[FieldTrip] localspheres

[Johanna Zumer]

Dear Allison,

Thank you for your question.  There have been some changes to
ft_prepare_headmodel recently (partly implemented by me) and my apologies
that the documentation for these changes was not made thoroughly.   I
assume that you are refering to a very recent FT version.   :-)

The way that you call ft_prepare_headmodel looks almost correct, except
that cfg.vol is not needed.

If you have already a 'vol' or 'bnd' , then that can be used as the second
input argument to ft_prepare_headmodel, and the 'segmentedmri' is not
needed.

If you don't already have a 'vol' or 'bnd', then that will be created on
the fly within ft_prepare_headmodel from the segmentedmri that you include
as second input.  However, what are the fields within 'segmentedmri' that
you use?   If 'brain' or 'scalp' already exist, then those will be found
and used by default, and therefore a cfg.tissue is not needed.  However, if
you have other fields with different names, etc then cfg.tissue should
point to the name of the subfield of segmentedmri that you wish to use as
the headshape.   Please see ft_volumesegment for more details on which
tissue types or segmentation types can be computed as output and which can
then be used in subsequent functions.   Perhaps simply recompute the
segmentedmri with the newest version of ft_volumesegment and then it will
work?

In the meantime, I will update the documentation to make all this more
clear.

However, one more question.  I'm not sure what you mean by the error you
get with ft_getopt(cfg,'tissue').   If 'tissue' is not in cfg, then it will
return a default empty variable, and there should not be an error.    Can
you say exactly what line of what function gives the error, and what the
error exactly is?

And finally, when you successfully ran singleshell method, was that with
the segmentedmri (which would surprise me), or rather with a cfg.headshape
option?

Cheers,
Johanna








2013/2/5 Nugent, Allison C. (NIH/NIMH) [E] <nugenta at mail.nih.gov>

>  Hello, ****
>
> ** **
>
> I have what is possibly a naïve question, but I can’t seem to find
> anything on the tutorial pages.****
>
> ** **
>
> I’m trying to create a headmodel using the localspheres method, using the
> output of a segmented MRI.****
>
> ** **
>
> There is a tutorial page for using different types of headmodels, but it
> references ft_prepare_localspheres – which works, but it appears to have
> been deprecated.  When I try this:****
>
> ** **
>
> hdr=ft_read_header(‘mydata.ds’);****
>
> cfg=[];****
>
> cfg.method=’localspheres’;****
>
> cfg.grad=hdr.grad;****
>
> cfg.vol=segmented_mri;****
>
> vol=ft_prepare_headmodel(cfg, segmentedmri);****
>
> ** **
>
> I get an error at ft_getopt(cfg,’tissue’);****
>
> ** **
>
> Although the documentation for ft_prepare_headmodel states that the only
> additional field needed by localspheres is “cfg.grad” it seems that
> cfg.tissue may also be required?  If so, how do I set this – I can’t find
> any documentation that explains.****
>
> ** **
>
> I should note that I’ve run ft_prepare_headmodel successfully using a
> singleshell method.****
>
> ** **
>
> Thanks,****
>
> ** **
>
> Allison****
>
> ** **
>
> Allison Nugent, PhD****
>
> MRI Physicist****
>
> Experimental Therapeutics and Pathophysiology Branch****
>
> NIMH/NIH/DHHS****
>
> Ph. 301-451-8863****
>
> nugenta at mail.nih.gov****
>
> ** **
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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