Hi Bruce, Thanks for your suggestions. If I manually erase ( whether I can modfiy control point just like modify wm) the dura on the brainmask.mgz to correct pial surface. Then I shoud re-run command: recon-all -autorecon2 -autorecon-3 sub01? or just recon-all -autorecon2-pial -autorecon3 sub01? Thnanks! Best Regards, Qian Ran At 2017-02-08 10:57:23, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> 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" <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 >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
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