Thankyou! It worked when I removed the trailing “ / “. However after it finished running, I received this error:

ERROR reading /usr/local/DTI_processed_data/freesurfer_data_dir/fsaverage/label/lh.BA1_exvivo.label

Because the “lh.BA1_exvivo.label” file for some reason, when I checked, was not in my subjects_dir.

What should I do?

Thankyou very much!

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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