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 CautionMany 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Greve, Douglas N.,Ph.D. DGREVE@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 CautionDear 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
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