I'll leave this for Doug and/or Nick On Wed, 5 Jan 2011, 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
