Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo –E recon-all –s bert –all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
Matt,
Can you send me the actual recon-all.log file? It might be helpful for me to diagnose the issue. Thanks.
-Zeke
On 10/23/2014 07:48 AM, Matthew Riddle wrote:
Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo –E recon-all –s bert –all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Zeke,
Here¹s the recon-all.log file. I didn¹t erase the old one before I started the run, so all the original bert information is there, my stuff starts near the bottom.
Thanks again for taking a look.
-Matt
On 10/23/14, 10:33 AM, "Z K" zkaufman@nmr.mgh.harvard.edu wrote:
Matt,
Can you send me the actual recon-all.log file? It might be helpful for me to diagnose the issue. Thanks.
-Zeke
On 10/23/2014 07:48 AM, Matthew Riddle wrote:
Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I¹m still experiencing an issue with freesurfer that I¹m hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo E recon-all s bert all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn¹t provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
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.
Hi Zeke,
So I may have solved the issue. Since /applications is write protected by default, I had to run the recon-all with sudo. But it seems like the subroutines of recon-all don't inherit the permissions, so I moved my Subjects directory to Documents, and then I can run recon-all without the initial crash, since permissions are no longer an issue. Hopefully it will run all the way through.
Best
-Matt
Sent from my iPhone
On Oct 23, 2014, at 10:34 AM, "Z K" zkaufman@nmr.mgh.harvard.edu wrote:
Matt,
Can you send me the actual recon-all.log file? It might be helpful for me to diagnose the issue. Thanks.
-Zeke
On 10/23/2014 07:48 AM, Matthew Riddle wrote: Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo –E recon-all –s bert –all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
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.
Interesting. Ive never encountered that issue before but Ive also never conducted an install test on subject bert on Mavericks or Yosemite. Ill take a look. Thanks for the update.
-Zeke
On 10/23/2014 12:03 PM, Matthew Riddle wrote:
Hi Zeke,
So I may have solved the issue. Since /applications is write protected by default, I had to run the recon-all with sudo. But it seems like the subroutines of recon-all don't inherit the permissions, so I moved my Subjects directory to Documents, and then I can run recon-all without the initial crash, since permissions are no longer an issue. Hopefully it will run all the way through.
Best
-Matt
Sent from my iPhone
On Oct 23, 2014, at 10:34 AM, "Z K" zkaufman@nmr.mgh.harvard.edu wrote:
Matt,
Can you send me the actual recon-all.log file? It might be helpful for me to diagnose the issue. Thanks.
-Zeke
On 10/23/2014 07:48 AM, Matthew Riddle wrote: Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo –E recon-all –s bert –all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
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
I tried to run a recon-all on a brand new subject and ran into the same issue, so I just moved the subjects directory on a hunch. I'm used to running Freesurfer on a CentOS system, so I'd never really considered OSX being as picky as it seems to be about write permissions. Bert's recon has been running for a couple of hours now without an issue, so let's hope it keeps going. I'll get back to you after it (hopefully) completes and let you know if it solves the issue.
-Matt
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 23, 2014 12:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
Interesting. Ive never encountered that issue before but Ive also never conducted an install test on subject bert on Mavericks or Yosemite. Ill take a look. Thanks for the update.
-Zeke
On 10/23/2014 12:03 PM, Matthew Riddle wrote:
Hi Zeke,
So I may have solved the issue. Since /applications is write protected by default, I had to run the recon-all with sudo. But it seems like the subroutines of recon-all don't inherit the permissions, so I moved my Subjects directory to Documents, and then I can run recon-all without the initial crash, since permissions are no longer an issue. Hopefully it will run all the way through.
Best
-Matt
Sent from my iPhone
On Oct 23, 2014, at 10:34 AM, "Z K" zkaufman@nmr.mgh.harvard.edu wrote:
Matt,
Can you send me the actual recon-all.log file? It might be helpful for me to diagnose the issue. Thanks.
-Zeke
On 10/23/2014 07:48 AM, Matthew Riddle wrote: Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I'm still experiencing an issue with freesurfer that I'm hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo -E recon-all -s bert -all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn't provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
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
?Hello,
I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped.
Anthony
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthew Riddle mriddle@nyspi.columbia.edu Sent: Thursday, October 23, 2014 7:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I'm still experiencing an issue with freesurfer that I'm hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo -E recon-all -s bert -all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn't provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
Hi Anthony,
wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a place where you have write permissions (as User).
Best, Martin
On 11/05/2014 12:56 PM, Anthony Dick wrote:
Hello,
I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped.
Anthony
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthew Riddle mriddle@nyspi.columbia.edu *Sent:* Thursday, October 23, 2014 7:48 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite) Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I'm still experiencing an issue with freesurfer that I'm hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo --E recon-all --s bert --all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn't provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Martin,
I did this (ran it from both the Desktop and Documents). Also tried re-installing Freesurfer. The subjects folder also has permissions:
drwx------+ 1632 adick staff 54K Nov 5 13:01 Desktop drwx------+ 42 adick staff 1.4K Nov 5 12:48 Documents
I also set permissions for freesurfer/bin using the chmod command: chmod -R a+x freesufer/bin/*
Not really sure what the issue is, but it seems to be related to the upgrade to Yosemite.
Anthony
On 11/5/14, 1:39 PM, Martin Reuter wrote:
Hi Anthony,
wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a place where you have write permissions (as User).
Best, Martin
On 11/05/2014 12:56 PM, Anthony Dick wrote:
Hello,
I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped.
Anthony
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthew Riddle mriddle@nyspi.columbia.edu *Sent:* Thursday, October 23, 2014 7:48 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite) Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I'm still experiencing an issue with freesurfer that I'm hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo --E recon-all --s bert --all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn't provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Martin Reuter
Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web :http://reuter.mit.edu
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.
Hello Anthony,
The problem isnt with the location of the bert folder but rather with the permissions of the bert folder itself (and the permissions within).
To run the bert case please 'cd' into the directory containing the bert folder and type the following:
sudo chmod -R a+wr bert
-Zeke
On 11/05/2014 02:42 PM, Anthony Dick wrote:
Hello Martin,
I did this (ran it from both the Desktop and Documents). Also tried re-installing Freesurfer. The subjects folder also has permissions:
drwx------+ 1632 adick staff 54K Nov 5 13:01 Desktop drwx------+ 42 adick staff 1.4K Nov 5 12:48 Documents
I also set permissions for freesurfer/bin using the chmod command: chmod -R a+x freesufer/bin/*
Not really sure what the issue is, but it seems to be related to the upgrade to Yosemite.
Anthony
On 11/5/14, 1:39 PM, Martin Reuter wrote:
Hi Anthony,
wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a place where you have write permissions (as User).
Best, Martin
On 11/05/2014 12:56 PM, Anthony Dick wrote:
Hello,
I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped.
Anthony
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthew Riddle mriddle@nyspi.columbia.edu *Sent:* Thursday, October 23, 2014 7:48 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite) Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo –E recon-all –s bert –all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Martin Reuter
Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web :http://reuter.mit.edu
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
Hello Zeke,
I have tried giving permissions to multiple folders (freesurfer, bin, Documents, bert etc.) using this command with no luck. Here is where it keeps dying. Is it possibly an issue with something else other than permissions?
#@# Talairach Wed Nov 5 23:58:06 EST 2014 /Users/adick/Documents/013_new/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin dizzy.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s 013_new exited with ERRORS at Wed Nov 5 23:58:13 EST 2014
For more details, see the log file /Users/adick/Documents/013_new/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 11/5/14, 2:51 PM, Z K wrote:
Hello Anthony,
The problem isnt with the location of the bert folder but rather with the permissions of the bert folder itself (and the permissions within).
To run the bert case please 'cd' into the directory containing the bert folder and type the following:
sudo chmod -R a+wr bert
-Zeke
On 11/05/2014 02:42 PM, Anthony Dick wrote:
Hello Martin,
I did this (ran it from both the Desktop and Documents). Also tried re-installing Freesurfer. The subjects folder also has permissions:
drwx------+ 1632 adick staff 54K Nov 5 13:01 Desktop drwx------+ 42 adick staff 1.4K Nov 5 12:48 Documents
I also set permissions for freesurfer/bin using the chmod command: chmod -R a+x freesufer/bin/*
Not really sure what the issue is, but it seems to be related to the upgrade to Yosemite.
Anthony
On 11/5/14, 1:39 PM, Martin Reuter wrote:
Hi Anthony,
wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a place where you have write permissions (as User).
Best, Martin
On 11/05/2014 12:56 PM, Anthony Dick wrote:
Hello,
I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped.
Anthony
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthew Riddle mriddle@nyspi.columbia.edu *Sent:* Thursday, October 23, 2014 7:48 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite) Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo –E recon-all –s bert –all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Martin Reuter
Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web :http://reuter.mit.edu
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
Anthony,
Im a few hours in running bert on Yosemite with no issue so far. Could you please send me you log file for the case below? Thanks.
-Zeke
On 11/06/2014 12:02 AM, Anthony Dick wrote:
Hello Zeke,
I have tried giving permissions to multiple folders (freesurfer, bin, Documents, bert etc.) using this command with no luck. Here is where it keeps dying. Is it possibly an issue with something else other than permissions?
#@# Talairach Wed Nov 5 23:58:06 EST 2014 /Users/adick/Documents/013_new/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin dizzy.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s 013_new exited with ERRORS at Wed Nov 5 23:58:13 EST 2014
For more details, see the log file /Users/adick/Documents/013_new/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 11/5/14, 2:51 PM, Z K wrote:
Hello Anthony,
The problem isnt with the location of the bert folder but rather with the permissions of the bert folder itself (and the permissions within).
To run the bert case please 'cd' into the directory containing the bert folder and type the following:
sudo chmod -R a+wr bert
-Zeke
On 11/05/2014 02:42 PM, Anthony Dick wrote:
Hello Martin,
I did this (ran it from both the Desktop and Documents). Also tried re-installing Freesurfer. The subjects folder also has permissions:
drwx------+ 1632 adick staff 54K Nov 5 13:01 Desktop drwx------+ 42 adick staff 1.4K Nov 5 12:48 Documents
I also set permissions for freesurfer/bin using the chmod command: chmod -R a+x freesufer/bin/*
Not really sure what the issue is, but it seems to be related to the upgrade to Yosemite.
Anthony
On 11/5/14, 1:39 PM, Martin Reuter wrote:
Hi Anthony,
wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a place where you have write permissions (as User).
Best, Martin
On 11/05/2014 12:56 PM, Anthony Dick wrote:
Hello,
I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped.
Anthony
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthew Riddle mriddle@nyspi.columbia.edu *Sent:* Thursday, October 23, 2014 7:48 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite) Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about.
Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal:
sudo –E recon-all –s bert –all
The processes crashes in a minute or two at the same place each time, and this is the last bit of output.
MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
I tried this on an almost identical machine running Mavericks, and got the exact same problem.
From my bugr output:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal.
Thanks,
-Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Martin Reuter
Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web :http://reuter.mit.edu
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Anthony Dick -
Martin Reuter -
Matthew Riddle -
Z K