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_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;
    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/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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1iz623RDpG7jX-8vTchfFOWMqWMqqANGChsGlp8WXSurTf7...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1iz623RDpG7jX-8vTchfFOWMqWMqqANGChsGlp8WXSurTf7... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1POG2n7wGXIhbgOgyia5pGK1aSOOR0Gvvs206k_qbLIkthj... <https://secure-web.cisco.com/1POG2n7wGXIhbgOgyia5pGK1aSOOR0Gvvs206k_qbLIkthj... rYnR1nOUxgeGZ6nN8ocj2CtVx45LtpGdn5WQ7k0M-RXzxI0eV3ZLwvQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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-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 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_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;
     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/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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1iz623RDpG7jX-8vTchfFOWMqWMqqANGChsGlp8WXSurTf7...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1iz623RDpG7jX-8vTchfFOWMqWMqqANGChsGlp8WXSurTf7... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1POG2n7wGXIhbgOgyia5pGK1aSOOR0Gvvs206k_qbLIkthj... <https://secure-web.cisco.com/1POG2n7wGXIhbgOgyia5pGK1aSOOR0Gvvs206k_qbLIkthj...

uX

...

rYnR1nOUxgeGZ6nN8ocj2CtVx45LtpGdn5WQ7k0M-RXzxI0eV3ZLwvQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ML8btI03azV7iRVpNzy_YbcSPpP4ysn2P905NUBgNT26Kg...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ML8btI03azV7iRVpNzy_YbcSPpP4ysn2P905NUBgNT26Kg... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1TsWwfzN0HiA239aQtTeK2lnPi1k7gXRM9KsjhlC1ntM85I... <https://secure-web.cisco.com/1TsWwfzN0HiA239aQtTeK2lnPi1k7gXRM9KsjhlC1ntM85I... XCEGxQzaH9-/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer