Hi Bruce,
I am a little confused about it. I found 'Manual-Intervention Workflow Directives' on recon-all free surfer wiki web.
It said if edits made to correct pial, run-autorecon2-pial.
If I only edit pial, I run >recon-all -autrecon-pial -s <subject id> -sd <subjects_dir> to fix this issue, I also should rerunning autorecon3? or which command I should use to continue to next step? Thanks a lot.
Best Regards,
Qian Ran
At 2017-02-09 08:55:34, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: >Hi Qian > >if you just want to regenerate the pial, then yes, edit the >brain.finalsurfs.mgz and run: > >recon-all -autrecon-pial -s <subject id> -sd <subjects_dir> > >note that it is NOT autorecon2-pial, but just autorecon-pial (leave out the >'2') > >cheeers >Bruce > > >On Thu, 9 Feb 2017, Ƚٻ wrote: > >> Hi Bruce, >> If I use brain.finalsurfs, then I run recon-all -autorecon2-pial -subjid >> sub01 or recon-all -autorecon2-pial -autorecon3 -subjid sub01? autorecon3 >> still need rerunning? Thanks! >> Best Regards, >> Qian Ran >> >> >> >> >> At 2017-02-08 12:19:35, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: >> brain.finalsurfs is fine if you are just rerunning the pial. Edit >> brainmask if you are starting earlier so all the downstream volumes >> including brain.finalsurfs will have the dura removed >> Cheers >> Bruce >> >> On Feb 7, 2017, at 10:45 PM, Ƚٻ <fskrq002076@163.com> wrote: >> >> >> >> >> brain.finalsurfs.mgz? not brainmask.mgz? >> or brain.finalsurfs.mgz for pial surface edit and brainmask for >> wm surface edit? >> >> >> At 2017-02-08 11:41:40, "Douglas Greve" >> <greve@nmr.mgh.harvard.edu> wrote: >> >> You should edit the brain.finalsurfs.mgz to remove >> the non-brain then run with -autorecon-pial >> >> >> On 2/7/17 10:37 PM, Ƚٻ wrote: >> >> >> Hi Prof.Douglas Greve, >> >> Yes, probematic surface normally existed near >> supeiror dura ( aroun superior frontal lobe or >> parietal lobe or central gry area). Just now I am >> confused about the next steps. 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? Thanks! >> >> Best Regards, >> Qian Ran >> >> At 2017-02-08 11:21:57, "Douglas Greve" >> <greve@nmr.mgh.harvard.edu> wrote: >> >> 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, Ƚٻ 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, >> 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 >> st >> eps >> >> 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 pi >> al >> >> (-pial ) at the >> same time, then I run: >> >> >> recon-all >> ¨Cautorecon2-cp >> ¨Cautorecon2-wm >> ¨Cautorecon2-pail >> ¨Cautorecon3 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 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 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >>