Freesurfer error..recon-all fails

List overview All Threads
Download

newer

older

mri_nu_correct.mni

v 5.3 pial- FLAIR vs T2

Manish Dalwani

4 Jun 2013 4 Jun '13

12:13 p.m.

Hello Freesurfer's

I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine.

I have checked the permissions to various and folders and they look ok to me.

When I run the following command: recon-all -i MR1000200001.dcm -s test2

I get the following error server:anat_5214 manishdalwani$ recon-all -i MR1000200001.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64

recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013

For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I am attaching the log file as well, and would appreciate if people can help with this issue.

Best Regards, Manish Dalwani

Attachments:

attachment.html (text/html — 5.9 KB)
recon-all.log (application/octet-stream — 16.7 KB)

Show replies by date

Douglas N Greve

4 Jun 4 Jun

12:15 p.m.

Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote:

...

Hello Freesurfer's

I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine.

I have checked the permissions to various and folders and they look ok to me.

When I run the following command: recon-all -i MR1000200001.dcm -s test2

I get the following error server:anat_5214 manishdalwani$ recon-all -i MR1000200001.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz

ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64

recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013

For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I am attaching the log file as well, and would appreciate if people can help with this issue.

Best Regards, Manish Dalwani

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Manish Dalwani

12:29 p.m.

yes, there is a file called LICENSE in the freesurfer folder. Should I look for something else? Thanks, Manish

________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, June 4, 2013 10:15 AM Subject: Re: [Freesurfer] Freesurfer error..recon-all fails

Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote:

...

Hello Freesurfer's

I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine.

I have checked the permissions to various and folders and they look ok to me.

When I run the following command: recon-all -i MR1000200001.dcm -s test2

I get the following error server:anat_5214 manishdalwani$ recon-all -i MR1000200001.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz

ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64

recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013

For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I am attaching the log file as well, and would appreciate if people can help with this issue.

Best Regards, Manish Dalwani

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.

Manish Dalwani

12:31 p.m.

Ok I checked the other version of freesurfer and I do have .license file in the freesurfer folder. How can I get this file?

Best, Manish

Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote:

...

Hello Freesurfer's

I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine.

I have checked the permissions to various and folders and they look ok to me.

When I run the following command: recon-all -i MR1000200001.dcm -s test2

I get the following error server:anat_5214 manishdalwani$ recon-all -i MR1000200001.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz

ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64

recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013

For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I am attaching the log file as well, and would appreciate if people can help with this issue.

Best Regards, Manish Dalwani

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Manish Dalwani

12:35 p.m.

Sorry for the bunch of emails. I registered and got the license file. I have been using this software after a long time and feel silly that this was the thing that was causing trouble. Thank you Doug! Manish

Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote:

...

Hello Freesurfer's

I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine.

I have checked the permissions to various and folders and they look ok to me.

When I run the following command: recon-all -i MR1000200001.dcm -s test2

I get the following error server:anat_5214 manishdalwani$ recon-all -i MR1000200001.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz

ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64

recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013

For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I am attaching the log file as well, and would appreciate if people can help with this issue.

Best Regards, Manish Dalwani

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

4746

Age (days ago)

4746

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

4 comments

2 participants

tags (0)

participants (2)

Douglas N Greve
Manish Dalwani