Hi Doug, No that file does not exist.I am using freesurfer -Linux-centos6_x86_64-dev-20160617-428ca78
Thanks -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, 26 August 2016 12:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all error using Freesurfer 6.0 Does this file exist? $FREESURFER_HOME/subjects/fsaverage/label/lh.BA1_exvivo.label If not, what version of FS are you using? On 08/24/2016 08:14 PM, Elpiniki Andrew wrote: > > Thankyou! It worked when I removed the trailing “ / “. However after > it finished running, I received this error: > > ERROR reading > /usr/local/DTI_processed_data/freesurfer_data_dir/fsaverage/label/lh.B > A1_exvivo.label > > Because the “lh.BA1_exvivo.label” file for some reason, when I > checked, was not in my subjects_dir. > > What should I do? > > Thankyou very much! > > Elpiniki > > Douglas N Greve > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&; > q=from:%22Douglas+N+Greve%22> > Mon, 22 Aug 2016 13:12:24 -0700 > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&; > q=date:20160822> > > Nothing looks suspicious. Try setting > > setenv SUBJECTS_DIR /usr/local/DTI_processed_data/freesurfer_data_dir > > ie, removing the trailing "/" > > On 08/22/2016 02:12 AM, Elpiniki Andrew wrote: > > > Hello Freesurfer experts, > > > > > > I'm having a bit of difficulty running the recon-all command. I > > > recently downloaded Freesurfer version 6.0. > > > > > > The command that I'm running is: > > > > > >recon-all -all -s $name -hippocampal-subfields-T1 > > > > > > However I keep receiving this error: > > > > > > If: Expression Syntax > > > > > > I've attached the output using the -debug flag. > > > > > > I'm using Linux ( centos6.3). Not sure if this is related but I > > > initially had an issue with recon-all stopped with an error when I > > > first ran the same dataset. There was an error in the log file " too > > > many levels of symbolic links". > > > So, I created a new subjects directory and created a symlink to the > > > fsaverage dir as per the instructions on the freesurfer wiki page. > > > > > > > > > Thankyou very much in advance for your time and efforts! > > > > > > Kind regards, > > > Elpiniki > > > > > > > > > _______________________________________________ > > > 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 -- 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/ _______________________________________________ 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
