Re: [Freesurfer] Set Up question

Hi David, Just put the commands into your .cshrc file (or .bashrc if you're using bash). Also, please post questions to the FS list instead of us directly so that it gets logged in our archive, other people can answer, and everyone can see the answer. Thanks! doug

On 06/10/2013 04:39 PM, David Dalton wrote:

Thank you so much! Do you also know how to get FreeSurfer to run automatically when I open the terminal? Right now I have to run the startup sequence every time.

Thanks, David

On Mon, Jun 10, 2013 at 2:42 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi David, it is not a problem if you're not going to run FS-FAST.
If it
bugs you, you can
setenv NO_FSFAST 1
in your cshrc file prior to sourcing the FS env

doug




On 06/10/2013 03:35 PM, David Dalton wrote:
> Hello FreeSurfer experts,
>
> I recently downloaded and installed FreeSurfer on my Mac
computer, but
> I have a few questions about the startup.
>
> 1. When I run FreeSurfer, I get the following.  I know the Wiki says
> to ignore the warning, and FreeSurfer does run normally after this,
> but I wanted to be sure it really was not a problem.
>
> [SiriasBook:/] csirias% setenv FREESURFER_HOME
Applications/freesurfer/
> [SiriasBook:/] csirias% source
Applications/freesurfer/SetUpFreeSurfer.csh
> -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   Applications/freesurfer/
> FSFAST_HOME       Applications/freesurfer//fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR      Applications/freesurfer//subjects
>
> WARNING: The /Users/csirias/matlab/startup.m file does not
appear to be
>          configured correctly. You may not be able
>          to run the FS-FAST programs
> Try adding the following lines to /Users/csirias/matlab/startup.m
> -----------------cut---------------------
> fshome = getenv('FREESURFER_HOME');
> fsmatlab = sprintf('%s/matlab',fshome);
> if (exist(fsmatlab) == 7)
>     path(path,fsmatlab);
> end
> clear fshome fsmatlab;
> fsfasthome = getenv('FSFAST_HOME');
> fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
> if (exist(fsfasttoolbox) == 7)
>     path(path,fsfasttoolbox);
> end
> clear fsfasthome fsfasttoolbox;
> -----------------cut---------------------
>
> MNI_DIR           Applications/freesurfer//mni
> [SiriasBook:/] csirias%
>
>
> 2. When I type in 'freeview' to the command line, I get several
other
> messages as the program opens.  I am not sure if they are a problem,
> but here they are. I seem to be able to run freeview despite these
> messages, but some others have told me that these messages do not
> appear on their computers, so I am wondering why they appear.
>
> [SiriasBook:/] csirias% freeview
> 2013-06-10 12:22:57.739 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.740 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.754 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.755 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.768 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.769 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.781 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.782 Freeview[1200:303] invalid drawable
>
> 3. And my last question. How do I run FreeSurfer automatically
when I
> open the terminal window? I would like to just type 'freeview' into
> the command line to have the program run, but I currently have
to type
>
> setenv FREESURFER_HOME Applications/freesurfer/
>
> followed by
>
> source Applications/freesurfer/SetUpFreeSurfer.csh
>
> in order for the program to run.
>
> Thank you so much for any help you can give!  Like I said, the
program
> appears to run normally despite the messages, but I just want to
know
> why they are appearing. The last question is more of a
convenience issue.
>
> Thanks,
> David
>
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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