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 steps
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 pial
(-pial ) at the same time, then I run:
recon-all –autorecon2-cp –autorecon2-wm –autorecon2-pail –autorecon3 sub01
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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