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 On Wed, 2013-05-08 at 11:52 -0500, Nick Jones wrote: > Hi Nick, > > I included that just to illustrate there are no "cut" lines or newlines, it > is not the information I entered, but rather an obfuscated license file. The > license file I'm using works fine on an older version of Opensuse (11.4) and > the 5.3 BETA, but not the newer 12.3 and 5.3 BETA. > > Thanks > > Nick > > On 05/07/2013 05:06 PM, Nick Schmansky wrote: > > Nick, > > > > Can you request another license file? The info in the .license file > > that is shown in your email below does not appear to be valid. There is > > no record of it in our license system (or more accurately, number 14743 > > has different data than that shown). Was it obtained recently? > > > > Our current licensing scheme has been used since at least 1999, so I > > think the history of how it came about has been lost. Changing it now I > > think might skew the stats we've collected over the years. > > > > Nick > > > > > > On Tue, 2013-05-07 at 13:57 -0500, Nick Jones wrote: > >> Hi Nick, > >> > >> It complains about libtix8.1.8.4.so missing. I add > >> $FREESURFER_HOME/lib/tcltktixblt/lib/ to the LD_LIBRARY_PATH variable, but > >> it still complains about the license and does not open bert. > >> > >> Tried the dev build and 5.3 beta, which also fail at the license. > >> > >> Why not remove the requirement and have people agree to a license prior to > >> downloading? Lots of folks probably enter bogus information into the > >> registration form anyway. > >> Just trying to be constructive. > >> > >> Thanks very much for your help > >> > >> Nick > >> > >> On 05/07/2013 12:14 PM, Nick Schmansky wrote: > >>> Nicola and Nick, > >>> > >>> Can you try the tkmedit.bin found here: > >>> > >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ > >>> > >>> copy it to the freesurfer/tktools directory (the wrapper script > >>> 'tkmedit' in the bin dir calls the binary in the tktools dir). > >>> > >>> I'm hoping the problem you are seeing is the same one that others have > >>> seen on Fedora 19 and Ubuntu 13 which is fixed for the upcoming 5.3 > >>> release. > >>> > >>> Nick > >>> > >>> > >>> > >>> On Tue, 2013-05-07 at 12:15 -0400, Nicola Toschi wrote: > >>>> Hi Nick, hi List, > >>>> > >>>> I have been having the exact same problem (also posted it on this list) > >>>> with every freesurfer version on Opensuse 12.3, and haven't been able to > >>>> sort it out. > >>>> > >>>> Any luck with it? Any pointers would be highly appreciated. > >>>> > >>>> Thanks in advance, > >>>> > >>>> Nicola > >>>> > >>>> On 5/1/2013 4:42 PM, Nick Jones wrote: > >>>>> Hi, > >>>>> > >>>>> I've run into a license problem with the latest version of Freesurfer > >>>>> on OpenSuse 12.3. 64 bit. > >>>>> > >>>>> FREESURFER_HOME: /usr/freesurfer > >>>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > >>>>> Kernel info: Linux 3.7.10-1.1-desktop x86_64 > >>>>> > >>>>> When running a test: > >>>>> > >>>>> /usr/freesurfer>echo $shell > >>>>> /bin/tcsh > >>>>> > >>>>> /usr/freesurfer>source SetUpFreeSurfer.csh > >>>>> -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 -------- > >>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) > >>>>> FREESURFER_HOME /usr/freesurfer > >>>>> FSFAST_HOME /usr/freesurfer/fsfast > >>>>> FSF_OUTPUT_FORMAT nii.gz > >>>>> SUBJECTS_DIR /usr/freesurfer/subjects > >>>>> MNI_DIR /usr/freesurfer/mni > >>>>> FSL_DIR /usr/fsl > >>>>> > >>>>> /usr/freesurfer>tkmedit bert orig.mgz > >>>>> -------------------------------------------------------------------------- > >>>>> ERROR: Invalid FreeSurfer license key found in license file > >>>>> /usr/freesurfer/.license > >>>>> If you are outside the NMR-Martinos Center, > >>>>> go to http://surfer.nmr.mgh.harvard.edu to > >>>>> get a valid license file (it's free). > >>>>> If you are inside the NMR-Martinos Center, > >>>>> make sure to source the standard environment. > >>>>> -------------------------------------------------------------------------- > >>>>> > >>>>> /usr/freesurfer>cat .license > >>>>> hotm...@hotmail.com > >>>>> 14743 > >>>>> *C5.JPynIz8mt > >>>>> /usr/freesurfer> > >>>>> > >>>>> This license file has been obfuscated. > >>>>> > >>>>> /usr/freesurfer>ll -a .license > >>>>> -rw-r--r-- 1 root root 46 Apr 29 09:38 .license > >>>>> > >>>>> /usr/freesurfer>cat VERSION > >>>>> freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 > >>>>> > >>>>> /usr/freesurfer>zypper targetos > >>>>> openSUSE-12.3-x86_64 > >>>>> > >>>>> /usr/freesurfer>uname -a > >>>>> Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC > >>>>> 2013 (82d3f21) x86_64 x86_64 x86_64 GNU/Linux > >>>>> > >>>>> Name: tcl > >>>>> Version: 8.5.12-3.1.3 > >>>>> Name: tk > >>>>> Version: 8.5.12-3.1.1 > >>>>> > >>>>> Thanks to anyone who can provide some insight or workaround. I'm also > >>>>> curious if anyone knows the reasoning behind using this type of license > >>>>> mechanism, as opposed to agreeing to a license prior to downloading, > >>>>> like FSL or 3DSlicer? > >>>>> > >>>>> Nick > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer@nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> > >>>>> The information in this e-mail is intended only for the person to whom > >>>>> it is > >>>>> addressed. If you believe this e-mail was sent to you in error and the > >>>>> e-mail > >>>>> contains patient information, please contact the Partners Compliance > >>>>> HelpLine at > >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you > >>>>> in error > >>>>> but does not contain patient information, please contact the sender and > >>>>> properly > >>>>> dispose of the e-mail. > >>>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>> > >>> > >> > >> > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
