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 -- 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.
