At 2017-02-08 10:57:23, "Bruce Fischl" <fischl@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, 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
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >> 
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>> >> 
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
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>>  
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