
> asaf
>
> On Jan 23, 2009, at 8:12 PM, Keller, Corey J. wrote:
>
>
>
>
> Hi MNE users,
>
>
>
> In the past to pull a timeseries from a specific vertex point I
> have always made stc files and then pulled them out in matlab.
> However, now I am trying to run at TF analysis on the data and need
> the whole data set at a given vertex, not just the averaged
> timecourse. Is there an easy way to do this? To pull out the epoched
> data from a vertex? Thanks again.
>
>
>
> Best,
>
> Corey
>
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