If the topology correction has not been done, then the stream cannot proceed. If you really want to skip the topofix, then just copy lh.orig.nofix to lh.orig and run with -nofix, but this is not recommeneded
On 8/25/2020 11:04 AM, k3...@free.fr wrote: > External Email - Use Caution > > Hi FS team, > > I am having an error when disabling (-nofix) the topology correction with the > recon-all command. > The "-nofix" option is skipping the topology correction as expected but then > the next step is failing because "?h.orig" file does not exist. > > When reading the recon-all table here: > https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 > it looks like "-fix" step (topology correction) is first copying the > following file: "cp ?h.orig.nofix ?h.orig" > So if this step is ignored with the "-nofix" option then "?h.orig" files are > not created, which is causing a failure with next step (cannot read ?h.orig). > > Do you have any solution to that? > My goal is to run FreeSurfer without topology correction because for some > cases it is running in an infinite loop (more than 2 days of processing). > > Thanks, > Florent > > FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 > Platform: Ubuntu 18.04 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
