Hi Isabelle

when you say you reanalyzed it from scratch, did you actually delete the subject dir and start over or just rerun autorecon1? If the latter, that won't reanalyze from scratch but will keep existing edits and such.

Did you do anything out of the ordinary the first time you ran it?

To check what is going on you can run:

mri_info /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brain.mgz

and

mri_info /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brainmask.mgz

they should both be 256^3

cheers Bruce

On Mon, 16 Nov 2015, Isabelle Deschamps wrote:

Dear FreeSurfer experts,

After running the following command:

recon-all -autorecon2 -autorecon3 -subjid S08_FS

I get the following error:

/Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 ERROR: dimension mismatch between source and mask Darwin Isabelles-iMac.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s S08_FS exited with ERRORS at Mon Nov 9 18:56:20 EST 2015

I read in a post that it might be a problem with registration, so following a post found on the forum, I re-analyze this participant (from scratch) using:

recon-all --autorecon1 -use-mritotal -subjid S08_FS

then I ran recon-all -autorecon2 -autorecon3 -subjid S08_FS

However, this did not solve the problem. Is there a workaround that I could use after the pial edits and running the -autorecon2 and 3?

Thank you very much in advance,

Isabelle _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer