All,
The solution suggested in the link that Mehul has sent works for me. It would be great to have this bug ironed out in future releases of FS :-)
Thanks
On Fri, Aug 3, 2012 at 11:45 PM, Mehul Sampat mehul.sampat@ieee.org wrote:
Hi James, I had the same issue. The following workaround was mentioned on the FS mailing list: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20335.html It works for me. Mehul
On Fri, Aug 3, 2012 at 10:11 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Delete that dir and run recon-all with -debug as the first option. Pipe the output to a file, eg, recon-all -debug ... |& tee recon-all.log And send me recon-all.log. Note it will likely be very big! doug
On 08/03/2012 12:52 PM, james pardon wrote:
works fine. Even I can cp expert.opts to scripts folder on my own. Sorry forgot to reply all at first
On Fri, Aug 3, 2012 at 9:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
So /home/dir/subject/subname/scripts does not exist? If so that is wrong. What happens if you mkdir /home/dir/subject/subname/scripts doug On 08/03/2012 12:09 PM, james pardon wrote: Nick or Doug could you help us here? On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi James can you post to the list so others can answer? I'm not sure what's going on, but Nick or Doug might Bruce On Fri, 3 Aug 2012, james pardon wrote: Hi Bruce, subject's folder is empty, there is no scripts folder,or
anything else. Again if I omit -expert everything works fine. Thanks On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi James what happens if you run: ls -l /home/dir/subject/subname/scripts/expert-options touch /home/dir/subject/subname/scripts/expert-options Bruce On Fri, 3 Aug 2012, james pardon wrote: Dear all, I'm trying to pass the following flags for mri_normalize through -expert flag in recon-all, with a file, named expert.opts with the following single line: mri_normalize -b 20 -n 5 my command line is: recon-all -i inputfile -subject subname -all -expert <pathname>/expert.opts I receive the following error: cp: cannot create regular file: '/home/dir/subject/subname/scripts/expert-options' The directory of the subject has been created, but it is completely empty. At first glance I thought it might be some sort of permission problems, however I have rwx permission for all the paths (even running under the root username the same error comes up).Secondly, I
checked my disk quota, it is completely fine. Please note that, if I do not pass -expert flag recon-all works completely fine. Any input is much appreciated. Regards, James 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 thePartners
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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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