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
> 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 <fis...@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"<charujing...@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 <fis...@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"<charujing...@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 <fis...@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"<charujing...@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
> > > > >
> > > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >
> > > >
> > > > 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 He
> > > >
>
> > lp
> > > Li
> > > > 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
> > > >
>
> > p
> > > ro
> > > > perly
> > > > dispose of the e-mail.
> > > >
> > > >
> > > >
> > >
> > >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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.
> >
> >
> >
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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