Hi Eli, the -make all flag contains a bug in the 6.0 release. This can be fixed if you download this script - https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_pub_dist_freesurfer_dev-5Fbinaries_centos6-5Fx86-5F64_recon-2Dall.makefile&d=DwIGaQ&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=NdmdZKAguIV8eXD4q6jw5Ub-tV1C8ZYAQonZaC5Moj4&s=OVTOQexQaYiTh7MsmChOewxSfa3PnCfztVjr2RDlnM8&e= - and overwrite the current $FREESURFER_HOME/bin/recon-all.makefile

Let me know if you still have issues

best,
Andrew


On 7/31/18, 3:15 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

    hmmmm, maybe -make all has changed (or my memory of what it does is
    incorrect). I'll find someone else here to help you out
   
    cheers
    Bruce
    On Tue, 31 Jul 2018,
    Bruce Fischl wrote:
   
    > did you run
    >
    > recon-all -s <subject name> -make all
    >
    > ?
    >
    >
    > I don't see it in the log
    > On Tue, 31 Jul 2018, Rockers, Elijah D. wrote:
    >
    >>
    >>          External Email - Use Caution       
    >>
    >>  Oh, yep, sorry about that. I copy the list on this e-mail, and attach the
    >>  log. I think the list
    >>  blocks attachments, but if anyone wants to see full log I can send it.
    >>
    >>
    >>  Thanks to all,
    >>
    >>  -Eli
    >>