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