[FieldTrip] localspheres

[Johanna Zumer]

Sorry, I meant if you have a 'bnd'.   Of course you won't have the 'vol',
that is the purpose of calling ft_prepare_headmodel!

Johanna


2013/2/6 Johanna Zumer <johanna.zumer at gmail.com>

> 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****
>>
>> ** **
>>
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>>
>
>
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