Hi all,
I would like to pull out and save timecourses from 40 or so vertex points on
10 individual subjects brains. I have the vertex number I want to use to pull
this timecourse out. Is there a way to pull these out and save them by command
line and not using mne_analyze? Thanks.
Best,
Corey
Hi Corey,
If you don't want to do this manually, you can create stc files using
mne_make_movie, and read the data out from matlab of just the
vertices you are interested in.
Dan
?
Hi all,
I would like to pull out and save timecourses from 40 or so
vertex points on
10 individual subjects brains. I have the vertex number I want to
use to pull
this timecourse out. Is there a way to pull these out and save them
by command
line and not using mne_analyze? Thanks.Best,
Corey_______________________________________________
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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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Hi,
the relevant command it mne_compute_raw_inverse. It will allow you to
extract the raw time course from a specific label.
asaf
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
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
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.f
if --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/l
PSTG-lh.label
mne_epochs2mat --raw
/space/multnomah/3/users/gow/ck_analysis/3_Reference_Labels/PROZ06006/lPSTG-lh-m
ne_raw.fif--mat VP16001_block1_trig3 --event 3 --tmin -200 --tmax 1000 --inv
/space/multnomah/3/users/gow/VP16/subj_VP16001/averages_covariances/VP16001_runs
1234_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
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: