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, dgreve@mgh.harvard.edu wrote:
Date: Tue, 25 Aug 2020 11:24:28 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Cannot disable the topology correction To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5284d1e1-011c-2e25-9d22-e222bd9e5989@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, k3ops@free.fr wrote:
External Email - Use CautionHi 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
I don't think so. You might be better off fixing the error manually. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...
On 8/28/2020 4:57 AM, k3ops@free.fr wrote:
External Email - Use CautionHi 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, dgreve@mgh.harvard.edu wrote:
Date: Tue, 25 Aug 2020 11:24:28 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Cannot disable the topology correction To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5284d1e1-011c-2e25-9d22-e222bd9e5989@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, k3ops@free.fr wrote:
External Email - Use CautionHi 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@nmr.mgh.harvard.edu
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Douglas N. Greve -
k3ops＠free.fr