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