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Thanks Doug.
Jim
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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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:
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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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto: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<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits
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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:
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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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