ah, I see. OK, I've fixed this in dev. On 4/4/2023 4:59 PM, Christopher Markiewicz wrote: > External Email - Use Caution > > 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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve > <dgr...@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 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 >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://secure-web.cisco.com/1iz623RDpG7jX-8vTchfFOWMqWMqqANGChsGlp8WXSurTf7Cz8elbzrjKirHbvATP_qaqv_KoLTkXONA83ZcZSCEC3AC8F9tXylylG1U5rojlEiuJ2cquf910LkQmkwZO91NGSzZIT6ZdjjGVoyppmiAWQWVX2LzZH5_DZevRY6KpGwQQAGftGMcIA5ZvdtpRJMrG41XL6ZS6tTW6O9o21zA0DFo_U4_EPRZqXvowfGGMDYtO79ZAM8zStmKz3FgYaf5r-_KiiGtKSLm_AIznuNafWcT-3lDXNYu13CyoeypNUqVGOpbbpCaMkAkBkoXlNvhwV9Oo1v9AosVjUEtXQw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1iz623RDpG7jX-8vTchfFOWMqWMqqANGChsGlp8WXSurTf7Cz8elbzrjKirHbvATP_qaqv_KoLTkXONA83ZcZSCEC3AC8F9tXylylG1U5rojlEiuJ2cquf910LkQmkwZO91NGSzZIT6ZdjjGVoyppmiAWQWVX2LzZH5_DZevRY6KpGwQQAGftGMcIA5ZvdtpRJMrG41XL6ZS6tTW6O9o21zA0DFo_U4_EPRZqXvowfGGMDYtO79ZAM8zStmKz3FgYaf5r-_KiiGtKSLm_AIznuNafWcT-3lDXNYu13CyoeypNUqVGOpbbpCaMkAkBkoXlNvhwV9Oo1v9AosVjUEtXQw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> The information in this e-mail is intended only for the person to whom it is >> addressed. 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