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 fischl@nmr.mgh.harvard.edu 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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 fischl@nmr.mgh.harvard.edu 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 fischl@nmr.mgh.harvard.edu 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

can you send me the file rsx.gii? how was it created? is it readable/convertable by other gifti compliant applications?

n.

On Wed, 2011-01-05 at 05:09 -0200, Leonardo Barbosa wrote:

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 fischl@nmr.mgh.harvard.edu 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 fischl@nmr.mgh.harvard.edu 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

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