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