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
________________________________
From: Douglas N Greve <gr...@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
gr...@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/
_______________________________________________
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
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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.
