[ 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<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<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<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >
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