Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

Hi Bruce, Thanks for your reply.

For this, I think pial surface (the location where I circle) already located outside of brain. 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 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" 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 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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer