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.moeller1@rwth-aachen.de To: Nisser ali umar nisser.au@usa.net Cc: ryorrickster@gmail.com, Freesurfer@nmr.mgh.harvard.edu, Obisesan Thomas O tobisesan@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 fischl@nmr.mgh.harvard.edu To: Nisser ali umar nisser.au@usa.net Cc: Freesurfer@nmr.mgh.harvard.edu, ryorrickster@gmail.com, Obisesan Thomas O tobisesan@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 moeller@caltech.edu

Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer