[FieldTrip] localspheres

[Lilla.Magyari at mpi.nl]

hi Allison,

this was a small a bug in FieldTrip a few weeks ago. It has been fixed
since then already, so I think if you download the latest version, you can
run ft_prepare_headmodel with method 'localspheres' without the
specification of tissue-type. In this case, the geometry of the 'brain'
tissue will be used for the headmodel by default. Therefore, it will work
only if your segmentation contains a binary mask of the brain (i.e. your
segmentation should have a 'brain' field with binary values) or if your
segmentation contains the probability tissue maps of 'gray','white','csf'
tissue. In this later case, the brain mask will be created from gray,
white and csf by the function.

But actually, if you want to run ft_prepare_headmodel with your version,
you can just specify the name of the tissue that is in your segmentation.

Best,
Lilla


> 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
>
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