there used to be something built into tksurfer to do soap bubble smoothing. You can try smooth_vals_spare from the tcl prompt. I think it depends on setting the fixedval field in the vertex struct to 1 for the stationary points of the soap bubble. You can first read in a file that is 1 for the fixed points and zero elsewhere then call fix_nonzero_vals. Then load the vals you want and try the soap bubble. It's pretty old code and hasn't been used in ages though, so it is likely to have problems.
I guess writing a stand-alone soap bubble would be pretty trivial, so if you find this doesn't work and this is important to you let us know and I'll add it to our to-do list. cheers Bruce On Mon, 9 Nov 2015, Douglas N Greve wrote: > > Sounds like you are trying to do soap bubble interpolation (?). I don't > think we have a binary for that. Maybe Bruce knows of one. You could > hack something together, with smoothing (mri_surf2surf), creating binary > masks (mris_binarize), and masking (mri_mask), and basic math operations > (fscalc). > > > On 11/09/2015 02:07 PM, Gardus III, John D wrote: >> Hello all, >> >> I'm in the process of mapping some non-FreeSurfer derived outcomes to >> a curv file containing the vertices of the pial surface mesh. I have >> values at roughly 100 vertices, leaving some 37000 with 'nan'. >> >> I then run an intra-subject surf2surf command in an attempt to >> interpolate between vertices for which I have values. The problem is >> that the NaNs pull the existing values down, resulting in a >> smearing/dilution of my outcomes. >> >> Is there any way to interpolate and make the intervening vertices >> purely a function of nearby vertices for which values exist? >> >> Thanks, >> >> John >> >> >> This e-mail message, including any attachments, is for the sole use of >> the intended recipient(s) and may contain confidential and privileged >> information. Any unauthorized review, use, disclosure or distribution >> is prohibited. If you are not the intended recipient, please contact >> the sender by e-mail and destroy all copies of the original. >> >> >> _______________________________________________ >> 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 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.
