Hi Paul
can we take a step back. What are you trying to achieve by avoiding these
steps?
cheers
Bruce
On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:
Thanks Bruce. Another question, since " -no segmentation " flag skips the
white matter segmentation step of recon-all. Can I also use the same
logic as the "-noskullstrip" flag to replace the wm.seg.mgz file? That's,
run " recon-all -autorecon1 -autorecon2 -nosegmentation -s subjid ". Then
copy/convert my already segmented brain and name it wm.seg.mgz. After
that, treat it as if I had freesurfer's wm.seg.mgz and finally, run "
recon-all -autorecon3 -s " to complete the process. What do you think?
Best, Paul
Sent from my BlackBerry 10 smartphone.
Original Message
From: Bruce Fischl
Sent: Friday, November 4, 2016 10:50 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] Fw: recon-all steps question
Hi Paul
we required the T1.mgz, brainmask.auto.mgz and brainmask.mgz volumes so
must create them somehow. I think if you copy/convert your already-stripped
and name it brainmask.mgz we should treat that as if you had edited our
skull stripping and you should be able to run from their forward
(autorecon2 and autorecon3 I believe)
cheers
Bruce
On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:
Please can someone answer this. Thanks
"
Hello Freesurfer, I have couple of questions. While going through the
frequently asked questions on your
pagehttp://freesurfer.net/fswiki/UserContributions/FAQ I came across a
question regarding how to integrate a skull stripped from another problem
into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid ---->
create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
from brainmask.auto.mgz to brainmask.mgz ------> after run the finall stages
of recon-all: recon-all -autorecon2 -autorecon3 -s subjid).
First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
during skull stripping? why are they present if I included the "-no
skullstrip" flag?
Second question, where do I insert my already skull stripped data in the
symbolic link?
Last question, the final stages of recon-all ( recon-all -autorecon2
-autorecon3) doesn't include skull stripping, how can I be sure my skull
stripped data was incorporated into the freesurfer recon-all process?
Best,
Paul
Sent from my BlackBerry 10 smartphone.
From: miracoo...@gmail.com
Sent: Wednesday, November 2, 2016 9:39 AM
To: Freesurfer support list
Subject: Fw: recon-all steps question
Sent from my BlackBerry 10 smartphone.
From: miracle ozzoude <miracoo...@gmail.com>
Sent: Monday, October 31, 2016 8:39 AM
To: Douglas N Greve
Subject: recon-all steps question
Hello Freesurfer, I have couple of questions. While going through the
frequently asked questions on your
page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a
question regarding how to integrate a skull stripped from another problem
into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid ---->
create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
from brainmask.auto.mgz to brainmask.mgz ------> after run the finall stages
of recon-all: recon-all -autorecon2 -autorecon3 -s subjid).
First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
during skull stripping? why are they present if I included the "-no
skullstrip" flag?
Second question, where do I insert my already skull stripped data in the
symbolic link?
Last question, the final stages of recon-all doesn't include skull
stripping, how can I be sure my skull stripped data was incorporated into
the freesurfer recon-all process?
Best,
Paul
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