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Hi,
We are finding that the skull-stripping in standard FS 7.1.1. in a few of our 3yo subjects is a little aggressive and is removing brain from the brainmask primarily in the occipital pole region. We decided to use the "cloning to T1 method", using the Recon Edit tool in Freeview for adding brain back to the brainmask.mgz.
Once the revised brainmask.mgz is re-saved with the same file name, what command needs to be run to regenerated the entire pipeline?
We originally ran: recon-all -s -i -hires -all
Do we run the same command again or should we use: recon-all -s -make -hires all
Thanks.
Jim
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That is fine. You could save a few min by not starting from scratch, but the brainmasking happens very close to the beginning.
On 2/17/2021 3:57 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Hi,
We are finding that the skull-stripping in standard FS 7.1.1. in a few of our 3yo subjects is a little aggressive and is removing brain from the brainmask primarily in the occipital pole region. We decided to use the “cloning to T1 method”, using the Recon Edit tool in Freeview for adding brain back to the brainmask.mgz.
Once the revised brainmask.mgz is re-saved with the same file name, what command needs to be run to regenerated the entire pipeline?
We originally ran: *recon-all -s -i -hires –all*
**
Do we run the same command again or should we use: r*econ-all –s –make –hires all***
**
Thanks.
Jim
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Thnaks. Some of the data may have been copied from different places so I'm concerned the time stamps might not be accurate which is why I'd prefer to run from scratch using recon-all -s -i -hires -all
Nothing else is needed, correct? Only FS output from the original run with the new/revised brainmask.mgz.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, February 19, 2021 9:23 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits
* External Email - Caution * That is fine. You could save a few min by not starting from scratch, but the brainmasking happens very close to the beginning. On 2/17/2021 3:57 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Hi,
We are finding that the skull-stripping in standard FS 7.1.1. in a few of our 3yo subjects is a little aggressive and is removing brain from the brainmask primarily in the occipital pole region. We decided to use the "cloning to T1 method", using the Recon Edit tool in Freeview for adding brain back to the brainmask.mgz.
Once the revised brainmask.mgz is re-saved with the same file name, what command needs to be run to regenerated the entire pipeline?
We originally ran: recon-all -s -i -hires -all
Do we run the same command again or should we use: recon-all -s -make -hires all
Thanks. Jim
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Yes, that is right. Not sure whether the time stamp thing will cause a problem. Mostly, we don't look at time stamps, but some parts do. When you make a copy, you can include the -p flag when running cp and it will preserve time stamps (and permissions)
On 2/22/2021 4:58 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Thnaks. Some of the data may have been copied from different places so I’m concerned the time stamps might not be accurate which is why I’d prefer to run from scratch using *recon-all -s -i -hires –all*
**
Nothing else is needed, correct? Only FS output from the original run with the new/revised brainmask.mgz.
Jim
**
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Friday, February 19, 2021 9:23 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits
** External Email - Caution **
That is fine. You could save a few min by not starting from scratch, but the brainmasking happens very close to the beginning.
On 2/17/2021 3:57 PM, Alexopoulos, Dimitrios wrote:
* External Email - Use Caution * Hi, We are finding that the skull-stripping in standard FS 7.1.1. in a few of our 3yo subjects is a little aggressive and is removing brain from the brainmask primarily in the occipital pole region. We decided to use the “cloning to T1 method”, using the Recon Edit tool in Freeview for adding brain back to the brainmask.mgz. Once the revised brainmask.mgz is re-saved with the same file name, what command needs to be run to regenerated the entire pipeline? We originally ran: *recon-all -s -i -hires –all* ** Do we run the same command again or should we use: r*econ-all –s –make –hires all*** ** Thanks. Jim ------------------------------------------------------------------------ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1yVGlVUCWMffIMDXzwJm0lFeE15XORpaqp-eEKE_Wbu6H25t-uHnMUZL109S5kke75bGMMlqKQiD4kNUpErU0UQyUKPd7Gft6fg2THuY2noLLr30YDu8Hdk3xFJtieU2shCjVwKijZGFrgFQgiryhwlzDz0iyias18GRiKH0U6wTJqCJjkoqIybbse98DF2ypb1r0-zA3WY5cjwpcAkhvY7wJADRXokW3cToSBifigK26Ga1FbMg8eLl-eZPOL-PQl501pYoTnLWHRTWx98ljAg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks Doug.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, February 23, 2021 8:12 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits
* External Email - Caution * Yes, that is right. Not sure whether the time stamp thing will cause a problem. Mostly, we don't look at time stamps, but some parts do. When you make a copy, you can include the -p flag when running cp and it will preserve time stamps (and permissions) On 2/22/2021 4:58 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Thnaks. Some of the data may have been copied from different places so I'm concerned the time stamps might not be accurate which is why I'd prefer to run from scratch using recon-all -s -i -hires -all
Nothing else is needed, correct? Only FS output from the original run with the new/revised brainmask.mgz.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, February 19, 2021 9:23 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits
* External Email - Caution * That is fine. You could save a few min by not starting from scratch, but the brainmasking happens very close to the beginning. On 2/17/2021 3:57 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Hi,
We are finding that the skull-stripping in standard FS 7.1.1. in a few of our 3yo subjects is a little aggressive and is removing brain from the brainmask primarily in the occipital pole region. We decided to use the "cloning to T1 method", using the Recon Edit tool in Freeview for adding brain back to the brainmask.mgz.
Once the revised brainmask.mgz is re-saved with the same file name, what command needs to be run to regenerated the entire pipeline?
We originally ran: recon-all -s -i -hires -all
Do we run the same command again or should we use: recon-all -s -make -hires all
Thanks. Jim
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________
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________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
freesurfer@nmr.mgh.harvard.edu
-
Alexopoulos, Dimitrios -
Douglas N. Greve