Mark,

Creating empty directories for the subjects and fsl/bin was the right solution to the warning messages you were seeing.  I need to add stub directories with READMEs to the directory structure.

The FreeSurferEnv.csh file (which I am guessing you 'source' in your .cshrc file) has some text on the environment variables it references, including SUBJECTS_DIR and FSL_DIR, which pertain to your question (remember to set these before sourcing FreeSurferEnv.csh).  Here's a snippet from that file:

#############################################################################
# Name:    FreeSurferEnv.csh
# Purpose: sets up the environment to run FreeSurfer and FS-FAST
# Usage:  
#   1. Create an environment variable called FREESURFER_HOME and set it
#      to the directory in which FreeSurfer is installed.
#   2. From a csh or tcsh shell or (.login):
#      source FreeSurferEnv.csh
#   3. There are environment variables that should point to locations
#      of software or data used by FreeSurfer. If set prior
#      to sourcing, they will not be changed, but will otherwise be
#      set to default locations:
#        FSFAST_HOME
#        SUBJECTS_DIR
#        MINC_BIN_DIR 
#        MINC_LIB_DIR 
#        FSL_DIR
#   4. If NO_MINC is set (to anything), then all the MINC stuff is ignored.
#   5. If NO_FSFAST is set (to anything), then the startup.m stuff is
#      ignored
#   6. The script will print the final settings for the above variables
#      as well as any warnings about missing directories. If
#      FS_FREESURFERENV_NO_OUTPUT is set, then no normal output will
#      be made (only error messages).
#
#   The most convenient way to use this script is to write another
#   script that sets FREESURFER_HOME and possibly SUBJECTS_DIR for
#   your set-up, as well as NO_MINC, NO_FSFAST, or
#   FS_FREESURFERENV_NO_OUTPUT as appropriate, and then source this
#   script.

Nick


On Sat, 2005-06-11 at 00:21 -0400, Mark Pinsk wrote: 
Hi Nick,

Thanks for the Tiger installation.  I just installed it on my ibook
just to see if it worked, and so far so good.  I was able to get the
csurf GUI to pop up, so I'll have to run thru a subject on my G5
desktop in the next few weeks after I get back from HBM.

1 question:
When I sourced my .cshrc file it could not find a 'subjects' directory
and a  'fsl/bin' directory within the freesurfer folder.
I went ahead and just created empty folders with those names so that
it wouldn't complain.
But for future reference, where can I define the location of my
subjects folder and of my FSL installation if they aren't within the
freesurfer folder?

Thanks !
Mark


On 6/10/05, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote:
>  Mark,
>  
>  I don't think dlcompat is required to run freesurfer.  I am able to run it
> on a tiger machine without it.
>  
>  There is a new freesurfer build for Tiger just posted on the ftp site.  Its
> a .dmg file, which is a compressed installation package.  After download, a
> .mpkg file will appear, and clicking on that will begin the installation.
>  
>  The 'full' installation includes freesurfer binaries, support libraries and
> the MINC toolkit, all newly created on tiger from source.  All install in
> /usr/pubsw/packages, thus Administrator access is required.  The install
> location is not relocatable, as freesurfer depends on some fixed paths.  A
> Fink installation is not necessary, as the support-libs packages includes
> everything freesurfer needs: jpeg, tiff, glut, tcl/tk, tix, blt and gsl.
>  
>  The full install file is at:
>  
>  ftp://surfer.nmr.mgh.harvard.edu 
> and the file is called freesurfer-Darwin-tiger-full.dmg
> 
>  
>  This is a work-in-progress, so I'd appreciate any comments, especially if
> it works for you.
>  
>  Nick
> 
>  
>  
>  On Fri, 2005-06-10 at 16:11 -0400, Mark Pinsk wrote: 
>  
> 
> Hi, I just tried a fresh installation of freesurfer on a new OS X Tiger
> machine.
> 
> Turns out that Fink is not longer offering the dlcompat library for
> download.
> 
> Can anyone wrap those binaries up and send them to me, or post them
> for download by any chance?
> 
> thanks so much!
> Mark
> 
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