Yes, that's it. It just back to the command line after that. What do you think the problem is?
BW Karen Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Douglas Greve Sent: 07 February 2017 23:08 To: [email protected] Subject: Re: [Freesurfer] Recon-all - finished with errors Is that the entire terminal output? On 2/7/17 6:46 AM, Bunday, Karen wrote: > Hi > > Thank you for your email. > > I checked the disk space and there is over 300 GB left. > > I ran the code as you suggested, this is the output: > > "WARNING: # of slices=-92 in header - assuming 124... > Read_signal (/Applications/Freesurfer/subjects/subjKZ/surf/I.001): > could not open file > > No such file or directory > > mris_calc: could not establish read access to 'lh.area.mid' > > No such file or directory" > > It's odd as I did manage to run this subject before, but needed to re-run > with a different .nii and now it will not complete. > > BW > Karen > > Karen Bunday, PhD > Research Associate > Sobell Department of Motor Neuroscience and Movement Disorders > Institute of Neurology, University College London > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Douglas N > Greve > Sent: 06 February 2017 18:05 > To: [email protected] > Subject: Re: [Freesurfer] Recon-all - finished with errors > > That is a strange error. Can you run the following command to try to > replicate: > > cd /Applications/freesurfer/subjects/subjKZ/surf > > mris_calc -o lh.area.mid lh.area.mid div 2 > > also, make sure that you have not run out of space on that disk > > > On 02/06/2017 09:56 AM, Bunday, Karen wrote: >> Dear FS members >> >> I am having trouble with using the "recon-all" function on one >> particular subject. "recon-all" does not complete and finishes with >> errors, it seems it does not complete both hemispheres. I am no >> expert in FS so I don't really understand why this is happening and I >> am unable to understand the log (attached). Could someone help >> interpret the log so that I may be able to process this subject? >> >> Many thanks >> >> Karen >> >> Karen Bunday, PhD >> >> Research Associate >> >> Sobell Department of Motor Neuroscience and Movement Disorders >> >> Institute of Neurology, University College London >> >> 33 Queen Square >> >> London >> >> WC1N 3BG >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > [email protected] > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
