Hi Qian
if you just want to regenerate the pial, then yes, edit the
brain.finalsurfs.mgz and run:
recon-all -autrecon-pial -s <subject id> -sd <subjects_dir>
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.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" <[email protected]> wrote:
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 <[email protected]> wrote:
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"
<[email protected]> 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, 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 am
confused about the next steps. 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 sub01? Thanks!
Best Regards,
Qian Ran
At 2017-02-08 11:21:57, "Douglas Greve"
<[email protected]> wrote:
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 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 for your reply.
[IMAGE]
For this, I think pial
surface (the location
where I circle)
already
located outside of
brain.
[IMAGE]
For this, pail surface
(near hippcamps I
think) located inside
of cortical I
think.
I mean if I manually
modify surface, how do
it? Thanks very much!
Best Regards,
Qian Ran
At 2017-02-08
09:54:30, "Bruce
Fischl"
<[email protected]>
wrote:
>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 wrote:
>
>> >> >> Dear
Prof.Douglas Greve,
>> Thanks for your
reply. I add parts of
problem screenshot of
white/pial
>> surface.
>> >> When I did
freesurfer for
structure analysis, I
was confused by some
st
eps
>> and results. The
analysis stream was:
>> >> 1st: check data
orientation
>> >> 2nd : convert
nii.gz to mgz
>> >> 3rd: recon-all
–all –subjid sub01
>> >> After these
steps finished , I
checked skullstrip,
segmentation quality.
The
>> problems as
following:
>> >> 1st: skullstrip
result not very well,
almost need manually
operation.
>> >> After
manually operation, I
run:
>> >> recon-all
–autorecon2
–autorecon3 –subjid
sub01
>> >> 2nd: parts of
white surface and pial
surface not very
exactly. I only did
>> adding control
points to modify white
surface, then I run:
>> >> Recon-all
–autorecon2-cp
–autorecon3 –subjid
sub01 brainmask.mgz
>> >> Several parts of
pial surface exit
errors. I added these
as screenshot:
>> >> >> >> >> [IMAGE]
>> >> [IMAGE]
>> [IMAGE]
>> [IMAGE]
>> >> [IMAGE]
>> >> So when I met
such issues, I should
add control points for
pial surface as
>> white surface did
(or how I correct or
edit pial; still use
tkmedit tool?
) ?
>> Then I run:
>> >> recon-all
–autorecon2-pial
–autorecon3 sub01 ?
>> >> If white surface
and pial surface all
needed manually
operated, whether I
>> could do like this:
I add control points
(-cp), edit wm (-wm),
correct pi
al
>> (-pial ) at the
same time, then I run:
>> >> recon-all
–autorecon2-cp
–autorecon2-wm
–autorecon2-pail
–autorecon3 sub0
1
>> or recon-all
-autorecon2-cp brainmask.mgz
-autorecon2-wm
-autorecon2-pial
>> -autorecon3 sub01?
>> >> or any other
suggestions?
>> >> Thanks very
much!
>> Best Regards,
>> Qian Ran
>> >> At 2017-02-08
07:18:51, "Douglas
Greve"
<[email protected]>
wrote
:
>>
>> 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 is the
problem. In the
>> second
question, you had some
problem with the
quality of the
>> white/pial
surfaces, but there
was not much detail or
a picture.
>> >> >>
>> On 2/7/17
8:22 AM, 冉倩 wrote:
>> Hello
Freesurfer Developers,
>> I have had last
September Freesurfer
course. When I
operated my
>> data following that
stream I met some
problem in reon-all
-all
>> step. Because I
need put some
screenshout to
exaplain that
>> problems, I add
word document in
attachment. Thanks
very much!
>> Best Regards,
>> Qian Ran
>> >> >>
>> >> >> >>
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>> Freesurfer mailing
list
>>
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>>
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