Hi Rujing,
About tksurfer visualization, we had the same problem, it was because the
graphic card in the server, you cannot do anything about it (well, install
a different one).
If I remember correctly, you need a graphic card that supports OpenGL.
Regards,
Gari
On Friday, December 20, 2013, Rujing Zha wrote:
> Thanks Doug.
> All the best.
>
> 2013-12-20
> ------------------------------
> *Rujing Zha*
> School of Life Science
>
> University of Science and Technology of China
>
> E-mail:
>
> zh...@mail.ustc.edu.cn <javascript:_e({}, 'cvml',
> 'zh...@mail.ustc.edu.cn');>
>
> charuj...@gmail.com <javascript:_e({}, 'cvml', 'charuj...@gmail.com');>
>
> charujing...@163.com <javascript:_e({}, 'cvml', 'charujing...@163.com');>
>
>
> ------------------------------
> *发件人：*Douglas N Greve <gr...@nmr.mgh.harvard.edu <javascript:_e({},
> 'cvml', 'gr...@nmr.mgh.harvard.edu');>>
> *发送时间：*2013-12-20 00:14
> *主题：*Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit
> *收件人：*"Rujing Zha"<zh...@mail.ustc.edu.cn <javascript:_e({}, 'cvml',
> 'zh...@mail.ustc.edu.cn');>>,"Bruce
> Fischl"<fis...@nmr.mgh.harvard.edu<javascript:_e({}, 'cvml',
> 'fis...@nmr.mgh.harvard.edu');>
> >
> *抄送：*"freesurfer"<freesurfer@nmr.mgh.harvard.edu <javascript:_e({},
> 'cvml', 'freesurfer@nmr.mgh.harvard.edu');>>
>
>
> On 12/19/2013 07:22 AM, Rujing Zha wrote:
> > Hi Doug, Bruce and others.
> > Would you please help me deal with 2 problems?
> > The 1st one is :
> > There is a excellent segmentation in -surfs after editing the pial and
> > running -autorecon-pial. Some voxels was removed from the
> > brainmask.mgz(i.e. picture 2 in the attachment),but neither did -aseg
> > image which had those voxels(i.e. picture 1 in the attachment) which I
> > have removed from the brainmask.mgz when I ran "tkmedit subject
> > brainmask.mgz -aux wm.mgz -surfs -aseg". Does this incorrect aseg
> > image will influence my group thickness analysis? If so, what can I do
> > to fix it?
>
> I don't think you need to fix that. It is dura but it does not look like
> it is affecting the surfaces. The cortical segmentation in the aseg is
> not that important since all cortical statistics are computed from the
> cortical surfaces, not the aseg.
>
> > The 2nd one is :
> > I could not visualize the inflated image properly in tksurfer by this
> > command:
> > tksurfer yizhihui rh inflated
> > I could see little thing in the tksurfer after typing the command
> > above. The result can be got in picture 3 of the attachment and the
> > standard output message can be seen in the picture 4. I visualized the
> > inflated image in the freeview tool by typing "freeview -f
> > $SUBJETCS_DIR/yizhihui/surf/rh.inflated ". The result can be seen in
> > picture 5.
>
> I don't know, looks like a problem with the libraries needed for
> display. Maybe Zeke or Ruopeng can weight in.
>
> > CentOS 5.8 is used in my server
> > and I use "freesurfer-Linux-centos4-stable-pib-v5.3.0".
> > Thanks in advance.
> > All the best.
> > 2013-12-17
> > ------------------------------------------------------------------------
> > /Rujing Zha/
> > School of Life Science
> >
> > University of Science and Technology of China
> >
> > E-mail:
> >
> > zh...@mail.ustc.edu.cn <mailto:zh...@mail.ustc.edu.cn>
> >
> > charuj...@gmail.com <mailto:charuj...@gmail.com>
> >
> > charujing...@163.com <mailto:charujing...@163.com>
> >
> > ------------------------------------------------------------------------
> > *发件人：*Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> > *发送时间：*2013-12-16 23:57
> > *主题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from
> > the command-line ERROR
> > *收件人：*"Rujing Zha"<charujing...@163.com>
> > *抄送：*"freesurfer"<freesurfer@nmr.mgh.harvard.edu>
> > Hi Rujing
> > you can use either our FTP site or our file drop. Info for this is at
> > http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
> > and
> > https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > cheers
> > Bruce
> > On Mon, 16 Dec
> > 2
>
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