[MINC-users] MNI tools in Freesurfer

[Andrew Janke]

Wierd, I had thought all the packages from now on were using static
libraries.  Anyhow, I presume you got the .deb packages from
packages.bic.mni.mcgill.ca/deb?

If so, then I'd still like to know why they are using shared libraries
but the fix is to simply add:

   /usr/local/mni/lib to your LD_LIBRARY_PATH

andrew

On 01/06/05, Fornito, Alexander <Alexander.Fornito@wh.org.au> wrote:
> Hi all,
> I've been having trouble with the MNI tools packaged together with Freesurfer. We are running a  linux kernel 2.4.26 debian 3.0 (woody).
> We've installed the freesurfer and the packaged MNI tools in the apporpriate directories and set the appropriate environment variables.
> When I run Freesurfer's segmentation algorithm, I get the following error messages:
> 
> 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'
> 
> On their own some of the MNI tools work (eg., Display), whereas others don't (eg., mritotal, which returns with the mincinfo: error while loading shared libraries: libvolume_io.so.0 message).
> Any help would be greatly appreciated!!!
> Thanks,
> Alex
> 
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
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> 


-- 
Andrew Janke      (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor)
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