[Mne_analysis] FW: forward solution retransmission
Kirk Gregory R.
GKirk at uwhealth.org
Tue Dec 1 12:30:08 EST 2009
can you help me with the forward solution problem described below so i can get tononi's lab set up
using the mne software ?
i think i have solved the .elp->htps problem - the ordering of the cardinals they
gave me was wrong, i figured it by making them the 256 electrode and seeing where it went.
ill send the files so you can see what is going with the .elp files being kicked out by nextstim
but making a script that just yanks out the coords and makes a .htps file is good for me.
my current issue is with mne_do_forward_solution --spacing oct-6 --meas Fabio_raw.fif --eegonly
gives
mne_forward_solution version 2.9 compiled at Jun 10 2009 23:37:23
Source space : /home/gkirk/mne/mne/sample_data/subjects/Fabio/bem/Fabio-oct-6-src.fif
MRI -> head transform source : ./Fabio_raw-trans.fif
Measurement data : Fabio_raw.fif
BEM model : /home/gkirk/mne/mne/sample_data/subjects/Fabio/bem/Fabio-5120-5120-5120-bem.fif
Accurate field computations
Do computations in head coordinates.
Free source orientations
Destination for the solution : ./Fabio_raw-oct-6-fwd.fif
Reading /home/gkirk/mne/mne/sample_data/subjects/Fabio/bem/Fabio-oct-6-src.fif...
Read 2 source spaces a total of 8196 active source locations
Coordinate transformation: MRI (surface RAS) -> head
0.996425 -0.060723 -0.058740 -3.22 mm
0.076219 0.946048 0.314934 10.63 mm
0.036447 -0.318285 0.947294 73.73 mm
0.000000 0.000000 0.000000 1.00
Read 257 EEG channels from Fabio_raw.fif
MEG not requested. MEG channels omitted.
Some EEG channels do not have locations assigned.
Forward computation failed (see above)
there are 256 channels of data + ref
mne_edf2fiff --edf TSDpilotDS_FF_B1_AEP.edf --hpts Fabio_head_coord.htps --meters --fif Fabio_raw.fif
gives
mne_edf2fiff version 1.4 compiled at Jun 10 2009 23:37:18
EDF/EDF+/BDF file (input) : TSDpilotDS_FF_B1_AEP.edf
hpts file (input) : Fabio_head_coord.htps
fif file (output) : Fabio_raw.fif
Parsing EDF/EDF+/BDF header...[done]
Reading the digitization data from Fabio_head_coord.htps (coordinates in meters)...
Read a total of 260 digitization points. 257 electrode labels present
Transformed LPA : -70.1 0.0 0.0 mm
Transformed NAS : -0.0 89.6 -0.0 mm
Transformed RPA : 63.8 -0.0 -0.0 mm
Transformed 260 locations to the head coordinate frame.
256 EEG electrode locations assigned
Reference electrode at : -18.4 21.1 158.2 mm
Note: Annotation channel present but trigger map not specified.
Annotation channel will not be converted into a trigger channel.
Coverting raw data file TSDpilotDS_FF_B1_AEP.edf to Fabio_raw.fif...
Converting...[done]
Adding directory...[done]
I think I have responded to all your requests. Good bye.
so it seems to give all 256 channels + ref a location
so i don't know what it's flopping over dead about
seems i should be close to making a movie as soon as i can get the forward solution to compute sucessfully
the .elp and htps are attached , for ref since you most likely don't have the egi electrode layout
channels 241,242,243 are left anterior electordes
and 238,239,240 are right anterior
the last 3 coordinate triples i.e. electrode 257 258 259 are a second digitization of the cardinals
and there is no digitization of the vref, i added a fale near the electrodes at the apex where egi puts it's ref ( but not an exact copy of an electrode location )
thanks bunches
Greg.
-----Original Message-----
From: Matti Hamalainen [mailto:msh at nmr.mgh.harvard.edu]
Sent: Thu 11/5/2009 7:12 AM
To: Kirk Gregory R.
Subject: Re: [Mne_analysis] topo plot
Hi Greg,
On Nov 3, 2009, at 1:16 PM, Kirk Gregory R. wrote:
>
> Hi,
>
> im trying to get tononi's lab set us using the mne tools, everything
> pretty
> smoth exept the eeg geometry.
>
> included a tiff of the topoplot the electrodes at the vertex ( top)
> of the head appear out at the boundary instead
> rather than at the center. seems i remember something that it was
> supposed to work that way years
> ago when i was there, or maybe i just need a memory circuit replaced ?
>
> also the digitization data im using is from the nextstim optical
> system, the electrode positions did not
> seem all to make sense, had a few on the bottom of the neck ? . the
> numbers are all less than 1.0 so i assumed that i needed to use the
> --meters option to
> import the digitize data. i just make a .htps file out of the .elp
> file from nextstim as the .elp file was not recognizable by the mne
> import function, ie.
> seems the nextstim .elp was written by somebody with a different
> standard manual than matti cited in the doc and it seemed much
> easier to just
> yank out the numbers and make a .htps
>
>
> trying to get a movie of an auditory erp made as a some people
> from egi will be here tomorrow and i would like to show them, got
> the freesurfer processing
> and bem surfaces made, forward model, import the eeg data fine and
> can compute an average,
> so if i can just get a sensible mri->eeg coord tran i should be able
> to make a movie.
Can you send me the elp and hpts files and I can have look what is
going on.
- Matti
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Fabio_head_coord.htps
Type: application/octet-stream
Size: 8397 bytes
Desc: Fabio_head_coord.htps
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20091201/2be260db/attachment.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Fabio_Head_Coordinates_10_14_2009.elp
Type: application/octet-stream
Size: 25320 bytes
Desc: Fabio_Head_Coordinates_10_14_2009.elp
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20091201/2be260db/attachment-0001.obj
More information about the Mne_analysis
mailing list