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
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
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Elpiniki Andrew