fit volume segment and sensors?

Fri May 7 17:24:25 CEST 2010

Dear Marc,

we use nutmeg to do co-registration.

http://nutmeg.berkeley.edu/index.php?title=Main_Page

in a first step we define fiducials manually, similar to volumerealign. in a second step -with the help of a magic button doing "complex things" (or was it stuff)- you can use the headshape to get even some better matching.

then from the command line:
global nuts st

%mri is the MRI structure read into firldtrip with read_fcdc_mri
mri.transform=inv(nuts.coreg.meg2mri_tfm)*st.vols{1}.mat;

from there on you can continue with your forward modeling as before.

good luck,
nathan

On 07.05.2010, at 16:59, Marc Recasens wrote:

> Thanks Jan for the rapid response,
>
>  I followed the steps using ctf coords and the segmented volume fits perfectly well in the skull using sourceplot. The volume seems to fit better into the headshape. However, as can be seen in the picture, there's still a big space from the posterior part of the brain to the posterior part of the head shape. I suppose this Can be due to a bad realignment (?).  As I mentioned, I have no fiducial points in the MRI scans, so I have to select the nas, lpa and rpa with no physical reference. I guess there is no alternative in this case but using another volume or trying to align the volume manually until it fits in the headshape, isn't it? Can the volume segment be aligned in connection to the headshape automatically?
>
> thank you for the help!
>
> Bests,
>
> <CTFvolume.jpg>
>
>
>
> On Fri, May 7, 2010 at 9:01 AM, jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl> wrote:
> Dear Marc,
>
> It seems to me that there is an issue with the coordinate system in which your original MRI is expressed. This could be related to the order of the steps you take, so I would permute the order and see whether this makes any difference at all (for me it usually works fine as follows:)
>
> First do a call to ft_volumerealign using your single subject's MRI. This step should give you the transformation matrix from voxel to headspace according to CTF's convention (which happens to be the same as 4d).
> Then do a segmentation of the output of ft_volumerealign, but note that you should specify ctf.coordinates = 'ctf'.
> Then you can proceed to create the single shell volume conductor model (after checking whether the segmentation worked fine with respect to the orientation etc of the resulting volumes; I believe there is some documentation about this on the website) and plot the results.
>
> Hopefully this helps,
>
> Best,
>
> Jan-Mathijs
>
> On May 6, 2010, at 8:38 PM, Marc Recasens wrote:
>
>> Hello,
>>
>> I'm new in Fieldtrip and I find myself needed of some help :)
>> I'm currently analysing some MEG data (4D-Neuroimaging, Magnes 2500WH) and trying to create a Single-Shell headmodel using a segmented mri.
>> . I've read all the documentation on FT website but I'm still stuck. The volume never fits in the correct position inside the sensor helmet.
>>
>> First of all, I create a segmented MRI  using Analyse images (.img'), and the segmentation is performed using:
>> cfg.coordinates  = 'spm';
>> cfg.template     = 'C:\...\MATLAB\R2007a\toolbox\spm2\templates\T1.mnc';
>> segmentedmri = ft_volumesegment (cfg, mri);
>> segmentedmri.anatomy = mri.anatomy;    <--- I use that for posterior volumerealign.
>>
>> Then, I do a volumerealign by selecting manually the fiducial points (Nas, Lpa, Rpa), as I actually don't have fiducials on the MRI scans.
>> cfg.method = 'realignfiducial';
>> cfg.fiducial.nas = Nas;  <--- (I get this from headshape.fid)
>> cfg.fiducial.lpa = Lpa;
>> cfg.fiducial.rpa = Rpa;
>> segmented_r = ft_volumerealign (cfg, segmentedmri);
>>
>>
>> Finally I create a volume through the ft_prepare_singleshell (cfg, segmented_r) function and plot it.
>> I have the fiducials or head position coils and the scalp registered by means of a Polhemus digitizer..
>> Though the segment via ft_sourceplot (doing the: segment.avg.pow = segment.gray+...) looks right, the headmodelplot shows that the volume and the headshape don't fit.
>>
>> Is there any possibility to realign the segmented mri according either to the headshape points either to the MEG fiducials? I'm afraid the answer is no in both cases (as the MRI  and MEG coordinates are different). I tried to realign the segment interactively by selecting the positions where the coils in the MRI should be... but as the picture shows, it doesn't fit.
>> am I doing something wrong or skipping some important step?
>> Is it possible to transform MRI coordinate system to MEG-head coordinate system? Would it help?
>>
>>
>> <singleshell.jpg><singleshell2.jpg>
>>
>> I attach a picture of what i've managed to do till now!
>>
>>
>>
>> Thanks for all!!!
>>
>>
>>
>> --
>> Marc Recasens
>> Tel.: +34 639 24 15 98
>>
>> ----------------------------------
>>
>> 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/
>>
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3668063
>
> ----------------------------------
>
> 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/
>
>
>
>
> --
> Marc Recasens
> Tel.: +34 639 24 15 98
> ----------------------------------
>
> 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/neuroimaging/fieldtrip.
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