Hello, Nick

I tried mri_convert work, glxgears,tksurfer, qdec,freeview. It all respond as "Command not found"

two questions:

1) How should I initiate freesufter evey time i turn on the computer?

2) The other day when I installed freesurfer,i typed  ¡°tkmedit bert orig.mgz¡±, it reponded ¡°Illegal instruction¡±. If I typed in ¡°recon-all¡±, it showed
¡° Required Arguments:
 -subjid <subjid>
-<process directive>¡­... ¡±

and the other arguments.

But when i tried the ¡°recon-all¡± today, it said "Command not found".

Another thing is i installed the freesurfer in my Document folder, instead of the local folder. Although i am the administrator, Ubuntu would not allow me to move any file to the local folder..

Any idea of the problem of freesurfer in my computer?

thanks

Jie





> From: nicks@nmr.mgh.harvard.edu
> To: rememberer@hotmail.com
> Date: Wed, 23 Feb 2011 18:32:58 -0500
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] installation problem
>
> does mri_convert work?
>
> glxgears?
>
> tksurfer?
>
> qdec?
>
> freeview?
>
> your installation should work on ubuntu, as it has for other people, so
> i'm a bit at a loss.
>
> n.
>
> On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote:
> > Hello, Nick
> >
> > the output of uname -a is
> >
> > "Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21
> > 17:40:48 UTC 2011 i686 GNU/Linux"
> >
> > thanks
> >
> > Jie
> >
> >
> >
> >
> > > Subject: Re: [Freesurfer] installation problem
> > > From: nicks@nmr.mgh.harvard.edu
> > > To: rememberer@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Date: Wed, 23 Feb 2011 11:59:16 -0500
> > >
> > > what is the output of
> > >
> > > uname -a
> > >
> > >
> > > On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote:
> > > > Hello, Freesurfer experts:
> > > >
> > > >
> > > >
> > > > I emailed some installation problems a couple days ago, but
> > haven¡¯t
> > > > answered yet. I am new to freesurfer and try to install the newest
> > > > version of freesurfer in Ubuntu system. I closely followed the
> > > > instructions, and the only difference is that I installed it in my
> > > > Documents, instead of local folder.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Below is the output after ¡°source
> > $FREESURFER_HOME/SetUpFreeSurfer.sh¡±
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > -------- freesurfer-Linux-centos4-stable-pub-v5.0.0 --------
> > > >
> > > >
> > > >
> > > > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > > >
> > > >
> > > >
> > > > FREESURFER_HOME /home/jie/Documents/freesurfer/
> > > >
> > > >
> > > >
> > > > FSFAST_HOME /home/jie/Documents/freesurfer//fsfast
> > > >
> > > >
> > > >
> > > > FSF_OUTPUT_FORMAT nii
> > > >
> > > >
> > > >
> > > > SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects
> > > >
> > > >
> > > >
> > > > MNI_DIR /ho me/jie/Documents/freesurfer//mni
> > > >
> > > >
> > > >
> > > > Everything seems fine and I also added the .license file to the<
> > br>> > freesurfer folder. But when I test it by ¡°tkmedit bert
> > orig.mgz¡±, it
> > > > reponds ¡°Illegal instruction¡±
> > > >
> > > >
> > > >
> > > > If I type in ¡°recon-all¡±, it will show
> > > >
> > > >
> > > >
> > > > ¡° Required Arguments:
> > > >
> > > >
> > > >
> > > > -subjid <subjid>
> > > >
> > > >
> > > >
> > > > -<process directive>¡­... ¡± and the other arguments.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > How to fix the problem and make Fressurfer run? Any help is
> > > > appreciated. Thanks a lot!
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer.
> > > >
> > > >
> > > >
> > > > Jie
> > > >
> > > > _______________________________________________
> > > > 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 is
> > > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > > contains patient i nformation, please contact the Partners Compliance
> > HelpLine at
> > > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > > but does not contain patient information, please contact the sender
> > and properly
> > > dispose of the e-mail.
>
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