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:
zharj@mail.ustc.edu.cn <javascript:_e({}, 'cvml', 'zharj@mail.ustc.edu.cn');>
charujing@gmail.com <javascript:_e({}, 'cvml', 'charujing@gmail.com');>
charujing123@163.com <javascript:_e({}, 'cvml', 'charujing123@163.com');>
*发件人：*Douglas N Greve <greve@nmr.mgh.harvard.edu <javascript:_e({}, 'cvml', 'greve@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"<zharj@mail.ustc.edu.cn <javascript:_e({}, 'cvml', 'zharj@mail.ustc.edu.cn');>>,"Bruce Fischl"<fischl@nmr.mgh.harvard.edu<javascript:_e({}, 'cvml', 'fischl@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:
zharj@mail.ustc.edu.cn mailto:zharj@mail.ustc.edu.cn
charujing@gmail.com mailto:charujing@gmail.com
charujing123@163.com mailto:charujing123@163.com
*发件人：*Bruce Fischl fischl@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"charujing123@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