External Email - Use Caution Thanks Bruce, this is my command line (note that because of a different organization of the data, the subject dir is /Data/48/ and the subject is MRI_sMRI_fs_reconall_fs_reconall_gcv6s):
mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s --srcsurfval /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi.fsaverage6.mgh --trgsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s --trgsurfval /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi.fwhm5.fsaverage6.mgh --surfreg sphere.reg --hemi lh --fwhm 5 so I could use the fsaverage6/surf/lh.sphere.reg for the --surfreg flag instead, right? But then I would need to copy and rename it in the subject folder, is that correct? Thanks a lot! Rachele ________________________________________ Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Bruce Fischl <fis...@nmr.mgh.harvard.edu> Gesendet: Freitag, 7. Dezember 2018 19:14 An: Freesurfer support list Betreff: Re: [Freesurfer] fsaverage6 FS6 Hi Rachele what is your command line? The ?h.sphere.reg is in register with fsaverage, but it looks like your data has been mapped to the fsaverage6 subject (which has 40962), but you are specifying the individual subject surface. If that is the case, use the fsaverage6 surface instead cheers Bruce On Fri, 7 Dec 2018, Sanfelici, Rachele wrote: > External Email - Use Caution > > Many thanks Doug, that worked! > > Now that I resampled my data I'm having the next issue: smoothing. > I'm using mri_surf2surf specifying the same source and target subject > (resampled to fsaverage6), but apparently to skip the registration I need to > also specify the ?h.sphere.reg. I get this error: > > Reading source surface reg > /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.sphere.reg > Loading source data > ERROR: dimension inconsistency in source data > Number of surface vertices = 151901 > Number of value vertices = 40962 > > Which I guess it's because the sphere is not "registered" to fsaverage6, > right? > My solution would be to copy and rename fsaverage6 ?h.sphere.reg to the > subject directory to bypass this problem. Can you please confirm that this > approach is valid? Or otherwise would you have a better solution? > > Thanks a lot in advance! > Rachele > > ________________________________________ > Von: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Greve, Douglas > N.,Ph.D. <dgr...@mgh.harvard.edu> > Gesendet: Donnerstag, 6. Dezember 2018 18:33 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] fsaverage6 FS6 > > Try using mris_apply_reg. The command line is simpler (but otherwise > gives the same result). > > On 12/06/2018 11:44 AM, Sanfelici, Rachele wrote: >> >> External Email - Use Caution >> >> Dear FreeSurfer experts, >> >> >> I am encountering a problem when trying to downsample to fsaverage6 >> with FreeSurfer v.6.(see below): >> >> >> mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s >> --srchemi lh --srcsurfreg fsaverage6.sphere.reg --trgsubject >> fsaverage6 --trghemi lh --trgsurfreg sphere.reg --tval >> ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh >> --sval >> /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi >> --sfmt curv --noreshape --cortex >> >> srcsubject = MRI_sMRI_fs_reconall_fs_reconall_gcv6s >> srcval =/Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi >> srctype = curv >> trgsubject = fsaverage6 >> trgval = >> ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh >> trgtype = >> srcsurfreg = fsaverage6.sphere.reg >> trgsurfreg = sphere.reg >> srchemi = lh >> trghemi = lh >> frame = 0 >> fwhm-in = 0 >> fwhm-out = 0 >> label-src = lh.cortex.label >> label-trg = lh.cortex.label >> OKToRevFaceOrder = 1 >> UseDualHemi = 0 >> Reading source surface reg >> /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.fsaverage6.sphere.reg >> No such file or directory >> >> I guess it's because the naming of the sphere file is now different >> compared to v.5.3 (it was sufficient to run recon-all with the >> additional -qcache -target fsaverage6 flag), so it can't be found by >> mri_surf2surf. I tried to run mris_preproc instead of recon-all but I >> still get the same error. Could you please help me with the right command? >> >> Thank you very much in advance! >> >> Best >> Rachele >> >> >> >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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
