Nicola and Nick,
Hi, its Nick (the other Nick :)). This looks like a new issue we haven't seen before that is specific to opensuse. Can you try downloading the file libcrypt.so.1 from this location:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
copy it to your freesurfer/lib dir, then set a lib path prior to setting-up (sourcing) freesurfer, like this:
setenv FREESURFER_HOME <whereever you installed freesurfer> setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib source $FREESURFER_HOME/SetUpFreeSurfer.csh
this libcrypt lib is from centos6, and i'm thinking that possibly opensuse implements crypt differently (working theory anyway).
you can confirm that mri_convert is using this new lib by typing:
cd $FREESURFER_HOME/bin ldd ./mri_convert
and you should see libcrypt in the list with a path to the freesurfer/lib dir.
Nick
Hi Nick (Schmansky),
sorry to jump back in on this thread - I have exactly the same issue (license file not valid) on the same OS (and not on others) with *all* fs commands. I have tried multiple license files from other working installations.
Is there anything else i can try?
Thanks a lot
nicola
On 5/8/2013 3:09 PM, Nick Schmansky wrote:
Nick
Can you email me the .license file that is being used?
Thanks,
N.
On Wed, 2013-05-08 at 13:21 -0500, Nick Jones wrote:
Hi Nick,
Truncated the email. I'm getting a license error for both the mri_convert command and the tkmedit command that you provided. The original also yields a license error (no segfault). You are right, my earlier test called tkmedit.bin directly.
Thanks
Nick
On 05/08/2013 12:07 PM, Nick Schmansky wrote:
Nick,
Hi, I found what might the source of the problem and posted new versions of mri_convert and tkmedit.bin to this directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
before trying the new mri_convert though, can you try the following?
cd <some writable directory> mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz
I'm guessing it will segfault or print the license problem.
Now copy the new mri_convert (from the ftp link above) to the freesurfer/bin directory and try again. It should work. You can then also try the new tkmedit.bin. Remember to copy the tkmedit.bin to the freesurfer/tktools directory and leave freesurfer/bin/tkmedit untouched (its a wrapper-script that sets-up paths to the tcl/tk/tix/blt libs, so tkmedit.bin cannot be run directly)
Thanks,
Nick
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