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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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