RE: [Freesurfer] Missing libraries? - Freesurfer

5 Jun 2005


      Thanks Nick, 
We'll give it a try and keep you posted.
A.
-----Original Message----- 
    From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] 
    Sent: Sat 6/4/2005 7:41 AM 
    To: Fornito, Alexander 
    Cc: Freesurfer Mailing List 
    Subject: Re: [Freesurfer] Missing libraries?
Alex,
    
    I've just posted a source code bundle of most of the MNI-BIC tools,
    along with a Makefile for building/installing/testing this software.
    
    The README file is here:
    
    ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README
    
    and the gzip file is here:
    
    ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz
    
    Although the README says the ideal place to install is
    at /usr/pubsw/packages/mni/current, I've installed the set in a local
    home directory, and the segment_subject works for me (on Mac OS X, and
    Linux CENTOS 4)
    
    However, you may be able to get your existing install working by just
    adding the environment var DYLD_LIBRARY_PATH.  See the README for an
    example.  Your error (not finding a .so file) is indicative of this
    problem.
    
    Let me know how things go.
    
    Nick
    
    
    On Fri, 2005-05-27 at 14:38 +1000, Fornito, Alexander wrote:
    > Hi,
    > We're really stuck on this one...
    > We are running a linux kernel 2.4.26 debian 3.0 (woody).
    > We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables.
    > We can't get the MNI tools to work through freesurfer, and only some limited MINC tools work if we try to run them on their own (eg., we can use MINC display, but can't do anyting with the images). It seems like there are some libraries missing (see below). Can you tell us why the MINC tools that came packaged with fressurfer aren't working? Is there something else that needs to be installed?
    > If I try to run mri_convert from the GUI after checking the MNI Linear
    > Register option in expert preferences, I get a message saying MNI align
    > not yet implemented.
    > If I run segment_subject I get :
    > 
    > segment_subject 190
    > cp: cannot stat
    > `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat'
    > : No such file or directory
    > /data/flanders/work/alex/freesurfer/subjects/190/scripts
    > /data/flanders/work/ale
    > x/freesurfer/subjects
    > registering 190
    > mri_convert orig orig/orig.mnc
    > reading from orig...
    > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    > i_ras = (-1, 0, 0)
    > j_ras = (0, 0, -1)
    > k_ras = (0, 1, 0)
    > writing to orig/orig.mnc...
    > mincinfo: error while loading shared libraries: libvolume_io.so.0:
    > cannot open shared object file: No such file or directory
    > Error executing mincinfo on orig/orig.mnc
    > Error:  could not open file
    > "/data/flanders/work/alex/freesurfer/subjects/190/mr
    > i/transforms/talairach.xfm".
    > System message: No such file or directory
    > mri_add_xform_to_header: could not read xform file
    > '/data/flanders/work/alex/fre
    > esurfer/subjects/190/mri/transforms/talairach.xfm'
    > 
    > Any help would be much appreciated!!!
    > Thanks,
    > Alex
    >
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