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
__
Rujing Zha
__
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
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
__
__
Rujing Zha
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The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
