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