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, 冉倩 <fskrq002...@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" <gr...@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, 冉倩 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" <gr...@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, 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 >>>> >> >> >> >> >> >>>> >> >> >> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> _______________________________________________ >>> 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
