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
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