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Hi Doug,
Sorry for the delay. CAReg shows up, but not GCAReg:
$ grep -A6 "case .-autorecon2-volonly" $FREESURFER_HOME/bin/recon-all case "-autorecon2-volonly": set DoRemoveNeck = 0; set DoSkullLTA = 0; set DoSegStats = 0; set DoCANormalize = 1; set DoCAReg = 1; set DoCALabel = 1;
Best, Chris
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, March 30, 2023 09:29 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -gcareg dropped from -autorecon2-volonly
In my version, it appears just after DoCANormalize. Can you have grep print out one more line?
On 3/28/2023 9:05 AM, Christopher Markiewicz wrote:
External Email - Use CautionHi Doug,
$ cat $FREESURFER_HOME/build-stamp.txt freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 $ grep -A4 "case .-autorecon2-volonly" $FREESURFER_HOME/bin/recon-all case "-autorecon2-volonly": set DoRemoveNeck = 0; set DoSkullLTA = 0; set DoSegStats = 0; set DoCANormalize = 1;
I'm also not seeing it in `dev` on GitHub: https://secure-web.cisco.com/19BPC0I5kosNy_-RSRAWv0WGSAh5adNjGaAo84dO6_vclc0...
Best, Chris
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, March 27, 2023 11:16 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -gcareg dropped from -autorecon2-volonly
In 7.2 it appears to be there (and in 7.3 and in dev and in 7.0 and 7.1)
case "-autorecon2-volonly": set DoGCAReg = 1; set DoRemoveNeck = 0; set DoSkullLTA = 0; set DoCANormalize = 1; set DoCAReg = 1; set DoCALabel = 1; set DoSegStats = 0; set DoNormalization2 = 1; set DoMaskBFS = 1; set DoSegmentation = 1; set DoFill = 1; breakswOn 3/24/2023 9:57 AM, Christopher Markiewicz wrote:
External Email - Use CautionHi all,
This is a duplicate of a bug report on GitHub (https://secure-web.cisco.com/1C5EnDIMtZh6wk0SJMqe8l166ycKmSdnL5atT3CIHDPAY15...):
`DoGCAReg` was removed from `-autorecon2-volonly` in commit 4b9af5fc8c559e944400b885ef89f3682f94e0da, but this seems unrelated to the commit message. It's still in `-autorecon2`. Is there a reason it shouldn't be present, or was this a mistake?
This issue affects versions 7.3.0+. Apologies for doubling up if you saw it; my impression is the mailing list is more actively monitored.
Best, Chris
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