Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug
Bruce Fischl wrote: > Hi John > > Doug can say for sure, but I think you want to give it the switch > --sval-xyz so it knows to expect a surface not a scalar field over the > surface. > > cheers > Bruce > On Wed, 7 Dec 2011, John Griffiths wrote: > >> [ Douglas and Dan - sending this again as I didn't sent it to the list >> address before. Sorry. ] >> >> Thanks guys. >> >> When I run mri_info on the .mgz file I was using before it seems crash >> (nothing happens, and have to press ctrl+c to get the console back). >> So I >> suppose that partially explains mri_surf2surf not working. Not sure >> what's >> going wrong there - the command I used was >> mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial >> /home/jdg45/lh.pial_converted.mgz >> >> For the original question - I was using a converted .mgz file because >> when I >> just give it the path to the 'lh.pial' file in the same directory it >> says it >> cant determine the file type - >> mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval >> /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval >> /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 >> Standard output: >> ERROR: could not determine type of >> /work/imaging5/Freesurfer/CBU070282/surf/lh.pial >> Standard error: >> >> Is there a .xxx suffix for those files I should be using? >> Incidentally, the reason I'm doing this is that I want to downsample a >> surface file; someone suggested to me to use mri_surf2surf with the >> 'trgicoorder' flag. Is this a good way to downsample a surface? >> Thanks, >> john >> >> >> On 6 December 2011 19:02, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> wrote: >> >> surf2surf actually takes surface overlays (not surfaces >> themselves) as input, and they can be in any format that FS >> reads. The wiki is probably not up-to-date as those options are >> ok. >> doug >> >> Daniel Wakeman wrote: >> Hi John, >> >> It seems weird that you are using .mgz files (this >> suffix is for >> volume files) with mri_surf2surf (whose inputs >> should be surfaces). >> Also, it seems that several of the options you are >> trying I don't >> believe exist at least according to the wiki (e.g. >> -cortex -fwhm). Are >> you sure you are using the right command? >> >> D >> >> On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths >> <j.davidgriffi...@gmail.com> wrote: >> >> Dear list, >> >> I am having the following memory >> allocation problem when running >> mri_surf2surf. Can't find any mention of >> this error on the list or the >> internet - sorry if I've missed >> anything. >> >> mri_surf2surf --cortex --fwhm 5.0000 >> --hemi lh --sval >> /home/jdg45/lh.pial_converted.mgz --tval >> /home/jdg45/CBU070282_smoother_surf.mgz >> --s CBU070282 >> Standard output: >> srcsubject = CBU070282 >> srcval = >> /home/jdg45/lh.pial_converted.mgz >> srctype = >> trgsubject = CBU070282 >> trgval = >> /home/jdg45/CBU070282_smoother_surf.mgz >> trgtype = >> srcsurfreg = sphere.reg >> trgsurfreg = sphere.reg >> srchemi = lh >> trghemi = lh >> frame = 0 >> fwhm-in = 0 >> fwhm-out = 5 >> label-src = (null) >> label-trg = lh.cortex.label >> OKToRevFaceOrder = 1 >> Reading source surface reg >> /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg >> Loading source data >> Standard error: >> MRIalloc: could not allocate 2032167524 >> slices >> >> Cannot allocate memory >> Return code: 254 >> >> >> Any suggestions? >> >> >> Thanks, >> john >> >> _______________________________________________ >> 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 >> >> >> >> >> >> -- >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
