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 hotmail@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

Hi Nick,

sorry - I should have been more specific.

I get the same error with *any* FS command or script (recon-all, mri_glmfit), so in effect ever since the upgrade I am not able to use FS at all.

The tkmedit patch you posted is only missing a library on my system though, which I can fix - so maybe that's a pointer towards the root of the problem?

Thanks again,

Nicola

On 5/7/2013 2:57 PM, 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 hotmail@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

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 hotmail@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

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

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

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.

Thanks Nick,

well that did change something... here is what i get now with any fs command:

/bin/tcsh: /lib64/libfreebl3.so: version `NSSRAWHASH_3.12.3' not found (required by /work2/rootbackup/usr/local/freesurfer/lib/libcrypt.so.1)

Should I update/substitute /lib64/libfreebl3.so al well?

thanks a lot,

Nicola

PS when running ldd ./mri_convert inside the bin dir, I get

"not a dynamic executable"

On 05/09/2013 06:02 AM, Nick Schmansky wrote:

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

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.