subject:"\[Freesurfer\] crypt

Re: [Freesurfer] crypt_gkey = (null)

2018-06-12 Thread Dicamillo, Robert

Hello Aaron,

The build timestamp from the output below shows mri_convert is from 8/2014.
When I look at the build timestamp on our stable 5.3 version of mri_convert I
see it is from 5/2013. So the version that you listed is about 1 year newer
than the 5.3 release I can see. It is possible that someone downloaded a
daily/dev build of freesurfer at that time.

You might want to consider running the latest 6.0 release of Freesurfer
(released in January 2017), which should be fine on CentOS 7. It can be
downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

I also suggest that you start out in a default/clean shell, set
FREESURFER_HOME, and then source the setup script for linux, You can see the
instructions on that same web page under “Setup and Configuration”. The setup
steps should work for version 5 or 6.

- rob

On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum
mailto:aaron.b.tanenb...@gmail.com>> wrote:

External Email - Use Caution

I checked my system is not encrypted. I had someone else run the command on the
same machine. It worked for them. So I changed my BASH environment to a default
environment. I still get the same error.

I tried this again but with a different FreeSurfer 5.3. turns out the one I was
using has been altered version of FreeSurfer. I do not know how it was
altered. It worked. so it has to do with the altered FreeSurfer.
I ran the command mri_convert -version on both FreeSurfer.

for the unaltered i get the out put
mri_convert -version
stable5
altered version i get
mri_convert -version
dev build (use --all-info flag for full version info)

with this output i type in mri_convert --all-info
mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $
TimeStamp: 2018/06/12-18:32:17-GMT BuildTimeStamp: Aug 22 2014 21:04:47 CVS:
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: tanenbauma
Machine: rocky Platform: Linux PlatformVersion: 3.10.0-862.el7.x86_64
CompilerName: GCC CompilerVersion: 40400
Wondering is this version of mri_convert a developmental version?
Also both version are the CentOS 6 build.

On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert
mailto:rdicami...@mgh.harvard.edu>> wrote:
Hello Aaron,

You could check to see if the CentOS 7 system is using disk encryption, e.g.,
if the
following command return 1, then it would mean encryption is in use (which can
be
an issue with FreeSurfer).

$ cat /proc/sys/crypto/fips_enabled

If it returns zero, it could be an issue with a system library like glibc on
CentOS 7.5
(that does not happen on older versions of CentOS).

Either way, this is not your doing ;-)

On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum
mailto:aaron.b.tanenb...@gmail.com>> wrote:

External Email - Use Caution

I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i
get to the part where MRI_convert is creating the the orig001.mgz its gives me
a segmentation fault. if i run this on a centos 6 system it works fine. below
is the output of the program.

/data/gizmo/data1/freesurfer5.3/bin/mri_convert
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
/data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
crypt_gkey = (null)
Segmentation fault (core dumped)

Did I do anything wrong?
___
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

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

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, plea

Re: [Freesurfer] crypt_gkey = (null)

2018-06-12 Thread Aaron Tanenbaum

External Email - Use Caution

I checked my system is not encrypted. I had someone else run the command on
the same machine. It worked for them. So I changed my BASH environment to a
default environment. I still get the same error.

I tried this again but with a different FreeSurfer 5.3. turns out the one I
was using has been altered version of FreeSurfer.  I do not know how it was
altered. It worked. so it has to do with the altered FreeSurfer.
I ran the command mri_convert -version  on both FreeSurfer.

for the unaltered i get the out put

*mri_convert -version stable5*
altered version i get

*mri_convert -version dev build (use --all-info flag for full version info)*

with this output i type in mri_convert --all-info
*mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name:  $
TimeStamp: 2018/06/12-18:32:17-GMT  BuildTimeStamp: Aug 22 2014 21:04:47
CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User:
tanenbauma  Machine: rocky  Platform: Linux  PlatformVersion:
3.10.0-862.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400*
Wondering is this version of mri_convert a developmental version?
Also both version are the CentOS 6 build.

On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert <
rdicami...@mgh.harvard.edu> wrote:

> Hello Aaron,
>
> You could check to see if the CentOS 7 system is using disk encryption,
> e.g., if the
> following command return 1, then it would mean encryption is in use (which
> can be
> an issue with FreeSurfer).
>
> $ cat /proc/sys/crypto/fips_enabled
>
> If it returns zero, it could be an issue with a system library like glibc
> on CentOS 7.5
> (that does not happen on older versions of  CentOS).
>
> Either way, this is not your doing ;-)
>
>
> On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum 
> wrote:
>
> External Email - Use Caution
>
> I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3.
> When i get to the part where MRI_convert is creating the the orig001.mgz
> its gives me a segmentation fault. if i run this on a centos 6 system it
> works fine. below is the output of the program.
>
>
> /data/gizmo/data1/freesurfer5.3/bin/mri_convert
> /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
> /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
> $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
> reading from
> /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
> crypt_gkey = (null)
> Segmentation fault (core dumped)
>
>
>
> Did I do anything wrong?
> ___
> 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
>
>
> 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

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] crypt_gkey = (null)

2018-06-12 Thread Dicamillo, Robert

Hello Aaron,

You could check to see if the CentOS 7 system is using disk encryption, e.g., 
if the
following command return 1, then it would mean encryption is in use (which can 
be
an issue with FreeSurfer).

$ cat /proc/sys/crypto/fips_enabled

If it returns zero, it could be an issue with a system library like glibc on 
CentOS 7.5
(that does not happen on older versions of  CentOS).

Either way, this is not your doing ;-)


On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:


External Email - Use Caution

I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i 
get to the part where MRI_convert is creating the the orig001.mgz its gives me 
a segmentation fault. if i run this on a centos 6 system it works fine. below 
is the output of the program.


/data/gizmo/data1/freesurfer5.3/bin/mri_convert 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
 /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
crypt_gkey = (null)
Segmentation fault (core dumped)



Did I do anything wrong?
___
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


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] crypt_gkey = (null)

2018-06-12 Thread Aaron Tanenbaum

External Email - Use Caution

I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3.
When i get to the part where MRI_convert is creating the the orig001.mgz
its gives me a segmentation fault. if i run this on a centos 6 system it
works fine. below is the output of the program.


/data/gizmo/data1/freesurfer5.3/bin/mri_convert
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
/data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
crypt_gkey = (null)
Segmentation fault (core dumped)



Did I do anything wrong?
___
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] crypt_gkey = (null)

Re: [Freesurfer] crypt_gkey = (null)

Re: [Freesurfer] crypt_gkey = (null)

[Freesurfer] crypt_gkey = (null)

4 matches

Site Navigation

Mail list logo

Footer information