Hi,
I managed to connect the surfaces, but now I'm having this error when
I try to convert it back to freesurfer format (from gifti)
mris_convert rsx.gii subjects/rs/surf/whole.white
mrisReadGIFTIfile: malformed coords data array in file rsx.gii:
num_vertices=3 num_cols=238032
mris_convert: could not read surface file rsx.gii
It seams that the matrix is transposed or something like that... but
it works perfectly within Matlab..
>> rsx
rsx =
vertices: [238032x3 single]
mat: [4x4 double]
faces: [476064x3 int32]
>> save (rsx, 'rsx.gii')
Best Regards
Leonardo
On Tue, Jan 4, 2011 at 12:18 PM, Bruce Fischl
<[email protected]> wrote:
> Hi Leonardo,
>
> you would need to connect the 2 ?h.orig surfaces, then I guess try running
> the combo through mris_sphere and mris_fix_topology. No idea what the
> results will be as we've never tried such a thing. Or maybe you should
> correct the topology first then create a topology-preserving connection if
> you can, and just run the combo through mris_sphere.
>
> cheers
> Bruce
>
>
> On Mon, 3 Jan 2011, Leonardo Barbosa wrote:
>
>> Hi Bruce,
>>
>> Thanks for the quick reply.
>>
>> I really need the sphere representation of the surface.
>>
>> When you say its harder, do you mean that mris_fix_topology wouldn't
>> be able to automatically project it onto the unity sphere? I would
>> need to make manual adjustments to fix handles and holes and then use
>> mris_sphere to create the sphere surface?
>>
>> Can you please send more information about where or how it has been done
>> before?
>>
>> Thanks in advance for any help,
>> Leonardo
>>
>> On Fri, Dec 31, 2010 at 12:52 PM, Bruce Fischl
>> <[email protected]> wrote:
>>>
>>> Hi Leonardo,
>>>
>>> we don't generate such a surface by default although we have created them
>>> on
>>> occasion. There's no standard procedure for doing so. It would be easy to
>>> create one that isn't topologically correct (e.g. run mri_mc on the white
>>> matter of the aseg), but harder to create one that is.
>>> cheers
>>> Bruce
>>>
>>>
>>> On Fri, 31 Dec 2010, Leonardo Barbosa wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm trying to save the white matter surface as a gifti file so I can
>>>> use it outside the freesurfer to implement an EEG dipole fitting, but
>>>> I'm not sure if this is the best way to do it. I searched old posts in
>>>> the list, but didn't find an answer.
>>>> The problem is how to export the whole cortex, and not only one
>>>> hemisphere.
>>>>
>>>> I'm using
>>>>
>>>> mris_convert subjects/subj1/surf/lh.white ~/subj1.lh.white.gii
>>>> mris_convert subjects/subj1/surf/rh.white ~/subj1.rh.white.gii
>>>>
>>>> and trying to mix the two surfaces inside my program, but I guess it's
>>>> not right, because the middle of the brain is opened. I have two
>>>> closed surfaces, and I would like to have one close mesh, without
>>>> creating new faces and ignoring vertices in the middle.
>>>>
>>>> Sorry i this is confusing, but the question is: Can I export one
>>>> closed surface of the whole brain with freesurfer?
>>>>
>>>> Thanks in advance for any help... and Happy New Year!
>>>>
>>>> Leonardo Barbosa
>>>> www.if.usp.br
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>>>>
>>>>
>>>
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>>
>>
>>
>
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