[FieldTrip] Problem with Template Model for Source Reconstruction

[Paolo Belardinelli]

Dear Britta,
I have been working with the bias correction of my subject's MRI these
days, and while working extremely well for some of them, some others appear
to be even worse after correction.
I don't have much experience with MRI images, so maybe the combination of
parameters that I am setting may be not optimal.
At the moment, I am playing around with the Bias correction parameter (from
extremely light to no correction) and the FWHM bias (from 30mm to 150mm).
In the original images I can see some non-uniformity in terms of contrast
and usually they look quite smooth/low frequency to me. After correction I
can observe an improvement in the MRI images themselves, but no improvement
or even worsening in terms of not covered surface in the source
localization.
Do you have any suggestion how to find some quantificable parameters to
help me out in this procedure? How can I quickly check whether the quality
of the image is enough to guarantee that the cortex is fully covered,
without going through the whole forward model production? Sometimes, even
though the grid is well positioned, I still have the aforementioned
problem.

Best wishes,

Paolo

On Fri, Mar 18, 2016 at 3:35 PM, Paolo Belardinelli <
paolo.belardinelli at gmail.com> wrote:

> Dear Britta,
> I was deeply involved in the processing and I forgot to update this post.
> Thank you: it worked out!
> Eliminating the bias from MRI images (using light/very light
> regularization) leads to more accurate grids and correct results.
>
> Best,
>
> Paolo
>
>
>
> On Thu, Feb 18, 2016 at 10:10 AM, Britta Westner <
> britta.westner at uni-konstanz.de> wrote:
>
>> Dear Paolo,
>>
>> I experienced similar problems and found that correcting the field bias
>> in the participant's MRI (e.g. doing a "bias correction" with SPM) can
>> help. My explanation would be that the field bias either leads to small
>> inaccuracies in the segmentation and volume which then "get visible" when
>> warping the grid based on the non-segmented MRI, or that the warping
>> algorithm itself is affected by this bias. Maybe you can give that a try!
>>
>> Hope this helps,
>> Britta
>>
>>
>>
>>
>> Am 17.02.2016 um 20:20 schrieb Paolo Belardinelli:
>>
>> Dear Fieldtrippers,
>> we are encountering a problem with a template model for source
>> reconstruction. In particular, we are warping (non linearly) a template
>> grid to the individual subject's MRI.
>> Doing that, it appears that the very top of the brain is not fully
>> covered by dipole locations.
>> We found that this issue has been already reported:
>>
>>  http://www.fieldtriptoolbox.org/template/sourcemodel
>>
>> Apparently, since March 7th 2013, this issue has been fixed.
>> However we are using August 28th 2015 Fieldtrip version and we are still
>> dealing with the same issue.
>> Any suggestions?
>> Here are our code lines:
>>
>> cfg = [];
>> cfg.grid.warpmni = 'yes';
>> cfg.resolution = 6; % resolution of the template grid in mm
>> cfg.grid.nonlinear = 'yes'; % use non linear normalization
>> cfg.mri = mri_spm; % use subject's mri in mni coordinates
>> cfg.grid.unit = 'mm';
>> sourcemodel = ft_prepare_sourcemodel(cfg);
>>
>> Thank you in advance.
>>
>> Paolo
>>
>>
>>
>>
>> --
>> --
>> Paolo Belardinelli, PhD
>> Neurology Department
>> University Hospital Tuebingen
>> Eberhard Karls University Tuebingen
>> Hoppe-Seyler Str. 3
>> D-72076 Tuebingen
>> Tel: +49 7071 / 29 80478
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> --
>> Britta Westner, M.Sc.
>> Neuroelectromagnetic Oscillations Laboratory
>>
>> Fachbereich Psychologie
>> Universität Konstanz
>> Postfach 905
>> 78457 Konstanz
>>
>> Telefon: +49-(0)7531-88-5703
>> Fax: +49-(0)7531-88-5709
>> www.psychologie.uni-konstanz.de/nemo-lab
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> --
> Paolo Belardinelli, PhD
> Neurology Department
> University Hospital Tuebingen
> Eberhard Karls University Tuebingen
> Hoppe-Seyler Str. 3
> D-72076 Tuebingen
> Tel: +49 7071 / 29 80478
>
>


-- 
--
Paolo Belardinelli, PhD
Neurology Department
University Hospital Tuebingen
Eberhard Karls University Tuebingen
Hoppe-Seyler Str. 3
D-72076 Tuebingen
Tel: +49 7071 / 29 80478
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160320/7820a83c/attachment-0002.html>