I don't think so. You might be better off fixing the error manually. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 8/28/2020 4:57 AM, k3...@free.fr wrote: > 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, dgr...@mgh.harvard.edu wrote: >> Date: Tue, 25 Aug 2020 11:24:28 -0400 >> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] Cannot disable the topology correction >> To: <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <5284d1e1-011c-2e25-9d22-e222bd9e5...@mgh.harvard.edu> >> 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, 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
