Hi Nisser,
On Dec 17, 2010, at 10:14 , Nisser ali umar wrote:
> Hi Sebastian,
>
> Thank you very much for the input. We tried but weren't able to get the
> problem resolved. Can you please shed more light on what you meant by
> "replace the directory in FREESURFER_HOME, and define your subjects
> directory", please?
Well, you install freesurfer from the .dmg into /Applications? Then I
assume it should be:
export FREESURFER_HOME=/Applications/freesurfer
(basically the same directory where you placed the .license file)
the SUBJECT_DIRS variable has to point at the directory in which you place all
the directories for the single sessions for which you want to reconstruct
surfaces. This really is your choice, just make sure the directory actually
exists :)
For example you could put all the data into a subdirectory called subjects in
your desktop directory:
first create the directory:
mkdir ~/Desktop/subjects
then put the following in your ~/.bashrc:
export FREESURFER_HOME=/Applications/freesurfer
. ${FREESURFER_HOME}/SetUpFreeSurfer.sh
export SUBJECT_DIRS=$HOME/Desktop/subjects
export doublebufferflag=1
But this will only work if the sourcing part (.
${FREESURFER_HOME}/SetUpFreeSurfer.sh) works correctly. And sorry my first
instruction was misleading in that . /opt/freesurfer/SetUpFreeSurfer.sh was
wrong for your setup, but I thought this was obvious. Also your initial error
might be simply that "source $FREESURFER?SetUpFreeSurfer.csh" should not have a
question mark but a slash ("source $FREESURFER/SetUpFreeSurfer.csh") but this
might just be a transcription to e-mail issue. In addition if you use bash as
your shell (the default in snow leopard) you would do better to use ".
$FREESURFER/SetUpFreeSurfer.sh". Note the dot followed by a space and the
extension .sh instead of .csh. No these issues are all basic unix/linux issues
and not related to freesurfer at all, you might want to try finding a local
unix expert to help you get started...
Good luck
Sebastian
>
> Once more, thank you very much.
>
> Nisser
>
>
>
>
>
> ------ Original Message ------
> Received: Fri, 17 Dec 2010 02:26:28 AM GMT
> From: Sebastian Moeller <sebastian.moell...@rwth-aachen.de>
> To: Nisser ali umar <nisser...@usa.net>
> Cc: ryorricks...@gmail.com, Freesurfer@nmr.mgh.harvard.edu, Obisesan Thomas O
> <tobise...@howard.edu>
> Subject: Re: [Freesurfer] Difficulty running FreeSurfer
>
>
> Hi Nisser,
>
>
> On Dec 16, 2010, at 12:09 , Nisser ali umar wrote:
>
> > Dear all,
> >
> > Thanks for the prompt responses to our query.
> >
> > Where do we create the .licence file? in the applications folder or the
> > freesurfer main folder.
>
> in the directory you put in $FREESURFER_HOME (would be the freesurfer main
> folder, just I always install freesurfer outside of applications so I do not
> know the installers default behaviour).
>
>
> >
> > In addition, we are also having difficulty setting up the FREESURFER_Home
> > enviroment. When we type the command: setenv
> > FREESURFER_HOME</Applications/freesurfer>freesurfer, it retuens a %, but
> > when we put in the command "source $FREESURFER?SetUpFreeSurfer.csh", it
> > returns a "/SetUpFreeSurfer.csh:No such file or directory."
>
> Well, per default the macosx terminal (at least for recent OS versions) uses
> bash, so you would have to edit .bashrc in your home directory. Please ignore
> any to verbose description, I just want to cover all bases...
> open a terminal and type nano ~/.bashrc (the editot nano seems to be part of
> snowleopard, no idea about older versions)
> add the following (but replace the directory in FREESURFER_HOME, and define
> your subjects directory, the doublebuffer flag might or might not speed up
> certain freesurfer components you just have to try it):
>
> export FREESURFER_HOME=/opt/freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
> . /opt/freesurfer/SetUpFreeSurfer.sh
> export SUBJECT_DIRS=$HOME/subjects
> export doublebufferflag=1
> then use control x to save and exit the file. Quit and reopen the terminal
> application to make sure any newly started bash shell will have executed your
> modified .bashrc.
>
>
> best
> sebastian
>
>
>
>
> >
> > Regards,
> >
> > Nisser
> >
> >
> >
> > ------ Original Message ------
> > Received: Thu, 16 Dec 2010 01:11:18 AM GMT
> > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> > To: Nisser ali umar <nisser...@usa.net>
> > Cc: Freesurfer@nmr.mgh.harvard.edu, ryorricks...@gmail.com, Obisesan Thomas
> > O <tobise...@howard.edu>
> > Subject: Re: [Freesurfer] Difficulty running FreeSurfer
> >
> >
> > Hi Nisser,
> >
> > put it in a file named $FREESURFER_HOME/.license
> >
> >
> > cheers
> > Bruce
> >
> > On Thu, 16 Dec 2010, Nisser ali
> > umar wrote:
> >
> > > Hi,
> > >
> > > We installed freesurfer on a mac computer but could not find where to
> > > paste the license code, thus have difficulty getting the freesurfer
> > > running.
> > >
> > > Can anyone help, please.
> > >
> > > Nisser
> > >
> > >
> > >
> > >
> > >
> > >
> >
> >
> > 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 information, 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.
> >
> >
> >
> > _______________________________________________
> > 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 information, 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.
>
>
> --
> Sebastian Moeller
>
> telephone: 626-807-5242 / 626-395-6523 / 626-395-6616
> fax: 626-395-8826
> German GSM: 0 15 77 - 1 90 31 41
> US CDMA: + 1 - 626 - 807 - 5242
> moel...@caltech.edu
>
> Division of Biology
> MC 114-96
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> 1200 East California Boulevard
> CA 91125, Pasadena
> USA
>
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>
>
--
Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616
fax: 626-395-8826
German GSM: 0 15 77 - 1 90 31 41
US CDMA: + 1 - 626 - 807 - 5242
moel...@caltech.edu
Division of Biology
MC 114-96
California Institute of Technology
1200 East California Boulevard
CA 91125, Pasadena
USA
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