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?
Once more, thank you very much.
Nisser
------ Original Message ------
Received: Fri, 17 Dec 2010 02:26:28 AM GMT
From: Sebastian Moeller <[email protected]>
To: Nisser ali umar <[email protected]>
Cc: [email protected], [email protected], Obisesan Thomas O <[email protected]>
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 <[email protected]>
> To: Nisser ali umar <[email protected]>
> Cc: [email protected], [email protected], Obisesan Thomas O <[email protected]>
> 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
> [email protected]
> 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
[email protected]
Division of Biology
MC 114-96
California Institute of Technology
1200 East California Boulevard
CA 91125, Pasadena
USA
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <[email protected]>
> To: Nisser ali umar <[email protected]>
> Cc: [email protected], [email protected], Obisesan Thomas O <[email protected]>
> 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
> [email protected]
> 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
[email protected]
Division of Biology
MC 114-96
California Institute of Technology
1200 East California Boulevard
CA 91125, Pasadena
USA
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list [email protected] 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.
