Hello

In a very similar situation to a post I found in the Freesurfer archive, I have low-resolution (3T) and high-resolution scans (7T) of the same subject - and would like to put the surfaces from the low-resolution scan into the space of the hi-res data. The instructions from the previous thread say to check example 4 when running ‘mri_surf2surf --help’ - which I tried, but I cannot get the result to overlap in freeview.

I have a registration file which looks very good from running bbregister on the high-res data into the low-res space - but I cannot perform the registration the other way around as I’m still having trouble getting the hi-res data to process properly through recon-all (it’s acquired at 350um, and I’m currently running it downsampled to 500um, but that’s still a work-in-progress…).

So this is the command-line that I tried to apply the transformation from the registration to a surface:

mri_surf2surf --reg-inv hires_to_lowres.dat ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --hemi lh --sval-xyz white --tval-xyz ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --tval lh.white.hires --s subj_lowres

If I then try to view the result:

freeview -v ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz -f ${SUBJECTS_DIR}/subj_lowres/surf/lh.white.hires

it is clear that the two are far from being aligned…

I’m afraid I may be misunderstanding how to control the coordinate systems in the mri_surf2surf command - especially as the source and targets are different ’subjects’ (the same actual subject, though…). I can’t used the ‘--trgsubject’ option because recon-all has not completed properly on the hires data, and there is no sphere.reg file (although I have to confess, I haven’t understood why it would need it if I am specifying my own registration file…) . Any suggestions very gratefully received.

Thanks

Daniel