DICS Localization Problem
Vladimir Litvak
v.litvak at ION.UCL.AC.UK
Tue Aug 5 10:10:10 CEST 2008
Dear Nathans,
I think Nathan2 is in the right direction. I don't see anything in
Nathan1's code that performs coregistration of the head model and the
sensors, Robert and people at the Donders use CTF software to prepare
their MRIs. In that software they specify the three fiducials and then
the MRI is saved with transform from voxels to CTF head coordinates,
the same coordinate system that the sensors are in. Thus when one uses
MRI preprocessed with CTF software there is no need to coregrister.
But this is not true in general, but rather an exception. Nathan1 uses
MRI preprocessed with SPM. This MRI is most probably in MNI or some
native coordinates in mm. The sensors are in head coordinates in cm
(although I'm not sure about your particular system). The latest
versions of FT, of the last month or so complain if there is a
mismatch in units but they don't complain if your sensors are rotated
90 degrees for instance. So indeed you should become very well
familiar with headmodelplot. Also look at volumerealign,
electroderealign and interactiverealign. In general coregistration is
quite tricky business, which is not very well reflected at the FT
website because at the Donders they do it in one particular way, which
makes it not so tricky for them.
In SPM8 which will be released in October and is integrated with FT
there will be a semi- automatic tool for coregistration that works
with the 3 common MEG systems. But until then you have to figure it
out. It's useful in the long run if you don't want to do things
blindly.
Best,
Vladimir
On Tue, Aug 5, 2008 at 6:34 AM, Nathan Weisz <nathanweisz at mac.com> wrote:
> dear nathan,
> we see nice mu desynchronizations nicely localized to motor cortex when
> subjects prepare responding to a target using a 4-D 2500 WH (the one with
> 148 sensors).
> Have you already done localizations with your MEG system using a segmented
> brain? If not, then I suggest to check if you get the same results using a
> more 'standard' headmodel, e.g. multisphere (like in the tutorial). this
> assures you always are in the MEG-coordinate system, and have no weird
> mixture between coordinate systems. you need a headshape for that (pretty
> standard with 4D; i can provide you with one if you don't have one). also
> you might want to check if your volume / grid makes sense relative to the
> sensor position using 'headmodelplot'.
> good luck,
> yet-another-nathan
> On 05.08.2008, at 02:45, Nathan Dees wrote:
>
> Dear Fieldtrippers,
>
> Have been struggling a long time to produce a viable image of beamforming
> analysis. We are using a 4D-Magnes3600 Magnetometer MEG unit to record a
> prompted finger tapping motor task with variable ISI of 2.5 - 3.0 seconds.
> Our time-frequency plots show evident beta and alpha
> desynchronization at movement onset. We are using the beamforming tutorial
> as a guide. After calculating dataPre and dataPost, and verifying our mri
> has been properly segmented by SPM, our code is:
>
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'powandcsd';
> cfg.tapsmofrq = 2;
> cfg.foilim = [18 20];
> cfg.pad = 0.5;
> freqPre = freqanalysis(cfg,dataPre);
>
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'powandcsd';
> cfg.tapsmofrq = 2;
> cfg.foilim = [18 20];segmentedmriF.transform = mri.transform;
> segmentedmriF.anatomy = mri.anatomy;
> cfg.pad = 0.5;
> freqPost = freqanalysis(cfg,dataPost);
>
> segmentedmri.transform = mri.transform;
> segmentedmri.anatomy = mri.anatomy;
> [vol, cfg] = prepare_singleshell([], segmentedmri);
>
> cfg = [];
> cfg.grad = freqPre.grad;
> cfg.vol = vol;
> cfg.reducerank = 2;
> cfg.channel = {'MEG'};
> cfg.xgrid = -30:1:30; % 'AUTO' does not work!
> cfg.ygrid = -30:1:30; % 'AUTO' does not work!
> cfg.zgrid = -40:1:40; % 'AUTO' does not work!
> [grid] = prepare_leadfield(cfg);
>
> cfg = [];
> cfg.frequency = 20;
> cfg.method = 'dics';
> cfg.projectnoise = 'yes';
> cfg.grid = grid;
> cfg.vol = vol;
> cfg.lambda = 0;
>
> sourcePre = sourceanalysis(cfg,freqPre );
> sourcePost = sourceanalysis(cfg,freqPost);
>
> %Plot of deep sources in the center of the brain looks reasonable.
>
> sourceDiff = sourcePost;
> sourceDiff.avg.pow = (sourcePre.avg.pow - sourcePost.avg.pow) ./
> sourcePost.avg.pow;
> cfg = [];
> cfg.downsample = 2;
> sourceDiffInt = sourceinterpolate(cfg, sourceDiff , mri);
>
> cfg = [];
> cfg.method = 'slice';
> cfg.funparameter = 'avg.pow';
> cfg.maskparameter = cfg.funparameter;
> cfg.funcolorlim = [0.0 .2];
> cfg.opacitylim = [0.0 .2];
> cfg.opacitymap = 'rampup';
> figure
> sourceplot(cfg,sourceDiffInt);
>
> We expect localization of desynchronization to be in the motor cortex,
> predominantly on the left side. The result we get is diffusely localized,
> and with weak signal. I have images to possibly help diagnose the problem,
> but for now, can anyone spot the errors?
>
> Thank you!!
>
> ----------------------------------
> 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/fcdonders/fieldtrip.
>
> --------------------------------------------
> Attention: New Contact Details
> --------------------------------------------
> Dr. Nathan Weisz
> OBOB-Lab
> University of Konstanz
> Department of Psychology
> P.O. Box D23
> 78457 Konstanz
> Germany
> Tel: ++49 - (0)7531 - 88 45 84
> Email: nathan.weisz at uni-konstanz.de
> Homepage: coming soon
> Bob-wisdom: It's better to do one job well than two jobs... not so well.
>
> ----------------------------------
>
> 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.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/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/fcdonders/fieldtrip.
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