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" fischl@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 sub01brainmask.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"
greve@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 skullstripping.
It looks like you had to make a manual edit. This is expected sometimes. If it is more than that, what is the problem. Inthe
second question, you had some problem with the quality of the white/pial surfaces, but there was not much detail or apicture.
>>
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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