Do I need to run the SetupFreeSurferEnv.csh every time before I start the Freesurfer? I thought it is only for initial intallation?
PS: even after I run the SetupFreeSurferEnv.csh when i installed Freesurfer the other day, it showed
-------- 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
But it did not work for the test "tkmedit bert orig.mgz"; it reponded¡°Illegal instruction¡±
Any suggestion for the problem?
Thanks
Jie
> From: nicks@nmr.mgh.harvard.edu
> To: rememberer@hotmail.com
> Date: Sat, 26 Feb 2011 18:30:31 -0500
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] installation problem
>
> the SetupFreeSurferEnv.csh file needs to be run. see installation
> instructions:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration
>
> n.
>
> On Fri, 2011-02-25 at 08:25 +0800, Liukarl wrote:
> > 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 clos
ely 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
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> > Compliance
> > > > HelpLine at
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> > > > > but does not contain patient information, please contact the
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> > > > > dispose of the e-mail.
> > >
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