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
Freesurferv6.0_recon-all_error
Description: Freesurferv6.0_recon-all_error
_______________________________________________ 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.
