On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting
ls brain*
brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz
mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./brain.mgz... Segmentation fault (core dumped)
Any ideas?
Thanks
Joshua
Can you send the full terminal output? Or is that it? Do you have enough disc space or is it running out? what is the result of ls -l brain.mgz
On 06/02/2016 03:07 PM, Joshua Lee wrote:
On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting
>>ls brain* brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./brain.mgz... Segmentation fault (core dumped)Any ideas?
Thanks
Joshua
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Yes the quoted lines were output fromt her terminal.
ls -l brain.mgz
-rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
I have many Tb of disk space. I can chmod 777 the files and still seg faults.
Thanks Josh
- Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you send the full terminal output? Or is that it? Do you have enough disc space or is it running out? what is the result of ls -l brain.mgz
On 06/02/2016 03:07 PM, Joshua Lee wrote:
On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting
>>ls brain* brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./brain.mgz... Segmentation fault (core dumped)Any ideas?
Thanks
Joshua
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Is this a virtual machine? (The username seems odd...)
What is the output of whoami?
What is the output of ls -l ../?
hth d
On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Hi Doug,
Yes the quoted lines were output fromt her terminal.
ls -l brain.mgz -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
I have many Tb of disk space. I can chmod 777 the files and still seg faults.
Thanks Josh
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you send the full terminal output? Or is that it? Do you have enough disc space or is it running out? what is the result of ls -l brain.mgz
On 06/02/2016 03:07 PM, Joshua Lee wrote:
On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting
>>ls brain* brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./brain.mgz... Segmentation fault (core dumped)Any ideas?
Thanks
Joshua
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
I had replaced the user name in the output I posted to the listserv for security reasons. I am not on a virtual machine. Fresh install on bare metal. ls -l ../
...
drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri ...
- Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:25 PM, dgw dgwakeman@gmail.com wrote:
Is this a virtual machine? (The username seems odd...)
What is the output of whoami?
What is the output of ls -l ../?
hth d
On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Hi Doug,
Yes the quoted lines were output fromt her terminal.
ls -l brain.mgz -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
I have many Tb of disk space. I can chmod 777 the files and still seg faults.
Thanks Josh
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve <
greve@nmr.mgh.harvard.edu>
wrote:
Can you send the full terminal output? Or is that it? Do you have enough disc space or is it running out? what is the result of ls -l brain.mgz
On 06/02/2016 03:07 PM, Joshua Lee wrote:
On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting
>>ls brain* brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz mri_convert ./brain.mgz --in_type mgz --out_type nii -o./brain.nii
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./brain.mgz... Segmentation fault (core dumped)Any ideas?
Thanks
Joshua
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I do note that I can enter "freeview ./brain.mgz" and the image opens. Then I can manuall save it as a .nii
- Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee jkilee@ucdavis.edu wrote:
I had replaced the user name in the output I posted to the listserv for security reasons. I am not on a virtual machine. Fresh install on bare metal. ls -l ../
...
drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri ...
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:25 PM, dgw dgwakeman@gmail.com wrote:
Is this a virtual machine? (The username seems odd...)
What is the output of whoami?
What is the output of ls -l ../?
hth d
On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Hi Doug,
Yes the quoted lines were output fromt her terminal.
ls -l brain.mgz -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
I have many Tb of disk space. I can chmod 777 the files and still seg faults.
Thanks Josh
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve <
greve@nmr.mgh.harvard.edu>
wrote:
Can you send the full terminal output? Or is that it? Do you have
enough
disc space or is it running out? what is the result of ls -l brain.mgz
On 06/02/2016 03:07 PM, Joshua Lee wrote:
On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting
>>ls brain* brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz mri_convert ./brain.mgz --in_type mgz --out_type nii -o./brain.nii
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./brain.mgz... Segmentation fault (core dumped)Any ideas?
Thanks
Joshua
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Perhaps something to do with
libcrypt-2.*.so ??
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528...
- Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee jkilee@ucdavis.edu wrote:
I do note that I can enter "freeview ./brain.mgz" and the image opens. Then I can manuall save it as a .nii
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee jkilee@ucdavis.edu wrote:
I had replaced the user name in the output I posted to the listserv for security reasons. I am not on a virtual machine. Fresh install on bare metal. ls -l ../
...
drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri ...
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:25 PM, dgw dgwakeman@gmail.com wrote:
Is this a virtual machine? (The username seems odd...)
What is the output of whoami?
What is the output of ls -l ../?
hth d
On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Hi Doug,
Yes the quoted lines were output fromt her terminal.
ls -l brain.mgz -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
I have many Tb of disk space. I can chmod 777 the files and still seg faults.
Thanks Josh
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve <
greve@nmr.mgh.harvard.edu>
wrote:
Can you send the full terminal output? Or is that it? Do you have
enough
disc space or is it running out? what is the result of ls -l brain.mgz
On 06/02/2016 03:07 PM, Joshua Lee wrote:
On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting
>>ls brain* brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgzbrain.mgz
mri_convert ./brain.mgz --in_type mgz --out_type nii -o./brain.nii
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./brain.mgz... Segmentation fault (core dumped)Any ideas?
Thanks
Joshua
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If you must use 5.1 (I would recommend upgrading), then try what Zeke suggested there.
You beat me to the email ;)
hth d
On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Perhaps something to do with
libcrypt-2.*.so ??
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528...
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee jkilee@ucdavis.edu wrote:
I do note that I can enter "freeview ./brain.mgz" and the image opens. Then I can manuall save it as a .nii
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee jkilee@ucdavis.edu wrote:
I had replaced the user name in the output I posted to the listserv for security reasons. I am not on a virtual machine. Fresh install on bare metal. ls -l ../
... drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri ...
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:25 PM, dgw dgwakeman@gmail.com wrote:
Is this a virtual machine? (The username seems odd...)
What is the output of whoami?
What is the output of ls -l ../?
hth d
On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Hi Doug,
Yes the quoted lines were output fromt her terminal.
ls -l brain.mgz -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
I have many Tb of disk space. I can chmod 777 the files and still seg faults.
Thanks Josh
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you send the full terminal output? Or is that it? Do you have enough disc space or is it running out? what is the result of ls -l brain.mgz
On 06/02/2016 03:07 PM, Joshua Lee wrote: > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on > Ubuntu 16.04 LTS > mri_convert is seg faulting > > > >>ls brain* > brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz > brain.mgz > > mri_convert ./brain.mgz --in_type mgz --out_type nii -o > ./brain.nii > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from ./brain.mgz... > Segmentation fault (core dumped) > > > Any ideas? > > Thanks > > Joshua > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
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.
Unfortunately this does not seem to work.
locate libcrypt-2
*/lib/x86_64-linux-gnu/libcrypt-2.23.so http://libcrypt-2.23.so/lib32/libcrypt-2.23.so http://libcrypt-2.23.so*
cp /lib/x86_64-linux-gnu/libcrypt-2.23.so $FREESURFER_HOME/lib/libcrypt.so.1
[verified it copied, and added to lib path to environment]
echo $LD_LIBRARY_PATH
*/home/myuser/Tools/freesurfer/lib:/usr/lib/fsl/5.0*
cd ~/data/APP_FreeSurfer/APP_longitudinal/100604-200/mri ls brain.*
*brain.mgz*
mri_convert -i ./brain.mgz -o ./help.nii
*$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from ./brain.mgz...Segmentation fault (core dumped)*
- Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:44 PM, dgw dgwakeman@gmail.com wrote:
If you must use 5.1 (I would recommend upgrading), then try what Zeke suggested there.
You beat me to the email ;)
hth d
On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Perhaps something to do with
libcrypt-2.*.so ??
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528...
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee jkilee@ucdavis.edu wrote:
I do note that I can enter "freeview ./brain.mgz" and the image opens. Then I can manuall save it as a .nii
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee jkilee@ucdavis.edu wrote:
I had replaced the user name in the output I posted to the listserv for security reasons. I am not on a virtual machine. Fresh install on bare metal. ls -l ../
... drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri ...
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:25 PM, dgw dgwakeman@gmail.com wrote:
Is this a virtual machine? (The username seems odd...)
What is the output of whoami?
What is the output of ls -l ../?
hth d
On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee jkilee@ucdavis.edu
wrote:
Hi Doug,
Yes the quoted lines were output fromt her terminal.
> ls -l brain.mgz > -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
I have many Tb of disk space. I can chmod 777 the files and still
seg
faults.
Thanks Josh
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: > > Can you send the full terminal output? Or is that it? Do you have > enough > disc space or is it running out? what is the result of > ls -l brain.mgz > > > > On 06/02/2016 03:07 PM, Joshua Lee wrote: > > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on > > Ubuntu 16.04 LTS > > mri_convert is seg faulting > > > > > > >>ls brain* > > brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz > > brain.mgz > > > > mri_convert ./brain.mgz --in_type mgz --out_type nii -o > > ./brain.nii > > > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp
$
> > reading from ./brain.mgz... > > Segmentation fault (core dumped) > > > > > > Any ideas? > > > > Thanks > > > > Joshua > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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.
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
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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
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Maybe its because its not an older version of that file from Ubuntu 12.04.
All the data is processed on a different machine, but I then import it on my local machine for running different kinds of analyses (e.g. qdec). Will it matter if I use the latest FreeSurfer version with data processed on 5.1?
Josh
- Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 1:13 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Unfortunately this does not seem to work.
locate libcrypt-2
*/lib/x86_64-linux-gnu/libcrypt-2.23.so http://libcrypt-2.23.so/lib32/libcrypt-2.23.so http://libcrypt-2.23.so*
cp /lib/x86_64-linux-gnu/libcrypt-2.23.so $FREESURFER_HOME/lib/libcrypt.so.1
[verified it copied, and added to lib path to environment]
echo $LD_LIBRARY_PATH
*/home/myuser/Tools/freesurfer/lib:/usr/lib/fsl/5.0*
cd ~/data/APP_FreeSurfer/APP_longitudinal/100604-200/mri ls brain.*
*brain.mgz*
mri_convert -i ./brain.mgz -o ./help.nii
*$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from ./brain.mgz...Segmentation fault (core dumped)*
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:44 PM, dgw dgwakeman@gmail.com wrote:
If you must use 5.1 (I would recommend upgrading), then try what Zeke suggested there.
You beat me to the email ;)
hth d
On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Perhaps something to do with
libcrypt-2.*.so ??
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528...
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee jkilee@ucdavis.edu wrote:
I do note that I can enter "freeview ./brain.mgz" and the image opens. Then I can manuall save it as a .nii
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee jkilee@ucdavis.edu
wrote:
I had replaced the user name in the output I posted to the listserv
for
security reasons. I am not on a virtual machine. Fresh install on bare metal. ls -l ../
... drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri ...
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:25 PM, dgw dgwakeman@gmail.com wrote:
Is this a virtual machine? (The username seems odd...)
What is the output of whoami?
What is the output of ls -l ../?
hth d
On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee jkilee@ucdavis.edu
wrote:
> Hi Doug, > > Yes the quoted lines were output fromt her terminal. > >> ls -l brain.mgz >> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz > > > I have many Tb of disk space. I can chmod 777 the files and still
seg
> faults. > > Thanks > Josh > > > > - > Joshua Lee, Ph.D. > Post-Doctoral Researcher > MIND Institute > University of California, Davis > 530.747.3805 > > On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve > greve@nmr.mgh.harvard.edu > wrote: >> >> Can you send the full terminal output? Or is that it? Do you have >> enough >> disc space or is it running out? what is the result of >> ls -l brain.mgz >> >> >> >> On 06/02/2016 03:07 PM, Joshua Lee wrote: >> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed
on
>> > Ubuntu 16.04 LTS >> > mri_convert is seg faulting >> > >> > >> > >>ls brain* >> > brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz >> > brain.mgz >> > >> > mri_convert ./brain.mgz --in_type mgz --out_type nii -o >> > ./brain.nii >> > >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve
Exp $
>> > reading from ./brain.mgz... >> > Segmentation fault (core dumped) >> > >> > >> > Any ideas? >> > >> > Thanks >> > >> > Joshua >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. > _______________________________________________ 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
Installing the latest version of FreeSurfer has resolved this problem. So as long as the post-processing tools are compatible with these data then I should be fine.
Thanks.
Josh
- Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 1:20 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Maybe its because its not an older version of that file from Ubuntu 12.04.
All the data is processed on a different machine, but I then import it on my local machine for running different kinds of analyses (e.g. qdec). Will it matter if I use the latest FreeSurfer version with data processed on 5.1?
Josh
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 1:13 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Unfortunately this does not seem to work.
locate libcrypt-2
*/lib/x86_64-linux-gnu/libcrypt-2.23.so http://libcrypt-2.23.so/lib32/libcrypt-2.23.so http://libcrypt-2.23.so*
cp /lib/x86_64-linux-gnu/libcrypt-2.23.so $FREESURFER_HOME/lib/libcrypt.so.1
[verified it copied, and added to lib path to environment]
echo $LD_LIBRARY_PATH
*/home/myuser/Tools/freesurfer/lib:/usr/lib/fsl/5.0*
cd ~/data/APP_FreeSurfer/APP_longitudinal/100604-200/mri ls brain.*
*brain.mgz*
mri_convert -i ./brain.mgz -o ./help.nii
*$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from ./brain.mgz...Segmentation fault (core dumped)*
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:44 PM, dgw dgwakeman@gmail.com wrote:
If you must use 5.1 (I would recommend upgrading), then try what Zeke suggested there.
You beat me to the email ;)
hth d
On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee jkilee@ucdavis.edu wrote:
Perhaps something to do with
libcrypt-2.*.so ??
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528...
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee jkilee@ucdavis.edu
wrote:
I do note that I can enter "freeview ./brain.mgz" and the image opens. Then I can manuall save it as a .nii
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee jkilee@ucdavis.edu
wrote:
I had replaced the user name in the output I posted to the listserv
for
security reasons. I am not on a virtual machine. Fresh install on
bare
metal. ls -l ../
> ... > drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri > ... >
Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805
On Thu, Jun 2, 2016 at 12:25 PM, dgw dgwakeman@gmail.com wrote: > > Is this a virtual machine? (The username seems odd...) > > What is the output of whoami? > > What is the output of ls -l ../? > > hth > d > > > > On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee jkilee@ucdavis.edu
wrote:
> > Hi Doug, > > > > Yes the quoted lines were output fromt her terminal. > > > >> ls -l brain.mgz > >> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz > > > > > > I have many Tb of disk space. I can chmod 777 the files and still
seg
> > faults. > > > > Thanks > > Josh > > > > > > > > - > > Joshua Lee, Ph.D. > > Post-Doctoral Researcher > > MIND Institute > > University of California, Davis > > 530.747.3805 > > > > On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve > > greve@nmr.mgh.harvard.edu > > wrote: > >> > >> Can you send the full terminal output? Or is that it? Do you have > >> enough > >> disc space or is it running out? what is the result of > >> ls -l brain.mgz > >> > >> > >> > >> On 06/02/2016 03:07 PM, Joshua Lee wrote: > >> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed
on
> >> > Ubuntu 16.04 LTS > >> > mri_convert is seg faulting > >> > > >> > > >> > >>ls brain* > >> > brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz > >> > brain.mgz > >> > > >> > mri_convert ./brain.mgz --in_type mgz --out_type nii -o > >> > ./brain.nii > >> > > >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve
Exp $
> >> > reading from ./brain.mgz... > >> > Segmentation fault (core dumped) > >> > > >> > > >> > Any ideas? > >> > > >> > Thanks > >> > > >> > Joshua > >> > > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> greve@nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> Outgoing: > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >> _______________________________________________ > >> 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. > > > _______________________________________________ > 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@nmr.mgh.harvard.edu
-
dgw -
Douglas N Greve -
Joshua Lee