[FieldTrip] localspheres

Lilla.Magyari at mpi.nl Lilla.Magyari at mpi.nl
Wed Feb 6 11:19:31 CET 2013

dear all,
sorry for the multiply posting. My email browser is not working properly.

> 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
>> Ph. 301-451-8863
>> nugenta at mail.nih.gov
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