External Email - Use Caution Hi Douglas,
thanks for your answer. I agree that desabling the topology correction is not recommended but I am dealing with subjects having many lacunar infarcts that impact this step (running for more than 2 days sometimes and leading to segmentation errors like removing gyri from cerebral cortex). Is there a way to configure the behavior of the topology correction (like number of iterations, ...) from the "recon-all" command line? Thanks, Florent On 8/25/2020 11:24 AM, [email protected] wrote: > Date: Tue, 25 Aug 2020 11:24:28 -0400 > From: "Douglas N. Greve" <[email protected]> > Subject: Re: [Freesurfer] Cannot disable the topology correction > To: <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8"; format=flowed > > 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, [email protected] 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 > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
