Hi Jidan,
Can you upload one of these subjects so I can take a look?
You can use these options to upload data:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Best,
Lee
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Jidan Zhong [jidanz@gmail.com] Sent: Wednesday, August 20, 2014 10:48 PM To: freesurfer maillist Subject: Re: [Freesurfer] no improvement for recon-all result after edits
Hi
I am reposting my message, hoping someone can give me some hint to get my problem solved. Thanks in advance!!
On Mon, Aug 18, 2014 at 10:42 PM, Jidan Zhong <jidanz@gmail.commailto:jidanz@gmail.com> wrote: Hi Freesurfer experts,
I was doing some manual editing on our subjects which are patients with lesions. I managed to correct most of them, however, 4 subjects have the same problem that I can't fix no matter what edits I tried.
So, the 4 subjects, they all have the same problem, which is: frontal part of superior temporal gyrus region is not segmented as white matter, thus they are just "missing" from the final surfaces and final segmentations. But when just do eye check, there is nothing wrong with this part, even the intensity looks the same of other white matter parts.It's just suddenly cut.
When I went back to those subjects, first I tried with control points. - It didnt help.
I confirmed that white matter is present connected to the main brain white matter volume. -- I reran from recon-all autorecon2-wm, didnt help.
Then I checked the aseg.mgz, that part is segmented as white matter correctly. I even modified the aseg.mgz (although not suggested), it still didn't work
It is just weird that the surface was just cut from the middle of STG.
So, is there any other way I can tell FreeSurfer that this is really STG and please keep it?
Thanks!! -- Regards,
Jidan
-- Regards,
Jidan