preparing leadfield for Phantom

[Vladimir Litvak]

Dear Jim,

The example scripts:

http://fieldtrip.fcdonders.nl/example/make_leadfields_using_different_headmodels

and

http://fieldtrip.fcdonders.nl/example/shift_electrode_positions_into_the_same_coordinate_system_as_the_corresponding_mri_for_using_individual_headmodels


contain some ideas that you can use to do what you want. However, the
trickiest part is coregistration. In the CTF system this problem is
solved by the CTF software. Also for an expert it is easy to do with
just a few lines of code. This is why there is no easy-to-use generic
solution for it in Fieldtrip as far as I know.

I would recommend you looking at SPM8
(http://www.fil.ion.ucl.ac.uk/spm/software/spm8/) which is another
free Matlab toolbox. In SPM8 you can go through all the steps for
leadfield computation using GUI (see the manual, imaging source
reconstruction chapter). It support BTi data and is tightly integrated
with Fieldtrip so you can later get the coregistered vol and grad from
SPM and use them in your Fieldtrip script. See:

https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0905&L=SPM&P=R8906

Also SPM saves leadfields for its 'canonical cortical mesh' in a
mat-file and you can just use those.

Best,

Vladimir


On Fri, May 8, 2009 at 12:43 AM, Jim Li <megjim1 at gmail.com> wrote:
> Hi all,
>
> Actually I just observed something: "hdr.grad.pnt" doesn't contain the
> coordinates of digitization points, but instead seems to be sensor coil-related.
>
> My question regarding how to prepare the lead field using the
> single shell modeling still remains. Any suggestion will be greatly appreciated!
>
> Thanks,
>
> Jim
>
> On Thu, 7 May 2009 02:08:47 +0200, Jim Li <megjim1 at GMAIL.COM> wrote:
>
>>Dear FTer:
>>
>>I'm trying to test a localization algorithm with some epoch data collected on
>>our phantom. Can anyone suggest a way to prepare the lead field using the
>>single shell modeling? I'm using 4D's system right now.
>>
>>While playing with "prepare_singleshell" and  "prepare_leadfield", I
> encountered
>>two questions:
>>
>>1) How can I get my headshape points in head coordinate system?
>>
>>I can run
>>--------
>>hdr = read_fcdc_header(FileName);
>>cfg.headshape = hdr.grad.pnt;
>>[vol] = prepare_singleshell(cfg);
>>-------
>>but that doesn't seem to give me headshape points in head coordinate
> system
>>and it'll crash "prepare_leadfield" later on.
>>
>>2) Do I need to define "cfg.vol.r = 7.5; cfg.vol.o = [0,0,0];" before
>>running "prepare_leadfield"? If not, I'll get weird stuff like "1 dipoles inside, 26
>>dipoles outside brain".
>>
>>I'd appreciate it if anyone can show me your complete script of preparing
> lead
>>field from beginning to end.
>>
>>Cheers,
>>
>>Jim
>>
>>----------------------------------
>>The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and
> EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.