Hi Gari,
Thanks for your helpful prompt. I see.
All the best.
2013-12-21
Rujing Zha
发件人：Garikoitz Lerma-Usabiaga <gariko...@gmail.com>
发送时间：2013-12-21 15:47
主题：Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit
收件人："Rujing Zha"<zh...@mail.ustc.edu.cn>
抄送："freesurfer"<freesurfer@nmr.mgh.harvard.edu>
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
charuj...@gmail.com
charujing...@163.com
发件人：Douglas N Greve <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>,"Bruce
Fischl"<fis...@nmr.mgh.harvard.edu>
抄送："freesurfer"<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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