Re: [Freesurfer] License problem
Regarding any license issue under Opensuse 12.3 and the libcrypt incompatibility. So grab a libcrypt from an older opensuse (one where freesurfer was working, for me, I used libcrypt.so from 11.3, but 12.1 may be a better candidate if it works). Place it somewhere ($FREESURFER_HOME/lib is a good candidate), then add the location to the LD_LIBRARY_PATH environment variable so that freesurfer finds the old libcrypt. There is another workaround but you must contact Nick Schmansky, I don't remember the details. Thanks 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] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
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/freesurferecho $shell /bin/tcsh /usr/freesurfersource 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/freesurfertkmedit 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/freesurfercat .license hotm...@hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer This license file has been obfuscated. /usr/freesurferll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfercat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurferzypper targetos openSUSE-12.3-x86_64 /usr/freesurferuname -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
[Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
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 ___ 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.
Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
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/freesurferecho $shell /bin/tcsh /usr/freesurfersource 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/freesurfertkmedit 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/freesurfercat .license hotm...@hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer This license file has been obfuscated. /usr/freesurferll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfercat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurferzypper targetos openSUSE-12.3-x86_64 /usr/freesurferuname -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
[Freesurfer] Freesurfer License issue/bug on Opensuse 12.3
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/freesurferecho $shell /bin/tcsh /usr/freesurfersource 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/freesurfertkmedit 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/freesurfercat .license hotm...@hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer This license file has been obfuscated. /usr/freesurferll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfercat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurferzypper targetos openSUSE-12.3-x86_64 /usr/freesurferuname -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.
