Hi Qian
if you look at the recon-all help you will see:
USAGE: recon-all
Required Arguments:
-subjid
-
Fully-Automated Directive:
-all : performs all stages of cortical reconstruction
-autorecon-all : same as -all
Manual-Intervention Workflow Directives:
-autorecon1
Hi Bruce,
I am a little confused about it. I found 'Manual-Intervention Workflow
Directives' on recon-all free surfer wiki web.
It said if edits made to correct pial, run-autorecon2-pial.
If I only edit pial, I run >recon-all -autrecon-pial -s -sd
to fix this issue, I also should rerunning
Hi Qian
if you just want to regenerate the pial, then yes, edit the
brain.finalsurfs.mgz and run:
recon-all -autrecon-pial -s -sd
note that it is NOT autorecon2-pial, but just autorecon-pial (leave out the
'2')
cheeers
Bruce
On Thu, 9 Feb 2017, 冉倩 wrote:
Hi Bruce,
If I use brain.fina
Hi Bruce,
If I use brain.finalsurfs, then I run recon-all -autorecon2-pial -subjid sub01
or recon-all -autorecon2-pial -autorecon3 -subjid sub01? autorecon3 still need
rerunning? Thanks!
Best Regards,
Qian Ran
At 2017-02-08 12:19:35, "Bruce Fischl" wrote:
brain.finalsurfs is fine if you ar
brain.finalsurfs is fine if you are just rerunning the pial. Edit brainmask if
you are starting earlier so all the downstream volumes including
brain.finalsurfs will have the dura removed
Cheers
Bruce
> On Feb 7, 2017, at 10:45 PM, 冉倩 wrote:
>
>
>
>
> brain.finalsurfs.mgz? not brainmask.mgz
brain.finalsurfs.mgz? not brainmask.mgz?
or brain.finalsurfs.mgz for pial surface edit and brainmask for wm surface edit?
At 2017-02-08 11:41:40, "Douglas Greve" wrote:
You should edit the brain.finalsurfs.mgz to remove the non-brain then run with
-autorecon-pial
On 2/7/17 10:37 PM,
You should edit the brain.finalsurfs.mgz to remove the non-brain then
run with -autorecon-pial
On 2/7/17 10:37 PM, 冉倩 wrote:
Hi Prof.Douglas Greve,
Yes, probematic surface normally existed near supeiror dura ( aroun
superior frontal lobe or parietal lobe or central gry area). Just now
I a
Hi Prof.Douglas Greve,
Yes, probematic surface normally existed near supeiror dura ( aroun superior
frontal lobe or parietal lobe or central gry area). Just now I am confused
about the next steps. If I manually erase ( whether I can modfiy control point
just like modify wm) the dura on the
I think Bruce is referring only to the first image. For the second
image, it looks like most of the problematic surface is going through
the amygdala or hippocampus in which case it does not need to be fixed.
On 2/7/17 9:57 PM, Bruce Fischl wrote:
oh yes, it's grabbing a bit of dura. If you ha
Hi Bruce,
Thanks for your suggestions. If I manually erase ( whether I can modfiy control
point just like modify wm) the dura on the brainmask.mgz to correct pial
surface. Then I shoud re-run command: recon-all -autorecon2 -autorecon-3 sub01?
or just recon-all -autorecon2-pial -autorecon3 s
oh yes, it's grabbing a bit of dura. If you have a 1mm-ish T2 or FLAIR
you can use it to automatically correct this type of problem. Or you can
erase the dura in those regions on the brainmask.mgz and recreate the pial
surface
cheers
Bruce
On Wed, 8 Feb 2017, 冉倩 wrote:
Hi Bruce,
Thanks fo
Hi Qian
I'm not sure I understand what you think is wrong in the images you
included. The first two locations look quite accurate to me, and I'm not
positive but I think the third image the locations you circle are amygdala,
so not neocortical at all
cheers
Bruce
On Wed, 8 Feb 2017, 冉倩
Hi Qian, things will be a lot easier if you imbed your comments and
images in the email. From the text, I can't tell what you want exactly.
The first question had to do with skull stripping. It looks like you had
to make a manual edit. This is expected sometimes. If it is more than
that, what
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