can you send me the whole .mgz volume? And your recon-all command line that fails?

On Tue, 28 May 2013, LAOUCHEDI MAKHLOUF wrote:

hi   i send you the rawavg.mgz of the subject with the massive artefact. i inform you that i proceeded differently by splitting the recon-all -all into three steps (as in freesurfer wiki) : (1) recon-all -autorecon1, (2) recon-all -autorecon2 (3) recon-all -autorecon3. i just finished with the first step which still didn't work for some subjects so i deleted then in my SUBJECTS_DIR then i run "recon-all -i" to regenerate them. after that i re-run "recon-all -autorecon1" and it worked even for the subject with the artefacted rawavg.mgz i am sending you.

i noticed also that some extra cerebral structures like dura is not fully removed after the skullstripping step, and i reviewed some of my previous datasets i processed with freesurfer and i noticed that the cortical ribbon (containing the cortical parcellation) fits well the gray matter. so is a wise idea to not bother a lot about these "some" extra cerebral structures left and just go forward with the rest of the recon-all pipeline (but of course i'll take a look a posteriori).

Thanks