Re: [Freesurfer] Surface-based kernel operations
Hi Victor the sphere files are lh.sphere and rh.sphere in the surf dir. You could write out the metric tensor (or first fundamental form) of the mapping to compute Euclidean distances from spherical coordinates, or probably just use the 3D euclidean distances on the sphere as the sampling is dense enough that it won't make much difference unless you have pretty large kernels. cheers Bruce On Wed, 29 Nov 2017, Victor Montal Blancafort wrote: > Thanks Bruce and Doug! > > Bruce, I think the option of the sphere is the one that better fits my needs, > since I need to perform conv operations + > derivatives. How should address this issue? I am not very familiar with > sphere files (nor metric tensors) and do not know > how to open/where to find those files. > > Thank you once again! > Bests, > > Victor M > > > ___ 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.
Re: [Freesurfer] Surface-based kernel operations
Thanks Bruce and Doug! Bruce, I think the option of the sphere is the one that better fits my needs, since I need to perform conv operations + derivatives. How should address this issue? I am not very familiar with sphere files (nor metric tensors) and do not know how to open/where to find those files. Thank you once again! Bests, Victor M ___ 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.
Re: [Freesurfer] Surface-based kernel operations
read_surf.m will read in a surface including the nearest neighbors. the vertices are not ordered in an ordered way On 11/28/2017 11:38 AM, Victor Montal Blancafort wrote: > Dear Freesurfer experts, > > I would like to preform several operations in surface files using > spatial kernels (i.e mean value in a 3x3 grid, nearest neighbour > value, etc). In summary, perform operations in the surface such as a > 2D matrix/image. > > Is it possible to do it with Freesurfer? I tried to open the surfaces > using Python and Matlab, but as far as I am concerned, the vertex > orders does not follow any "continous" or topological order. > > Any insight would be very appreciated. > Thanks in advance! > > Victor M > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
Re: [Freesurfer] Surface-based kernel operations
Hi Victor the order of vertices/faces is somewhat arbirtry. If you want to write out a convolution I would do it on the sphere (and account for the metric tensor of the chart functions), or flatten and do it in the plane. cheers Bruce On Tue, 28 Nov 2017, Victor Montal Blancafort wrote: > Dear Freesurfer experts, > > I would like to preform several operations in surface files using spatial > kernels (i.e mean value in a 3x3 grid, nearest neighbour value, etc). In > summary, perform operations in the surface such as a 2D matrix/image. > > Is it possible to do it with Freesurfer? I tried to open the surfaces using > Python and Matlab, but as far as I am concerned, the vertex orders does not > follow any "continous" or topological order. > > Any insight would be very appreciated. > Thanks in advance! > > Victor M > > ___ 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.
