External Email - Use Caution
Hi 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_vclc0xTDdaWDhzjw4v7ppIcDpDNswchLRbpmE36ysQBkiSWjw92p1HKyrkhU-0zbtFv4PraKshl7lT1z-a16c9dB0tN4yZo_820XxuOeTrje-GYr8LsSd--qY_M5HRd1G6fSraiGRRAops64STReDvpoi0BXA-zlhMdnAhELxhrvob5NlWaNnWqeDe6wSEbT-hxMaP2uo-Bt_piurh13j7769MK9sNR0k-7Y9JyehZM_3gicUwLa4OuBnJ0Y_Ciig6EqP4woHYnsEIVljYRyK8kXmAy_9umFAvwvA9MpVIJmg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Frecon-all%23L7020-L7031
Best,
Chris
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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;
breaksw
On 3/24/2023 9:57 AM, Christopher Markiewicz wrote:
> External Email - Use Caution
>
> Hi all,
>
> This is a duplicate of a bug report on GitHub
> (https://secure-web.cisco.com/1C5EnDIMtZh6wk0SJMqe8l166ycKmSdnL5atT3CIHDPAY15Ixtf93Rif0FmPFCZaftXbqlhK5AbXT22OXXCJq9JgIiSOyglr8IF1n3lOAzrtCIHcr8C2aLwqsXcMciJwp9Mz2DV4vmcWjm2v_xTUmw6hoea4u37a4hkUyIkSRKIBbOEC9mKcGdJ41Nbz86rmDYbEm3v5pV6zuR3zISglz0_aPe4hJhmj_y7BHipJWdwr3J3pwKPc5BT5WbnmtOEJ6hBkSswM8xHN-3ZfID-bPa2VEltISdFH8ITDhpQJKlPlhEYwtkSxcoWugX9kNCGiWbWsbTqR4PbpJPvp4qp4e5w/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F1081):
>
> `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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