Hi Bruce,
Thanks for your reply.
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, Ƚٻ 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 ¨Call ¨Csubjid 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 ¨Cautorecon2 ¨Cautorecon3 ¨Csubjid 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 ¨Cautorecon2-cp ¨Cautorecon3 ¨Csubjid 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 ¨Cautorecon2-pial ¨Cautorecon3 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 ¨Cautorecon2-cp ¨Cautorecon2-wm ¨Cautorecon2-pail ¨Cautorecon3 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, Ƚٻ 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 >> >> >> >> >> >> >> >>