tksurfer visualization and -aseg option in tkmedit

19 Dec 2013

      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?
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.
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
charujing@gmail.com
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  
2013, Rujing Zha wrote:
...
Hi Bruce, 
Maybe 163 email has some problems. I will try my gmail to send you and Louis 
my data. But I donot know whether your email can get attachment size 289M? 
Thanks. 
All the best.
2013-12-16

Rujing Zha

发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 
发送时间：2013-12-16 22:37 
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
no, I didn't get it  
On Mon, 16 Dec 2013, Rujing Zha wrote:
...
Dear Bruce,  
Thanks Bruce. That's all right.  
I want to know if I e-mail to you my subject's data successfully. The  
subject's image had a incorrect segmentation in surfs after recon-all.  
Thanks in advance.  
All the best.
2013-12-16

...
Rujing Zha

...
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu  
发送时间：2013-12-16 22:24  
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
sorry, I don't know that code very well. Doug is probably the right one t
o  
?? ?
...
help you   
Bruce
On Mon, 16 Dec 2013, Rujing Zha wrote:
...
Dear Bruce,   
I did setup the "-run 015" not "013" in unpacksdcmdir as I told in prev
io
...
us
...
message. But it generated the "013" folder automatically after running
?? ?
...
...
...
unpacksdcdir, which made me so confused.   
As it created the "013" folder, I guess unpacksdcmdir didnot recognized
...
...
structure image correctly which was in the "15th" line of the scan.info
.  
?? ?> Thanks Bruce.
...
...
All the best.
2013-12-16

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...
Rujing Zha

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发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu   
发送时间：2013-12-16 22:12   
主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from th
e  
?? ?> command-line ERROR
...
...
收件人："Rujing Zha"charujing123@163.com   
抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
but why are you giving recon-all the path to run 013 instead of 015? I
?? ?
...
?? ?> don't know the fsfast file structure, but your scan.info says that 01 
3 is
...
?? ?an EPI fun and 015 is the mprage
...
On Sat,     
14 Dec 2013, Rujing Zha wrote:
...
Hi Bruce,    
It generated a 013 subfolder in after running this code "unpacksdcmdi
r  
?? ?
...
...
...
-src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3dana
t  
?? ?mg
...
...
z
...
001.mgz". It is 15 that I can see the number of  t1_mpr_ns_sag_iso_zh
an
...
g   
?? ?in
...
...
the unpack.log.    
Then I ran "recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liuj
un
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ha
...
o",
...
and it finished without error.    
"recon-all -s liujunhao -all" was run and ERROR would be displayed:
?? ?
...
...
...
...
ERROR: input(s) cannot have multiple frames!    
The recon-all.log unpack.log and scan.info were unloaded in the attac
hm
...
en
...
t.
...
Thanks.    
All the best.
2013-12-14

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__
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...
Rujing Zha

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2013-12-20