Hi Bruce,


I performed the -autorecon-pial as a means of regenerating the surfaces as instructed on the Freesurfer skull strip tutorial. The brainmask.mgz file does not have the skull but it has some dura left over. The issue I had before was that the skull would re-appear after the subject finished processing and the surfaces would be outlined on the dura and skull. 


Would it be okay if I could send screenshots of the my processed subject?


Thanks for your help.


Arsenije



From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Sent: Wednesday, November 22, 2017 11:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 165, Issue 35
 
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Today's Topics:

   1. Job opening: postdoc in AFNI group of NIH (P Taylor)
   2. Re: Problems when loading surface and mesh showing        vertices
      (Rosalia Dacosta Aguayo)


----------------------------------------------------------------------

Message: 1
Date: Wed, 22 Nov 2017 12:50:37 -0500
From: P  Taylor <neon.taylor@gmail.com>
Subject: [Freesurfer] Job opening: postdoc in AFNI group of NIH
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAB790KVuR-gAU__TTz0CoGSTFriKNEPCrDSSxg9wAdK3qBF+GQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello-

The Scientific and Statistical Computing Core (a.k.a. the AFNI group) at
the NIMH, NIH (Bethesda, MD, USA) is lookin' to hire a postdoc,
particularly someone with C and/or C++ experience, with Python and OpenGL
skills also being quite useful.

If you like problem solving and working with a fun group of people, then
check out the attached advertisement for details.  (And please feel free to
forward on.)

--pt
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Message: 2
Date: Tue, 21 Nov 2017 18:25:17 +0100
From: Rosalia Dacosta Aguayo <rdacostaa@gmail.com>
Subject: Re: [Freesurfer] Problems when loading surface and mesh
        showing vertices
To: fischl@nmr.mgh.harvard.edu, Freesurfer support list
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAPBdvhiXTvB-gh3CBgxgq=Le34Fc+u949KioRS2WRh9ws_fihg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Sorry Bruce,

I prefer sending it to your email directly, then if you want to make it
available to the other memebrs, there is not problem at all...

Kind regards,
Rosalia

2017-11-21 18:17 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:

> tar and gzip the entire subject dir and upload it following these
> instructions:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange


>
>
> On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo wrote:
>
>  Hi Bruce,
>>
>> Thank you for answering.
>>
>> Not, it is not a bug...in fact recon-all...-all had not problems. Just I
>> was
>> looking at the outputs...and as I am running FreeSurfer for my first time
>> I
>> wanted to ask about if this was a problem or I can go on....
>>
>> Where I should upload the subject and which files? I mean, in order to do
>> not overload the mail list...
>>
>> Kind regards,
>> Rosalia
>>
>> 2017-11-21 18:09 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
>>       hmmm, that is odd looking. Can you upload that subject so we can
>>       see if
>>       it is just a display bug or not?
>>       On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo
>>       wrote:
>>
>>       > Dear FreeSurfer Developers,
>>       >
>>       > I am checking the OutputData_freeview after running recon-all
>>       following your
>>       > tutorial:
>>       >
>>       https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputD
>> ata_freeview
>>       >
>>       > I have loaded T1.mgz, wm.mgz, brainmask.mgz and aseg.mgz, and
>>       then the
>>       > surfaces: rh.pial, rh.white, lh.pial and lh.white.
>>       >
>>       > In general, I did not see any problem...but when I wanted to
>>       see the
>>       > surface&mesh with vertices I saw something estrange I do not
>>       know if it is a
>>       > problem or it is normal (see the vertices in the temporal pole
>>       in grey
>>       > scale)...as this is my first run with FreeSurfer. I attach you
>>       the image.
>>       >
>>       > 1. FreeSurfer version:
>>       > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>       > 2. Platform: CentOS release 6.7
>>       > 3. uname -a: Linux rosalia-PORTEGE-Z930 4.4.0-98-generic
>>       #121-Ubuntu SMP Tue
>>       > Oct 10 14:24:03 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>>       > 4. Recon-all.log; see attached (although it ended without
>>       errors)
>>       >
>>       > I haven't come across this error in my searches, but I may be
>>       using the
>>       > wrong key terms. Would anyone be able to point me in the right
>>       direction or
>>       > trouble-shoot fixing this?
>>       >
>>       > Thank you for your time,
>>       > Rosalia
>>       >
>>       >
>>       >
>>       >
>>       >
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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