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" <fis...@nmr.mgh.harvard.edu>
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"
<gr...@nmr.mgh.harvard.edu> 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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>> >> >> >> >>
>> >> >>
