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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